My “Why I Am an Atheist” Post

PZ Myers of Pharyngula has a long-running series where he posts “why I am an atheist” essays written by ordinary atheists across the world. He has probably posted well over a hundred so far. Today he posted mine; feel free to head over and read it.

Why I Am an Atheist, by Libby Anne

About Libby Anne

Libby Anne grew up in a large evangelical homeschool family highly involved in the Christian Right. College turned her world upside down, and she is today an atheist, a feminist, and a progressive. She blogs about leaving religion, her experience with the Christian Patriarchy and Quiverfull movements, the detrimental effects of the "purity culture," the contradictions of conservative politics, and the importance of feminism.

  • http://www.freeratio.org/ Brian63

    I am curious—What prompted you to read the God Delusion by Dawkins? Fundamentalists that I have come across tend to abhor the thought of reading or watching or listening to anything that promotes atheism. Did someone recommend it to you? Were you already well on your way, and it was not a scary thought to read it (or maybe it still was)?

    Brian

    • http://patheos.com/blogs/lovejoyfeminism Libby Anne

      Oh, I was already on the way at that point – I had turned to Catholicism but was becoming increasingly disillusioned and starting to have some serious questions – and my husband was further down the path and had a copy of the book. I don’t agree with everything in The God Delusion, but reading it was a long series of “WTF why didn’t I see that before?” moments.

  • Karen

    Oh, that *was *yours! I was wondering if you were that Libby Anne. Vaya sin Dios, my new favorite poster.

  • LittLBob

    Hi Libby Anne

    I’m glad that you are interested in getting to the truth, I fear you may have taken the a wrong detour though. Kudos for being open and honest about your feelings and musings. Perhaps I could also raise a couple of questions.

    1. You mentioned the God delusion, have you read Flew’s take on it and its argumentation? http://www.amazon.com/There-Is-God-Notorious-Atheist/dp/0061335290

    2. You mentioned that college challenged many of your beliefs, I suspect biology/evolution was the primary source. Do you know where the information contained in our DNA (and related carriers) come from? Naturalistic processes do not produce complex and specified information. The cell is full of machines that act on this information to perform work, produce proteins and preserve integrity.
    If this information is not produces by naturalistic processes, where did it come from and what can science tell us about it?

    3. If you want to know if God exists all you have to do is look at the state of Israel. God said that He will declare the end from the beginning as a proof of who He is. He’s made promises to Israel and yet they remain, despite many attempts to exterminate them.

    I could add many more questions, but I think these 3 would hopefully cause you to examine the evidence, assumptions, the sources and methods more closely.

    Regards

    LittLBob

    • http://cfiottawa.com Eamon Knight

      “Complex and specified information” is a bogus concept invented by the Intelligent Design/Creationist movement. It is nowhere rigorously defined, and the pseudo-arguments of people like Bill Dembski have been soundly refuted by experts in both biology and information theory. See for eg:
      http://talkorigins.org/faqs/information/infotheory.html
      http://talkorigins.org/design/faqs/nfl/
      http://talkorigins.org/origins/postmonth/feb01.html
      Like most creationist arguments, “information theory disproves evolution” is an elaborately constructed lie.

    • Contrarian

      You mentioned the God delusion, have you read Flew’s take on it and its argumentation? http://www.amazon.com/There-Is-God-Notorious-Atheist/dp/0061335290

      Have you read There is a God? Its argument is really very poor.

      You mentioned that college challenged many of your beliefs, I suspect biology/evolution was the primary source. Do you know where the information contained in our DNA (and related carriers) come from? Naturalistic processes do not produce complex and specified information. The cell is full of machines that act on this information to perform work, produce proteins and preserve integrity.
      If this information is not produces by naturalistic processes, where did it come from and what can science tell us about it?

      High information content is selected over low information content. Requiring a “source” for information is a red herring; what matters is whether or not mutations add variety to a gene pool, and whether or not selection occurs. Since the existence of selection is abundantly clear, creationists have invented “information” to attempt to argue around the empirical observation that mutations add variety to a gene pool. Once you have conceded both mutational variety and natural selection, you have conceded the Darwinian synthesis.

      If you want to know if God exists all you have to do is look at the state of Israel. God said that He will declare the end from the beginning as a proof of who He is. He’s made promises to Israel and yet they remain, despite many attempts to exterminate them.

      Have you considered any other hypotheses for the existence of the state of Israel?

      • LittLBob

        I have read it.
        Information systems require error correction and transmission mechanism.
        I have considered other hypotheses, the problem remains, people keep trying to wipe them out and against all odds don’t seem to succeed.

      • Contrarian

        It’s NOT an information system.

    • plch

      3. If you want to know if God exists all you have to do is look at the state of Israel. God said that He will declare the end from the beginning as a proof of who He is. He’s made promises to Israel and yet they remain, despite many attempts to exterminate them.
      what about Cuba? have they been chosen too?

      • LittLBob

        I’m not sure what you are asking. God seeks to save all people, however he has chosen a people for his own purposes. If you are trying to compare Cuba to the people of Israel , I suspect you don’t know much about their history? Are the people of Cuba an ethic people? Did they make a covenant with God? where they exiled, scattered and ultimately regather back as a nation after being exiled for 2000 years?

  • LittLBob

    Eamon, where did the information come from?

    • http://patheos.com/blogs/lovejoyfeminism Libby Anne

      Did you read his comment and his links?

      • LittLBob

        I’ve raised a simple question, Eamon’s concern is with the concept of CSI. The fact remains that there’s information in there and it drives us.

      • http://patheos.com/blogs/lovejoyfeminism Libby Anne

        How are you defining “information?” Also, did you read Eamon’s links? They deal with a whole not more than “the concept of CSI.”

    • Froborr

      Information is not a conserved quantity, and therefore any reaction can change the amount of information in a system in either direction. It need not “come from” anywhere.

      Here is a thought experiment: A plate sits on a slightly tilted table. The plate slowly slides to the edge of the table, then drops off. When it hits the ground, it cracks, dramatically increasing the information content of the system (it is now two irregular shapes instead of one regular shape). Did this information come from anywhere? No, it was created at the moment the plate hit the ground.

      Here’s another: Someone puts a powerful magnet dangerously near your computer and wipes all your data. Did that information go anywhere? No, it was simply destroyed.

  • LittLBob

    I’m sure they do, as I’ve said before we are dealing with an information carrier and machines that act upon them. There is no known naturalistic process that can account for them.

    • http://patheos.com/blogs/lovejoyfeminism Libby Anne

      That is false. You clearly haven’t read much evolutionary science.

      • http://cfiottawa.com Eamon Knight

        He also hasn’t read much *information theory* either. The entire class of arguments is an attempt to provide a pseudo-mathematical “proof” that evolution (or naturalism or materialism) can’t produce life-as-we-know-it.
        No, Bob: we are dealing with *molecules* and their *chemical interactions*. Information, machinery — these are abstractions *we* impose by (imperfect) analogy to our own technology. And to the extent we apply information theoretical concepts to DNA, we know a lot about the mechanisms of transmission (eg. DNA polymerase — IOW: chemistry) and error correction (hint: evolution *depends* on imperfect error correction). So here’s the deal, Bob — in order to make the kind of argument you’re trying for, you need to:
        1) Specify your information metric — ie. tell me your definition of “information” and how to measure the amount of it in an entity (eg. a genome).
        2) Demonstrate the existence of a conservation law that prevents that kind of information from increasing by mundane natural processes. Note, I said “demonstrate”, not “wave hands and assert”. BTW, I believe in one of those FAQs I pointed you to, it mentions the counter-intuitive fact that, according to at least one metric used by real mathematicians (ie. ones that aren’t creationist hacks), introducing random errors into an orderly string *increases* its information content.
        Go thou and learn!

      • LittLBob

        What is false, the fact that DNA contains codes / information or that naturalistic processes can produce them?

  • LittLBob

    And yet what we observe is information systems at work. I guess you don’t like the fact that we have a coding scheme using molecules? Do you truly believe that random genetic changes filtered by natural selection produced all we see? Now that would be a miracle.

    • Paula G V aka Yukimi

      I truly believe it and the scientific theories and facts about molecular biology and DNA make perfect sense to me. What doesn’t make an iota of sense to me is that information system you keep mention without defining them. You should inform yourself and take a few courses on biochemistry, biology and physiology before going desestimating solid scientific theories without understanding them.

    • http://cfiottawa.com Eamon Knight

      You keep repeating this as if that will make it true. Reality doesn’t work that way. You don’t actually know how to compose an argument, do you?

      • LittLBob

        So all the codes, copying, coding, decoding, error correction, preservation, etc is just an illusion?
        http://www.nature.com/nature/journal/v484/n7395/pdf/nature10965.pdf

      • Caravelle

        Of course not, except insofar as any attribution of function is an illusion (which it can be if we assume function requires a conscious agent, but isn’t if we use a more operational definition).
        But you give no reason why those things can’t arise by natural processes, except that you don’t think they can.

        One thing that may not be completely obvious is how chemistry works. Atoms react with other atoms to form molecules because that’s what they do; their attributes like mass and their electron configuration cause them to react that way. The same thing is true of organic molecules in the cell. They don’t need to be told what to do, or directed to meet each other; they diffuse passively until they encounter another molecule, which they react with according to their chemical composition. Put simply, there is no hardware/software distinction.

        Now we can attribute functions to all of those chemical processes such as “coding”, “copying”, “correcting” and so on because they’ve developed through evolution, which is an optimizing process. And optimizing processes imply something you’re optimizing *to*; in evolution’s case it’s “reproducing” (overall; optimizing reproduction overall will often imply optimizing sub-structures for some other purpose like “coding”, “copying”, “seeing”, etc. But the final arbiter is reproductive capacity). Hence those structures function AS IF they had goals, and we can talk about them in terms of goals.
        But nothing about that requires intelligent or conscious goal-setting.

      • Paula G V aka Yukimi

        That’s why my physiology teachers corrected us when we made false tautologies.

    • Ben

      As it happens LittleBob, I am a biologist. Yes. The largest problem with your set of assertions is that you are trying to claim that a chemical system that obeys certain laws of nature is analogous to a system based on symbolism and abstraction. When I am doing bioinformatics (say, I am trying to annotate a genome), I can apply many of the same assumptions I do when trying to crack a military code. However, this is only a useful simplification. Like assuming that the cannon ball you are trying to place inside an enemy fortification is free of drag. This is a big difference. A military code contains symbols, and those symbols contain information a human mind both creates and reads. The symbols are used as stand-ins for sounds, and those for ideas. A chemical system like DNA is not like that. A DNA codon specifies information. However, that information is written into the laws of chemistry and is not an abstraction. It no more requires an intelligent creator than a combustion reaction requires an intelligent creator to specify its outputs (CO2 and H2O for the scientifically disinclined).

      That the system is complex is irrelevant. That there are transport molecules is irrelevant. They did not start out that complicated. They started out as nucleotide sequences with some simple enzymatic function that created something the proto-cell needed (such as manufacturing more simple fatty acids for the proto-cell-membrane) and from there, natural selection takes place. The proto-cell can swallow smaller proto-cells (through membrane fusion, like soap bubbles coalescing), those that get larger faster are over-represented in the system. Bigger ones hold more nucleotides, which allows more enzymatic function. All DNA is, is a huge nucleotide enzyme with many many active sites that over time has produced more stuff that gives a cell an advantage over other cells. It even increases its information content by self-replication (in fact, some non-DNA nucleotides are capable of doing it with other enzymes. DNA happened later), and in modern cells, gene and even whole genome duplication happens due to errors in proof-reading mechanisms do happen. This creates a new substrate upon which natural selection can occur without damaging the cell’s other functions.

  • Collegiate

    I’ve been reading your blog for a couple weeks and I have one main question. You have mentioned several times that going to college challenged your beliefs. Maybe you don’t want to say exactly which college for privacy reasons, but what type of college was it? Apparently one that taught proper science, so not a fundamentalist christian college. I also know you mentioned that you were expected to go to college in order to be a better helpmeet for a man, which sort of makes sense. But I can’t understand why your parents would send you to a college that teaches modern science, after all that effort homeschooling you and everything. I don’t know if I’mm articulating this very well… but could you do a post on what factors went into you going to college, choosing a college, meeting peolpe there that challenged beliefs, etc? I guess I would just expect a family like the way yours is described to either keep daughters from going to college at all, or insist that they only go to fundamentalist schools. I’m curious about the details. Did you live at home while you were in college? Did your parents see that you were changing your mind? Did htey try to get you to quit school? I’d love to see a post on all that stuff.

    • http://patheos.com/blogs/lovejoyfeminism Libby Anne

      Haha, long question. Yeah, I should do a post, because I’ve been asked in the comments about this before and have replied, but keep getting asked it. Short answer: I went to a state school. My parents believed that I was so well taught and grounded in the truth that I was ready for that, and could witness to others. They really believe that everything they believe is factually true if you just examine it (including creationism), and the homeschool community promised that careful training would essentially make a child immune to being “led astray” intellectually. My parents valued education and were so sure they were right they just weren’t worried about a state school undoing all of their careful raising of me. I lived at college because it was a college some way from home, and my parents didn’t know I was changing my mind on things until it had happened. I wasn’t going to talk to them about it because I knew they might respond badly, and I’d always been taught to search for truth wherever it went, so I didn’t feel wrong about exploring things. I mean, I figured I’d just end up back at my parents’ position, since it was RIGHT. They didn’t try to get me to quit school when they found out, they just tried to get me to believe their beliefs again and when I didn’t prove very ready to do that, well, I just left. I stopped taking any money at all from them and was fully independent after that, so they had nothing to hold over me. Hope that answers at least some of it.

  • ScottInOH

    I liked your post, Libby Anne, as usual. From reading many of your other posts, though, I didn’t realize that YEC was so central to your de-conversion. I remember the accounts of your realizing how varied–and conflicting–God’s messages were to His people, of your salvation anxiety, and so on. Maybe losing Creationism was essential for the other things to happen, but it seems to me you could have ended up where you are by a variety of paths.

    Just musing…

    • http://patheos.com/blogs/lovejoyfeminism Libby Anne

      YEC started it all off for me. Then I had to search for something new. After all, the evangelicalism I had been raised on was wrong. So that’s when I found Catholicism and other more liberal varieties of Christianity. However, my fascination with understanding where the Bible came from backfired and then basic Christian doctrine stopped making sense…and then that was that. In some ways I deconverted first from evangelicalism and second from Christianity, but had to do each separately.

  • smrnda

    I studied theoretical computer science which is a field which uses a lot of information theory; I have never seen it used in any way to further ideas of intelligent design or that high levels of ‘information’ necessarily mean that intelligence must have been displayed in arranging any sort of data. In fact, an important metric is entropy, which means the number of bits (quantity) of information needed to quantify the uncertainty of a particular variable in terms of the values it takes – a variable which takes on lots of values with little or no order would have high entropy. If we take the idea of transmitting information, transmitting information that has low entropy will have a greater probability of success because it can be encoded with smaller bits of information and, with fewer possible values, will be less prone to error. All said, as I have not studied biology I don’t pretend to know the implications of this to biology or evolution.

  • smrnda

    On a correction mechanism, in AI the ‘programmer’ who deals with machine learning has to build in a function normally called the critic that tells the program, effectively, whether it has succeeded or failed depending on its performance. (What actions it takes then are based on its initial state and later trials.) If we were looking at living organisms, survival or death would effectively erase the need for what is usually termed the internal critic of a program. Through machine learning, I’ve seen incredibly ‘simple’ programs (initially) become capable of handling extremely complicated tasks without much but a simple ‘thumbs up thumbs down’ rating, with the rest handled by pure trial and error. In fact, machine learning is often used in fields where the idea of a programmer actually making a program to handle the situation is just beyond our capacity – nobody could consciously design something as effective as what can be produced through random trial and error.

  • LittLBob

    @Caravelle you said “The same thing is true of organic molecules in the cell. They don’t need to be told what to do, or directed to meet each other; they diffuse passively until they encounter another molecule, which they react with according to their chemical composition. Put simply, there is no hardware/software distinction”
    Is this not an over simplification, there’s shepherds and transportation molecular machines?

  • Caravelle

    Is this not an over simplification, there’s shepherds and transportation molecular machines?
    There are some molecules whose main function (or if you don’t want to use that word, effect) is to transport other molecules from one place to another. I know some molecules react to others by moving along them as if on a rail, so that can serve to move molecules from one part of the cell to another. I think that plays a big role in cellular division for example. But the main things are still diffusion and reaction. And even in the case of physical transportation, it’s still diffusion that gets a molecule in contact with the transportation system, and its transport is a chemical reaction between it and the transportation system.

    I don’t know about shepherds; I don’t doubt such molecules exist but I haven’t been able to find anything of that name with Google. Do you have details on what you’re thinking of ?

    • Paula G V aka Yukimi

      I can’t think of anyone “shepherd” molecule.

      Trying to assign a will or an intent to a molecule or something similar is simply wrong. You can also see pretty clearly that many of these transporters, regulators and the like exist in more evolved beings. If you simply compare a procariotic cell with examples of different eucariotic cells or fish like a shark to river fish you can see how certain mutations who were benefitial were maintained (mitochondrias, flotation system, …) and it’s the same with organules and specific biomolecules and you can see it by studying it in deep. I don’t know if I’m explaining very well because I’ve never had to defend evolution since almost 100% people in Spain believe in it…

      • LittLBob

        Paula have a look a the protein folding process, there are chaperones that serve to shepherd during the process.

      • Caravelle

        @LittLBob : That’s got nothing to do with transport. And again, those “chaperone” molecules aren’t molecules that were given the *role* of chaperoning – it’s molecules that, given their composition and the composition of the protein, will inevitably cause the protein to fold the way it does in their presence. Their function isn’t some abstract substance they were imbued with – like a rock would be imbued with the function of “paperweight” or “souvenir” or “decoration” or “weapon” depending on what I want to use it for, and which has more to do with me than with the rock – it’s an effect they have that’s inextricable from their structure.

      • Paula G V aka Yukimi

        I haev studied the chaperone moleucles in class thank you very much but Cravelle has already veyr bautifully answered you for me ^^

  • LittLBob

    @Caravalle Amusing, let let me get this straight, you are comparing the function of a rock to that of a molecule that helps to fold a protein in a way it *wont* fold naturally?

    • Caravelle

      Nope; try again.
      If you’re confused by the aside about the rock just ignore it, it was meant as an illustration of how we usually think of “function” as something that can be separated from structure. It isn’t a vital to my point, which was that molecules’ “functions” cannot be separated from their structure.

      • LittLBob

        @ Caravelle, I’m not trying to separate the function from the structure. The point it that is “helps” to perform an unnatural function during folding. It’s only going to get harder and harder to sustain the naturalistic narrative as we discover more molecular machines that seem to ensure information integrity and access like Topoisomerase.

        @LibbyAnne I’ve made my 3 points, take it or leave it :)

      • http://patheos.com/blogs/lovejoyfeminism Libby Anne

        “The point it that is “helps” to perform an unnatural function during folding.”

        And Caravelle’s point is that it doesn’t. It’s completely natural. With that protein present, the chain has to fold like that. Furthermore, I think you’re anthropomorphizing a bit when you use the word “helps.” Does a rock in a stream “help” or “perform an unnatural function” when the water flows around it? You’re attributing agency to a protein.

  • LittLBob

    No I’m attributing purpose, it has a purpose. The protein will not naturally fold into the
    novel structure required for its function. You need to introduce something to help it fold.
    Just like the Topoisomerase, it has a purpose, it cuts, crosses over and rejoins coiled DNA.

    • http://patheos.com/blogs/lovejoyfeminism Libby Anne

      Same thing. Does the rock in the stream have a “purpose?” If it weren’t there the water wouldn’t flow around it, but would instead flow straight. When you put a ball down a pegboard and it hits the pegs and moves around them, do those pegs have a “purpose?” And you’re still talking about “introducing” something to “help.” It’s the wrong language. Think about it this way. There is a stream that flows. It ends up dammed up and a lack is created. That dam could be built by people, and then it would be people “helping” stop the water, and the dam would be built with a purpose. But if a tree falls in a storm, and then sticks coming down the stream get caught up against it, and then leaves that fall do the same, and the result is a damn, can we say that someone “introduced” something to “help” create a damn or that that damn has a “purpose?” No. No one planned that damn. No one put the leaves there so that they could block it up. It was just natural processes doing what they do naturally – and can’t not do.

    • Caravelle

      “You need to introduce something to help it fold.”
      … That’s right, you need to introduce another molecule. That’s just as natural as the protein it reacts with. If the protein can appear naturally, then why can’t the protein/folding molecules system appear naturally ? And if the protein/folding molecules system can’t appear naturally, why is that ? Is there something special about that system that the protein itself (already a complex system) doesn’t have ?

      The issue is that you’ve been talking about how things like codes, copying, error-correcting or information couldn’t have appeared through natural processes. But given that at the chemical levels structure absolutely dictates function, asking “how did this function arise ?” is exactly the same question as “how did these molecules arise ?”. And suggesting that “coding” couldn’t arise through natural processes is the same thing as saying deoxyribonucleic acid couldn’t arise through natural processes. So please explain, what is it about a molecule of deoxyribonucleic acid that makes it impossible for it to arise through natural processes ? (“it’s very complex” and “it’s optimized to have a specific effect” aren’t good reasons, the process of evolution can result in both of those attributes)

      So saying that “coding” couldn’t arise through natural processes is the same thing as saying that the DNA molecule itself couldn’t arise through natural processes. Or topoisomerase, since you brought it up. So, why couldn’t it ? It’s a natural molecule made of natural atoms. It’s also a very non-random molecule with very specific effects, but evolution is a process that results in non-random systems with specific effects, so that’s not a problem.

    • Froborr

      To attribute purpose is to attribute agency. Objects do not have inherent purpose; they have purpose *to* an agent. In other words, if I use a rock to hammer nails, that is its purpose *to me.* If I decide instead to use it to make a philosophical point, that is its purpose to me. The purpose is not a property of the rock, but rather something I–as an agent–assign to it. An agent can create an object to fulfil a particular purpose (we call this a tool), but that purpose is again a subjective attribute assigned by the agent using the object, not a property of the tool–if you want to use a hammer for some purpose other than hammering nails, you can do so.

      Only an agent can possess an inherent purpose–definitionally, an agent is an entity that can act with intent, and thus my actions have a purpose in my mind, which we could consider my inherent purpose. Thus, to say something has a purpose–in itself, not imposed from outside–is to assign agency to that object, as I said.

      If your question is, rather, “Who gives the molecule its purpose?” the answer is that you do, because that purpose exists solely in your mind, not in the molecule. The proper field for exploring purpose is psychology, not chemistry or biology.

    • Ben

      For large proteins, yes. They need help folding. Simple ones however, do not. Just because an object does something does not mean purpose can be ascribed to it. Rocks erode. That does not mean something intends that they erode. I can use the laws of physics to send an object to Neptune. That does not mean that some inexorable universal intelligence intended that use the laws of physics in that way.

      You are affirming the consequent. A logical fallacy. Stop.

  • LittLBob

    It’s not the same things. You are comparing an intricate system to a river, the comparison doesn’t work.
    The one produces functioning proteins and ultimately you, the other well a full dam.

    • http://patheos.com/blogs/lovejoyfeminism Libby Anne

      The point of the example was that attributing “purpose” to natural processes is silly.

      • LittLBob

        Libby Anne you assume a naturalistic explanation for all you see, I don’t.
        Naturalism is a philosophical position not a scientific one.
        Imagine for a second that you discovered the watermarks in Mycoplasma laboratorium, would you contend that a naturalistic process encoded them?

      • http://patheos.com/blogs/lovejoyfeminism Libby Anne

        Actually, naturalism is definitely a scientific position. Science is about investigating nature and understanding how it works. And so far, we have always, always, always found natural explanations.

      • http://patheos.com/blogs/lovejoyfeminism Libby Anne

        Also, if something has a naturalistic explanation, why would you reject that and go for a supernatural explanation instead? When the wind blows, do we have to decide whether it is the result of natural or supernatural forces? Of course not! We know what causes wind, and it’s completely natural. Why would we reject a perfectly adequate natural explanation? Believe it or not, there are similarly perfectly adequate natural explanations for the formations of proteins and inner workings of the cell. If we know how they work, and know that they operate based on natural processes and have natural explanations, why would we reject that and choose to believe a supernatural explanation for no reason?

  • LittLBob

    Libby Anne, if the naturalistic explanations are sufficient I’ll gladly accept them.
    I think my previous example is a good one, if you encountered or discovered the the watermarks in Mycoplasma laboratorium, would you contend that a naturalistic process encoded them?

    I think we are hardly in a position to claim that we fully understand the naturalistic processes in the cell not to mention codes and machines that operate on them. Do you truly believe that random genetic changes filtered by natural selection produced them?

    Your prior commitment to naturalism doesn’t give you any alternatives when it comes to interpreting the data.

    http://www.collinsdictionary.com/dictionary/english/naturalism

    • Caravelle

      That question is actually a lot more complex than you seem to think. For one thing, that watermark is a series of amino acids which, when coded as letters of the alphabet, taking out spaces and taking Us as Vs, makes fifteen-letter chains containing the names of the organism’s creators and their organization.

      Anyone who knows a little bit about cryptology and numerology knows that in a sufficiently long set of letters (say, a book) and using sufficiently ad-hoc coding algorithms you willalways find a string of letters you find significant.

      That doesn’t mean such a string of letters is NOT significant; in fact with Mycoplasma laboratorium we know for a fact they are, because the people who put them there told us. So when you don’t have something so convenient as direct testimony from the person who encoded the significant bits of texts, how can you tell it’s actually significant and not random ?

      Thankfully we’ve invented statistics to deal with just this kind of question. Here, by looking at the length of Mycoplasma laboratorium’s genome and all the different ways the words could have been coded (different amino-acid/letter mappings for example) and how many words we’d consider significant (names of people ? coherent sentences in English ? words in any language ? Do we accept misspellings ?), we can calculate the odds that such a string of letters would appear by chance. And the lower those odds are, the more likely it is this string is indeed significant.

      I have no idea what those odds actually are in this case. Given Mycoplasma laboratorium’s genome is really small IIRC and the actual names of the creators is a very significant string the odds are probably very low. On the other hand if I didn’t know who the creators were and didn’t know they were English then I’d be less likely to recognize the significance of those strings of letters and might not recognize the watermark as such.

      Now the thing is a watermark isn’t random, and by that I don’t mean it’s designed. I mean it’s designed for a specific purpose which means it has specific characteristics : it’s meant to unambiguously indicate who made or owns the object. This means it’s purposefully non-functional, or even counter-functional* (…because if it were functional then any designer would put it there so it wouldn’t point to anyone specific), and is linked to the designer or owner in some way. This is clearly the case of Mycoplasma laboratorium’s watermark.

      None of the natural systems you brought up are like watermarks in that sense. They are extremely non-random and significant, that is true, but they’re extremely functional, which means any process that results in non-random functional systems could have made them. And evolution is such a process.

      Also ? There ARE natural systems that are like watermarks, in that they’re non-functional and linked to the process that generated them. Turns out ? They point to common descent.

      *For example, IIRC mapmakers would protect their copyright by adding a few non-existent islands or towns to their maps. It’s the only think that can make a map *specific* to its maker, see

  • LittLBob

    Ironically I am quite familiar with cryptography, the point I was trying to make was that if Libby Ann didn’t have any knowledge of the organism and discovered the watermarks, without necessarily decoding them, she would have concluded that there had to be a naturalistic explanation for them. Decoding them would have been a bonus :)

    • Froborr

      There *is* a naturalistic explanation for the watermarks: Some scientists put them there. That is a naturalistic explanation that involves no supernatural entities whatsoever.

      However, with the diversity of life on Earth, such an explanation doesn’t hold. It is like if I were on trial for murder, there were fifteen eyewitnesses, security camera footage, and my fingerprints are on the murder weapon, but I claim that my friend Joe did it. Magically. From another continent. In such a way that it *looked* exactly like me doing it and left my fingerprints on the gun. Would anyone buy that explanation for a second?

      The answer is yes: A conspiracy theorist emotionally invested in the idea of Joe being a bad guy and/or me being a good one would accept the explanation in a heartbeat.

    • http://cfiottawa.com Eamon Knight

      Froborr touches on this, but it’s worth emphasizing: you’re conflating two issues that need to be kept separate:

      1) Does a phenomenon (eg. some bit of biochem) result from the action of a powerful, intelligent agent?
      2) What is the ontology of that agent? (The choices being: natural or supernatural).

      Only after you’ve answered #1 in the affirmative is it relevant to start arguing #2. We may very well get false negatives on #1 — detecting the Myco watermark requires a cultural context that includes knowledge of the standard amino acid shorthand notation, of letter frequencies and phonetic combinations. An alien biologist from Tau Ceti would almost certainly miss it. But note that this failure is not due to a prior assumption, it’s due to not knowing what to look for (or that there is, in fact, anything to look for).

      And here’s the problem with asserting divine action as an explanation: we know what humans can do, and like to do, so we know what to look for. We don’t know that about gods, or hyper-powerful space aliens. Thus, while we regularly (if not always accurately) ascribe human agency to putative crime scenes and archaeological finds, it’s far from clear what gods or ETs would do (and the claims we see on behalf of both seem to be retroactively constructed — with a large dose of speculation — to fit the phenomena).

      • LittLBob

        @Eamon In my example I wasn’t asserting a divine hand. I was trying to demonstrate that our prior commitments can lead us down the garden path.

      • http://cfiottawa.com Eamon Knight

        our prior commitments can lead us down the garden path
        Thanks, but I think we already knew that — what you haven’t done is to demonstrate that that’s what’s actually happening. Suggestions about what someone might be doing aren’t arguments.

    • Caravelle

      Yeah, and I told you that this isn’t the case. What Libby Anne concluded on the watermarks would depend on the statistical analysis she conducted to determine whether is was likely non-random, and if it was it would further depend on which causes could be inferred from the watermark itself. If this analysis yielded a higher likelihood of a supernatural cause than a naturalistic one, she’d go with that. If not, not. (I apologize for speaking for you Libby Anne. I mean to make a general point, but since the post I’m responding to is in the form “Libby Anne would to X” I find it more elegant to continue in that vein)

      Of course the former can only happen if supernatural causes are amenable to such analysis (i.e. are testable) in the first place, which depending on the definition of the word they often aren’t. And that is the problem with supernatural causes.

      I also note that human microbiologists don’t in fact fall under the umbrella of “supernatural causes”.

      • Caravelle

        In other words, if Libby Anne had no knowledge of the organism and didn’t attempt to decode or analyze the string of amino acids in any way, and concluded that the string had come about by random mutation and not direct human engineering, it wouldn’t be her “prior commitment” that led her down this path. It would be her woeful lack of information. With more information (such as gaining knowledge of the organism, or analyzing the string of amino acids and noticing things like their total lack of functionality and an otherwise-minimal organism and their repeating patterns), she’d come to more-accurate conclusions.

  • LittLBob

    @Froborr naturally :)

    • Froborr

      Naturally what? My point is that there are really only two possibilities with the diversity of life on Earth: either it’s a product of naturalistic processes that do not involve agents, or it is product of agents who are so good at hiding that in thousands of years of searching for them we have yet to find a shred of evidence for their existence, despite the fact that they must be tweaking every mutation and every death of every organism. Invisibly, at a distance.

      In short, these agents, if they exist, are either gods or Sufficiently Advanced Aliens, which amounts to the same thing.

      So, on the one hand we have naturalistic explanations that adequately explain the diversity of life on Earth, and on the other we have magical god-aliens introduced for no other reason than that you like them.

      Occam’s razor, my friend.

  • LittLBob

    @Froborr “There *is* a naturalistic explanation for the watermarks: Some scientists put them there. That is a naturalistic explanation that involves no supernatural entities whatsoever.”

    I have to disagree, an intervention by an person is not an naturalistic explanation, what law compelled him or his team to do it? My point is that your prior commitment to naturalism (which is philosophical) and not science forces you to conclude that a naturalistic process like RM+NS produced the watermarks, which is clearly incorrect.

    • Froborr

      I’m not going to get into debating free will and agency and such, especially seeing as you’ve declared your intent to depart.

      I will thank you to not tell me what I believe without asking, because you’re wrong. The actions of known naturally occurring agents, such as people, are perfectly acceptable as part of a naturalistic explanation.

      You clearly have no understanding of what the words “naturalism” and “science” actually mean. Science is the pursuit, construction, and testing of positive, naturalistic models of physical phenomena (yes, even the social sciences, they’re just dealing with very very complex physical phenomena). The scientific method is not capable of detecting supernatural entities (which makes the fact that it has nonetheless managed to adequately explain pretty nearly everything we’ve encountered verrrrry interesting) or addressing normative questions, because that’s not what it’s for.

  • LittLBob

    @Libby Anne this will be my final post, thanks to all for the civil discourse.
    I’d like to leave you with a final point. As we uncover more of the mysteries
    of the cell we will be forced to make inferences about it’s origin.
    We have to follow the evidence where it leads.

    Quantum mechanics is one of those areas that’s clearly showing us things
    about our reality that don’t square with the prevailing narrative.
    QM is showing us experimentally that information transcends space and time.
    This quantum information/entanglement is even evident in our DNA.
    If information transcends space and time, and it found in all living organisms it has to originate from an source outside our reality. The only worldview in which this makes sense is the Judeo/Christian worldview, where God claims that He transcends his creations. Where the “Word” became flesh.

    http://www.metacafe.com/watch/5936605/

    Cheers
    LittLBob

    • Froborr

      QM is showing us experimentally that information transcends space and time.

      Depends on how you define “transcends.” Quantum entanglement obeys clear laws. They’re not the laws our naive intuition expects, but they’re demonstrably there.

      If information transcends space and time, and it found in all living organisms it has to originate from an source outside our reality.

      This is *like* logic, in the sense that there are premises and a conclusion, but the conclusion does not remotely follow from the premises, the truth of the first premise has not been established, and the second present is only true in the sense that *everything* has information content. There’s nothing mystical about information; it’s an abstraction, and therefore, like all abstractions, something we invented to understand and categorize phenomena that pre-exist our abstractions. There is not some sort of mystical substance called “information” living inside DNA; the DNA interacts with chemicals around it in ways that we can more easily understand if we imagine the nucleotides as forming a “code” that the surrounding cell “reads.”

    • Froborr

      Also, as an ethnic Jew, I find the term “Judeo-Christian” highly offensive. Judaism is a completely distinct worldview from Christianity, with different beliefs, different values, different goals, different ethical standards, and very different understandings of the nature of the divine. Your following sentence makes it very clear you mean the Christian deity only, so your “Judeo-” is revealed for what it always is, an attempt to appropriate a misunderstood minority culture by the dominant majority.

      • http://cfiottawa.com Eamon Knight

        Or as I like to put it: “Ignore the fact we treated you like vermin for 16 or so centuries, now that we want your votes, we’ll let you be Honorary Christians” (say that last phrase with as much condescension as you manage).
        (My wife was raised Reform Jewish)

  • http://www.arizona-writer.com Kimberly Hosey | Arizona Writer

    @Libby: I have nothing new to offer to this ongoing discussion, but I do want to say how much I enjoyed your essay at Pharyngula. I can see a few echoes of my own experience (I was raised Catholic, with my teenage years spent in a stint in fundamentalism/evangelicalism/YEC, but oddly always with the admonition to question and investigate for myself), but more than that I see echoes of a loved one who was raised almost exactly in the same culture, and who is slowly, bit by bit, coming around. It gives me hope.

    I meant to write a post for my own blog yesterday, and sort of accidentally wrote the better part of my own “Why” essay instead. Maybe eventually I’ll have the guts to send it in. Much thanks for the ongoing inspiration.

    P.S. Apparently, Answers in Genesis read your essay too, and interpreted it exactly backward:
    http://blogs.answersingenesis.org/blogs/georgia-purdom/2012/05/03/answers-in-genesis-and-libbys-journey-to-atheism/

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  • Elizabby

    Interesting, thanks for writing. I think your journey is the exact opposite of mine. Suffice it to say that I reached the same crisis of faith, realizing that it is impossible to be a scientist with intellectual integrity AND a Creationist at the same time, and knowing that if Creationism is compulsory then Christianity is not an option. However, I resolved the dilemma differently and am a happily evolution-believing Christian. I agree with you though – that it is a terrible mistake to pin faith to Creationism. I was lucky that my faith was not based there, so I could jettison this without losing my faith, but at my seminary one of my classmates had a terrible crisis of faith exactly like this, and it was painful to watch. But this crisis is completely avoidable – the conflict is manufactured. Most Christians in the world are not Creationists, and I hope and pray that this ridiculous idea passes away, along with the Flat Earth and Geocentric Theory.


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