Beyond Tribal Theology

The blog Psephizo shared this graphic, developed by Jon Kuhrt:

Although I line up more on the liberal side of many things, I am delighted to be part of a church that isn’t liberal, nor moderate, nor conservative. It is diverse, and finding a church where you can not only be welcome and fit in, and not only be encouraged by a community where your views are understood and shared, but also challenged by others who do not see things as you do, is not always easy. And so as my church gears up to celebrate a membership drive next month which we’re calling “Novembership” (one thing that the pastor and I share is a love for bad puns), let me invite you to Crooked Creek Baptist Church in Indianapolis, if you are in its vicinity. You won’t always like what you hear. But your freedom to be yourself and think differently will be welcome as part of this community. And isn’t that better than simply surrounding yourself with a group of people who simply nod in agreement to whatever you say, because you all think alike?

  • Spaced-Out SCIENCE

    I like some of what you say. Stop and think though–do those who are in charge of educating your children allow for diversity of thought…or do they routinely circle the wagons and vilify anyone who dares suggest that evolutionary assumptions are errant? Did you happen to see the movie NO INTELLIGENCE ALLOWED with Ben Stein? Have you noticed the vitriolic ad hominem leveled against Michael Behe for his carefully-thought-out elaboration of the limits which evolution has? His very scientific research is intolerable to those who have already sacrificed their souls on the altar of Naturalism.
    In your previous post about the cutest response to creationism, did you ever think that it was really a cartoon applicable to those who worship at the shrine of evolutionism; those who essentially say things like, “evolution is the answer…..now, what’s the question?” And, “No, I refuse to see that evolution has serious limitations, because I’ve already decided I don’t like your God…therefore I must eliminate him from the picture at all costs. Evolution must be all-powerful because that’s the logical way to eliminate a Creator. But, by the way, if Behe is correct, then I’m O.K. with the “cosmic seeding” hypothesis, as long as I only have to believe in little green men coming to earth and not God!”

    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

      I’ve extensively dealt with this topic on this blog in the past. Here is a link to a good place to start:

      http://www.patheos.com/blogs/exploringourmatrix/2008/09/blogging-intelligent-design-the-highlights.html

      I don’t think that anyone should judge the merits of Intelligent Design on the basis of what is clearly a poor treatment of the matter, namely Stein’s movie. And unless one is opposed to naturalistic meteorology on religious grounds, then applying this criticism only to biology is illogical and hypocritical.

      • Spaced-Out SCIENCE

        I respectfully decline your invitation to duel on the subject of whether or not ID was “adequately” treated in Ben Stein’s work. That would only serve as a diversion from the point. But surely you knew that. I wasn’t asking you to judge the merits of ID but rather the merits of a group of people who claim to be fair and impartial with the evidence while at the same time exercising the kind of
        heavy-handed political bigotry and dirty tricks that a medieval bishop would be proud of!

        I suspect that God is less interested in whether we assent
        to a belief in creation versus Darwinism than He is in our comprehension of good versus evil and what we do with that knowledge. If you think that the hostility and discrimination
        shown to proponents of ID or creationism makes God proud of your supposed grasp of “the facts”, then I would conclude that we worship very different gods.

        • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

          Well, I am part of a community where there is no censoring either of ID and YEC views or of ones that are actually scientifically well-informed. But personally I am opposed to pseudoscience and pseudoscholarship, whether it be Intelligent Design, Jesus-mythicism, or anything else. Associating God with bunk does no one any favors, in my own personal opinion.

          • Spaced-Out SCIENCE

            I’m sooo tempted to address the monumental irony contained within your own statements, but instead, I would ask you to satisfy my curiosity on a very important related issue.
            What do you believe, and then what would you guess the majority of the group which you represent believes, regarding resurrection of the dead?

            • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

              I seem to recall another troll very recently trying to change a discussion on the subject of evolution, about which they clearly had strong views and weak knowledge, to the subject of the resurrection. I understand why this tactic appeals, but let’s deal with things one at a time.

              Hume’s Dialogue Concerning Natural Religion gave excellent articulation to the case that the design argument is at odds with Christian piety, even before Darwin’s time and our much more extensive knowledge about the workings of living organisms.

              Michael Behe views malaria as an intelligently-designed killing machine. The laryngeal nerve in the giraffe makes the designer seem inept. And so why do you adopt a position that depicts God as malicious and/or incompetent?

              • Spaced-Out SCIENCE

                Really? “another troll”? Are you serious? I look forward to your definition of terms. In the meantime I will give you
                the benefit of the doubt, however small it might be, that you were not resorting to ad hominem. I’m sure you are aware that attacking others via negative labeling belies faults and insecurities in one’s own logic.

                I would greatly appreciate you directing me to the site where you previously discussed resurrection if you are unwilling to engage here.

                As for Behe…did he really say what you are inferring? I’ve read several of his books and articles and also seen him speak in public. He has always seemed to be very careful not to overreach in his conclusions. His legacy of scientific arguments consistently and unashamedly points out that mutations and natural selection do not have the power to do what Darwin might have hoped they could. As to who is then responsible is another subject entirely which Behe usually avoids.

                Really…isn’t this where religion might legitimately come in,
                demonstrating evidence for realities of the universe which cannot be tested or measured by current scientific tools? Can you measure “good” and “evil”, love, hatred, honor or dishonor? Of course, neither can you measure the strings in string theory or the 11th dimension or the “dark matter”
                in the universe!!! This reality should bring humility to the otherwise arrogant assertions about what science “knows”!!!

                • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                  It isn’t necessary to go to another site. Just search on this one. I am perfectly willing to answer questions, and indeed have regularly brought that topic up. But I am unwilling to play the game of “uh oh, he’s figuring out I don’t have sufficient knowledge of this topic, so let me see if I can divert the conversation to something else.”

                  A major problem with design arguments is the willingness of propnents to say “this was intelligently designed” but not “this was poorly designed.” If one is logical, why not the other?

                  • Spaced-Out SCIENCE

                    Yes, that’s a reasonable question to ask. It seems logical if you have access to all the facts—if it’s as simple as some folks want to believe, i.e. “god did it and that’s enough for me”. The problem is…don’t try to paste that logic onto the Bible as so many have. When I make room for the subtleties and nuances of the Bible and I read just a little between the lines, I see that it supports belief in a kind of evolution…or maybe “de-volution” would be more appropriate. The idea seems to be that in the beginning everything was created “very good” (notice I didn’t say perfect, as some want to infer…perhaps the recurrent laryngeal nerve is merely evidence of necessary pragmatism in the implementation phase) and later on several influences or factors acted upon the creation to slowly change it over time.

                    For instance, now days we know that cell phones cause cancers by inhibiting the normal DNA repair mechanisms in our cells. No one could probably prove what massive
                    amounts of similar radiation might have existed a few thousand years ago, or longer. Also, reading the book of Job, I can easily accept that Satan has the power to affect biology and chemistry, considering what he did to Job’s body in that story. It’s only a small leap beyond that to believe that he has done numerous things along the way to hurt and destroy the original creation. Yes, malaria may be one of those things. That’s not a point worthy
                    of intense arguing, however, it’s simply a hypothesis that has brought harmony to numerous elements of science and religion in my own mind.

                    None of us dare call God “inept” until we create something better. You may have heard of Craig Venter’s recent claim to have created “the first artificial cell”. That’s actually a false claim because it was only partially man-made. He used an already-existent cell and merely injected a string of DNA into it! Create your own cell from scratch before you dare to criticize God’s creation. BTW—there’s
                    a huge lesson that biologists can learn by seeing how difficult it was for Venter to succeed at his efforts, even as limited as they were. He exerted intense efforts of intelligence and design and he barely succeeded. Yet
                    evolutionists say that blind evolution could accomplish the same task and billions of similar tasks without question?
                    Me thinks you aren’t asking the right questions!

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      If the result of your thinking is that you attribute creation to the devil rather than God, you have already departed dramatically from the Bible. In which case, you shouldn’t take comfort from rejecting evolution, as though that made your Gnostic stance any less deviant from the perspective of historic Christianity.

                    • Spaced-Out SCIENCE

                      You must be testing my ability to spot errors of logic. Don’t make the mistake of assuming an all-or-none argument. I
                      never suggested that Satan is responsible for “the creation”. My suggestion is that he may have dabbled and tinkered maliciously with it, to some degree, since Adam and Eve rebelled against God.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      I understood that. Is your point to suggest that you are a Manichaean rather than some other sort of Gnostic?

                    • Spaced-Out SCIENCE

                      No, my purpose was not to declare my own belief system or to tell you in any way what you should or should not believe. Rather, my intent was to clarify your thoughts, profuse as they seem to be, and suggest that you have more room to allow for other people’s beliefs which are different than yours, instead of so quickly mischaracterizing them, scoffing sarcastically at them and vilifying them. But this may be only my impression—you
                      may have had alternate motives in mind. I simply hope you realize how some of your statements come across to
                      others.

                      But all this is a distraction from the subject matter. I was hoping to share an important thought earlier about resurrection. I would suggest that rethinking this idea might allow you to look more charitably upon folks who hold a different belief in origins than you. The logic goes something like this: if A is greater than B and if B is greater
                      than C…then A is greater than C.

                      Extrapolated to theology, this suggests that if Lazarus was indeed dead x 4 days and “stinking”, as the Bible says, and yet God had no trouble reassembling his molecules into living order, and all of that within a blink of the eye (in
                      our dimension, at least!), then it would be reasonable to assume that God had the ability, in the beginning, to create the entire world as it was then, in a period of one week (and with the appearance of being mature at that point, just like Lazarus, Jesus and others were resurrected in mature form). I’m not telling you I know these things to be absolutely true. I’m simply trying to remind you that if you state that it’s ridiculous to believe this scenario, then you do a disservice to your assertion of being open-minded and welcoming to those with diverse beliefs. You may also be doing a disservice to the peace, love and unity upon which the church was founded.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Ah, so your real aim is to appeal to a story about a miracle in order to try to justify not merely the Gnostic conclusions to which Intelligent Design leads, but the utter pseudoscientific garbage that young-earth creationism peddles, suggesting that, if God can do miracles, then we can assume that the Creator made the cosmos, the Earth, and everything else appear to be a particular age, and condemns those who mistakenly think that the Creator is trustworthy and would not deliberately deceive in this way.

                      I am part of a community that welcomes me despite there being many in the church that would disagree with me, and welcomes others with whom I disagree in a similar way. But recognizing the appropriateness of being inclusive does not mean sitting by quietly while people make nonsensical claims, and worse, try to use the generosity of spirit of others to deceive and mislead. I presume that taking a vocal stance opposing a Holocaust denier would not, in your view, be “doing a disservice to the peace, love, and unity upon which the church was founded.” So why should the same not be true in opposing those who mislead about matters of science in a comparable way?

                    • Spaced-Out SCIENCE

                      Why didn’t you equate denying the holocaust with denying creation? Wouldn’t that be a more direct comparison for a Christian to make? The fact is that neither comparison adds an iota of evidence or even legitimate logic to the discussion. And that is really my overall point; that such tactics aimed at diminishing your ideological opponent’s
                      views are hypocritical to your lofty claims of being open-minded. You apparently use the emotional element of
                      the holocaust to justify your antagonistic voice of contempt towards YEC’s or ID’ proponents. But comparing apples to
                      oranges is always an error of logic.

                      If you feel that strongly about your perceived opponent’s
                      ideas, why don’t you respectfully “attack” those ideas instead of using personal attacks consisting only of your opinionated labeling? Examples exude from your last post: “utter pseudoscientific garbage”… “deceive and mislead”… “make nonsensical claims”… How might you respond to someone throwing those labels at you? Wouldn’t it be better to use a more respectful approach? If a person does not believe in the holocaust, wouldn’t it make sense to investigate why? If you carefully looked at their reasoning, you might find many areas of agreement. It may in fact NOT mean that they like Hitler or they want Jews to be persecuted.
                      It’s a faulty analogy, but what I’m saying is…if the young earther and the old earther agree on love, peace, honor, faith, etc., then why start WWIII on the basis of disagreements regarding origins? What is so important about your beliefs on these things that it justifies hateful tactics?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      It depends what you mean by creation, of course. The question of what simply exists, giving rise to other things which are not eternal, is one to which there cannot be a definitive answer. And so adopting one view or another on that does not necessarily involve completely denying existing evidence, but merely interpreting that evidence differently. Holocaust denial and young-earth creationism and other forms of denialism, however, involve denying what the available evidence clearly indicates. And for someone to support views that involve such dishonesty, and then accuse those who point out the dishonesty of being “hateful,” simply shows just how despicable those viewpoints are, and that those who adopt them have no sense of decency and no concern for truth.

                      I have been blogging about young-earth creationism and Intelligent Design (as well as other forms of denialism) on this blog for a very long time. If you are new to the blog, then why not start here: http://www.patheos.com/blogs/exploringourmatrix/2010/02/blogging-creationism-and-intelligent-design-the-highlights-revisited.html

                      When someone writes extensively about something over the course of many years, it really isn’t fair to them to pretend that hasn’t happened.

                    • Spaced-Out SCIENCE

                      What I’m saying is that before you judge someone else’s ideology as “dishonest” and all the rest of your diatribe, you might be gracious enough to understand the internal
                      consistency which actually does exist in their beliefs. I would also suggest this same remedy to those who attack your beliefs! The bare facts of science, as we know them today, unedited by those with presupposed conclusions, contain elements which can easily support three or more views on origins. None of them are all-conclusive, however, and it is irresponsible to declare that they are.
                      For example, I could point out to you the well-documented fact that our moon is moving away from this earth by about a yard per year. Extrapolating that fact into the past in the same fashion as evolutionists extrapolate many other
                      things backwards would lead you to logically conclude that life could not have existed on this earth 20 or 30 thousand years ago. Similar conclusions can be arrived at when looking at the scientific evidence of magnetic field changes and temperature changes.
                      But hanging your hat on these things alone is as silly as Naturalists appealing to their interpretation of genomic evidence and what they think might have occurred millions of years back, while ignoring evidence which would preclude that possibility. They cannot acknowledge these things because of what’s called “paradigm inertia”—roughly meaning that their philosophical attachment to their theory is such a speeding freight train of hasty conclusions that they can’t stop to evaluate whether or not they are on the right track. Have you written about that?

                    • Nick Gotts

                      The usual creationist nonsense. There is abundant evidence of multiple magnetic field reversals, and of repeated temperature changes in both directions. As for the earth-moon system, your statement that the moon is moving away from the earth at about a yard per year is simply wrong: the best estimate is 3.82±0.07 cm/year. The same article explains the clear evidence that this rate is not constant, and why the current rate of recession is unusually high.

                    • Spaced-Out SCIENCE

                      Though my poorly-recalled facts about the moon’s recession were off (it would actually be about a yard in
                      24 years), the point still stands that applying uniformitarian assumptions results in catastrophic conditions in the relatively recent past by anyone’s evolutionary paradigm. Maybe this is why evolutionists are being very careful to elucidate theories which explain away that catastrophic possibility. They MUST
                      depart from uniformitarian assumptions in this area but they seem very reticent to do so regarding other areas, like the so-called geologic record and the decay rate of radioactive elements. The fossil record looked at from a common-sense view seems to be screaming out CATASTROPHY rather than slow and gradual processes.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      No, what is off is your embracing bogus information without fact checking it. It is a fundamental problem of approach, and not just a minor error of detail, that is wrong with your claims.

                    • beau_quilter

                      Let me get this straight – Spaced-Out actually thinks the fossil record is the evidence of a global flood? And that somehow the flood disbursed completely different species in each geologic strata? (you never find human bones next to dino bones)?

                      It is hard to believe that such ignorance still exists in the world.

                    • arcseconds

                      Doesn’t it strike you as remotely strange that the world’s scientists should accept a framework which is so obviously flawed any idiot can see through it?

                      I mean, if it’s really this simple, they’re either a bunch of fools, or engaged in some huge confidence trick.

                      The former seems contradicted by the fact they can build something like the Hubble. The later seems incredibly unlikely. It requires the sort of conspiracy theory normally attributed to shadowy, possibly non-existent groups like the Freemasons or the Illuminati, but unlike them is a completely open ‘organisation’ that virtually anyone can join simply by enrolling in a science degree at a suitable tertiary institution, or even just subscribing to a suitable journal.

                      I put ‘organisation’ in scare quotes because unlike the Freemasons, there is no overarching hierarchy, no way of making collective decisions, and no really effective means of punishing people for not toeing the line. You might not be able to get your creationist ideas published in peer-reviewed journals, but no-one will stop you publishing your chemistry papers because you hold unpopular opinions in other areas.

                      At the higher echelons of professional scientists, there are millions of people from all around the world involved, many of them are Christians or members of other faiths.

                      Under these circumstances, it’s really hard to see how a conspiracy could possibly work, especially as according to you it’s ‘covering up’ things which are transparently obvious.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      This sums it up so nicely that I would like to quote you in a blog post, if you wouldn’t mind!

                    • arcseconds

                      Be my guest :-)

                      Of course, I expect proper citation stylez!

                      arcseconds (2013), Commentary , ‘Beyond Tribal Theology’, 1100332665, Exploring our Matrix, Oct. 2013.

                      (no i don’t)

                    • Spaced-Out SCIENCE

                      Really?
                      No reprisals towards those who don’t toe the line? You might re-watch Ben Stein’s documentary NO
                      INTELLIGNECE ALLOWED to test the veracity of you wishful thinking. He, nor I, suggest that an organized or
                      official international group is responsible for a conspiracy of discrimination. The Bible says there is an ideological battle
                      going on with “principalities and powers of evil in high places”. It also says that Satan is the father of all
                      lies. Might that include the lie that
                      macro-evolution has been demonstrated and is a fact? This would certainly fit his agenda of
                      defaming God.

                    • beau_quilter

                      Since you seem to enjoy doing Wiki research, be sure to read the wiki post on NO INTELLIGENCE ALLOWED – all about the overwhelmingly poor reviews, the dishonesty of the filmmakers with their participants, the way that Stein deceptively misquoted Darwin, to make it appear that Darwin supported eugenics, when a full quotation clearly reveals that Darwin had the completely opposite point of view, and the theft of intellectual property from Harvard!

                      If the makers of NO INTELLIGENCE ALLOWED are your source of opinion, you’ll have to check your honesty at the door!

                    • arcseconds

                      Is this supposed to answer my question?

                      How do you think the scientific community keeps lids on obvious things like the moon spiraling out too far too fast for it to be in orbit for billions of years?

                      I mean, let’s just imagine a young, keen, physics student who decides to investigate the Earth-Moon system. They do a google search, and find out you’re right! The Moon moves out by nearly 4cm a year! Then they do some calculations and work out that the Moon can’t have been in orbit that long.

                      So, what happens next? They tell their supervisor, who tells them to keep quiet about it? When they ask “why”, what is said? What kind of threat of punishment or payoff would be sufficient to stop them? And not just this one example, but every time this comes up, which, if you were right about it, must be tens or hundreds of times every year. There must be hundreds of thousands of physics students in the world.

                      Are we talking about some kind of heinous, ultra-efficient science mafia here that will actually kill anyone who steps out of line, but for some reason won’t touch creationists?

                      Because that’s the only way I can remotely see how the moon could so obviously contradict an old earth and yet no-one except creationists seems to have noticed.

                      Or maybe they will touch creationists! Perhaps your very life is in danger now you’ve let the secret out! I hope you were using an anonymizer…

                    • Nick Gotts

                      You are simply wrong in thinking that “uniformitarian assumptions” means “assume everything always happened at the same pace it does now”. That’s just a YEC straw man. Rather, it means you can’t arbitrarily assume that physics has changed in ways that you need to accommodate your pet ideas, as creationists routinely do. If you didn’t have your head so firmly in the sand, you might have noticed that paleontologists believe there to have been at least 5 mass extinctions in the past, the most recent, at the Cretaceous-Tertiary boundary, almost certainly caused by a massive meteor hitting what is now the Gulf of Mexico – a catastrophe in anyone’s language. That the earth is at least millions of years old was consensus science decades before evolution was accepted as the explanation for life’s diversity. The huge depth of strata, quantities of shells so vast they could not possibly have been contemporaneous, interspersed strata of the types laid down in deeper and shallower waters, the existence of geological unconformities – where strata that were evidently laid down flat are found upended, and covered with further strata at different angles, made this quite clear to geologists – all of them, as far as I know, Christians, but unlike modern creationists, honest scientists – by the 1830s.

                    • Spaced-Out SCIENCE

                      <>Granted, that was a nutshell characterization of what
                      Lyell seemed to believe. It’s obvious that his position is untenable; thus the new theories and beliefs you cite. It’s like the abandonment of Darwinism, now subscribing to “Neo-Darwinism” instead. What’s next…neo-neo-Darwinism? I’m curious…since you see how frequently and substantially “science” changes what it thinks it knows, might you construct a type of regression analysis and imagine what it might think it knows in a hundred years from now? Now, take the brief Bible stories in Genesis and look at them as mere sketches of much
                      greater realities. For example, “the flood” may have consisted of a huge meteor strike, catastrophic disruption of the earth’s crust and atmosphere, gravitational and magnetic alterations, rapid tectonic plate movements, huge tsunamis, release of core elements from deep
                      within the earth, including the associated heat and radiation, as well as solar radiation’s effect through an atmosphere temporarily lacking defenses, etc. Try to responsibly factor in what all of this might do to the various dating methods of life on earth. I’m not talking primarily about how long the earth may have existed “without form and void” as Genesis states. I have no problem accepting that state as being very old, in theory. More later.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      This comment is bizarre, and not just the formatting. You seem to know nothing about the progress made in science – is heliocentrism not an improvement over geocentrism? What is wrong with biology gathering more and more data, doing more and more research, and changing as a result?

                      You should read The Bible, Rocks, and Time. Then you will get a Christian perspective that will disabuse you of this “uniformitarianism” nonsense you have been spouting.

                    • stuart32

                      “the flood may have consisted of a huge meteor strike, catastrophic
                      disruption of the earth’s crust and atmosphere, gravitational and
                      magnetic alterations, rapid tectonic plate movements, huge tsunamis,
                      release of core elements from deep within the earth, including the
                      associated heat and radiation, as well as solar radiation’s effect
                      through an atmosphere temporarily lacking defenses, etc.”

                      But during this a large wooden ship managed to stay afloat.

                    • Spaced-Out SCIENCE

                      It is only logical to assume that if God can take a stinking human corpse and instantly reorganize its molecules back into a live person, he can protect a wooden ship in an otherwise un-survivable cataclysm.

                    • stuart32

                      In that case why not invoke even more miracles. There would be no need to appeal to natural events like a meteor strike or the release of water hidden in the earth’s crust. The water for the flood could have appeared by magic and then just vanished when the flood was over.

                    • Spaced-Out SCIENCE

                      That’s not an illogical argument. I can only guess that God acts parsimoniously in regards to stepping outside our usually-understood laws of physics. It might actually take a lot of effort on His part. I don’t suggest He is lazy but if you can work with naturally-occurring processes…why not?

                    • stuart32

                      That’s a good start. It’s better to think that God works with nature. Which do you think is the cleverer God, one who creates a universe in which life can arise through natural processes, or one who starts by creating the Universe and then needs to go on creating everything in it separately, including all the stars and planets and life forms?

                    • Spaced-Out SCIENCE

                      I’m not sure God cares that we think he is clever. I’m pretty sure He cares more about honoring our free will and free thoughts and somehow impressing us of the differences between good and evil. I think He also intentionally refuses to overwhelm us with His existence and presence because for some people that might impede the achievement of the more
                      important tasks.

                    • Nick Gotts

                      Granted, that was a nutshell characterization of what Lyell seemed to believe.

                      It’s reasonable to say that Lyell confounded methodological principles with substantive hypotheses, and that the latter have been modified as evidence of catastrophic events has been found – but it’s absurd and indeed dishonest to fail to distinguish Lyell’s views of uniformitarianism from those of modern geology. Science, unlike creationist pseudoscience, advances by collecting evidence, and testing and (where the evidence justifies it), modifying or abandoning hypotheses.

                      Darwinism has not been abandoned, of course, but amended, deepened and broadened in accordance with discoveries made since Darwin’s time. You evidently don’t know what “neo-Darwinism” means: it’s the fusing of Darwin’s central theories of common descent and evolution by natural selection, with Mendelian genetics, as developed into population genetics by Fisher, Haldane and Wright.

                      For example, “the flood” may have consisted of a huge meteor strike, catastrophic disruption of the earth’s crust and atmosphere, gravitational and magnetic alterations, rapid tectonic plate movements, huge tsunamis, release of core elements from deep

                      within the earth, including the associated heat and radiation, as well as solar radiation’s effect through an atmosphere temporarily lacking defenses, etc. Try to responsibly factor in what all of this might do to the various dating methods of life on earth.

                      But such a catastrophe would have left clear evidence of its occurrence, which it has not – you are just making stuff up. If it had disrupted radioactive dating methods, it would have made them incompatible with each other, and with the geological sequence which was already worked out from the Cambrian onwards before radioactivity was even heard of. It has not. Again, you are just making stuff up.
                      According to the biblical timetable, the flood cannot have been more than a few thousand years ago, but we have ice cores going back hundreds of thousands of years – utterly impossible if the kind of catastrophe you blithely invent had occurred. Stop making stuff up to protect your religious dogma.

                    • Lee

                      Yes I love it when creationists say “It COULD have happened this way or that way” as if that means anything. Like the misused word “theory” which most people believe means wild speculation. Before you even get to the theory, you have to come up with a REASONABLE hypothesis based on OBSERVATION.

                      Yeah one of the biggest problems with creationism is trying to fit in the ice age. They proclaim that it was a RESULT of the flood. Yet apparently the writers of the bible never noticed this? What about the other cultures? What is really stupid is that civilizations existed BEFORE the supposed flood and apparently magically re-appeared AFTER the flood with no disruption at all?

                    • http://irrco.wordpress.com/ Ian

                      the point still stands that applying uniformitarian assumptions results in catastrophic conditions in the relatively recent past by anyone’s evolutionary paradigm.

                      Erm, how does that point still stand?

                      Where in the mathematics of the dynamics of the earth-moon system is there the implication of “catastrophic conditions in the relatively recent past“? Or even of “uniformitarian assumptions”?

                      And why does an “evolutionary paradigm” have anything to do with the nonlinear dynamics of planetary motion?

                      After having your claim shown to be totally false in both detail and effect, you don’t get to say “well my conclusion stands”, if you do the math how I do it.

                      As on the other thread, you’ve simply invented this fiction of scientists using assumptions you’ve projected onto them, and then you come to conclusions no scientist ever would and attack that as if you were doing something useful. I think the metaphor I used before is even more strong here. You seem to be rather a Don Quixote character in this discussion. For all your talk of worldviews and presuppositions, you seem to be unable to actually describe what your opponents position is, in ways they would understand. So you’re off galloping through the windmills imagining you’re winning great battles against the giants.

                    • stuart32

                      The geologic column was worked out before the development of radiometric dating. That is very convenient because then radiometric dating can be used as an independent test of the order in the geologic column. For example, we determined that Cambrian rocks were older than Jurassic rocks before knowing their absolute ages. Radiometric dating confirmed this.

                      The interesting thing is that the conclusion stands even if the rate of radioactive decay has changed. If the rate had changed we would be mistaken about the absolute ages of the rocks but not about the fact that Cambrian rocks are older than Jurassic rocks.

                      Of course, the rate couldn’t have changed enough to make a 6000 year earth look like a 4.5 billion year old earth without turning the earth into a molten inferno.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      When someone has looked into a subject in detail, having previously been a young-earth creationist and then changed his mind as a result of the evidence, it is rather silly for you to complain that I ought to do this or that before judging the viewpoint in question. You clearly have gullibly embraced things that you were told without fact-checking them. I encourage you to do so. Why not turn to someone like Francis Collins? An Evangelical Christian, and one of the leading biologists in the world? Why turn to the dubious sources that you’ve accepted without question and accept them on authority?

                    • Spaced-Out SCIENCE

                      But I’m confused—why should I accept your word–because you changed your opinion in one direction? You know as well as I that people can change their opinions based upon faulty information. I could cite other people, including myself, who changed their views in the other direction, but that adds nothing credible to the discussion. Maybe we all should more highly regard people like Behe, who has been fairly consistent all along or folks like John Lennox who consistently and charitable deals with the philosophical elements of science and religion.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      You should not under any circumstances accept my word, particularly if it is about a matter of science in which I have no expertise. Nor should you accept a fringe view just because the individual who holds it does have relevant expertise, since you can always find someone with relevant credentials who holds a particular view. You should ask what the consensus of experts is. Academics are required to try to challenge prevailing views in order to publish. If we agree on anything, the evidence for it must be pretty strong indeed.

                    • Spaced-Out SCIENCE

                      The problem with that logic is that no consensus of so-called scientists has provided any observed evidence of macro-evolution and yet plenty of astonishingly arrogant statements
                      abound regarding their certainty that it did happen. Given the lack of credible evidence, this “certainty” would have to be classified as faith, belief and even “religion” of some sort. Also, if Lazarus or anyone else were resurrected today in front of Richard Dawkins, he would be powerless to prove scientifically that a miracle had or had not occurred. Science, nor a consensus of scientists, can provide all the answers. Having an automatically dismissive attitude towards God, faith and religion or even a possible young creation is arrogant and unwise.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      You are misinformed about the evidence, and the consensus, because you choose to blindly accept what you are being told, without consulting even Christian experts in biology, assuming you consider others untrustworthy. Might I recommend anything by Francis Collins or Francisco Ayala, and in particular, Ken Miller’s Finding Darwin’s God?

                      It is as though you have never read Proverbs 18:17: “The one who states his case first seems right, until the other comes and questions him”. Having gathered information from the dubious sources you have, why have you sought no second opinions? Does this matter really mean so little to you that you would gladly hear charlatans but refuse to read works reflecting genuine expertise? If so, then why proclaim your view in such blatant ignorance? Or are you deliberately trying to damage the reputation of the Christian faith?

                    • Spaced-Out SCIENCE

                      I’m afraid you are resorting again to attacks of my intentions, research capability and scientific discernment. Accusing me of “blindly accepting” a position which you so easily mischaracterize is nothing but a naked assertion. Why do you presume to know whom I have read
                      or not? You have tried to label essentially all my reading as “from dubious sources”. Well, I read Ken Miller’s so-called answer to Behe’s explanation of why the bacterial flagellum demonstrates irreducible complexity. I would say that Miller’s answer way definitely dubious. You accuse me of not seeking second opinions. Don’t be ridiculous. What you may really mean is; why haven’t I arrived at the same opinions as you? You accuse me of taking these things too lightly and consulting charlatans. None of that is factual but merely ad hominem. Then you ask if I am deliberately trying to damage the reputation of the Christian faith. That’s quite ironic considering that I’ve spent the last 3+ years studying and researching certain biblical ideas and
                      their integration with certain scientific thoughts. My book is called God’s Reputation in the Balance…have we really gotten it right? After I read your thoughts on hell, I think
                      we might actually agree on more than we don’t, at least on that subject. Certain declarations regarding hell have certainly damaged the reputation of God, unfortunately.

                    • beau_quilter

                      Oh, don’t worry, no guess-work needed. You make it as clear as day how limited your reading is. How many other Biologists have you read (besides Behe) who support Intelligent Design? Ken Miller is not, by a long shot, the only scientist who has completely debunked Behe’s ideas (not hypotheses, not theories) about irreducible complexity.

                      Behe is a laughing stock in the scientific community. Even his own department at Lehigh University posted a complete disowning of his ideas on their website:

                      http://www.lehigh.edu/~inbios/news/evolution.htm

                    • Spaced-Out SCIENCE

                      Please show me who has credibly refuted the following article:

                      MichaelJ. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘TheFirst Rule of Adaptive Evolution’,” Quarterly Review of Biology,Vol. 85(4) (December, 2010).

                    • beau_quilter

                      Well, there’s not that much to refute because Behe’s assertions in this particular review (note, no original research, no experimentation – it’s just a review), are extremely limited in scope, as he himself makes clear.

                      But if you would like to read useful responses:

                      http://biologos.org/blog/series/behe-lenski-and-the-edge-of-evolution
                      http://whyevolutionistrue.wordpress.com/2010/12/12/behes-new-paper/
                      http://bcseweb.blogspot.com/2010/12/behes-review-in-context-or-whats-point.html

                      The real measure, of course, is that there are so Few responses. Field-changing studies are not ignored, they are pounced upon by the academic/scientific community prompting frequent citations and continued research. Behe’s dull little review has landed on the scientific landscape like a drop in the ocean, if it even has that much effect.

                      Do you know what really astounds me about you, though, Spaced-Out? You are only referencing people that are useful to you, when they are useful to you. As you brandish these studies by “scientist” Behe, do you even realize that he believes in common descent, an ancient age to the earth confirmed by geology, and no literal global flood?!!

                      You have such inconsistent beliefs, you can’t even find sources that agree with you!

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      I would just add to SPACED OUT that, in my opinion, when there is an overwhelming consensus among experts in a field, those outside the field really have no business picking a views held by a small number of people in that field who are clearly motivated by ideology, and embracing that instead of the consensus. I don’t care if the subject is Intelligent Design, aliens building the pyramids, or the health impact of smoking. Hunting for rogue experts who say what we want to hear always leads to finding some such person. But the whole reason for having a system of higher education with experts is to help prevent ourselves, individually and corporately, from being so easily led into error. This isn’t to say that the consensus can’t be wrong. But if it is, it will come to light either as a result of the ongoing study of the matter by the experts themselves, or by someone outside the field learning that field’s methods and content and making an overwhelmingly persuasive case that persuades the experts. Despite what some say, the latter is not entirely impossible, just rare and unlikely. But either way, we should all be suspicious of those who cannot persuade their peers and yet try nonetheless to convince the public that they are right and the majority of experts are wrong.

                    • Spaced-Out SCIENCE

                      I seem to recall that the researcher who discovered that Helicobacteria pylori causes gastric ulcers was ridiculed for years and years. Everyone wanted to continue to believe that type A personality, stress and a whole lot of other things were the culprits.
                      The fact that Behe may have, at some time in the past, said he agrees with certain “mainline” beliefs only gives him more credibility in his area of expertise. If he aligned himself completely with a YEC type model, you would assassinate his character based upon that! The areas mentioned are not in his area of expertise and so I say he is allowed some latitude. The fact that I agree with his assessment of evolutionary limits doesn’t mean I have to worship him as an ideologue in general. Nor should anyone else.
                      I believe that Behe may have been influenced by Hugh Ross. I have studied Ross’ synthesis and find that it certainly has merit. I do not believe he should be called a heretic as some have done. Ross is also not a biologist and is a little weak in certain areas. I also believe he makes some potentially wrong assumptions about the Bible and about God, but in the grand scheme of things, I’m not sure how much they matter. I think his influence adds more good than confusion.

                    • beau_quilter

                      I see. You only agree with “scientists” in matters where they agree with you. How convenient for you.

                    • Spaced-Out SCIENCE

                      You seem to be suggesting that appealing to popularity or appealing to authority are not actually errors of logic! I choose to think for myself and it matters little to me that someone like Behe largely avoids conclusions on the issues you raise. I’ve seen him speak and debate in public and I don’t recall him making any dogmatic proclamations except to show, as he has always argued, that mutations and natural selection have very definite limits. Have you read his book THE EDGE OF EVOLUTION?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Here’s a link to my review of The Edge of Evolution way back when: http://www.patheos.com/blogs/exploringourmatrix/2008/03/reviews-of-michael-behes-the-edge-of-evolution.html

                      Your suggestion that Behe’s views are not even what he has published is silly. I can say that Richard Dawkins is a young-earth creationist who is just pretending to be a supporter of mainstream science, setting himself up to have a dramatic conversion at some point in his life. If we are willing to deny what is written, then any view is possible – which of course is precisely what it takes to be a young-earth creationist.

                    • Spaced-Out SCIENCE

                      Edge of Evo was published in 2007. I say him speak publically 4 years of so after that. Which would you say matters more? Regarding the other issues, did he merely express limited opinions or did he venture to provide scientific evidence to support them? There’s a big difference. I don’t subscribe to anyone’s opinions because of who they are. I simply agree with the evidence which Behe has cites to support his concept of irreducible complexity. I realize that his view on this is unpopular because it tears at the very soul of the evolutionary paradigm and too many people are far too committed to that ideology than to following the facts.
                      I wonder, have you looked at Hugh Ross’ biological/mathematical analysis of why evolution is not possible, except for organisms less than one centimeter in size and reproductive cycles of 3 months or less, as he says???

                    • beau_quilter

                      So you’ll quote Hugh Ross when he agrees with you about evolution. But you’ll discount him when he disagrees with you about the age of the earth?

                      How convenient for you.

                      “I saw him speak publically 4 years after that. Which would you say matters more?”

                      Are you saying that you have heard Behe change his views about common descent since 2007?

                    • Spaced-Out SCIENCE

                      In case you missed my previous post, I will repeat part of what I said re. Ross:

                      I have studied Ross’ synthesis and find that it certainly has merit. I do not believe he should be called a heretic as some have done. Ross is also not a biologist and is a little weak in certain areas. I also believe he makes some
                      potentially wrong assumptions about the Bible and about God, but in the grand scheme of things, I’m not sure how much they matter. I think his influence adds more good than confusion.

                      As for Behe, it is meaningless to debate something unless you clearly define your terms and premises. In the final Q & A session in a debate including Hugh Ross and Terry Mortenson (YEC proponent), I recall Behe saying that his beliefs fell somewhere in between the other two or that his beliefs regarding the synthesis between science and the Bible might be malleable. He seemed to have an open mind, willing to look for further evidence. I like that. I’m in a similar position.
                      My point of entry into this thread was to point out the hypocrisy of pretending to be open minded while calling someone who supports YEC a dolt. Ridiculing one model of thought or the other, or hurling labels of heresy, are not helpful. What might be helpful is to periodically remind ourselves of the factual existence of paradigm inertia. We can all succumb to it if we’re not careful. Before ridiculing someone else’s inertia, Jesus suggested cleaning up your own inertia first (Hezekiah 3:16 or something like that!).

                    • beau_quilter

                      Assuming for the moment, it is completely unflawed, and putting aside the lack of attention it has received, what, exactly, do you think Behe’s review actually says?

                      I don’t think it says what you think it says …

                      And if you think Behe doesn’t actually “avoid conclusions” when it comes to the age of the earth and common descent, then apparently you are the one who hasn’t read THE EDGE OF EVOLUTION:

                      “Evolution from a common ancestor, via DNA changes, is very well supported” (p. 12).
                      “[O]ne leg of Darwin’s theory—common descent—is correct” (p. 65).
                      “The bottom line is this: Common descent is true” (p. 72).
                      “Despite some remaining puzzles, there’s no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives” (p. 72).

                    • Spaced-Out SCIENCE

                      Ah…we’re just now getting to the meat. Does Behe state clearly what levels of taxonomy he believes common ancestry to pertain? Sure, we all agree that all finches come from a common ancestor. But do finches and
                      dogs have one? Do Dogs, Finches and Daisies have a common ancestor? Behe certainly seems to lean towards a concept of universal common ancestry, but leaning is
                      not proof of dogma, doctrine or science of any flavor. More importantly, Behe’s entire emphasis is on the HOW could it happen question. He started his book basically stipulating to certain assumptions and conclusions others have made in order to set up his discussion of HOW. Further on page 72 he says; common ancestry (within a genus) “although fascinating, is in a profound sense trivial. It says merely that commonalities were there… It does not even begin to explain where those commonalities came from… Something that is nonrandom must account for the common descent…”

                      Computer programs can change over time. They can also be copied, replicated or reproduced. Because you
                      find some odd feature deep within the bits of Microsoft Word program and it looks just like what you find in a PowerPoint program, do you assume they had a common ancestor? Do you assume that they all came about by only natural processes including mutations and natural
                      selection? Rather silly, wouldn’t that be?

                    • beau_quilter

                      Sorry, Spaced-Out (really fitting handle by the way), but arguing over what Behe believes is hardly getting at the meat of anything. The more I read of Behe, the more I realize I am wasting time.

                      As I seem to be doing with you. Since you never really address the critical questions asked of you.

                      Where do you get bizarre “analogies” like comparing software programs? What do engineered software programs have in common with organisms that produce offspring through known biological processes?

                      You began this latest meaningless argument by challenging us to produce a refutation for a Behe review. But you never said why. What do you think the review says that demands refutation?

                    • Spaced-Out SCIENCE

                      If I recall correctly, Behe revisits Miller’s so called refutation of irreducible complexity in the bacterial flagellum. I’m not aware of a credible come-back by Miller or anyone else. Behe’s point has always been that mindless evolution must have a credible pathway—a mechanism of accumulating useful genes.
                      That pathway must logically conform to the maxim that Darwin gave—that each small successive step along the way must have an advantage to survival and/or reproduction of the cell or organism. Otherwise, “selection” is inoperable. It is ludicrous to assume that 17 genes which together in perfect harmony produce anything like a flagellum could ever spontaneously arrive by any know mechanisms of mutation and/or replication errors. Each gene would have to sequentially appear and have an advantage in and of itself.
                      No such pathway or mechanism has been demonstrated. Miller nor anyone else has even given us a
                      comprehensive theoretical pathway to such a thing regarding complex structures, especially because they require specific direction and regulation of the assembly
                      process. Just because a house and an outhouse have the same nails does not mean that the one can spontaneously go on to produce the other.

                    • beau_quilter

                      The flagellum is Behe’s old argument. You’re out of touch. Behe doesn’t use it anymore because he knows it doesn’t hold water.

                      You’re still ignoring the question. What idea in Behe’s 2010 review do you think needs to be refuted?

                    • Spaced-Out SCIENCE

                      A similar protein can be used as one element in the construction of a mitochondria and also the endoplasmic
                      reticulum, let’s say. Miller would tell you that this refutes irreducible complexity of one or the other. What he fails to see is that completely different assembly instructions, regulation of insertion timing and limiting of overproduction, etc. are necessary components which completely eclipse the
                      superficial comparison he has made. This fact brings I.C. right back to an extremely valid argument, despite your
                      appeals to popularity and your ad hominem against Behe.

                    • beau_quilter

                      Do you even know what you’re talking about? There are multiple independent peer-reviewed articles demonstrating the evolutionary relationships between type 3 secretion systems and the flagellum. Do you know how many peer-reviewed articles Behe has produced to refute these findings? None.

                      I.C. was never a valid argument to begin with – it is unprovable notion that has never been vetted by peer review and has no experimental ramifications whatsoever.

                    • Spaced-Out SCIENCE

                      You: “demonstrating the evolutionary relationships between type 3 secretion systems and the flagellum”

                      Me: A truthful statement would replace the word demonstrate with the word hypothesize. These articles proved nothing, nor did they demonstrate anything about the past. They only surmised, from their Naturalistic
                      biases, a possible link between the two things.
                      These possible links are so insignificant, however, because they ignore the vast amount of specific and complex information necessary for the placement, timing and regulation involved in the two different processes of
                      construction. A brick can be found in a house and a mausoleum. Entirely different blueprints are needed, however, as well as other things to complete each project. The thing which they have in common is the intelligence that created those plans, directions, instructions.

                    • beau_quilter

                      Demonstrating is quite truthful.

                      But it would also be truthful to say that, as you aver, that these are true scientific hypotheses based on the fact that these systems share complex protein structures with the flagella that Behe insisted were “irreducible”. Whether or not you “buy into” evolution theory (as 99% of scientists do), what is undeniable is that there, in the lab, are Behe’s “irreducible” structures – clearly existing in reduced forms.

                      Behe’s notion of an irreducible flagella, on the other hand, doesn’t even qualify as a hypothesis, as he has never published any scientific studies on the topic (only popular books like Darwin’s Black Box) and there is no peer reviewed research or publications of any kind supporting the notion of irreducible complexity.

                      Behe himself has had to concede that “There are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred.”

                      Even Behe hasn’t published scientific articles or research arguing for irreducible complexity.

                    • Spaced-Out SCIENCE

                      You still don’t get the fact that somewhat similar
                      structural elements means almost nothing when you consider that all the rest of it, especially the assembly instructions, timing and regulation, etc. is very complex and completely unique. For it to work, all parts, instructions etc. have to be there together in working order before natural selection can start selecting. Applying reasonable math to that kind of complexity should blow anyone’s mind. I wonder…at what infinitesimal probability would you or anyone else agree that something is actually impossible? If the answer is that it
                      would take more molecules than exist in the entire world, just to randomly arrive at a DNA sequence which would make only one component to the flagellum, would you then agree that it is impossible under known natural conditions?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      This is a silly question, since no one is suggesting that this all simply assembled randomly – except science-deniers like yourself who misrepresent what scientists say, since tackling what scientists actually have to say is too hard for you.

                      And as for similar elements of DNA not proving anything, you are welcome to try that as your defense in court, but if the paternity test results come back and determine that you are the parent, the court will rightly require you to pay child support, because the court understands what DNA evidence means, even if you do not.

                    • Spaced-Out SCIENCE

                      I did not say “similar elements of DNA”, I clearly said “somewhat similar structural elements”. And similar is not identical! I suspect that the DNA coding for each is substantially different. And that’s the point you fail to see. The rest of your post is simply off-point. If you bothered to read Behe’s book, you would understand that Darwin’s maxim of evo’s progression having to be shown as slow and incremental accumulation of new traits MUST be applied to DNA, since that is what we know produces it all. You have to evaluate the DNA which codes for each protein AND ALSO the segments which are necessary for its proper folding, insertion, regulation, etc. No gene is an island! It’s all interrelated in very complex ways that defy simplistic descriptions. It is those inappropriate simple descriptions which deceive you into thinking they might have occurred spontaneously. The solution is to responsibly apply the math to known cell biology.

                    • beau_quilter

                      Spaced Out, you make me laugh!

                      The notion that “all parts, instructions etc. have to be there together in working order before natural selection can start selecting” is a completely false premise. Irreducible complexity is unproven and rejected by scientists. There is no, I repeat NO scientific article or research demonstrating irreducible complexity.

                      Do you really think an anonymous blog commenter who believes in flood geology has the scientific credentials to insist that we “don’t get it”.

                    • Spaced-Out SCIENCE

                      “Proving” I.C. is like proving that you can’t drive a car until the steering wheel, gas pedal and brake pedal are installed. If you stop and think about it, everyone knows this is true but who would bother “proving” it? Behe is truly an original thinker, however, unlike so many Darwin lap dogs. He is one of the few scientists asking the incredibly relevant question of whether or not a Darwinian mechanism exists at the cellular level. His conclusion, and many people agree, is that extant genes can be altered slightly by mutations and acted on by natural selection, but no credible mechanism or path has been demonstrated for spontaneously amassing the complex specific instructions for assembly and regulation of structures and systems analogous to a mouse trap. Not one credible scientist or layperson would even dare to suggest that a mousetrap could function without one of its parts in place at the right time and ‘regulated’ by something/someone who would bait it and set the spring. But, I.C. is a kind of anti-theory, seriously challenging the assumptions and premises of
                      evolution-loving folks. Why would they want to study it? It’s a hell of a lot easier to engage in categorical denial, appeal to popularity, false appeal to authority, ad hominem, battling straw men, and other fallacies of logic, hoping
                      that others won’t notice that you aren’t doing real science at all, but rather dirty politics! BTW, you are still ignoring
                      the math.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Merely challenging assumptions and premises is not enough. The challenges must be persuasive, on the one hand, and some better framework needs to be offered on the other.

                      Scientifically speaking, counter-evidence for claims of irreducible complexity have been offered. Theologically speaking, depicting God as the designer of intelligently-designed killing machines like malaria and e coli is scarcely something a Christian ought to do.

                      But the heart of the matter is this: Claiming that your views are rejected because of a conspiracy against you is what all cranks and crackpots say. And so if you want ID to be taken seriously, you will need to stop presenting it as a crackpot theory and start doing the scientific research necessary to make an actual persuasive case for it.

                    • Spaced-Out SCIENCE

                      You keep resorting to old, tired and irrelevant
                      arguments, despite my previous dissection of them. I already explained a reasonable hypothesis for reconciling God the Creator with malaria’s existence. Your conspiracy straw man has also been previously asked and answered. Why don’t you quit dodging the real challenges?
                      Did you review Craig Venter’s work? Don’t you see that his team created a million-long sequence of DNA with
                      specific and recognizable uniqueness—distinct from anything “natural”? From the tiny changes that Lenski’s 20-year experiments over 35K+ generations of E. coli “produced”, is it responsible to say that these things could ever produce what Venter produced? You MUST run the math on that to realize the answer, otherwise you are engaging in pure magical thinking, not scientific. BTW, what would you call Craig Venter’s accomplishment…I mean, how did he do it? Did he use “artificial selection” of mutated genes, or any kind of gathering/reworking/recombining of extant genes? No. He
                      designed his idea on paper and then started with one nucleotide in the lab, adding successive ones until the chain was completed. Weeelll….. I got news for you ostriches with your heads in the sand…..what Venter did is called INTELLIGENT DESIGN!!! Yea…and nothing we have observed in anyone’s lab has shown that “nature” can do the same. No mythical DNA typewriter or “gene machine” has been found…no pathway or mechanism to macro-evolution demonstrated at all. And a responsible evaluation of mathematical probabilities says it’s impossible! There are not enough atoms on the face of this earth.

                    • beau_quilter

                      Spaced-Out, it’s clear that yours are the old, tired, and irrelevant arguments. You haven’t dissected anything.

                      And your understanding of Craig Venter’s work is banal. So … he “started with one nucleotide in the lab, adding successive ones until the chain was complete” … really?! Where did you get your kindergarten conceptions of genomic science?

                      You keep talking about mathematical probabilities, but I haven’t seen you produce one calculation. If you’d like to read about why the “probability” argument is bonkers, here is a good source:

                      http://scienceblogs.com/evolutionblog/2011/08/16/probability-and-evolution/

                    • Spaced-Out SCIENCE

                      Venter’s work proves that Intelligent Design works—it’s a fact! Lenski’s experiments fail to show a path or mechanism for similar accomplishment by only natural processes. No gene machine or DNA typewriter was shown to exist or be at work. But if it were to exist, it absolutely could not do what Venter did. How many excuses can you come up with for ignoring the math?
                      Forget about probabilities for the moment—there is a related fact which is easier to understand and incredibly significant. Simply calculate how many molecules would be used up in a random process of combining all possible sequences for a set length of DNA. Start with the number 10 (a tiny fraction of what Venter created). And
                      don’t forget that if a random process were at work creating such sequences, Natural Selection would have no power or influence whatsoever until each sequence were run through the ribosomes to see what resulted. But remember that DNA sticks together once formed—you can’t simply re-shuffle the cards and start over if it doesn’t work! Molecules that are attached into useless sequences are not only used up and are unavailable for recombination
                      but they can also gum up the works with clutter. How much clutter might that be? Run the numbers. Don’t be afraid. But then realize that a #10 sequence gives you virtually nothing to work with. The “start” and “stop” codons use up 6, which then leaves you with only 4. That only results in one amino acid—not even one protein and certainly not life! Realistically, you need to run the math on a DNA sequence of at least 100, just to get one small protein. If a random process were actually running off all the possible sequences, it would use up more molecules than exist on the face of this earth. It is purely magical thinking to suppose this process would simply stumble across the
                      right sequences before much clutter was produced and before running out of molecules for trial runs. Think about
                      it. Realize that the ENCODE project demolished previous ideas about “junk DNA” making up the majority content of
                      genomes and thus testifying to random origins. With no more “junk DNA” to appeal to, you have to admit that another creative force was at work—one like Venter!

                    • http://irrco.wordpress.com/ Ian

                      Why would you do such a ridiculous bit of math to show that a made-up version of evolution that no scientist claims is correct is incorrect?

                      All conversations with spaced ultimately end up with his inability to comprehend the position he is arguing against, even on the most basic level. He just knows they are wrong, and is willing to bodge any talking points he half remembers to prove it.

                      Once again (this must be about the fourth time now), can you describe evolution in a way that an evolutionist might recognize and agree expresses their opinion?

                      Lots of mud-slinging, no actual attempt to engage? So what is it spaced? Can you, or are you merely inventing enemies to slay with your lofty self-opinion?

                    • Spaced-Out SCIENCE

                      Refusal to honestly look at the math is usually followed with excuses like: it’s too difficult, we just don’t know all the
                      factors, it’s impossible to tell how natural selection helped here (circular reasoning, by the way), and; nobody can prove that nature has to be exactly this way–there may be millions of other life forms that could result with other DNA sequences…we just happen to be the lucky ones, etc. One fact rises above these excuses: the start and stop codons for any gene need to be in precise locations, regardless of what’s in between. Do the math on that. Any complex structure like a flagellum or an eye or wing needs at least 15 genes (probably much more). If you just consider how many molecules would get used up in a random process of trying start and stop codons in all possible locations, you would quickly use up every carbon atom on the face of this earth. Natural Selection might “park” the losers by the roadside, but they are still used up and unavailable for retrial and they are in the way. You MUST somehow
                      generate one cell with the starts and stops in just the right location, minus significant clutter, or you’ll never get a flagellum, much less an eye or a wing.

                      If you are hauled into court and tell the Judge that those fingerprints or DNA also belong to someone else, good luck. Common sense understands basic truths about
                      probabilities. If you go to Vegas and win at the tables every day for a week…look out…you’ll probably be arrested or at least thrown out. Most everyone will
                      be thoroughly convinced that random processes were replaced by some high form of intelligence. If one person won the Powerball lotto every day for a month, a Judge would be rightly petitioned for a search warrant of that person’s computer, phone records, etc., and he would
                      readily sign it, merely from common sense knowledge of statistics. “Probable cause” would be easily recognized. People generally know what can and can’t happen in the real world. But go into a science classroom and show that belief in spontaneous macro-evolution requires nature to win the lottery every day in a row for trillions upon trillions of years and suddenly people’s eyes glass over as if they just smoked some wacky grass and they say: … “yea, sure…that could happen”.

                    • http://irrco.wordpress.com/ Ian

                      I can do the math, it isn’t too hard. I did a PhD in the math of evolution. I’ve run the math literally hundreds of millions of times. I’ve done it. We absolutely don’t know all the factors (though we can put bounds on things, and check the math works for the range of values within the bounds), and it is absolutely crucial to factor in the lottery winner’s fallacy to any calculation of probability, regardless of how much you want to scoff at it. Both of which are simply basic parts of doing any probabilistic model (if you used math to argue in court, say, you’d do the same), neither are excuses for anything. Certainly neither are excuses for rejecting your math. Which is wrong simply because it is based on a bizarre misrepresentation of evolution.

                      Your math doesn’t correspond to any model of evolution that any scientist claims. Your model is just made up, conjured out of your ignorance of actual evolutionary biology. Of course if we consider silly scenarios we get silly results. The rule of garbage in – garbage out holds for maths. And the version of evolution you seem to imagine is garbage. Now i understand why you want to not understand it, because it feeds your ego, thinking you’re sticking it to those heathen and closed minded evolutionists. But all you’re really doing is showing your painful ignorance.

                      So again, please describe the evolutionary mechanisms in a way that an evolutionary scientist would recognize. Rather than another exercise venting your obvious incredulity, actually try to accurately and systematically describe what you think you’re arguing against. Then, if math is really your passion, we can talk about how to build a mathematical model of those mechanisms. And we can do the math, and see what happens.

                    • http://irrco.wordpress.com/ Ian

                      I would also like to point out the irony of your previous comment as to your intentions here:

                      No, my purpose was not to declare my own belief system or to tell you in any way what you should or should not believe. Rather, my intent was to clarify your thoughts, profuse as they seem to be, and suggest that you have more room to allow for other people’s beliefs which are different than yours, instead of so quickly mischaracterizing them, scoffing sarcastically at them and vilifying them.

                      Given that you’re entire interaction here has been to mischaracterise what scientists claim and then scoff at it!

                    • beau_quilter

                      Venter’s work prove’s evolution? It’s a fact only in your stunted imagination.

                      Well your strained effort at math only reveals that you have no idea how natural selection works. Have you ever wondered why Behe has never published such “mathematical proofs” against evolution in a scientific journal?

                      Sorry, but ID can’t take credit for predicting the value of “junk DNA”; that functions would be found for DNA previously deemed “junk” was predicted by legitimate evolutionary scientists long before and without the help of IDiots. And these functions were discovered by legitimate evolutionary scientists in the field. The bozos at the Discovery Institute have never “discovered” anything.

                      And what the heck do you think Venter “created”?! He sequences genomes. He’s not trying to create anything, except a process for figuring out the configuration of genomes.

                    • Spaced-Out SCIENCE

                      You apparently missed Venter’s recent claim to have created “the first artificial cell”. His team assembled a one-million-long string of DNA with specific sequences designed by them. It took multiple trials before it “worked” because they had one wrong molecule. The plain truth, however, is that this working ‘gene’ or ‘chromosome’ or whatever you wish to call it is clearly a product of intelligent design! Venter is very intelligent and he designed and constructed the one-million string from scratch. Imagine what a being with even higher intelligence could do!

                    • http://irrco.wordpress.com/ Ian

                      Beau,

                      Venter’s institute made a bacterium genome by sequencing genes from a Mycoplasma mycoides bacterium into a series of fragments, duplicating these fragments in yeast, then transplating the result into a M. mycoides cell that had had (as much as possible of its) DNA removed. The aim was to replace the coding for all biochemical pathways that would allow for homeostasis and replication. The PR from the project claimed that they’d created the first ‘artificial cell’ or ‘artificial organism’, which given what they used as raw materials, is rather over-egging it!

                      But still, while using the cell’s protein synthesis machinery, the actual genome looks nothing at all like any natural genome. It looks like a genome that was intelligently designed: it is modular, regular, and systematic.

                      So in one sense Venter’s work proves intelligent design. In the sense that it shows that something intelligent can design something! But then, it is more of Spaced’s weird imagined alternate universe that would suggest scientists think nothing can be designed by an intelligence. Venter is hardly the first there, we’ve been designing biological systems for decades, and as tools improve we’ll do it differently and better.

                      I think the creationist’s bizarre logic is somehow that scientists think genomes must have evolved, because we can’t possibly believe anyone could be capable of designing one. Which is, of course, nonsense. Part of the imagined scientific worldview that creationists love to bash.

                      If the suggestion is that Venter’s synthetic genomes have the same design characteristics as naturally occurring genomes, then the suggestion is fanciful. There is no genome scientist in the world who couldn’t tell the difference between Venter’s M. mycoides and the wildtype.

                      Once more, I’m afraid, Spaced is showing that he doesn’t actually understand the science, nor can he explain what a scientist would expect to see, in any way that any scientist would recognize. Instead he raises straw-men an yelps in glee as he cuts them down, imagining he is a brave defender of the faith.

                    • Spaced-Out SCIENCE

                      “any genome scientist could tell the difference” (between Venter’s DNA and wild type).

                      If you were paying attention, Venter stated that he specifically designed it that way. If he had not, other researchers might have doubted his claimed accomplishment.

                      All of your attempts to mock me do nothing to change the fact that micro-evolution has never been shown to produce macro-evolution or even get started along a pathway which we could reasonably extrapolate in that direction. Lenski’s long term evolution experiment (LLEE) started with E. coli which had around 4000 genes and ended with the exact same number of genes. Certainly, there were
                      minor changes in several of those genes but additions were not made—instead, merely minor alterations were made in extant systems of complex metabolism. It would be utterly irresponsible for any scientist to suggest that the changes seen in LLEE can be extrapolated in reasonable fashion to eventually produce a flagellum. The math says never in a trillion years. It would take someone like Venter working to add many new genes to the system in order to accomplish this kind of feat. Venter proved that ID is capable of this task. The math responsibly applied to
                      known cell biology proves that mutation + natural selection cannot do it. You cannot demonstrate that natural causes
                      are responsible for the creation of E. coli’s 4000 genes. If it could have started with 10 genes, it could never get to 11 genes via Lenski’s demonstrated results. Zero pathway, zero mechanism=zero macro-evolution. That’s an equation you can bank on.

                    • http://irrco.wordpress.com/ Ian

                      I’m not attempting to mock you. I’m asking you to simply express the position you’re arguing with in a way that people who hold that position would recognize.

                      This is now roughly the fifth or sixth time I’ve asked you. Each time you’ve either ignored my post, or tried to respond with more claims and misunderstanding.

                      I claim you are absolutely incapable of doing so, because you simply do not understand evolutionary biology.

                      Please feel free to prove me wrong.

                      Otherwise all your assertions about the probability of this, or the meaning of that, are transparently absurd. If you don’t even understand what you’re talking about. You arrived on this blog trying to claim that it is important to hear all sides of the discussion, and for people to learn and understand the ‘other’ position. It appears to me you have no inclination, or no ability, to do the same.

                    • Spaced-Out SCIENCE

                      I would love to engage in a real discussion of the math and
                      biology, but first we have to set the stage with some agreements.
                      Questions 1: What would you say is the bare minimum of genes which a cell could contain in order to “be alive” and survive? Most bacteria have about 4000, but a lot of redundancy exists in various enzyme systems and many genes may not be absolutely necessary for survival in optimal conditions. Go back in hypothesized evo history to a place where none of that redundancy existed. Take an educated guess—how many genes would be minimally required?
                      2. How much “junk DNA” could any cell accumulate and still be alive and reproduce (or divide)? Just take an educated guess—would it be around 50%, 70% or what?
                      3. What would you say is the shortest functional protein in any cell—how many amino acids make it up?
                      4. What probabilistic number would you say represents a falsification of macro-evolution theory? When the chance
                      of a theorized event happening is less than one in 10 to the what power would you agree that it’s essentially zero? If you cannot give a reasonable number, then aren’t you subscribing to a mere belief rather than a scientific theory?

                    • http://irrco.wordpress.com/ Ian

                      First we have to make sure you understand what you’re talking about. Which you’ve continually failed to do.

                      Now at the sixth time of asking, please lay out what you think the position you are arguing against is, and the grounds on which someone who holds it will have based their conclusions.

                      That you are trying every which way to avoid the question of whether you have any clue about what evolutionary biology actually says and why is deeply telling. I’m afraid you won’t divert me into discussing the conclusions of the science, until you can demonstrate you actually understand what the science is and how scientists think works. Then, and only then, is it worth discussing anything in more detail. You don’t have to agree, to be able to honestly and accurately describe your opponent’s position.

                      There’s no point discussing car maintenance strategies with someone who thinks cars have legs and live in the Serengeti.

                    • Spaced-Out SCIENCE

                      You seem to be trying to draw me into trying to satisfy you with some kind of proof of my knowledge. That’s a diversionary tactic. You also ask me to state a conclusion before you might consider answering my questions.
                      It is in the answering of those questions that you will learn what conclusions you might reasonably come to, aside from parroting arguments you read from TalkOrigins or elsewhere. Why not plow some original ground here? You
                      have consistently inferred your superiority in knowledge, which is why I asked you to respond to the relevant questions. I’ll try to work with the numbers that you are comfortable with and show you what it means in terms of probabilities. Or you can volunteer your answers first, if you want. My premise is simply this: that if
                      macro-evolution is possible at all, a mechanism or path must be elucidated or demonstrated which falls into reasonable bounds of known biology and known probabilistic limits. I do not accept the thinly-disguised
                      escape of saying “we just don’t know”, or “it’s just too difficult to specify conditions” etc. It’s precisely because
                      we do know so much that tells us an avoidance of careful analysis is cowardly. Also, saying that known mechanisms of micro-evolution can simply be amplified or added up in order to accomplish macro-evolution is specious—it indicates a refusal to carefully examine known cell biology and math. Macro-evolution would include something like a flagellated bacteria evolving from a non-flagellated one. Multiple new genes have to be added to the one in order to get the other. We can begin to do the math in order to see if this is remotely possible by any kind of mutation/natural selection scenario. You have the choice to examine the facts or simply hang on to your blind faith in evolution.

                    • http://irrco.wordpress.com/ Ian

                      You seem to be trying to draw me into trying to satisfy you with some kind of proof of my knowledge.

                      No, I’m asking you to demonstrate you’re not making up views to argue against. Because it looks very much like that’s what you’ve been doing all along. And I asked you to do this way before you started trying to ask me to pick probabilities to plug into your screwy maths.

                      It is a really simple request. If you can clarify what you think evolution actually is, and what grounds you think scientists have for it, then we can look at a) whether that is actually what scientists think and why, b) how to encode that into mathematics, and c) the implications of such calculations.

                      I’m pretty sure I could explain Intelligent Design in a way that an ID-er would recognize, and describe the theoretical basis put forward to justify it. If I was in a discussion with someone who promotes ID and they continuously suggested that I was misunderstanding what ID was and how it is understood by those who hold that position, I would gladly offer my interpretation and see where the mismatch is. Doing so doesn’t mean I would ‘lose’ the conversation, or concede anything. It just means I would potentially decrease my ignorance, or at the very least make the conversation more constructive.

                      Why can’t you do the same for evolution? If you think you know evolution well enough to be able to do probabilistic calculations on it, why can you not describe it in basic terms that an evolutionary biologist would recognise?

                      As I said before, no point discussing numbers, with someone who doesn’t understand what the numbers mean.

                      You appear to be all bluster, but no actual foundational knowledge. If you disagree, prove me wrong. Your manifold excuses and attempts at misdirection are fooling nobody.

                    • Spaced-Out SCIENCE

                      Me thinks you forget or ignore what I’ve said previously. Darwin’s theory rests on a premise that still stands unchanged by “Neo’s”—if the theory is valid, all life forms must be shown to have come from other life forms by a series of small incremental changes. The critical question you evo’s neglect or refuse to talk about is what the smallest increment of change would be in order to make a significant move up Darwin’s supposed tree of life. You conflate point mutations or rearrangements of extant genes as the smallest unit of evolutionary change. You would then propose that this is the appropriate place to apply any math to. You are mistaken, because these changes are dead ends, adding no new additional genes to a genome. (Lenski showed this.) They could rightly be termed parasitic changes only. To advance up the tree of life, you must generate new additional genes which produce new additional innovations and functions. One would be tempted, then, to think that a single gene would be the smallest unit of evolutionary change. This is where Behe’s work comes to light. In reality, one single new added gene would not likely get you much change. Most genes function in concert with numerous other genes to produce enzyme systems, complex structures and processes. The Kreb’s Cycle is a classic example of an
                      inter-related enzyme system which requires many genes in order to exist and function properly. The usual tactic to weasel out of acknowledging these things is to suggest that “it didn’t have to be this exact way…it might just as well have been other ways of doing the same thing”. You may be partially right, in theory at least. But whatever system of energy usage and transfer you might propose…still requires genes. And genes require specific start and stop signals for transcription then translation, as well as complex regulatory tools like operons, etc. So apply the math to that! Pick a modest number of DNA molecules that would be required to form the start and stop sequences, with simply an average number of codons in between.
                      Grant your theory the benefit of saying that the stuff in between doesn’t have to be very specific—that almost anything might work. Just don’t forget—the starts and stops are very specific. And if you have a process
                      of random generation of these, it would likely be the same process for the stuff in between. You can’t have your
                      cake and eat it too—the calculation of how many molecules would be irreversibly linked must be faced. All the wrong start and stop codons would be linked to useless strings of DNA called “junk DNA”, using up a limited supply. So, the questions I posed earlier remain extremely relevant—how much junk can a cell tolerate? What probabilistic or combinatorial number would you say represents a falsification of macro-evolution theory?

                    • http://irrco.wordpress.com/ Ian

                      Still avoiding the question, I see. Doesn’t surprise me. How many thousands of words are you going to spend avoiding a simple, straightforward question?

                      I’ve gone back and re-read every comment you’ve made on this site, and in none of them do you lay out the basic evolutionary science that you are claiming to mathematically model. If I’ve missed something feel free to copy and paste it in response.

                      This is important, because it is very common for folks to show up spouting talking points but unable to articulate the science they are trying to attack. By and large creationists and IDers get all their knowledge from creationist or ID resources, and only ever read any actual science with a narrow focus of derision. So although they can throw around the same examples they’ve read on creationist sites, they can’t actually engage in any sensible conversation on the science, because outside the talking points, they have no clue. They’ve never taken more than an intro to biology class, they’ve never done any practical science, they have no experience. So that’s why it is an important question. Do you actually know what you’re talking about? You appear not to – you appear to be stringing together vaguely remembered bits of the apologists you’ve read, with a bit of personal improvisation that makes less sense than the people you’re challenging.

                      Which is why you’re so afraid to actually give an account of your assumptions on what evolution is and why it is the way it is.

                      Chalk another one up to invincible ignorance, I guess.

                    • Spaced-Out SCIENCE

                      The assumption which Naturalism makes (and I refute) is that natural processes alone have, under any known circumstance, produced a new ADDITIONAL complex cell structure or enzyme pathway (AKA macro-evo), or even COULD do it. To pose the argument that evo theory does not propose this, is to ignore known cell biology and to ignore the absolute necessities involved in moving up Darwin’s tree of life. Using Lenski’s evidence in attempts to prove macro-evo is erroneous.
                      Damaging existing complex genes and playing shell-games with them is not the same at all. NO new gene was added—no new start and stop codons with anything new in between. It is not a pathway to moving up Darwin’s tree. Each significant step along taxonomy (i.e. genera, families, orders, and up) would require far more, at the gene level, than any demonstrated mutation + natural selection can produce—each step needs the de novo generation of multiple genes working in concert, all
                      present at once (and genomic data confirms this). In fact, each living cell we know of today is Irreducibly Complex by a simple irrefutable definition: Take away the cell wall and it dies. Or, take away the DNA and it dies. Take away the transcription & translation enzymes and the cell cannot replicate or reproduce. Take away the histones needed to keep DNA organized, and it likely dies. Take away the mitochondria…etc. etc. Multiple
                      structures, systems and enzymes MUST BE in place at the same time and place in order for a live cell to exist. And all those things require critical information to be encoded in the genes, each with very specific start and stop signals, among other things. And a very limited amount of random gunk can coexist in the same cell. What you Evo’s need to do is put your money where your mouth is and apply the math to known cell/molecular biology instead of getting all misty-eyed thinking about what “might have…..could-a,
                      would-a or should-a” happened. I have no doubt that your mythology is popular, but so what? Show me the beef. Show me you can do the hard work instead of
                      merely offering pretenses, excuses and fallacies of logic. Otherwise, get off your bigoted bashing of
                      ID/Creationism because Venter actually gave us proof if its validity, among other things. Yes…micro-evo is proven by other evidence…nobody doubts that. But
                      conflating MICRO- with MACRO- is unproven and thus represents only wishful thinking. I am asserting that
                      solid evidence indicates macro-evo is impossible. Do the math.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      I don’t think you grasp that what you are saying are old canards that we do not find persuasive, and for good reason. You seem to think that you are a genius and can see what the mass of foolish scientists cannot. Whenever you find yourself in that situation, it is wise to ask whether it is not more likely that the experts in their knowledge do not know something that you are missing.

                      In this case, you are trying to make an inept math-based case against something that can be observed, and thus any math which allegedly says that phenomena we observe are impossible must by definition be flawed.

                      Perhaps consider that the “language” of DNA has only four letters, all “words” are three letters long, and every word means something, and you will realize that your protestations about what random processes cannot do is off target.

                      http://www.patheos.com/blogs/exploringourmatrix/2007/09/monkeys-and-typewriters-on-the-edge-of-evolution.html

                      http://www.patheos.com/blogs/exploringourmatrix/2011/11/monkeys-typewriters-and-evolution.html

                      Perhaps, since you are clearly not an expert in either the math or the science related to this question, you have been misled by analogies that turn out to themselves be problematic?

                    • Spaced-Out SCIENCE

                      You: “you are trying to make an inept math-based case against something that can be observed”
                      Me: Have you observed a new “start” codon being added to a genome? Lenski did not! I’m sure it is possible to do this with enough trial and error combinations. And Darwin’s tree of life demands that millions of them be generated. But, no matter what your process of generating those sequences, you have to admit that 63 out of 64 of them are going to be wrong. That alone will mean that 98.5% of the genome is “junk”. Worse yet; once you happened to get a correct start codon, 66% of what randomly followed it would not be divisible by 3, hence it could never be correctly “read” by the ribosomes. We haven’t even discussed the actual content of the genes and the likely specificity required there, and yet our calculation is that 1/64th times 1/3 would be our success rate, at most. That’s 0.516%, leaving 99.5% failures or “junk DNA”, not to mention the huge amount of junk amino acid combinations that would result. Now review what the ENCODE project revealed about how little junk is actually present in cells. There is no known mechanism for purging random junk out of cells. Natural selection cannot do it. Mutations cannot do it. What other “tools” does evo have? Nothing. The demonstrable lack of random junk in cells obviously means that another mechanism had to have been responsible for their creation.
                      Put your money where your mouth is–find any reputable cell biologist to refute this math. Find one reputable scientist that would agree that there are enough carbon atoms in this world to allow for the inevitable number of junk sequences to form in a random process of generating the first cell on earth. Then, show me evidence that such a prolific process actually exists in nature, for combining all the possible trial-and-error sequences. Lenski failed to show it. No one else has either.

                    • http://irrco.wordpress.com/ Ian

                      Put your money where your mouth is–find any reputable cell biologist to refute this math.

                      Or alternatively, find any reputable cell biologist who recognises your characterisation of what evolutionary theory contains, expects or predicts. You do that, and then we can talk about the math.

                    • Spaced-Out SCIENCE

                      So, you refuse to answer my legit questions and you refuse to offer your own refutation of my math. Isn’t that the definition of someone with their head in the sand? Really…it’s not so hard…why don’t you take a good collegiate try. How many molecules do you think would have been used up long ago just trying to get the first string of 300 DNA molecules OF THE CORRECT ISOMER? That’s really short, but in theory it might give you 3 genes producing 3 proteins of 31 amino acids in length. Never mind anything else–just calculate the odds of flipping a coin and getting 300 consecutive heads in a row. This would be appropriate because natural environments with any nucleotides at all would contain roughly equal isomers of left and right hand. The correct answer is that 2 to the 300 power # of molecules would be used up in trial and error fashion, on average, to accomplish this minimal task alone–and that is more molecules…no…it’s actually more ATOMS than exist on our planet. And at this point you haven’t even begun to create specific codons, genes, proteins, cell walls, mitochondria or anything else necessary for life.

                    • http://irrco.wordpress.com/ Ian

                      I can’t even begin to ‘refute’ your math, because it isn’t based on any recognizable concept of evolution. So I’m asking you to clarify. And you’ve refused on nine requests to describe the biology on which it is based! Anyone can make up random numbers and demand that people ‘refute’ them. But that’s meaningless unless we can start from the basis of making sure your numbers correspond to something.

                      Honestly, how hard is it to understand?

                      I get that you want to play some bizarre kind of projection or distraction card and make out like I’m failing to answer your questions or not producing any evidence to refute your devastating critique. Perhaps you’ll continue this charade for weeks more and claim victory because nobody on here was able to ‘refute’ your maths, so therefore clearly you were right and everyone was slain by the devastating force of your arguments.

                      But my response is far simpler. Please describe, in detail, the evolutionary biology that you think you are modelling!

                      Then we can talk about whether your biology corresponds to evolutionary theory, and if so what are reasonable ways to model that mathematically, and the conclusions that might then arise. Who knows, that process might actually lead to the conclusion you are claiming. In doing so we might discover that the math of evolution doesn’t work. If you are genuinely confident in your mathematic ability, and the conclusions it will lead it, why does building it around a model of evolutionary theory, that actual scientists would recognise, scare you so much?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Interesting. It took only seconds to fact check your claim against online lecture notes, textbooks, and journal articles, and to learn about the phenomenon of overprinting, which is one of the documented ways that new genetic information is produced when a new start codon results from a mutation. If it took me a matter of seconds to fact check your claim and find it to be false, then that suggests that you have put even less time into trying to understand this field in the first place.

                    • Spaced-Out SCIENCE

                      You are mistaken again and as usual, you did not pay attention to the details. If a mutation creates a start codon where one did not exist before, you might get something usable, if and only if you have the right number of nucleotides from there to the stop codon. More importantly, that mutation just parasitized or destroyed an existing gene. So, where is the ADDITION of a new functional gene to the genome? BYW, did Lenski demonstrate this hypothetical mechanism? No. Show me one example that has been scientifically demonstrated, showing that one functional gene gave rise to two different functional genes via the process of overprinting. Throwing hypotheticals around as if they are fact is bad arguing. All along you have been telling me that, although you just don’t know how it happened…”trust me, macro-evo is true”. Sorry…I’m not buying it, and frankly, for a guy who claims to believe in God, you mystify me with your incredible faith in evolution (macro). Where, if at all, do you see God entering the picture?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Why not read some of the articles freely available online or through library databases about the evolutionary role of such mutations, instead of insisting that they can’t exist or can’t do anything useful for no better reason than that you have made up your mind in advance about this?

                    • Spaced-Out SCIENCE

                      I was actually looking forward to where you fit God into evo history. Anyway, I would ask you if you think men evolved from chimps and if you think that occurred purely by natural evolution? If so, use the data that Lenski’s bacteria actually demonstrated and use the know genomic differences between men and chimps and then tell me how many generations of men and how many years that would take to achieve the difference in genomes (if you are not aware, humans differ from chimps in 40 million places).

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      No one thinks humans evolved from chimps. If that is what you think evolution is then you know less than a well-informed Middle School student.

                    • Spaced-Out SCIENCE

                      Pay close attention:

                      (from Science Daily News, 2006)

                      The researchers paid special attention to gene number changes between humans and chimps. Using a
                      statistical method they devised, the scientists inferred humans have gained 689 genes (through the duplication of existing genes) and lost 86 genes ***** since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence, the total gene differences between humans and chimps was estimated to be about 6 percent.
                      Trying to hide behind word-games i.e. the use of “evolved” versus “common ancestor” is beneath the level of an informed AND HONEST Middle School student.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Since you did not provide a link, I can only assume that the source is talking about the number of genetic changes separating humans and chimps as a result of our evolution from a common ancestor. If it doesn’t mean that then there is a problem with the article.

                      Your arrogance about matters that you cannot even speak about accurately is a disappointing character flaw in anyone. But in someone who claims to be a Christian, it is a betrayal of what ought to be your core values. You have been duped by a satanic lie that is training you in deceit and hubris.

                    • Spaced-Out SCIENCE

                      Your feigned righteous indignation and straw-man techniques forces me to reiterate what you apparently overlooked in my last post:

                      Trying to hide behind word-games i.e. the use of “evolved” versus “common ancestor” is beneath the level of an informed AND HONEST Middle School student.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Adding words the meaning of which you seem not to know, and reference to logical fallacies which you do not understand well enough to recognize whether they are applicable, does not help your case.

                      Words matter. Concepts matter. And using them correctly matters. If you do not understand that “evolved” and “common ancestor” are not the appropriate contrast to make (presumably you meant “evolved from chimps” vs. “evolved from a common ancestor with chimps”?), and do not realize that many people misunderstand evolution at precisely this point, and that the difference between the two matters, and that the evidence supports one of those two and does so strongly, then why are you even having this discussion?

                      Would you discuss a subject about which you are so poorly informed if your identity was known and your reputation could be affected by the impression you give? I suspect not. And yet you are happy to sully the reputation of Christianity by associating that name with your ignorance. And so you clearly care less about Christianity than you do about yourself.

                    • Spaced-Out SCIENCE

                      Your persistence in quibbling and nit picking about terminology indicates that you prefer to attack straw men instead of addressing the substantive questions I’ve raised. You refuse to acknowledge common-usage language in place of technically correct jargon in an internet thread full of common language. If you cannot see that “evolved
                      from chimps” is an abbreviated way of saying “evolved from a chimp-like creature”, it is only because you refuse to grant me the common decency you would like for yourself. Where is your Golden Rule, thou professed Christian? And
                      where does your God fit in your evolutionary paradigm? Why do you continue to refuse an answer on that but instead Build Mountains out of grammatical or linguistic molehills?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      If I cannot see that you meant something other than what you wrote, then I am nit picking? But you still seem not to get the point. Evolution is not “from a chimp-like creature” as opposed to “from chimps.” It is from a population of common ancestors from which the populations of both chimps and humans descended.

                      The reason you think this is making a mountain out of a molehill is because you don’t understand the basics of biological evolution. Are you sure you want to continue illustrating this point? I’m very happy for you to do so, but I’m not sure why you want to!

                    • Spaced-Out SCIENCE

                      Let me ask you this: as I previously mentioned, Craig Venter created “the first artificial cell” by designing and building a unique genome then injecting it into a cell which he had removed a lot of natural DNA from. Now, assuming that cell proliferates many generations, how would you describe the “common ancestry” involved?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      When all else fails, try to change the subject?

                    • Spaced-Out SCIENCE

                      I’m on the same subject I’ve been on from the start–showing you that you aren’t as open-minded as all that posturing at the beginning. You have refused to engage on serious questions, preferring instead to offer sarcasm and hasty judgments. You have failed to address the substantive issues but in place you repetitively attack me on trivial semantics.
                      My question regarding Venter and his created genome is very central to the debate over whether ID makes sense or instead deserves to be scoffed at as you have consistently done. If someone unaware of Venter’s work were to examine his post-intervention cells, comparing them to the pre-intervention cells, they would notice striking similarities in parts of their genomes. They likely would assume “common ancestry”. But do we call it “natural common ancestry” or “artificial common ancestry”??? Perhaps “ID-ancestry” would do.
                      If you simply applied knowledge of cell and molecular biology with some basic math, as I have repeatedly, you should be convinced that macro-evo is in incredible trouble. The numbers just don’t add up at all–their not even close. But now look at the demonstrated abilities of intelligent design! Nuff said.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      So anything that humans can do in a laboratory cannot come about through natural processes? The actual fact is that humans regularly seek to replicate natural processes for experimental purposes. I can’t imagine why you think there is a basis for your case in this, unless your ignorance about evolution ranges to science more generally.

                    • Spaced-Out SCIENCE

                      You: So anything that humans can do in a laboratory cannot come about through natural processes?
                      Me: Bravo–that is exactly the kind of question you should be asking and then testing it with known chemistry and cellular biology–for example, the evidence which Lenski gave us. Did natural processes create any new start and stop codons with new functional sequences between? The answer is no…not in 35000+ generations. Now look at the chimp-human differences in genes–in the many hundreds. Is it rational to think that natural processes are capable of such successes…and with complete lack of the obligatory junk that natural processes tend to create? Don’t answer too quickly as is your habit–carefully study the real chemistry, cell biology and math first. If you need some help, I can send you a chapter that explains it well.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Seeing as you have shown that you don’t understand evolutionary biology, how can you possibly judge whether something “explains it well”? By all means share articles, but the chances are that, unlike you, I have actually read them, and also critiques of them, and so I understand what is wrong with them in a way that you either are unable to or choose not to because of your ideological biases and dogmatic refusal to accept correction from those with greater expertise than yourself.

                    • Spaced-Out SCIENCE

                      For a guy who claims to be a Christian, you are amazingly free with your insults. Your comments remind me of the guy who says “don’t confuse me with the facts…my mind is already made up”! They also remind me of the adage that says; “a man convinced against his will is of the same opinion still”. But I want you to understand one thing very clearly–my purpose in interring this thread was not to convince you to give up all you ideas about evolutionary modeling and accept an alternate explanation. It took me several years of study and reflection to make that decision. I sincerely hoped that you would simply see from the substantive questions and data I’ve shared, that you would temper your intolerant attitude towards ID/C folks and begin to actually live up to you “open minded” claim which began this thread.
                      PS–you haven’t read the articles I was referring to because I haven’t published them yet. Unfortunately, they are not yet in a form that I can share a shortcut link to access them. I mentioned in a previous response that I was just finishing a book by the title; GOD’S REPUTATION IN THE BALLANCE…have we really gotten it right? A couple of early chapters deal with actual evidence related to evolutionary modeling as opposed to ID/C, in a careful and detailed way.
                      But this is probably moot because you have refused at least tree times to share your own integration of your evo beliefs and where you think God fits in. I’m kind of wondering if you are actually what you profess to be or instead merely someone who found it occupationally convenient or even opportunistic???

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      This is quite amusing, given that you have been remarkably free with your denigration of scientists and their work, and you come across as someone whose view is precisely “I have made up my mind, don’t bother me with the facts.”

                      I have read the available arguments for ID and find them wanting, but more importantly the scientific community finds them wanting. And they are not fundamentally less problematic than the design arguments that many found impious already centuries ago.

                    • Spaced-Out SCIENCE

                      And how you fit God into your paradigm???
                      As I have already said, I am a person who actually changed my mind because I carefully studied the evidence and facts. If I denigrate anything, it is not personalities as such but instead the ideas of evolutionary bigotry which are so common in the halls of academia these days. I’m simply challenging them to re-evaluate the evidence, particularly some stunning recent evidence, instead of resting on their pompous tenured laurels. It’s not about me. It’s not about you. The facts are much more important than that.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      So your aim is to find a way of making room for God in a world that science increasingly explains? That’s a dangerous game that has been played time and time again, and religious faith never benefits from the losses. We need to make sense of the world as it is, and God in relation to that world. We cannot say that we want there to be room for God and then rewrite the evidence from the natural world to that end. At least, we cannot if we want to be honest and not to live in constant fear of science’s progress.

                    • Spaced-Out SCIENCE

                      Funny you mention “rewriting evidence”. So many examples of this have occurred involving
                      evo-loving “scientists”, your suggestion is beyond ironic. Look again at the “punctuated equilibrium” theory, the cosmic seeding theory, the multiverse theory, etc. These are examples of where scientists have honestly faced the fact that the actual evidence could not support their
                      desired beliefs, hence they reached for anything to prop up their failing paradigm. I see no reason to be
                      SCIENCE-PHOBIC. It’s 99% opinion and 1% science, so many times.

                      “religious faith never benefits from the losses” you said.
                      What is lost, aside from straw men? Making an example of old geocentric beliefs is specious because it clearly rested on such spurious interpretation of such minimal scripture. We should learn a lesson from this–to not be
                      dogmatic about such things. But throwing the baby out with the bathwater makes no sense. Too many areas of the Bible make it clear that God created us, without
                      saying how or exactly when. The fact that macro-evolution has never been demonstrated, never seen, never even facilitated by designed parameters of experiments, leads me to believe that the Bible is correct in its basic assertions…all subtleties and nuances notwithstanding.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      That’s simply ridiculous. The interrelatedness of all living things and the macroevolution that accounts for it are able to be demonstrated to a much higher degree of probability than historical claims in the Bible. If you have a different impression, then you must be as poorly informed about how historical study works and its application to the Bible as you are about science.

                    • Spaced-Out SCIENCE

                      What’s really ridiculous is that you attempt to prove the
                      validity of macro-evolution by appealing to “the inter-relatedness of all living things”. That is classic circular
                      reasoning! You are using a premise to prove a premise. The fact that two premises or two hypotheses seem to complement each other is not proof that association equals causation. And as to fearing science’s progress, go back to my example of someone examining Venter’s before and after cells without knowledge of what he did. Do you think Venter is afraid that this person(s) will use inferences of science to say that natural processes were responsible for the “common ancestry”? Maybe what you missed seeing is that what gets advertised as “science” is often nothing more that compatible theories committing mental masturbation over their agreement. It’s like a ‘scientist’ gleefully reveling in Hawking’s Multiverse hypothesis because he sees it somehow validating his belief in the “cosmic seeding” hypothesis or perhaps even the hypothetical “RNA world”, etc. Ask yourself one important question—how much actual scientific evidence stands behind each of these ideas? The answer is; nothing, nothing, and all-but nothing. Now, who’s afraid of nothing?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Ranting does not make your case sound more persuasive.

                      When there is a DNA match in a paternity test, it will always be theoretically possible that it is because both individuals were abducted by aliens and the match is due to alien manipulation of their DNA. But the court will rightly decide that there is a much simpler explanation, and not because they assume what they need to prove but because they understand the significance of DNA evidence and apply deductive reasoning to it in an appropriate manner.

                    • Spaced-Out SCIENCE

                      All automobiles may appear to be “inter-related”
                      but that means nothing unless you are combining that observation with premises (assumptions) about causation and origins. The inter-relatedness of all life forms on earth means nothing aside from presumptions regarding possible causation. Ontological Naturalism, which you apparently subscribe to, makes the brash premise that no other means of origins is possible that “natural” processes. This Ostrich technique might
                      be less objectionable if you could prove that natural processes alone can actually create a gene. All life on earth depends upon genes. Where did they come
                      from? What or who is capable of producing them? Let’s look at some actual evidence instead of wishful storytelling and jaundiced retrospecascoping:

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                      Ok then…it is proven that intelligence can create genes. Now for the evidence that spontaneous natural processes can do it:

                      Lenski’s long term evolution experiments…0 genes added to E. coli. Absolutely NO macro-evolution demonstrated. As for any other scientific experiments…zip, zilch, nada, the big Zero.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      You seem not to even understand what this conversation (if one can call it that) is about. And I really do understand how hard it is to admit that one is wrong or that one does not understand something. But asking for help in understanding matters of science outside one’s area of expertise is admirable and nothing to be ashamed of.

                      Saying that we should leave room for the supernatural is all well and good. But one should not jump to the conclusion that the supernatural is involved. If the police investigate a murder, at what point ought they to close the case and, in the absence of a clear human perpitrator, decide that God killed the victim?

                      If you want to dispute mainstream science, you will need to spend time in a lab, and not merely address one experiment that you think supports your position, but the multitude that clearly do not.

                    • Spaced-Out SCIENCE

                      You: “Saying that we should leave room for the supernatural is all well and good. But one should not jump to the conclusion that the supernatural is involved.”

                      Me: Sure, I agree, but
                      what’s good for the goose should be good for the gander—jumping to conclusions
                      that spontaneous processes can create genes is just as error-prone.

                      You keep alluding to some mythical laboratory evidence for macro-evolution in action—where is it? Hallucinations don’t count. Beliefs don’t count. That’s your arguments against God as Creator…so live by your own rules or else accept the label of hypocrite.

                      James, I think your fears related to what science might dig up in the future may indicate that you haven’t carefully evaluated your own religious beliefs in terms of Essential beliefs versus Non-essential beliefs. Some groups make unfortunate declarations, for example; that creation in 6 literal days is an essential belief, otherwise you are a lost heretic! That has never been my position.
                      Based upon the premise that resurrection is true (see I Cor. 15), I merely conclude that it would be silly to think God incapable of doing it that way if He so chose. As to the actual scientific evidence…well, you need to be extremely careful about labeling assumptions and biased interpretations of evidence as “science”. Exercising discernment here might bring some clarity to your beliefs, I think. Otherwise, you are perilously close to the descriptions of 2 Peter 3:5-7.

                    • Spaced-Out SCIENCE

                      Comparing forensic medicine with evolutionary modeling of origins is like comparing apples to asteroids. The comparisons made in forensic cases between
                      humans completely lack the huge differences which exist between men and chimps, for example, or any other “kinds”.
                      Because of these differences (which I previously cited) and the lack of evidence for spontaneous gene production, a responsible judge should throw the case for common ancestry between the groups out of court! The case is overwhelmingly in favor of intelligent intervention instead of naturalism.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Well, courts have actually decided differently than you think they ought to have. And you can keep saying “no new genes” but that just shows you have not understood the evidence presented to you.

                      Talking about “kinds” suggests that you are so steeped in misinformation that you probably have no idea just how badly you have been misled.

                    • Spaced-Out SCIENCE

                      You have already shown a propensity to play word games, so rather than use the word species with its debatable meaning, I used the word kinds. You also obfuscate my position by continual misquotations and assertions that you know what I’m thinking. Let me repeat clearly–I am telling you that no additional novel functional genes being added to a genome has ever been witnessed occurring in any lab. We have never seen E. coli go from 4000 genes to 4001 genes, with that new one creating a new functional protein or enzyme. All the giggly talk about what MIGHT have happened in the remote past is not a “demonstration” of anything but a wet dream. It is not science, it is something else.

                    • newenglandsun

                      Are you talking about speciation?
                      Google the rhea then the ostrich then the emu.

                    • Spaced-Out SCIENCE

                      No, I specifically avoided the word species and speciation because of the debatable meanings. I’m looking for scientific evidence from observed laboratory findings that a genome can spontaneously grow in number of unique and functional genes. This evidence is what would provide validation to the MACRO-side of the theory of theory of evolution. Without this evidence, Darwinism is just an incredible overreach–it is no more than opinions shared among those who wish it to be true.

                    • newenglandsun

                      So are you saying God deceived us? I, unlike James McGrath, can show that the God paradigm not only fits in well with the theory of evolution but does not suffer any bullets from it either.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      All this comment illustrates is that when you were presented with scientific articles you either did not read them or did not understand them or are pretending they do not exist. Which is it?

                    • Spaced-Out SCIENCE

                      What it may really illustrate is that I used critical thinking skills when reading those articles, instead of swallowing the propaganda hook-line-and-sinker, like so many others have. Can you tell the difference between
                      overreached opinionated conclusions about evidence versus the actual evidence? Again I give you an example which you previously ignored:

                      “The
                      researchers paid special attention to gene number changes between humans and chimps. Using a statistical method they devised, the scientists inferred humans have gained 689 genes (through the
                      duplication of existing genes) and lost 86 genes since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence, the total gene differences between humans and chimps was estimated to be about 6 percent.” (from Science-Daily News, 2006 link: http://www.sciencedaily.com/releases/2006/12/061219201931.htm

                      Without the Darwinian propaganda, it would read more like:

                      Chimps have 86 genes that humans do not and humans have 729 genes that chimps do not, in addition to 689 genes which appear duplicated in humans but not in chimps, for a total of 1504 apparent gene differences, based upon a devised statistical method of analysis. This infers about a 6 percent difference between the two gene groups.

                      From this point, an honest scientist might begin to wonder about possible causes and begin to hypothesize. No jumping to conclusions should be allowed. No confusion between premises, presumptions and
                      conclusions versus facts should take place.
                      It’s very important to think critically at all times.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Without the anti-evolutionary propaganda, your comment says “I can change what the results of science actually say and conform them to my preconceived notions, making them seem like they say something else.”

                    • Spaced-Out SCIENCE

                      Really? Shadow-boxing instead of engaging with the evidence again? Do you know your cell biology,
                      chemistry and math 101? Do you know the published mutation rates, the average size of human genes, the genetic code and its requirements in terms of start and stop codons, at the very least? Do you realize that within
                      these indisputable facts and features, and the previously-referenced data are the elements of a powerful refutation of macro-evolution having caused the observed differences in genomes? A true scholar would be eager to see it, to evaluate it, instead of appealing to old and stale
                      propaganda. I think for myself and my analysis is my own, but if you were patient, humble and moderately astute, you could also deduce it for yourself. I would be delighted to help you, if so desired.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      You keep repeating your assertions, and yet when challenged on the details you show that you can’t even get the terminology of the relevant scientific disciplines right, never mind the details. Why do you keep up this pretense? Why offer to help others instead of asking for help for yourself?

                    • Spaced-Out SCIENCE

                      I entered this discussion by challenging your assertion to being “open minded” and tolerant of other beliefs than your own. You countered by defending your open-mindedness while at the same time uttering ever-more opinionated scorn towards those who believe differently than you. That irony alone might, after careful reflection, cause you to reconsider. And that is really all I hoped for.
                      I did not expect you to embrace a different worldview but merely to give up your unfounded and arrogant intolerance of someone else’s interpretations of
                      the actual evidence. I gave you enough scientific evidence to see that your allegiance to Darwinism is, well, willfully blind allegiance. My repeated attempts to
                      engage you on the actual science have only resulted in your repeated avoidance of it like the plague.
                      Your reasoning seems to always return to a defense which essentially says; ‘you are not talking my language, therefore I am justified in attacking your thoughts and negatively labeling them’. What you are really
                      saying seems equivalent to; “if you don’t agree with my conclusions then I reject you and find any excuse to defame and scoff at you”.
                      I hope you eventually realize that you are caught in a death-spiral of ever-increasing bigotry only masquerading as being “open-minded”. If you have an honest interest in ‘hearing’ the other side and engaging on a discussion related to religion’s intersection with it, you might start by reading (or re-reading) Behe’s THE EDGE OF EVOLUTION and then seriously answering the question I have posed to you so many times: where do you see God fitting in here?
                      That could be a far more meaningful discussion than the inane jousting of opinions and insults you have engaged in.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Ah, but you see, you have not done the things you claim to have. What you have done is to repeat deceptive claims made by cdesign proponentsists in various places, which had already been considered and evaluated here, but more importantly, had been evaluated by the scientific community and been found wanting, or been investigated and found not to have the implications that the ID spin doctors claim.

                      What you have done, time and again, is to show that you do not have the necessary understanding of the relevant scientific disciplines to discuss these subjects, nor the wisdom to defer to the consensus of experts in the absence of such expertise.

                      It is not appropriate to ignore or oppose science because it seems not to leave room for divine action. That was tried in Newton’s day, but gravity carried the day. And yet many of the theological edifices built thereon proved to be misguided, not because Newton was wrong, but because we see and know in part and all our constructions have limitations – but even more so in theology than in science.

                    • Spaced-Out SCIENCE

                      Ah…what you have done is persistently refuse to engage in the real meaning of scientific evidence and facts, and instead you rely on casting aspersions as to
                      my “expertise” (which is irrelevant here and serves only as a diversion from addressing the real issues), while simultaneously you retreat to your usual hollow
                      appeal to authority. You obstinately fail to acknowledge the difference between evidence and interpretation of said evidence. You tirelessly assume that popular interpretations (among evolutionists) are equivalent to evidence. You and others have consistently failed to
                      cite any evidence that novel functional genes can spontaneously be added to genomes purely by mutation and natural selection. Yet, you persist in believing that
                      macro-evolution is true. That, my friend, is the blindest of all blind faiths! Please, don’t continue to insult my intelligence by further attempts to reassert your beliefs as “science”. They are not. Real scientists make clear
                      distinctions about where the science ends and the speculation begins. You, sir, have done nothing but muddy those waters. That approach only leads to
                      ignorant bigotry, not to educated “open-mindedness”. The Emperor has no clothes. Your response is to kiss up to his ‘expertise’ and authority. I prefer to keep my eyes
                      and intellect open to the truth rather than propaganda.
                      You persist in pressuring me to “defer to the consensus of experts”. Is that what Newton, Einstein and a thousand other independent thinkers did? Ludicrous! Did they instead appeal to their own ‘expertise’? Hell, no…they simply kept challenging others with the evidence. Eventually, others began to see the truth. This is what I hope you will eventually accept. In the meantime, I will be satisfied for you to simply release some of your bigotry towards ID/C ideas, since I have demonstrated that they are clearly tenable in light of the evidence.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      You misunderstand once again. I am not suggesting that those working in the natural sciences should not challenge consensuses. That would be ridiculous. Scientists and other scholars constantly seek to do precisely that. But not all such attempts are successful, and scientists and scholars typically know that the onus is on them to convince their peers. But you as someone outside of the field and with neither the ability nor apparently the interest to actually undertake pioneering scientific research deem yourself nevertheless wiser than not merely the scientists but than all those who have helped to shape the way scientific research is done over the years. It is only ideologically-driven denialists and ignorant fools who call it an appeal to authority to point to the consensus of experts on a subject. The fallacy is precisely to point to someone like Michael Behe simply because he is a scientist and to assert that, even though he has not persuaded his peers, nevertheless he must be right since he has the appropriate qualifications.

                    • Spaced-Out SCIENCE

                      Your repertoire of derisive and evasive rhetoric again circles around to previous vacuous positions. Opinions are not the same as evidence, no matter who is offering the opinion. You just refuse to get that. And yet, when someone presents clear evidence, it should not matter if they are a janitor or a rocket scientist. Truth is truth, facts are facts and evidence is evidence. Spontaneous generation of genes which lead to new genera is nothing more than fanciful speculation. You keep cloaking
                      that concept in a deceptive garb of legitimacy which is utterly false—it is a confabulation driven by evolutionary beliefs. When will you take your head out of the sand and begin to discuss the actual evidence?

                      .

                      You and others keep categorically bashing Behe without even beginning to address the evidence he brings to the table. You gleefully quote him by using your chosen sound-bites of misinformation while refusing to seriously study the evidence and contemplate its powerful
                      implications. Your assertion that “Behe has not convinced his peers” is nothing but ideologically-motivated propaganda. You keep playing fast-and-loose
                      with the facts. You are merely playing favorites by your choices of who you consider a peer, who you consider a
                      scientist and whose opinions you consider valid. What this tells me is that you are probably incapable of objectively evaluating the evidence for yourself. Therefore, you are merely functioning as a useful
                      lap dog for Darwin (or Jerry Coyne, Richard Dawkins, etc.).

                      .

                      This cultish thinking can be deprogramed though—it starts with facing the facts and with honestly grappling with the evidence. Macro-evolution is an unproven myth. No amount of evangelical hand-waving will change that. On the other hand, ID/C has demonstrated its ability to create novel genes instead of just tinkering with them slightly, as mutations have been proven to do.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      But you have not presented evidence. You have appealed to what you think is the evidence of others, and continue to simply assert that macro-evolution is an unproven myth even though you have been presented with evidence to the contrary. How can you be this dishonest and stubborn and consider yourself a Christian?

                    • Spaced-Out SCIENCE

                      Indeed I have presented evidence:
                      1. Review Lenski’s work — no new genes added
                      2. Behe’s analysis of AIDS virus, malaria etc. — no new genes added
                      Your assertion that “you have been presented with evidence to the contrary” is nothing more than obfuscation. Quit blowing smoke and face facts — macro-evo is nothing but speculation on what some people BELIEVE might have happened in the remote past. That is a far cry from demonstrating anything of substance. Furthermore, the calculation of what micro-evolution is maximally capable of is “evidence” in itself. You or anybody with a high school education can repeat that calculation with whatever variables you decide are reasonable. Why don’t you do that instead of blowing smoke? I’ll take you through it one step at a time if you like…
                      First, define the rate at which mutations occur in organisms (Behe said 1/100mil but other sources say 1/30mil. — choose one or provide a source that says otherwise).
                      Second, take a wild guess as to how many mutations might have to occur on a section of unused DNA to produce a functional new additional gene. (You are going to have to commit to a guess because no evidence exists that demonstrates an answer. But go ahead and choose low — choose a number which maximizes evo’s chances.
                      When you have answered these simple questions, we will move along to several others that need to be factored in. All of this is extremely basic science…no need to get cowardly and pretend it is too complicated. Man-up and answer the questions or else admit that you can’t think for yourself — you can’t rationally evaluate the evidence in an objective way.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      You are ignoring the counter-evidence for these claims that were presented you, and going back to simply repeating what Behe says. Why won’t you take this conversation seriously? If you don’t care about the truth, or the evidence, or anything else relevant to the discussion, then why do you persist in it?

                    • Spaced-Out SCIENCE

                      Again you fail to man-up and engage with the evidence. You keep offering naked assertions instead of honesty. Oh…wait a minute…one of your minions said that “Behe has been refuted”. But of course, no rational evidence was offered for that conclusion. And you, as usual, treat this baseless statement as if it were evidence or fact. How ridiculous.
                      .
                      I do not appeal to Behe as an authority. I do not rely upon his conclusions. Instead, I go directly to the evidence and correlate it with basic science facts which are readily available to anyone with an ounce of honest interest in facts rather than propaganda. The scientific analysis I began to share with you last post is not found in Behe’s work. Your empty disrespectful disdain for him is irrelevant when you simply look at the facts.
                      .
                      Go ahead and prove to me that you are more than just a talking head and an opinion jockey. Show me that you can actually handle an original thought. I will be glad to let you in on the secret that is so basic, so irrefutable and so profound that I promise you it will rock your world. Answer my previous two questions and then we will add several more bits of scientific evidence. Notice I’m not advancing my own opinion related to this discovery–instead, I allow you to give the opinion as to mutation rates and mutations necessary for the production of an added gene. Go ahead and advance any opinion you think is reasonably honest and rational and we will go from there. I will lead you to an amazing discovery if you are simply willing.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      As I have said since your first comment, a lot of these topics have been addressed on this blog before. Since then, many commenters responded to your assertions with relevant scientific studies that you showed you were incapable of understanding. You can keep making the assertions as at first while ignoring the responses offered to them, but readers of this blog are not as gullible as you seem to hope they will be.

                    • Spaced-Out SCIENCE

                      You: “many commenters responded to your assertions with relevant scientific studies”
                      .
                      Me: That is total hogwash and you know it…or else you are incredibly gullible. Over and over I have been asking for scientific evidence that natural processes alone can add a new unique useful gene to a genome. Obviously, you haven’t been paying attention because the only responses or references have been to mere theoretical ideas–essentially nothing but story-telling. No actual evidence has been cited because it is non-existent. Then, I repeatedly offer to show you evidence that refutes the fanciful story-telling…but you continue to evade. Your yellow stripes are showing, Mr. Opinion Jockey.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      I get that you are incapable of understanding the scientific studies that were offered to you in response to your appeals to Behe (and more ironically to Lenski). So why do you respond by ranting and simply asserting that no one presented evidence, when any reader can scroll through the comments and see that you are lying? Are you really an atheist troll trying to make Christians look unreasonable and dishonest?

                    • Spaced-Out SCIENCE

                      I’m just wondering…is there a book out there somewhere which fairly reasonably summarizes your beliefs as to the juncture of science and religion, specifically how God and evolution can best be reconciled? I’m guessing that Francis Collins’ THE LANGUAGE OF GOD might be the one but why don’t you simply tell me so I can search for the answers you persistently refuse to engage me on.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      I have not written a book with my own views on the subject, but Paul Tillich’s Dynamics of Faith does a good job of addressing the relationship between religion and science. Beyond that, authors like Keith Ward, Arthur Peacocke, and Ian Barbour can be recommended, but not as though reading any of them would give you precisely my own views. I would, however, recommend Ken Miller’s Finding Darwin’s God to help you understand why I think your claims about science have already been shown to be unpersuasive long before you made them here, and why I think that they are theologically and not just scientifically dubious.

                    • Spaced-Out SCIENCE

                      I’ve done some reading. Ken Miller portrays only two possible gods—his concocted quark-master photon-slinging otherwise uninvolved initiator of the laws of physics, or else one who micromanages everything at
                      all times and is thus responsible for all the imperfections and problems science is uncovering. This is a profane
                      and heretical false dichotomy and an example of the worst kind of pseudo-religion. Neither of Miller’s proposed gods fit with the Bible’s representations at all! Yet in bombastic rhetoric he likewise misrepresents the ID movement, incorrectly conflating it with the creationist
                      movement, and he egregiously misquotes and misrepresents Behe’s words and contribution to science.

                      .

                      Miller admits to ignorance regarding the science of life’s beginnings but only covers that with the usual smug inference that we’ll find it soon. What he fails to admit or provide any scientific hypothesis for, is how hundreds of genes appear while some disappear between every known different kind of animal (i.e. chimp-human) while their genomes remain virtually free of junk DNA (see the results of ENCODE project). What’s the mechanism, Mr. Professor? Surely you must have some idea??? He largely avoids the pivotal cell biology and chemistry, instead reverting to old and tired comparisons of incomplete fossils. This is the usual retrospective
                      speculation based upon equating similarities and association with causation. In the age of genomics, this is inexcusable pseudoscience. Answer the hard questions with real science or shut up.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Wow. Pretending you’ve read Miller now? Or perhaps you’ve just read him with such a bias that you dismissed all the important evidence he presented? Or is your “some reading” just an indication that you looked at something like the blurb on the back cover and considered that enough?

                      You’ve been presented hard science. The fact that some questions have not been answered is irrelevant – that has always been and always will be the case. The answers and evidence we do have points consistently in a particular direction, and proposing that there is a conspiracy working hard against your view which otherwise ought to persuade everyone is what all crackpots, cranks, and kooks say. And so what distinguishes your crackpot theory from ancient aliens, for instance? You are united in saying that mainstream scholarship unfairly dismisses the mountains of evidence that you’ve accumulated. What, if anything, separates you from other crackpots?

                    • Spaced-Out SCIENCE

                      Your harsh insinuations fall right in line with Miller and Dawkins. You misrepresent my ideas worse than Miller’s
                      treatment of Behe. I don’t recall saying I had mountains of evidence for “my theory” or anything like that. Over and over I have been simply trying to tell you that the genomic data I referenced is completely unexplained by any evolutionary cellular biology and chemical analysis. These unexplained gaps exist between millions of organisms as well as plants. What I repeat is that I am in possession of unique convincing evidence that evolution
                      can never jump any of those gaps. I’m in the process of having this peer reviewed and then hopefully published in a significant journal. I’ve offered several times to walk you through the scientific analysis, but you ignore. That, along with your apparent demeanor, reveals your unswerving commitment to your beliefs, evidence be damned. Your continual referral to “evidence given”
                      must mean the retrospective comparisons that you and others conclude causation from. In this age of known cell biology, this is lame, as well as a fallacy of logic.
                      Just admit that you haven’t understood the real science and I might be able to help. It’s really only dependent
                      on your attitude, and that continues to seem bigoted instead of open-minded. You only continue to confirm
                      the point of my original post.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      You seem still to not understand that you do not understand the relevant science sufficiently to be able to discuss the topic intelligently, since you have not responded to any of the scientific studies that were offered to you except in a manner that indicated a failure to comprehend the details of them and their significance for the matter at hand.

                      And since you are willing to proudly insist that you do understand, you obviously are leaving yourself open to being manipulated by promoters of pseudoscience.

                    • http://irrco.wordpress.com/ Ian

                      you do not understand the relevant science sufficiently to be able to discuss the topic intelligently

                      And refused to be clear about the genetic model that the ‘mathematical’ result was based on, despite being asked ten times.

                      But there’s no shortage of hinting at the some bizarre fantasy version of evolution.

                      Why not just come out with it, spaced? Detail your model of evolution in a way that a) fits your mathematical model and b) is recognizable to biologists.

                      Just admit that you haven’t understood the real science and I might be able to help.

                      Oh the irony!

                      I’m in the process of having this peer reviewed and then hopefully published in a significant journal.

                      Define ‘significant’ – as in a creationist journal, or an actual scientific journal? Because, if the latter, then you’ve going to have to spell out the genetic basis of your model in a way that other scientists might recognize. And if that will be in your paper, why the reluctance to do it now?

                      Other than the vain need to feel like you’re somehow sticking it to the ignoranti?

                    • Spaced-Out SCIENCE

                      Ad hominem is a pathetic excuse for substance. I have offered several times to walk you slowly point by point through the basic science and you seem to think that attacking me is an answer to that! If you had an ounce of honesty and integrity you might simply say; “O.K., I’ll take a look at it”. You falsely accuse me of “not responding to any of the scientific studies offered to you”. That is utterly ludicrous. I saw nothing in those studies to answer factually my most basic challenge to macro-evo ideas–how can mutations ever create a gene? I do not accept half-baked speculation. I want some real experimentally-backed evidence. If evo mechanisms cannot create genes, and a hell of a lot of them, then the fanciful ideas of Darwinists like Miller and you are simply equivalent to mental masturbation. I realize that it makes you feel good to believe that you are actually educated and participating in upholding the popular “consensus” against the challenges, but you’re shooting nothing but blanks here. You continually evade the substance and instead offer nothing but fluff. Sigh.

                    • http://irrco.wordpress.com/ Ian

                      I have offered several times to walk you slowly point by point through the basic science

                      I asked you ten times to lay out the basic biology in a way that matches your model and is recognizable by scientists. You made various excuses not to.

                      So maybe we got our wires crossed.

                      Yes, please walk us point by point through the basic science and show us how mainstream science leads to the probabilistic calculations you give.

                    • Spaced-Out SCIENCE

                      Great. First, I assume that you both are aware and reasonably versed in “the genetic code”–64 individual “codons” which represent “words”, while each of these is made up of three “letters”– triplets of DNA bases. Of course, they don’t stand separately, since DNA is usually present in very long helical strands. The determination as to what the codon actually is “reads” as…is determined entirely by the molecules which transcribe the genes and regulatory areas. -A-G-T-C-G- has 3 possible codons, depending on where the “frame reading” begins: AGT or GTC or TCG. All but three of the codons eventually get translated through ribosomes into amino acids. Therefore, the meaning of the codons is relatively specific and important. The degree of that specificity and importance is open to philosophical debate however. As an example of this, simply go to Amazon’s customer review of Meyer’s recent book; Signature in the Cell. Darwinists avoid like the plague any stipulation of specificity, complexity, “language”. Even the word “code” is anathema to some, as it infers a code-maker and designed code interpretation process. I’m fairly versed in the standard Darwinist responses to these thing (usually on the order of “with enough time and opportunity, anything can happen”, also the appeal to molecular affinities etc.
                      .
                      However, it is not necessary to resolve these types of philosophical differences because a much simpler and extremely basic scientific argument exists which makes all others seem moot. First, we must establish reasonably agreed upon premises.
                      1. Do you have any evidence or belief that any kind of natural selection operates within cells to prefer or select the placement of codons in any positions? Please advise. In other words, in a chance production process, do all 64 codons have the same relative chance of occurrence at each potential position? Yes or no?
                      2. If the “engine of evolution” is mutations, then these must occur prior to a new gene being formed, and the result of that become evident phenotypically before Natural Selection can begin to influence survival of the organism (or cell). Survival of individual genes is directly and only tied to the survival of the organism or cell as a whole. There is no process to select advantageous genes while discarding the duds from within the cell. If you have evidence to the contrary, please advise.
                      I’ll continue after response.

                    • http://irrco.wordpress.com/ Ian

                      You lost me a bit towards the end of the first paragraph, but I’ll try to interpret.

                      DNA is made up of a mutually complimentary pair of strings of four bases on a sugar phosphate spine. After a series of rather complex intermediate RNA products, some DNA is translated into polypeptides/proteins. In that translation triples of RNA bases, called codons, determine the amino acid which is added to the protein. The transcription of DNA is a probabilistic process, lots of DNA is transcribed, but there are a series of editing, fusing and absorption processes in the cell that limit what gets translated and how often. And even at the end, the machinery by which RNA polymerase ‘chooses’ what to transcribe is rather complex. We can go into it if needed.

                      Of course, not all RNA is used in ever destined for translation. RNA is also biochemically active and is a catalyst for various reactions in the cell. Ribosomes, for example, are RNA molecules operating as catalysts rather than codes. miRNA is a major player in gene regulation. Bacterial sRNA, for example, have roles in regulation of expression of various proteins. There are a dozen or so different types of ncRNA we know of.

                      All but three of the codons eventually get translated through ribosomes into amino acids.

                      [edit: I figured out what you mean here, I think.]

                      You’re referring to the fact that there are three stop codons, right?

                      Yes, at a very basic level. The actual chemistry here is much more complex. There are other codons that don’t get translated, and some that get translated in other ways. For example AUG may be used as a non-coding initiator, or as an amino acid. But yes, basically.

                      Therefore, the meaning of the codons is relatively specific and important. The degree of that specificity and importance is open to philosophical debate however.

                      Why is this philosophical? We know how tRNA binds to the large ribosomal subunits during translation, and how tRNA binds to amino acids, and why the binding tRNA to mRNA at the ribosome causes hydrolysis of GTP, moving the mRNA chain and causing the peptides to chain. So in that sense, the specificity of the code is a by-product of their biochemistry. Let’s not get caught up with debates on philosophy or religion here, let’s stay focussed on you explaining the science.

                      Your specific questions

                      1. No. Even at the base level, bases are not equally distributed in a genome. Despite a rather a lot of cellular machinery to limit its effects, different DNA sequences are not biochemically identical during replication, and transcription. This can be seen in the tendency of particular mutations to occur with many times the frequency of others. And of course, codon/amino acid mapping is degenerate, so the codon distribution is only indirectly related to the distribution of possible proteins.

                      As for the question about natural selection, your question doesn’t make a lot of sense to me. In locations in the DNA that are highly functionally dependent, natural selection has a big say on what is where. In locations that have weak effect, it has little say. On areas that have no effect, any influence of natural selection is highly indirect and almost certainly negligible, at least in the specific, on aggregate perhaps it might have a weak effect at best.

                      I suspect you’re asking a different question though, which I’m not getting, because you need to be clearer about Q2:

                      2. What must occur prior to a new gene being formed, mutations? Please walk us through how a new gene is formed, specifically in terms of what kinds of mutations you think give rise to a new gene, and what the starting point of that gene might be.

                    • Ian

                      You offered to continue after my response. But it is more than a month later. Are you still interested in describing the biology behind your calculations?

                      Are you willing to describe the mechanism of gene formation, according to scientists, and how that relates to your probabilities. I’m still interested to know how you get your calculations.

                      As it stands it looks like you ran away when the conversation turned to actual biology, and haven’t used your Disqus account since. I’m sure that wasn’t intentional though.

                    • Spaced-Out SCIENCE

                      Hello again,
                      You must have missed my last post which began to lay out the biological/molecular foundations of the argument. I would love to continue, but the premises need to first be understood and agreed to, or else it is only guaranteed to lead to confusion rather than clarity. If you find anything at all incorrect about the two premises and questions I posed, please help me clear that up…then we can proceed with the really interesting scientific review and discovery. If you did not understand the principle of “frame-reading”, for example, then it would be useless for me to proceed with any explanations which involve important considerations of this principle.
                      You ask if I’m “willing to describe the mechanism of gene formation”. Not sure if you really intended that to come off sounding singular. You realize, of course, that no ONE single mechanism has been postulated, much less witnessed in the lab. The kind of story-telling that Coyne, Miller, Shapiro and others so frequently do is far too superficial for me to even call “science”–it’s really just science-fiction. Unless you begin to carefully analyze genes at the molecular level and really get into the “nuts and bolts” of how they might have come about in the beginning, all the fanciful “could-a, would-a, should-a” scenarios are merely propaganda and not science. We know what genes are made of–we know the meaning of the 64 different codons–we know the language and how it is used. There are several very specific considerations which everyone else seems oblivious to, or perhaps they are intentionally ignoring. The key to clarity begins with understanding the basic science, not with rehearsing superficial sound-bites that evolutionists hope 6th-graders will simply swallow unchallenged.

                    • Ian

                      I replied to that comment. With clarifications and further questions.

                      You ask if I’m “willing to describe the mechanism of gene formation”. Not sure if you really intended that to come off sounding singular. You realize, of course, that no ONE single mechanism has been postulated

                      You gave a probability of a gene evolving. I’m asking you to describe the mechanism of gene formation that you are considering in your probability calculation. The one you use to get your number.

                      The key to clarity begins with understanding the basic science

                      I agree, so if you read my response and continue your explanation, perhaps we can make progress towards these “very specific considerations which everyone else seems oblivious to”

                    • Spaced-Out SCIENCE

                      Sorry, I don’t recall you answering the questions related to basic premises. Do you understand what a “frame shift” error is and how numerous mutations can lead to this?

                    • Ian

                      You don’t have to recall it, it is in the comment thread. You can read it!

                      Yes, I understand what a frame shift is, and how it is both caused and the effects it has. If you want to bring frame shifts into your explanation, feel free. But I would respectfully ask you to find and read my response, because otherwise we’ll just have to go over the same ground again. And it was long.

                    • Spaced-Out SCIENCE

                      “The calculation” can be done at several locations along the hypothetical history of evolution. The first would be to ask how correct chirality occurred in the creation of the first gene and also in the first protein products. We can easily calculate how many molecules would get used up in, for example, forming a chain 20 molecules long, all of the correct isomers. Each position has a 0.5 chance. Multiply that by itself 20 times, and you find out how many trial-and-error attempts it would take, on average, to produce a success. The answer is that over one million errors would be expected to occur, on average, for each hypothetical “win” of this very short length. Those molecules would now be locked together semi-permanently, and in the way of everything else. If you posit that the first initial “life-form” needed a minimum of 300 molecules all of the same isomer, then the number of incorrect combinations surpasses the total number of molecules, even atoms, on the face of this earth. And 300 is a really small number–much smaller than the vast majority of single genes!
                      The next calculation would consist of asking how a gene could be formed from that 300-long chain. Obviously, the first task would be to get a start codon near the beginning. We know that A-T-G is what starts virtually all genes in our world. In order to get this codon in “the right place”–i.e. at the beginning of a sequence of DNA or RNA which might just happen to be useful, would be a one in 64 chance. In other words, 63 duds would be created in the process, which would again use up an outrageous number of molecules.
                      But then comes the necessity of getting a stop codon near the end of the 300, or at any conceived appropriate place, and in the same frame reading as the start codon. If each of the 64 codons has the same relative chance of occurrence at each codon position, then you see that on average, one would show up at approx. every 21 codons along the chain (since there are 3 stop codons). Now, if you posit that an effective gene of any kind must be a minimum of 98 codons long (294 bases long), then you would again tie up hundreds more molecules, multiplied by the previous considerations.
                      And I would suggest that you would not even be close to generating anything which could be considered “life”. And similar calculations can then be applied to virtually every place along the “tree of life” where new genes are required to produce new characteristics. Most of the mutational events hypothesized, and those witnessed to occur, run the chance of interrupting a presumed previously-successful gene sequence, due to alteration of its frame-reading. What follows behind any interruption of frame-reading is essentially a randomization of codons, which risks the placement of a stop codon every 21 along the chain, on average. Now, look at the average length of the genes of any cell (in the thousands) and apply the math. How many molecules would get used up in simply getting the average human gene length of 9000+ codons without a premature stop codon occurring at 8998 places in the middle? That would be the inverse of 0.95 to the power of 8998, which is probably more molecules than exist in the entire universe!

                    • stuart32

                      Or you could create a new gene by duplication and divergence, in which case you automatically get the right reading frame and the start and stop codons.

                    • Spaced-Out SCIENCE

                      So, how do you propose to take the hemoglobin gene, for example, and transform it into the gene for any of the Krebs cycle enzymes? The vast diversity of genes and their products is well known, making your scenario a simplistic one which lacks believability. You just cannot take “Skoobydoobydoo” and magically transform it into a Shakespeare sonnet, much less the encyclopedia of specific information every cell requires for life. You are dabbling in science fiction instead of science. Show me how you propose to get the first gene in the world formed, and then how you turn that into any other useful gene, without getting the stop codons in all the wrong places, using up all the molecules in the world.

                    • stuart32

                      I think that your original point was that it was impossible in principle for a new functional gene to evolve. In order to refute that I only needed to give one example of the evolution of a new gene, which I did some time ago. Now it seems that the challenge is to explain how the first gene evolved. In fact, what you want me to do is to solve the problem of the origin of life. This is an unreasonable tactic. Let’s deal with one problem at a time.

                      The fact that you are thinking of the very first gene as having start and stop codons shows you have a naive view of the subject.

                    • Spaced-Out SCIENCE

                      Duplication and divergence or overprinting and divergence is not an accurate description of any mechanism–you are conflating causes with effects. “Divergence” is nothing more than a tautology…a place-holder for “evolution”. Evolution is an effect of something, not a cause. An accurate assessment of possibility and probability is not aided by the confusion. You need to grapple with a real nuts-and-bolts evaluation of causes. For that, you need a working knowledge of the genetic code and applied biochemistry.
                      It is humorous and ironic that Shapiro essentially refutes Coyne’s ideas of possible evolutionary mechanisms (see the book; Evolution: A view from the 21st Century), and yet he also fails to honestly grapple with the nuts and bolts biochemistry. Instead, he offers us another masked tautology called “Natural Genetic Engineering”. LOL. No evidence, no proof–only science fiction and circular reasoning. Clarity is only found when one applies the known math to the known biochemistry instead of dreaming about how these realities might have been avoided by some mystical properties of chemistry or some magical but yet-unknown mechanisms that we should believe in nonetheless. Deal honestly with reality first. The answer is right there within easy reach by anyone willing to look behind the misty curtain of evolutionary propaganda.

                    • stuart32

                      I take it that you don’t dispute the fact that genes are duplicated? You are aware that you have extra copies of certain genes that I don’t have and vice versa? Presumably, your objection is to the idea that the duplicated gene can acquire a new function.

                      Why don’t we compare the hypothesis of gene duplication/divergence with the alternative as potential explanations of the example I gave some time ago. The example, as you may recall, was the ability of certain primates to see in three colours, as compared to the two colour vision of most mammals.

                      Let’s say that God chose to give old world apes and monkeys the ability to see an extra colour. In the new world monkeys which don’t have the extra colour receptor, one gene for the receptor is on the X chromosome and the other is on a different chromosome. The two genes have quite different sequences. When God decided to give us the extra colour receptor He put the gene for it close to the other gene on the X chromosome, which is exactly where you would expect to find the gene if it was a duplicate. To make matters worse God chose to make the sequences of the two genes very similar, which is again exactly what you would expect if there had been duplication and divergence. Why did God do this?

                    • Ian

                      Im confused. I thought you were talking about the evolution of any new gene. You now seem to be talking about the evolution of the first ever gene.

                      My response will be different depending on which one.

                      What is a chain 20 molecules long? Do you mean a polypeptide with 20 amino acids? Why is there a 0.5 chance, and what is it a chance of? Of what do we have 300 molecules, and why, if they are all of the same isomer, are you worried about incorrect combinations?

                      Then you seem to use this 300 as if you’re talking about a chain of things: because you talk about ‘at the end’ of that chain.

                      Then you seem to get around to talking about a mechanism for gene formation.

                      So let me get this straight. Are you suggesting that genes are formed by starting with a random string of DNA that does nothing useful, and accumulates single nucleotide polymorphisms such that that, some time later, that stretch of DNA has all the correct codons to be translated into a working protein, then further SNPs add a start codon (and the additional transcription markers, which you ignore, but would be needed, and would be even more unlikely) and stop codon in exactly the right places, so now the gene finally gets chance to be made into a protein, and to see if it does anything? Is that the model of gene formation you are critiquing.

                      If it is, then I couldn’t agree more with you. The most basic probability calculations utterly refute that. There is simply no way, in the lifetime of the universe, that a new gene could evolve that way. It is the most ridiculous idea that no thinking person should take seriously.

                      Can you find any biologist or biology textbook that says that is how a gene is formed?

                    • Spaced-Out SCIENCE

                      I stated earlier that “the calculation” (meaning a very similar version) could be applied at multiple places along so-called evolutionary. It is easiest to understand and apply considering early requirements of chemical evolution. You realize, of course, that DNA or RNA will not form the nice organized helix if random isomers are included in the chain–they all need to be right-handed, or perhaps it might work if they all were left-handed. The 0.5 is the correct chance (50%) of being the correct isomer at each base molecule’s location, not of the entire string (such as the 300 I mentioned as a hypothetical one to apply calculations to). So, the 300 was primarily meant to refer to DNA or RNA, but the chimeric (optical isomer) consideration would also apply to polypeptides–throw a right-handed peptide into a chain of all-left-handed ones and it destroys the folding pattern necessary for so many enzymes and structural proteins. It is remotely possible that one particular version of this odd chain might function well as an evolutionary advancement. How in the world would you ever repeat it though? It’s impossible.
                      So, it would seem that we agree on the impossibility of at least one scenario for gene production. Yet, don’t straw-man me on this. I made it clear previously that MUMEROUS mechanisms might be involved, actually and theoretically. The great error I have noticed with evolutionists is that they love to fling around phrases like “genetic divergence” as if that is any kind of explanation of a mechanism or cause. That term is nothing but a tautology, virtually synonymous with “evolution”. You are describing an EFFECT, as if it were a CAUSE! What is the cause of genetic divergence–that is the real question. And it must be answered carefully with real biochemical analysis rather than word-smithing. And the math must be applied responsibly. This is where consideration of the stop codons is so vital. Even in the most liberal and creative of scenarios, say over-printing then splicing, you must consider the high likelihood (~66%) of frame-shifting, since no magical mechanism exists for causing splices to occur at just the right place. You have to honestly grapple with the realities of random chemistry and random mutations. Applying the math to the nuts-and-bolts of these things results in layer upon layer upon layer of impossibilities.

                    • Ian

                      It is certainly possible to find difficulties in evolutionary theory with regard to the origin of life. Because evolutionary theory is, at best, very very tenuous there. To figure out a naturalistic origin of life, we’ll need a theory that, at best is extends evolution dramatically, or may even need very different mechanisms. At the moment there is no theory of this. There are a few hypotheses. But they all have their own difficulties. So arguing that evolution is wrong because the origin of life is a puzzle is silly. Its like arguing that there is no India because the origins of India are not fully understood. If your point is purely that evolutionary theory is not an adequate theory of abiogenesis, then again you’re right. If your point is that SNPs of R/DNA, expression and natural selection is a very poor theory for the origin of life. You’re right, and that is very much the view of mainstream biology. Can you find a biologist who says otherwise?

                      I thought you were making a claim about the evolution of new genes (some thing that, if evolution is true, must have happened millions or billions of times since the first cell). You were claiming that the evolution of a new gene is impossible, and that there were features of the biology that, if scientists took notice of, would disprove it. So can we focus on the evolution of a gene – the bit where you seem to disagree with professional biologists? Instead of focussing on the bits where you agree. So not the first gene. Not the origin of DNA. But what you originally claimed: that evolution is simply not possible because new genes cannot evolve.

                      As for the comments on chirality: are you claiming that new genes cannot evolve, because every new gene has to go through a random chance process of selecting the chirality of its constituent parts? If so then that’s just plain wrong. The raw materials of translation are not available in both chiralities. This is simply a function of the cell’s biochemistry. While it is a question how that arose. It is not a mystery that, once it did arise, it would be retained.

                      So, it would seem that we agree on the impossibility of at least one scenario for gene production.

                      Yes, but let’s be clear. Inventing new biochemical mechanisms that are then impossible is neither impressive, nor does it challenge biology. You merely put forward a demonstration of something every professional biologist would have said if you’d have described your scenario.

                      Yet, don’t straw-man me on this.

                      I don’t want to, so if that scenario is a straw-man, can we move onto something you do think accurate represents the impossible mechanisms of evolutionary biology?

                      I made it clear previously that MUMEROUS mechanisms might be involved, actually and theoretically.

                      Yes, and you are claiming that ALL such mechanisms are impossible, right? I mean, you’re not here arguing that some mechanisms are likely and some less likely. Your whole thesis is that all mechanisms are so fundamentally unlikely as to be justifiably dismissed.

                      So that being the case, why did you use an example that you’d invented that no biologist claims. If you want to make that point, why not start with the mechanism for new gene evolution that biologists actually use? Do you know what that is?

                      You state that the math must be applied carefully to the biochemical reality. But throw in a 66% probability of frame shifts (you know we can directly measure the probability of a frame-shift, right? And it isn’t 66%!)

                      So let’s get back to the biology. Can you describe the actual mechanism that biologists think is responsible for the vast majority of new genes? Can you give a probabilistic analysis of that, and show it is vanishingly improbable? Can you grapple honestly with the realities of this and make your point?

                      Because so far you’ve only landed two points, I can make out, among the handwaving and vagueries:

                      1. That a mechanism for gene evolution that you put forward that no biologist has claimed cannot be correct.

                      2. That genetic evolution cannot explain the origin of life, or the origin of coding.

                      Both are true, that I can see. And both are very much what a professional biologist would think. So they hardly help your main point that evolutionary biology has fundamental errors.

                    • Spaced-Out SCIENCE

                      Great response…thanks…we’re finally getting to
                      clarify some things. Previously I said:

                      I made it clear previously that MUMEROUS
                      mechanisms might be involved, actually and theoretically.

                      You then said:
                      Yes, and you are claiming that all such mechanisms are impossible, right?

                      No, that’s not correct. Some semantics must be clarified. First, let’s look at the “actually” side of
                      things—the witnessed changes. What does “new
                      gene” mean to you? Did Lenski’s E. coli produce
                      any “new genes”? Some people want to say yes to that. But no new start and stop codons were added. How does that lead to any macro-evolutionary changes? Everyone agrees that micro-evolution occurred due to several relatively minor mutations. They now transport citrate across their cell membranes better during oxic conditions. The selection for that “trait” only occurred
                      because a very artificial and restrictive environment was forced on them for thousands of generations. But they
                      previously transported citrate in anoxic conditions and they always were able to metabolize it. So, that’s not a very big change that occurred, and certainly not the addition of a useful new gene to its genome. So, it’s only semantics to say that Lenski proved evolution in action. I would agree that it was micro-evolution but nothing more. Macro- will require substantially more than what was observed.

                      So, your friend Stuart says that genes can simply be
                      created by duplication followed by “divergence”. First of all, duplicating the hemoglobin genes might allow for higher production of hemoglobin, but that doesn’t create
                      cilia or mucoproteins or anything new. Divergence is not a cause but merely an effect—dependent upon
                      mutations. You could say that Lenski’s bacteria underwent genetic divergence but where did that get them? They are still bacteria. There is no evidence that they are becoming anything but bacteria of the same species and genera. Zero new start and stop codons formed, multiplied by billions of years, still equals no new start and stop codons. More later…

                    • Spaced-Out SCIENCE

                      As to the theoretical way new genes might be formed:
                      some form of splicing might be possible—accidentally combining parts of two genes, for example. Other splicing
                      scenarios can be thought of as well, but they all possess the distinct risk of frame shifting the previous reading with the associated danger of premature stop codons being encountered by that new reading frame. If you are unfamiliar with how this works, I can supply an example. The point is that these hypothetical mechanisms run at least a 66% chance of producing junk DNA. We now know from the ENCODE project that cells do not contain 66% junk DNA or anything close to that. An associated conundrum is how genes 80,000 bases long could ever be formed without premature stop codons occurring anywhere in the middle. There is no trial-and-error
                      process that could produce such genes without using up all the molecules in the world trying to do so. And Natural
                      Selection cannot prevent unwanted stop codons from occurring. It also cannot do “housecleaning” within the cell. So, what’s left? 50,000 generations of E. coli haven’t given us a clue.

                    • stuart32

                      I’m not sure if this comment was for me. Apologies if it wasn’t. If your theoretical understanding leads you to believe that a process is impossible in spite of clear evidence that it has happened then perhaps you need to reconsider your theoretical understanding.

                      You didn’t mention my point about the variation in the number of copies of genes within human populations. This is relevant to what you said about gene duplication leading to a build-up of junk DNA. Consider the extra copies that you have of certain genes but I don’t have. Are they junk DNA, or not?

                    • Spaced-Out SCIENCE

                      You make a good point worth clarifying. A duplicated gene that preserves the native frame-reading and all of the codons from start to stop is certainly NOT junk. But it is also not considered a new and unique gene added to a genome–it’s just a duplicate. A creature can never advance in terms of traits (i.e. building wings, eyes, brains, etc. by simply duplicating the hemoglobin gene). Any other partial duplication of genes as well as point mutations will, in more cases than not, disrupt native frame-reading which then does indeed create junk. Duchene’s muscular dystrophy compared with Becher’s is a great study in this phenomena, as is the study of malaria’s DXR gene, as mentioned previously.

                    • stuart32

                      Ok, so we’re making progress. A gene can be completely duplicated, with start/stop codons and reading frame preserved. Let’s say the duplicated gene is one that codes for a colour detector. At first the gene is just a back-up copy that does nothing new. Then the gene undergoes a number of mutations which enable it to detect a different colour. In the case we are talking about these are point mutations, not insertions or deletions, so the reading frame is unaffected.

                      So now we have a new gene with a new function. An animal has evolved the ability to see a new colour. Also, we have an example of entirely natural processes creating complex specified information.

                    • Spaced-Out SCIENCE

                      You said; “point mutations, not insertions or deletions…

                      What you obviously mean is “point substitutions” or “base substitution mutations”.

                      Yes, in theory this idea might work. This is theory involving only a small percentage of known types of mutation. Nevertheless, follow your idea through and consider the amount of Junk DNA a genome would contain if this were really the driving force behind ‘evolution’

                      Here’s an interesting source and quote:

                      http://en.wikipedia.org/wiki/Mutation

                      One study on the comparison of genes between different species of Drosophila suggests that if a mutation does change a protein [i.e. the substitution you suppose], this will probably be harmful, with an estimated 70 percent of amino acid polymorphisms having damaging effects [hence Junk protein resulting from Junk DNA], and the remainder being either neutral or weakly beneficial
                      The ENCODE project consortium clearly indicated that most cells contain at most around 20% junk DNA (really they just mean DNA for which we haven’t yet discovered the purpose of). Hence, your proposed mechanism fails to adequately address gene origins. You also fail to account for how a genome like ours contains genes with less than 100 nucleotides and also ones in the thousands, even tens of thousands long. Duplication and base substitution cannot get you that at all.

                    • stuart32

                      That isn’t what the ENCODE project found. What it discovered was that 80% of DNA was involved in some sort of activity. If you inserted a random sequence of DNA into the genome that would also be involved in some sort of activity.

                      By the way, single base substitutions are the most common type of mutation.

                    • Spaced-Out SCIENCE

                      Yes, of course. I simply stated the results of ENCODE in inverse fashion. If areas of DNA are involved in regulatory activity, they are not junk. Now, the areas of DNA involved in generating that 70% junk protein could not be involved in important regulatory functions. If you take a very nuts-and-bolts look at cell biochemistry instead of just vague impressions of what you think might have happened in the past, you should realize that what evolution theory claims to have occurred is completely unrealistic, based on actual evidence of how cells and molecules function.
                      As for single base substitutions–are you aware of how many diseases and problems are caused by these? Also, can you site one example of this type of mutation suddenly generating a completely new and usable gene product? Also, do you know how to calculate the probabilities of more than one of these mutations occurring within the same gene? This is very important, especially if you are proposing this mechanism as the main source of new genes in the past. Can you site any genomic data which shows two distinct genes differing in only one or two nucleotides which code for two different products, such as a component to the bacterial flagellum and a component of the type III secretory system? Vague ideas are fine to start out with, but if you never examine the specifics at the molecular level, you are simply repeating the presumptions of the past (evolutionary presumptions in your case).
                      Have you read The Language of God, by F. Collins? Did you notice how many times he repeats a statement that essentially says; “we just don’t know, and probably will never know, how evolution accomplished these things in the past”. Pray tell…how is this statement any more credible than one which says; “we just don’t know, and probably will never know, how God created these things long ago”?

                    • Ian

                      You really are obsessed with start and stop codons!

                      A unique gene, in this case, is an inheritable genetic sequence that codes for a unique protein (unique among other genes in the genome).

                      A new gene, then, would be a unique gene in some descendent that was not present in any of its ancestors.

                      I made it clear previously that MUMEROUS
                      mechanisms might be involved, actually and theoretically.
                      You then said:
                      Yes, and you are claiming that all such mechanisms are impossible, right?
                      No, that’s not correct.

                      So, is it your view that there are some mechanisms for the evolution of new genes that are possible and within the realm of probabilistic likelihood?

                      Because it seemed very clear that you were claiming that your knowledge of biology meant that no such mechanisms existed.

                      If you are willing to claim that such mechanisms do exist, which are they?

                      I understand you have a separate point about whether such mechanisms have been observed, but back when I responded to something you said to James, that wasn’t what I was interested in having you explain. We can perhaps return to the experimental science later. But I’m most keen that you to demonstrate your claims to be aware of features of the biochemistry that made new gene evolution vanishingly unlikely. Features you said scientists ignore.

                    • Spaced-Out SCIENCE

                      You can’t play poker with UNO cards. Just because you share some genes with E. coli doesn’t mean its 4000 genes were simply copied and tinkered with to get to your 25,000+ genes. At numerous places along the supposed evolutionary tree, new, unique and useful genes had to be ADDED to genomes repetitively. Now, for a surprising jaunt of computer research, try going to the gene databank and finding Plasmodium
                      falciparum . Take any gene from it and copy-paste it to your computer. Now, simulate a splicing event which would disturb the usual frame-reading of the gene (a 66% likelihood), and then count the resultant stop codons, due to the shift. Yes, in theory, it might be possible to create a “new” gene, but the length of it would be incredibly short and likely unusable. The DXR gene, however, is 1467 nucleotides long without a stop codon anywhere in the middle. Once you play with the numbers, especially considering how much junk DNA would be produced in naturalistic methods of producing a gene 1467 long with no stops, you should get the picture.

                      Here is the link to the database:

                      http://www.genedb.org/gene/PF3D7_1467300.1
                      hit the “view sequence” button on the right

                    • Ian

                      I say again, we can *directly measure* the proportion of frame-shift mutations. And it is not 66%, where are you getting this data. You said you can talk us through the basic biology that leads to your numbers. You’re just quoting numbers and handwaving again. Back to the biochemistry…

                    • Spaced-Out SCIENCE

                      66% comes from 2/3–2 0ut of 3 frame-readings of most every gene I studied resulted in premature stop codons at very frequent intervals, precluding the formation or existence of a typical functional gene, since most genes are hundreds if not thousands of nucleotides long without stop codons in their middles. If you would simply do as I suggested, using the gene databank on the DXR gene or any other, you would confirm for yourself the truth of what I’m saying.

                    • Ian

                      But this is my entire problem with your comments. We can actually check the proportion of frame-shift mutations, directly, and it isn’t 2/3 (not to mention the junior-high math gaff, that 2/3 isn’t 66%). The biochemistry disagrees with your naive probability calculations.

                      You’ve given us a probability calculation based on a mechanism for gene formation you yourself admitted nobody had ever suggested. And now you’re insisting that the probability of something we can actually measure should be generated by your calculation rather than reality.

                      You promised to tell us the biochemistry behind your numbers, but instead gave a rather sketchy high-school level summary of protein synthesis, and — as yet — no recognizable model of gene formation.

                      How can anyone take you seriously?

                    • Spaced-Out SCIENCE

                      You say “we can actually check the proportion of frame-shift mutations directly…:
                      Really? I think you might be confused. Have you checked the proportion of these in the muscular dystrophies?
                      Did you check them in Lenski’s lab experiments or any other actual real-time demonstrations of mutations in action? Is this what you so confidently refer to? Can you site a credible source to back up your claim that these things have been measured? Are you certain that we have not been talking apples and oranges? Perhaps you are referring to retrospective analyses which first Presume naturalistic evolution and then make an analysis of presumed results. If you analyzed Craig Venter’s created cells in this fashion, you would arrive at all the wrong conclusions.

                    • arcseconds

                      You’re making the unwarranted assumption that genes exist!

                      Please remove references to all theoretical entities, not just the ones you don’t personally like. Otherwise you’re not really thinking critically at all times, are you?

                      What would the data look like then?

                    • newenglandsun

                      A Christian can only accept evolution on certain qualifications, otherwise, our worldview becomes based entirely on rationalistic materialism. The soul has never been disproved and I think there are more reasons for it than against it.

                    • beau_quilter

                      newenglandsun

                      I can understand why you believe that “A Christian can only accept evolution on certain qualifications”, although I don’t agree with you. But if the theory of evolution doesn’t make room for your a priori Christian assumptions, then couldn’t you say the same about virtually every scientifc theory ever devised?

                      Couldn’t you take the word “evolution” out of your statement:

                      “A Christian can only accept evolution on certain qualifications …”

                      and substitute “quantum mechanics”, or “general relativity”, or “the Newtonian laws of motion”, or most any general scientific law or theory?

                    • newenglandsun

                      Yes. You absolutely can and should.

                      The issue is not with evolution vs. creation per se but how you are using the theory of evolution.

                      If you are maintaining to an historic Christian faith, then interpreting Genesis as allegory is fair game so long as you maintain monogenesis (note that this is a lot more complicated than it seems at first and Fr. Dwight Longenecker’s article which I will link to here explains it better), the existence of the soul, and original sin.

                      As for quantum mechanics and general relativity, you again need to maintain creation ex-nihilo. Same with the Newtonian laws of motion.

                      http://www.patheos.com/blogs/standingonmyhead/2013/05/difficulties-with-adam-and-eve.html

                      A Christian is by default a non-materialist and cannot use and abuse scientific theories to reject key doctrines. Evolution is distorted the most though when it comes to being abused in an attempt to dismantle Orthodox Christianity as we know it.

                    • beau_quilter

                      Is your main concern that scientific inquiry not intrude into areas of metaphysical philosophy and theology, by positing metaphysical naturalism?

                      Or do you envision a sort of scientific practice that does not limit itself to methodological naturalism?

                    • newenglandsun

                      I’m confused by your question.

                      All I’m saying is that one should not use anything in science to refute key doctrines of the faith. This turns Christianity into something entirely different.

                      http://anatheistbiblestudy.tumblr.com/post/7109645434/a-response-to-the-liberal-christians

                      I do not believe that science, when used properly, will refute any core Christian doctrines (monogenism, creation ex-nihilo, original sin, the existence of the soul). It’s fair to say I reject a good portion of modern neuroscience but I haven’t seen anything there that isn’t pure speculation.

                    • beau_quilter

                      You might be interested in looking up the difference between metaphysical naturalism and methodological naturalism. It is a debate regarding our approach to the sciences that gets to the heart of your issues.

                      As an atheist, of course, I don’t see any reason why the Bible should influence my views of science any more than the Quran, the Bhagavad Gita, the Tao Te Ching, or the Book of Mormon.

                      It strikes me as remarkably ironic that someone who espouses monogenism, creation ex-nihilo, original sin, and the existence of the soul would have a problem with pure speculation. There is far more speculation in your position than there is in modern neuroscience.

                    • newenglandsun

                      I am quite aware of the distinction between methodological naturalism and metaphysical naturalism. I thought we were discussing the notion of abusing science to reach metaphysical naturalism and change Christianity.

                      As for the soul, monogenism, creation ex-nihilo, and original sin, I think there is philosophical speculation on those things but I also think it’s far more rational to affirm those things in light of what I’ve explored so far than to deny those things.

                      Of course, this is primarily dealing with the soul’s existence and original sin. For instance, G.K. Chesterton once said, “Certain new theologians dispute original sin, which is the only part of Christian theology which can really be proved”.

                      After reading the Epicurean, Platonic, and Aristotelian view of the soul though, I was fairly convinced they all fell short. The Epicurean view turns us into animals, the Platonic model turns us into people denying our own bodies as sacred, the Aristotelian view gives us no future reunification.

                      Monogenism and creation ex-nihilo are core doctrines of the Christian faith. To use science (based on methodological naturalism) to refute them, is an abuse as I think both you and I can agree on, right?

                    • beau_quilter

                      Yes, I was aware of Chesterton’s comment on original sin. It’s not surprising that a Christian apologist would make a meaningless assertion about a vague concept such as sin.

                      No, I wouldn’t agree with your last statement. There are no “core doctrines” in science. Everything requires evidence, and a requirement of all scientific theories is that they are falsifiable.

                      Current biology has certainly demonstrated that all humans, regardless of race, are a single species with shared ancestry. First man and woman mythologies are not particularly useful to science in coming to this conclusion, however, since they have nothing to do with evolutionary biology. Incidentally, such mythologies are older than the Bible’s particular version in Adam and Eve.

                      As for creation ex-nihilo, I don’t know what you consider “abuse”, but the scientific study of the origin of the visible universe and what may lay outside the visible universe is an exciting field for which the Bible has nothing of value to offer.

                    • newenglandsun

                      “No, I wouldn’t agree with your last statement. There are no “core doctrines” in science. Everything requires evidence, and a requirement of all scientific theories is that they are falsifiable.”

                      I agree that *proper* science has absolutely no core doctrines. (Which I never said it did – please next time read what I said.) And based on previous statements of yours, you would agree with my last statement, “To use science (based on methodological naturalism) to refute them, is an abuse as I think both you and I can agree on, right?” Which if not, would make you intellectually dishonest at this point.

                      “Current biology has certainly demonstrated that all humans, regardless of race, are a single species with shared ancestry.”

                      I never said that theology didn’t teach this either. Again, please read what I have to say.

                      “First man and woman mythologies are not particularly useful to science in coming to this conclusion, however, since they have nothing to do with evolutionary biology. Incidentally, such mythologies are older than the Bible’s particular version in Adam and Eve.”

                      I never said they did have something to do with biology. You seem to embrace a teaching known as scientism (all things can be found in science) based on this statement of yours. This makes most people smack their heads on the face. Even my older sister who wrote her “anatheistbiblestudy” blog would contend against scientism. All I am saying is that the notion of monogenism dating to Adam and Eve is a theological concept that cannot be compromised with science. Nor though does science contradict it. Monogenism is an entirely theological concept.

                      “Yes, I was aware of Chesterton’s comment on original sin. It’s not surprising that a Christian apologist would make a meaningless assertion about a vague concept such as sin.”

                      I used to be a pretty dogmatic online atheist too (by dogmatic, I mean all religions are ridiculous and fed into the stereotypes of religions to attack them and ridicule them). I gave that up when I realized I had limited my intelligence. Yes, Chesterton’s argument had weight for me when I carefully considered it. Sin is not vague. Original sin indicates that *humans were born into a state where they just want to exercise arrogance and selfishness*. Now if only we could get a book about that subject on how there’s a selfish gene. Maybe some sort of Christian apologist will write that book, or plagiarize it from another atheist.

                      “As for creation ex-nihilo, I don’t know what you consider “abuse”, but the scientific study of the origin of the visible universe and what may lay outside the visible universe is an exciting field for which the Bible has nothing of value to offer.”

                      Of course the Bible has nothing of value to offer in this discussion. Creation ex-nihilo isn’t derived from the Bible. It’s an Abrahamic tradition (Islam, Christianity, Judaism) that was derived at from outside of the Bible *and* Quran to distinguish the faiths from the Pagan religions that taught creation ex-materia.

                    • beau_quilter

                      Despite your patronizing comments about my ability to read, I never said that you said science has core doctrines. I merely made the point that science (having no core doctrines) is not obliged to respect the core doctrines of religion. Neither did I say that you said that theology didn’t teach that all humans are a single species with shared ancestry. I read what you had to say, and I did not put words into your mouth. It is you who are putting words into my mouth.

                      And I don’t have to be “intellectually dishonest” (Good Lord!) to disagree with you about the question of whether science can address religious doctrines such as creation ex-nihilo. I pointed out the interesting differences between the approaches of methodological naturalism and the metaphysical naturalism; I did NOT say that I found metaphysical naturalism to be an abuse of science – so there is no disagreement with what I said later! I think you are the one who needs a bit of reading comprehension.

                      And speaking of face-palming, “scientism” isn’t a term that people generally use to describe themselves; it is a pejorative term, virtually always used in a derogatory manner. I don’t see how you can accuse me of scientism, unless you simply want to accuse anyone of scientism who doesn’t subscribe to biblical theology or who is willing to consider the perspective of metaphysical naturalism.

                      The “selfish gene” as Dawkins used the phrase is a metaphor for the way natural selection works to benefit the proliferation of genes – as opposed to each individual organism. In fact (as Dawkin’s book explains), natural selection quite often leads to “unselfish” behavior on the part of organisms, in parenting, often speeding death after procreation, and in altruistic behavior in service of a herd, hive, or clan.

                      The reason that I think the concept of sin is vague is that it is difficult to get different societies, religions, or even church members to agree on what individual acts could be called sin. I wish it were as easy as “selfish behavior”.

                      Theologians debate the question of whether the concept of creation ex-nihilo can be found in the bible or was a second century development in Christian thought. It is not a settled question in theological circles. However, I don’t really have a dog in that race.

                    • http://irrco.wordpress.com/ Ian

                      “you don’t understand evolutionary biology” or genetics, or evolutionary math, or probability theory, or computer programming.

                      Spaced’s imaginary science is legion, I fear.

                    • http://irrco.wordpress.com/ Ian

                      Right, as predicted, you still fail to answer the question. This is becoming rather predictable. I’ve asked you eight or nine times now to simply describe the position you arguing against, that you claim to be doing the math for. And still more delving into copy-and-paste talking points, and avoiding a very simple invitation to begin a conversation from a point of mutual understanding.

                      Sad, but not a surprise. And not unusual.

                    • beau_quilter

                      Spaced Out

                      Let me assume, for a moment, that you honestly want to understand what evolution theory entails. I will try to explain, as simply as I can, why the probability arguments you are borrowing from creationists simply do not work.

                      Consider this example:

                      The probability that my mother and father would have married, and that the particular sperm (out of billions produced by my father) would have joined with the particular egg to create me is astronomically low. Multiply that by the same probability that any of my ancestors would have been born, and the probability of my existence is so low as to be virtually impossible. Yet here I am.

                      You see the problem with this line of thinking? The probability that our human ancestors would have created me, specifically, is very low. But the probability that our human ancestors would have produced human descendants is quite high (knowing what we know about humans and their proclivity to reproduce).

                      Scientist estimate that there are at least 8.7 million distinct species of life on earth today. It is also estimated that these species represent only a tenth of a percent of the total number of species that have ever existed on earth. That’s trillions of viable life forms. And we’re only talking about life forms that have existed, which is only a tiny fraction of the number that might possibly have existed.

                      Evolutionary processes do not “predetermine” or “plan” what life forms will result, and that’s why your probability scenarios for any one protein forming are meaningless. All that life has to do in order to evolve is to continue replicating. It doesn’t care what form results from each successive mutation, evolution will continue as long as life replicates.

                      The likelihood that I might have been born is low, but the likelihood that people would be born, once the human species was established is high. By the same token, the likelihood that any one particular life form (or flagellum) might evolve once molecular replication is established is low, but the likelihood that life forms (with or without flagella) in general will evolve is quite high.

                    • Spaced-Out SCIENCE

                      Yes, I read those same hollow arguments on the evo link you posted earlier. Let me see if I can explain your errors. You’re really trying to compare apples and oranges.
                      YOU don’t have to be alive for life to go on, but many specific proteins and DNA sequences MUST EXIST for any life to happen! The start and stop codons for DNA
                      transcription are examples. If they don’t exist in appropriate places, life cannot exist. Many specific parts of the cell are absolutely necessary and cannot be
                      replaced with “whatever”. This is what a responsible scientist can indeed apply the math to. The analogy of a string of sand grains on the beach is similarly irrelevant because sand doesn’t stick together for millions of years like DNA has been reported to do, and sand grains are not necessary to life. Your arguments take the form of a fallacy
                      of logic called “begging the question” and circular reasoning. You are making a premise that evolution could
                      produce complexities of reproduction and then you are using the existence of those complexities to prove that evolution is factual (macro). Trial and error could certainly lead to many things, but don’t forget that you can’t instantly undo the myriads of wrong sequences and simply take a Mulligan every time! They would be in the way clogging up the works and sequestering molecules that would be in limited supply. Do the numbers—answer the very reasonable questions I posed and we can proceed with a rather interesting analysis.

                    • beau_quilter

                      I don’t think you understand what “begging the question” and “circular reasoning” mean. It’s also clear from your strange description of my “premise” that you have no understanding of the theory of evolution whatsoever.

                      You keep saying things like “do the numbers”, but you have, as yet, to produce even one legitimate calculation.

                      You also keep avoiding discussion of Behe’s 2010 article that you asked us to refute. Have you read it? Do you even know what he is arguing?

                    • beau_quilter

                      Spaced-Out

                      You’re making things up. The structures that you cite are necessary for the life that evolved with them, but they are not necessary for all forms of life. We don’t know what might have evolved had those structures not evolved, just as we don’t know what might evolved if dinosaurs had not gone extinct.

                      In addition to making false assertions you are committing the logical fallacy known as an argument from ignorance.

                      It’s becoming a bit tiresome arguing what 98% of the scientific community takes as a given with an anonymous blog commenter who clearly doesn’t understand the science.

                    • Spaced-Out SCIENCE

                      Your responses continue to be so typical of evo thinking: “we just don’t know what might have happened…” Yet, you have the audacity to keep asserting that I just don’t know how evolution works! LOL. Both of those statements reek of the fallacy called begging the question. You keep assuming, with no proof, that
                      macro-evolution does in fact work. You continue to use your premises as proof for your theory. That’s not how science works. You also continue to appeal to popularity,
                      referring to your presumed “98% of all scientists” wishful thinking. That is a fallacy of logic which I have pointed out before. Many times in human history someone had to stand apart from the crowd and challenge the popular
                      opinion. Forget about popularity. Forget about any appeals to so-called authority. Forget about who I might be or what I “know” and have the courage to think outside the limited box you have allowed your thoughts to be confined by. Have the honesty to ask yourself; “what if macro-evo is not true…what if it can’t be proved…what if it is actually impossible? How could I begin to prove that it is more than merely a shared wishful belief system with ‘98%’ of others?”

                      I would suggest you start by reading or re-reading a textbook on cellular and molecular biology and also Statistics 101. Then, begin to wrestle with the
                      legitimate questions I’ve posed. Put away any magical thinking about what you hope “might have happened” and recon with the specifics we do know. Whether
                      carbon-based or sulfur-based, life forms require specific instructions in their genomes. Extremely limited options exist for the start and stop signals for transcription and translation. Very limited options exist for the lengths of
                      genes—very short and very very long strings of nucleotides are not seen in any genes, for good reasons. Even-numbered strings are not seen—they must be divisible by 3, the number of nucleotides in one codon. These are basic known facts that you can apply math to quite responsibly, if you wanted to.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      Please, please, if you are going to keep commenting, then take the conversation seriously. You have disputed the work of scientists published in highly technical articles in science journals and refuse to present even minimal evidence for your claims when asked to do so. And you call the agreement of scientists “popularity” which simply shows that you don’t even understand how science works. If something is open to being challenged, it will be challenged, because those who are paid to research as part of their jobs are constantly seeking some room for innovation.

                      I am pretty sure that you only apply this argument to this particular area of evolution, and brush your teeth and take prescribed medication aware that the agreement of experts on a topic is not a trifling matter.

                    • stuart32

                      James, I actually gave Spaced-Out Science a specific and well-understood example of gene duplication earlier in this thread. He has ignored that comment and continued replying to other people, telling them that gene duplication is impossible. Perhaps he should go back to the example I gave and explain why it is flawed.

                      Just to clarify that point: an example of the creation of a new gene through gene duplication

                    • Spaced-Out SCIENCE

                      What I dispute is not the evidence offered but the interpretations placed upon it and the refusal to apply the math to the theories. What I dispute is the validity of offering excuses instead of doing the math. What I dispute is the representation that scientists being paid to study
                      evolution at any level (knowing that they will be scrutinized by strong believers in evo), have any significant incentive to call the theory itself (of macro-) into question. Job security normally dictates that they avoid such endeavors. Behe is
                      a notable exception, worthy of honor for this fact alone. And look how he is treated—character assassination is frequently offered in place of careful scientific evaluation. Will somebody please do the math instead of offering diversions and excuses?

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      You have not done any math, and so your request is odd. Behe has been criticized for trying to persuade the public of a view that he has not managed to persuade his peers with. If one picks books of that sort then I can tell you any number of contradictory things ought to be believed, since there is a scientists or other scholar who says them. That’s just silly. Why are you not treating this subject seriously? How can you with your spaced-out pseudonym dismiss an entire field of science and have the audacity to think that the burden of proof is on anyone but you?

                    • stuart32

                      Spaced-Out, I gave a specific, detailed example of evolution in action four days ago. It shows the creation of a new gene, with a new function. It also demonstrates how a naive calculation of probability can lead you astray. You ignored my comment.

                    • beau_quilter

                      Behe has published barely more than a dozen journal articles, which would hardly get you tenured, much less promoted at most research universities.

                      Do you know how many of these articles, have proposed a hypothesis of “intelligent design.” Precisely zero.

                    • Spaced-Out SCIENCE

                      You seem to forget–ID is no longer a hypothesis…Venter proved it a fact. Now, exactly where it came into play in the remote past is clearly up for debate, as well as which particular intelligent agent was involved. It is my argument that a careful analysis of the math gives a pretty good guess as to where along the taxonomic scale it must have occurred. After that, simple Mendelian genetics plus selection resulted in most observed changes, while mutations plus selection accounted for a small percentage more.

                    • beau_quilter

                      OK

                      I can’t take Spaced-Out seriously anymore. ID was never a “hypothesis” to begin with. It has never been proposed or stated as a scientific hypothesis in any scientific journal; no experiment has ever investigated the process of intelligent design … and now an evolutionary biologist (Craig Venter) has “proved it” somehow without even realizing it?

                      Spaced-Out, I have lost interest in your imaginary world. Good luck with your pseudo-science.

                    • http://irrco.wordpress.com/ Ian

                      I can’t take Spaced-Out seriously anymore

                      any more? ;)

                      I suspect spaced out is going to win this argument. He’ll keep repeating the same nonsense for weeks, until we all get bored with responding and move on, or until he gets kicked off the site.

                      At which point he’ll conclude that he slayed the dragons and once more proved that nobody could refute him or challenge his conclusion. He’ll probably go hang out with creationist buddies and share the stories of how his towering intellect was no match for the ignorant, ideologically compromised enemies of truth.

                      As they say “never wrestle with a pig. You’ll both get dirty, and the pig likes it,”

                      Still, I’ve enjoyed your responses on this thread. Sorry I didn’t up-vote them all. But it was fun to see you gamely try to respond.

                    • beau_quilter

                      Yes, I guess it’s been hard to take him seriously for some time now. At any rate, I’m bored with his illogical rants, so I’m moving on.

                      I’ve enjoyed your responses, too. I also enjoy your posts on Irreducible Complexity.

                      See you on the next thread!

                    • Spaced-Out SCIENCE

                      “The Nobel prize winner Francis Crick, along with Leslie Orgel proposed that life may have been purposely spread by an advanced extraterrestrial civilization.”

                      It’s hardly a stretch to believe that these ET folks are smarter than Venter and more prolific in their
                      accomplishments. Now, remember that way back in 1972, even the famous evolutionist Stephen J. Gould realized that the evidence was strongly suggesting that evo could not do what others hoped it could do, and so he iterated the “Punctuated Equilibrium Hypothesis”. It should be obvious that a reasonable expansion of these two ideas is that a great intelligence “injected” life in various forms into this world, in a process that in retrospect appears stepwise, and that life then changed over time due to Mendelian genetics plus a few mutations acted upon by selection (natural and intelligent). In reality, every time an animal breeder or a
                      plant hybridizer does their work, they demonstrate Intelligent Design. You need only to extrapolate this ability to a much higher intelligence in order to find the mechanism for macro-changes which have occurred in life forms…changes which micro-evo has proven
                      incompetent and impotent to produce.

                    • beau_quilter

                      Now you’re just being silly.

                      There is a massive amount of evidence for evolution, and if YOU actually read textbooks on cellular and molecular biology you would already know that. You are pretending to expertise that you so obviously do not posses.

                      Your spouting of random biological “facts” as though they support your premise is getting a bit old. And again you tell us to “apply the math”, without providing any sort of useful calculation of your own.

                      Your ignorance of science is especially clear from the fact that you don’t know the difference between popularity and scientific consensus.

                    • beau_quilter

                      Thanks, Ian, I had missed that news, and had no context for Spaced Out’s argument. Of course, now that I have the context, his argument seems all the more bizarre.

                    • arcseconds

                      You’re exaggerating what Venter has done.

                      But it doesn’t matter. It’s irrelevant. Everyone with any knowledge of the area and a bit of imagination can see that one day we will be making cells to order.

                      That cells can be designed doesn’t mean they were designed, any more than that some car ‘accidents’ are actually murders means that all car accidents are murders.

                      By the way, I’ve just had a creationist in another post tell me that scientsts haven’t managed to design and build cells, and therefore life is the domain of God. Perhaps you’d care to go and set them straight?

                    • beau_quilter

                      Well sure, but this proves intelligent design of all life how?

                    • beau_quilter

                      My apologies and thanks for the update on Venter. I had missed the artificial cell news.

                      Yes, I suppose you could say that Venter is an “intelligent designer”, but then so is an architect or a car engineer. Of course, you are modeling, in a vapid way, the usual strategy of the Discovery Institute, when they cite the work of hard-working evolutionary biologists and oddly claim it as their own.

                    • Spaced-Out SCIENCE

                      I think you misunderstand the valid point Venter’s work illustrates—it is clearly a path to macro-evolution-type changes. Lenski’s 2-decade, 35K+ generation view into
                      what nature alone can do failed to reveal a similar pathway. Venter created new genes with the requisite start and stop codons etc. Lenski’s bacteria simply displayed minor alterations to existing genes, actually damaging some and certainly not adding any to the genome. This completely fails to explain how E. coli might acquire the ability to, for example, produce flagella at some time in the future, no matter how long you allow.

                    • beau_quilter

                      If you’re inclined to hear real scientists explain why your “calculation” is bogus, read here:

                      http://ncse.com/cej/3/1/answers-to-standard-creationist-arguments

                      I doubt you will read it however, as you haven’t even read the 2010 Behe review that you challenged us to “refute”, yet couldn’t even explain what Behe’s review said in the first place.

                    • stuart32

                      It might be useful to consider a real example of evolution in action. Human beings have three types of colour detecting cells in their retinas. Each cell depends on a colour-detecting pigment, and each of these pigments is coded for by a specific gene. Most mammals have only two genes coding for two pigments. So at some stage one of our ancestors must have acquired a new gene. How likely is that?

                      If you think about it in terms of randomly throwing together the components of a gene the answer is fantastically unlikely. Each of the pigments is made up of about 360 amino acids, so the probability of getting one complete sequence by chance is 20^360. Impossible, in other words. Fortunately there is an easier way of doing it. Genes can be accidentally duplicated. In fact many people have extra copies of genes that the rest of us lack. So it is possible that one of the pigment genes was duplicated and then altered so that it became sensitive to a different colour. Is there any evidence for this?

                      When genes are duplicated the extra gene sits next to the one from which it was copied. This is exactly what we find. Two of our pigment genes sit next to each other on the same chromosome. The other pigment gene is on a different chromosome. Also, the two genes that sit next to each other are very similar. They differ by only fifteen amino acids. The fifteen amino difference didn’t have to arise all at once because most of the change in colour sensitivity comes from changing only three amino acids.

                      Also, if this evolutionary change occurred in a distant ancestor then all of the descendants of the ancestor should have it. It had already been worked out that all apes and old world monkeys share a common ancestor. Guess what? All apes and old world monkeys have the extra gene.

                    • beau_quilter

                      What math?! Your math?! You haven’t performed any math. Behe’s math has already been completely discredited. As has his mousetrap analogy, as has his notion of I.C. by far better scientists who actually do research and publish results every year.

                      Behe has published only one legitimate scientific article in years. It’s the one you cited, but haven’t read, since you can’t answer the basic question of what in the article (a review of other people’s work) actually needs to be refuted.

                    • stuart32

                      You say that Behe is a truly original thinker, but most people earn fame in science by explaining how things work, not by (allegedly) explaining how they don’t work.

                      A type III secretory system is the biochemical equivalent of a car without its steering wheel, gas pedal and brake pedal.

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      But we know that living things can produce offspring which differ from the parents. Outhouses do not reproduce. Your illustration is irrelevant.

                    • Spaced-Out SCIENCE

                      See my recent reply to beau_quilter

                    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

                      I did. It doesn’t help.

                    • http://irrco.wordpress.com/ Ian

                      Because youfind some odd feature deep within the bits of Microsoft Word program and it looks just like what you find in a PowerPoint program, do you assume they had a common ancestor?

                      Yes. In fact cases exactly like this have been tried in court. It is very common task in software forensics to prove that a piece of code that implements some functionality is an unlicensed copy of a piece of code in another piece of software. I’ve spent many weeks designing the statistical tests to come to the conclusion of common ancestry in code. And in the case of Powerpoint and Word, yes, there is common ancestry.

                      Incidentally, the reason why I’ve been paid to do this work is that I was able to draw from my research in biological evolution, where the same kinds of statistical tests are used to determine not just common ancestry, but when and how the two lines divided.

                      Do you assume that they all came about by only natural processes including mutations and naturalselection?

                      Who is assuming that in biological evolution. It is a conclusion, not an assumption.

                      You’re back to imagining what scientists think and why, and imagining you’re making some insightful criticism when you attack your own imagination.

                    • Spaced-Out SCIENCE

                      Me: Do you assume that
                      they all came about by only natural processes including mutations and natural selection?

                      You: Who is assuming that
                      in biological evolution. It is a conclusion, not an assumption.

                      Me: A premise is an assumption not a conclusion. Naturalism makes no pretenses or apologies about assuming that no “supernatural” events occur, hence inferring that God does not exist.

                      The question you dodge is whether Naturalism assumes that common ancestry results only from undersigned processes of reproduction, from one end of the taxonomic scale to the other, or whether it allows for the possibility
                      that a common designer created initial forms, similar to the way Craig Venter’s group created “the first artificial cell” (a misnomer, by the way).

                    • http://irrco.wordpress.com/ Ian

                      As I said, it is a conclusion, not a premise. Naturalism absolutely allows for the possibility that life was designed and multiple initial forms were created. The fact that that is not the conclusion reached is one of the evidence, not the assumption. The evidence is simply inconsistent with that hypothesis. It is a conclusion that could be overturned with additional data, but one that has been robust to scientific enquiry.

                      If you start with a computer program, one that may have been written by a skilled programmer, or that may have been assembled by natural selection and mutation, you could tell the difference very easily. To suggest that such a conclusion would be an assumption is simply wrong. Given two programs, you can conclude whether they were developed from the same original bit of code, or whether their similarities are due to similar functional requirements. Again, whether those bits of code are output from a human or a genetic algorithm. Again, to suggest that conclusion is an assumption is simply wrong.

                      To suggest that it is merely a matter of assumption that leads us to conclude that Word and Powerpoint were created by human designers rather than assembled by evolution, is bizarre in the extreme.

                      Creationists love to pretend that scientific conclusions are premises or assumptions, so they can go on about ‘worldviews’ and the idea that, if you started with their worldview and did science you’d come up with conclusions that backed up the bible. Which is simply nonsense

                      The question you dodge is, do you have any idea what scientists actually conclude and why? Can you express the reasons someone might hold the position you want to argue against in a way that someone who holds it would recognize? You arrived on this blog trying to pretend you were interested in balance and fairness, but you’ve not shown any inclination to accurate portrayal of the views you don’t hold. Instead you consistently set up and argue against straw men.

                    • stuart32

                      I think you are missing the point. It’s one thing to discover that evolution has happened; it’s another thing to discover every last detail about the evolution of every structure in the natural world. It doesn’t matter if we can’t say exactly how the flagellum evolved at the moment. It’s a matter for future research.

                      We already have overwhelming evidence for common ancestry. We know, for example, that human beings and chimpanzees have evolved from a common ancestor. That is hardly “trivial”. The most that you can argue at the moment is that evolution has been guided by God; you can’t deny that evolution has happened. But that argument is a hopeless one because it depends on our present ignorance about some of the biochemical details of evolution. Given the history of scientific progress, you won’t be able to exploit that ignorance for long.

                      Also. the analogy with computer programmes is ill chosen. If you want to interpret the evidence for common ancestry as evidence for a common designer then you have some explaining to do. For example, why did God decide to give humans and chimpanzees almost identical copies of a defective gene which should make vitamin c but doesn’t?

                    • Spaced-Out SCIENCE

                      You: For example, why did God decide to give humans and chimpanzees almost identical copies of a defective gene which should make vitamin c but doesn’t?

                      Me: In a typical creationist model, they were probably not defective “in the beginning” but came to be so after men rebelled against God, thus alienating His protection and blessings. It would be similar to Word and PowerPoint being made one way in the beginning but subsequently infected at the same susceptible site with an error or virus or similar thing, in those people’s computers who rejected Microsoft’s
                      freely-offered antivirus program.

                    • stuart32

                      There is a big problem with your way of looking at things. You see the theory of evolution and the theory of divine creation as two alternative explanations of the evidence. If I cite something as evidence for common ancestry you interpret it instead as evidence for divine creation. The problem is that you are putting an obstacle in the way of the theory of evolution that no other scientific theory has to face.

                      Normally, if a scientific theory explains the evidence and there is no other scientific explanation then the theory has done all that we can ask of it. You can come up with a supernatural explanation for the evidence if you like but then you are changing the rules of the game. You could use the possibility of a supernatural explanation to undermine every scientific theory. For example, the redshifting of light from distant objects is evidence for an expanding universe. All you have to say is that God caused the redshift and the theory is thrown into doubt.

                    • Spaced-Out SCIENCE

                      If you saw a snapshot picture of the far end of astring of dominos falling, you could know a few things and infer others. You could not, however, know who set the dominos up or what force started them falling.
                      The mistake that arrogant scientists make is in assuming that they will be able to accomplish this kind of task related to our universe. At what point did the common ancestry of certain animal groups begin to proceed because it was set up that way? Darwinism assumes that dominos could set
                      themselves up. Behe’s elucidation of the Irreducible Complexity concept simply clarifies the fact that they can’t. No pathway has been shown for spontaneous generation
                      of complex parts and systems which require numerous pieces to exist simultaneously, as well as the complex instructions for their assembly and regulation, for them to endow any evolutionary advantage. Applying an honest mathematical analysis to any one of the parts or processes involved should convince you that “natural” origins previous to that point of the domino track is impossible. Just because events from that point forward seem natural does not make it logical to assume that intelligent intervention was not required for the former. Also, assuming that science is the only thing that can inform you of who set up the dominos and started them going is simply narrow-minded, to say the least.

                    • stuart32

                      If I saw a snapshot of falling dominoes I wouldn’t think that the first half of the dominoes had been laid down to start with and that the second half had started upright and then been toppled and that all this had been done to deliberately deceive me. But seriously, I think you are wrong to accuse scientists of arrogance when they try to take scientific reasoning as far as it will go. There may be some cases where scientific speculation is unwarranted. For example, some physicists believe that string theory is in danger of becoming a branch of metaphysics. Clearly, this doesn’t apply to evolution.

                      You are also wrong to think that the argument from irreducible complexity can only be refuted by showing a complete evolutionary pathway for an irreducibly complex system. If I take a supposedly irreducibly complex system and break it in half and the remaing half still works then I have refuted the argument. A type III secretory system is basically half a flagellum. Admittedly, it has a different function, but that is the whole point. A system can evolve to do one thing and then acquire a different function. That is how feathers evolved. They originally evolved to provide insulation. In order to do that they only needed a primitive structure which wouldn’t have been useful for flight.

    • http://againstjebelallawz.wordpress.com/ Enopoletus Harding

      Stop and think though–do those who are in charge of educating your children allow for diversity of thought…or do they routinely circle the wagons and vilify anyone who dares suggest that evolutionary
      assumptions are errant?

      [Yawn.] You gonna complain about Big Math and its minions as well?

      Did you happen to see the movie NO INTELLIGENCE ALLOWED with Ben Stein?

      -Why, yes. I found it about five times as vacuous as I expected.

      Have you noticed the vitriolic ad hominem leveled against Michael Behe for his carefully-thought-out elaboration of the limits which evolution has?

      -Why, no, I haven’t.

      His very scientific research is intolerable to those who have already sacrificed their souls on the altar of Naturalism.

      -Calling our ignorance “ID” is very scientific. I speak sarcastically.

    • http://againstjebelallawz.wordpress.com/ Enopoletus Harding

      Also, evolution and naturalism aren’t “altars”, they’re frameworks of research. Do you have any real argument, or are you just a persecution fetishist?

      But, by the way, if Behe is correct, then I’m O.K. with the “cosmic seeding” hypothesis, as long as I only have to believe in little green
      men coming to earth and not God!

      -What the heck’s a God? What would falsify your religion? Also, I don’t love the smell of burning straw in the afternoon.

      • Spaced-Out SCIENCE

        ***-What the heck’s a God?

        Did you miss the graphic at the beginning? Theo=god and logy=knowledge. Which of the three columns might you identify more with, or are you an outsider merely wishing to stir up strife?

        The paragraph under the graphic included this sentence: “your freedom to be yourself and think differently will be welcome as
        part of this community”. I was simply pointing out the abject hypocrisy of that statement. You are apparently welcomed in this community that discusses “the kingdom of God” (left column), “focus of God’s concern” (middle column) and “relationship with God” (right column) but please, please, please, don’t suggest that He is a Creator God in the usual biblical sense of that!

        • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

          Umm, what on Earth are you talking about?

        • http://againstjebelallawz.wordpress.com/ Enopoletus Harding

          I’m an atheist. I think there are no gods.

    • Andrew Dowling

      Behe’s arguments were attacked because his assertions are simply false. The model he used in Protein Science has been proven numerous times to be a sham, as have his arguments about blood clotting being “irreducibly complex.” He’s a test case of someone of faith looking for evidence to fit his framework instead of just letting the evidence lead.

      As for “scientists sacrificing their souls on the altar of naturalism” . . ugh, hyperbole much?

  • http://againstjebelallawz.wordpress.com/ Enopoletus Harding

    The graphic’s pretty interesting and correct-looking, I have to admit.

  • beau_quilter

    Sounds like a welcoming, vibrant community, James – any atheists attending?

  • Eugenie Chaumont

    Thanks for linking. I actually think that *both* sides here are evangelical, in the sense that both are supported in the Scriptures, and that to be ‘theologically liberal’ is something else—so i actually address the questions here about limits and atheists.

    Jon in turn is making a slightly different points about tribalism in theology.

    http://www.psephizo.com/life-ministry/what-is-an-evangelical/

    (and I am Ian Paul, not whoever Disqus says I am!)

    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

      Both sides in the image certainly can be evangelical and are represented in evangelicalism. Neither has to be. And the view that Scripture includes diverse voices and perspectives is not at all incompatible with theological liberalism.

  • arcseconds

    And isn’t that better than simply surrounding yourself with a group of people who simply nod in agreement to whatever you say, because you all think alike?

    Or simply nod in agreement because although none of you really think alike, you’re all invested in keeping up the appearance that you do.

  • http://triangulations.wordpress.com/ Sabio Lantz

    Great list.

    It typifies two different views, but my experience is that the variety of Christians is actually huge. I looked at this list to see if I could supplement my table listing theological decisions Christians separate on.

    In this list, I found the following interesting:

    (1) Hermeneutic: On thing about progressives is how they differ so widely because what they do is figure out what they want their god to be, then they choose the scriptures to support it. I don’t mind that, but instead of admitting this strategy, they still pretend as if scripture has some authority for them that is greater than their intuitions, and it is clear that they aren’t acting like that.

    (2) Incarnational: I have a post in my draft pile on this word — it is a new fadish theological word. All very confusing for those of us no longer needing to hang on to the title “Christian”.

    I must say, James, your church sounds fantastic for you and they are fortunate to have you. And in light of your church, I think there is something missing from this list: Ecclesiology: Liberals are for local governance and Conservatives are often for Top Down rule. Your church allows variation. It is Baptist but different from other Baptists because Baptist ecclesiology is from the bottom up, not top down.

    That is a generality, but not totally true.

    The problem with that system is it invites cultish churches. Each system invites its own pitfalls.

    • http://www.patheos.com/blogs/exploringourmatrix/ James F. McGrath

      Yes, the autonomy of Baptist churches is an advantage and disadvantage. In fact, the emphasis on ‘soul freedom’ – the autonomy not just of churches but of believers and their freedom to follow their own conscience – ought to prevent some of the infamous abuses. But instead we see some Baptist churches becoming tiny authoritarian dictatorships in which it seems as though no one is even aware of such a principle, and indeed, quite happy to allow themselves to be dictated to by the pastor.

    • Spaced-Out SCIENCE

      You said:
      … progressives… figure out what they want their
      god to be… choose the scriptures to support it.

      [Also, of necessity, they choose to ignore a host of scriptures which are terribly inconvenient to their intuitions and desired god. ]…

      pretend as if scripture has some authority for them that is greater than their intuitions…
      [I would love to hear your expansion of
      this, with examples]

      Your characterization is profound and certainly true of “progressives” or “liberals” but perhaps it is also true in lesser degree to all of us at times—a universal temptation to make ourselves the god?

      “He who begins by loving Christianity more than Truth will proceed by loving his sect or church better than Christianity, and end in loving himself better than all.” –Samuel Taylor Coleridge

      2 Tim. 3:5-7 – “having a form of religion but denying the power thereof…ever learning but never able to come to the knowledge of truth”
      “…worshipping the creature more than the Creator” Romans 1

  • newenglandsun

    I think liberals and conservatives have difficulties marrying the two together. The two are one and must be married together to have the fullness of Christianity.

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