What’s With the Junk? (DNA that is) (RJS)

The topic of Junk DNA has come up a number of times in posts on this site over the last year or so. In particular one commenter has referred on several occasions to the supposed debunking of junk DNA as a serious blow to the theory of evolution. This is a fairly common misunderstanding. But the recent flurry of publicity over the release of a large series of papers by the ENCODE project the first week of September and a truly exceptional claim that 80% of DNA exhibits biochemical function has brought Junk to the fore once again.

A typical report from the New York Times: Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role.

And from the Washington Post (one of the worst examples of hype I found): ‘Junk DNA’ concept debunked by new analysis of human genome.

Another from Forbes looks at the reaction to the press surrounding ENCODE: Reports of Junk DNA’s Demise Have Been Greatly Exaggerated.

A response on the  Nature News Blog: Fighting about ENCODE and junk.

This is a real mess – a mixture of hype and real breakthroughs, straightforward commentary and polemic.

What does this mean for the arguments for evolution and common descent?

What is the non-scientist to think?

As a result the topic of junk DNA is probably worth a post.

We all learned in high school or college biology that the sequence of DNA codes for proteins. Each of the 20 natural amino acids is specified by one or more three base nucleotide sequences according to a genetic code. The stretch of DNA that codes for a given protein is called a gene. The human genome contains some 23,000 genes. Most of the DNA in each chromosome however, does not code for protein. The remainder either serves a different function or perhaps serves no function. This DNA has often been referred to as “junk” DNA as though it is uniformly without function in biology.

The presence and pattern of this so-called “junk” DNA is a persuasive argument for evolution and common descent. In his book The Language of God Francis Collins describes transposable elements or ancient repetitive elements (AREs) as one of many threads of evidence for common ancestors and common descent (p. 135-136).

Even more compelling evidence for a common ancestor comes from the study of what is known as ancient repetitive elements (AREs). These arise from “jumping genes,” which are capable of copying and inserting themselves in various other locations in the genome, usually without any functional consequences. Mammalian genomes are littered with such AREs, with roughly 45% of the human genome made up of such genetic flotsam and jetsam. When one aligns sections of the human and mouse genomes, anchored by the appearance of genetic counterparts that occur in the same order, one can usually also identify AREs in approximately the same location in these two genomes.

Some of these may have been lost in one species of the other, but many of them remain in a position that is most consistent with their having arrived in the genome of a common mammalian ancestor, and having been carried along ever since. Of course, some might argue that there are actually functional elements placed there by the Creator for a good reason, and our discounting them as “junk DNA” just betrays our current level of ignorance. And indeed some small fraction of them may play important regulatory roles. But certain examples strain the credulity of that explanation. The processes of transposition often damages the jumping gene. There are AREs throughout the human an mouse genomes that were truncated when they landed, removing any possibility of their functioning. In many instances, one can identify a decapitated and utterly defunct ARE in parallel positions in the mouse and human genome.

Do new discoveries of function for the so-called “junk” undermine this argument? Dennis Venema, an associate professor of biology at Trinity Western University in British Columbia, had a good series of posts on the BioLogos blog earlier this year discussing “junk DNA”: Is there Junk in your Genome. I recommend these posts to anyone with interest in more of the details.

The label “junk” is not entirely accurate as both Dr. Collins and Dr. Venema note, and functions of segments of the so-called “junk DNA” are being identified with some regularity. In fact is is not uncommon to see articles in the scientific literature, or more often in the popular press, with an opening paragraph that highlights the label and continues on to describe some function of some portion of the so-called “junk”.  Many small sequence of conserved noncoding elements (often abbreviated CNC or CNE) appear to serve regulatory functions turning genes on and off.

An NPR story last year Don’t Throw It Out: ‘Junk DNA’ Essential In Evolution highlighted the results of a paper published in Science, Three Periods of Regulatory Innovation During Vertebrate Evolution by Lowe et al. (Science 333,  1019-1024, 2011). This article discusses how the evolution of gene regulatory elements in the “junk” may be responsible for changes in the phenotypes (characteristic traits) of animals.

So what is the fuss?  The headlines for ENCODE claim something like 80% of the DNA exhibits features of biochemical function. This is a truly phenomenal claim, an excellent headliner and an attention grabber. But the definition of function used in the ENCODE study is, as Dennis Venema points out, very fuzzy. The kinds of function found range from a strict definition involving protein coding and gene regulation to a very loose definition. Dennis works though the details of this in two new articles posted just this week dealing with questions coming into BioLogos following the publicity arising from the ENCODE findings: ENCODE and “Junk DNA”  Part 1: All Good Concepts are Fuzzy and Part 2: Function: What’s in a Word?

The paper outlining the primary conclusions of the ENCODE project so far is available Open Access at Nature: An integrated encyclopedia of DNA elements in the human genome. I’m not the expert – so I may get some of this wrong. I will correct anything pointed out by a reader with more expertise. But here is the summary I can cull from the paper about the conclusions from ENCODE. Numbers are a little hard to pin down.

Something like 1.2% or so of our DNA codes for proteins.

Perhaps another 10-20% (many favor the low end of this range) functions as gene regulatory elements or serves other specific biochemical functions. According to the more conservative definitions of function the ENCODE project identifies 2.9% as “protein-coding gene exons” and 8.5% involved in “specific protein DNA binding.” The gene regulatory elements are critical, but operate under a different kind of evolutionary pressure for conservation of sequence. It appears, however, that more (much more) of our DNA is involved in gene regulation than in protein coding. This is a fascinating discovery. Biology is an incredibly complex topic. Quantum physics is trivial in comparison (perhaps).

Much of the rest of the DNA has function according to a very loose definition of function (see Dennis’s article for some more detail). Some of this “functional” DNA may have specific useful function to be uncovered in the future, but much of it probably doesn’t. I would bet very little of it does. Most, if not all, of it is under little to no selective pressure conserving the sequence of bases. In this 60% or so of the DNA that is loosely functional, and in the 20% for which ENCODE found no sign of biochemical function, we find ancient repeat units and pseudogenes, and other evidence for evolution recorded in the genome.

History in the Genome. It is interesting that as this story was breaking I was in Israel at a conference. One of the places I visited, and not for the first time, was the ancient site of Caesarea on the coast of the Mediterranean. Here we see both Roman ruins and the remains of a Crusader fortress. One interesting feature of the Crusader fortress is the recycling of material from the Roman city. The picture at the top of the post shows Roman pillars incorporated into the foundations and structures of the fortress. The picture to the right was taken in about the same location about a decade earlier (my camera wasn’t as good then – but the tree didn’t block some of the view). These pillars served a function for the Crusaders. They were not merely refuse carried along for no good purpose. Yet there is a history recorded in the details of the pillars independent of the function they served for the Crusaders, a history that points back to the Roman city.

A few percent of DNA codes for proteins, another 10-20% has specific function of various sorts, most importantly gene regulation. Much of the 80% of the DNA in the human genome that the ENCODE project finds to be functional only by the most liberal of definitions, or not functional even by that definition, carries a history written into the sequence of bases in the DNA chain. This history is something like the details, shapes, and carvings, of the pillars reused in the Crusader fortress. The details tell us something about the history of the genome. If this DNA serves a function, it is not a sequence specific function and the function does not obliterate the history encoded in the DNA sequence or disprove the theory of evolution.

Did the recent hype about Junk DNA cause you to wonder about the strength of arguments for evolution?

What is your reaction to the press and hype?  Where do we look for good information?

If you wish to contact me directly you may do so at rjs4mail [at] att.net.

If interested you can subscribe to a full text feed of my posts at Musings on Science and Theology.

  • Stuart B

    Thanks for this article.
    Collins book ‘The Language of God’ was primarily responsible for changing my stance from ambivalent to a firm supporter of theistic evolution. I’ll admit that the arguments for “junk DNA” were probably the most persuasive parts in changing my reasoning.
    I think that this line of evidence is easy for a layperson to understand, with Collin’s emotive challenge ‘Do you believe in a God who would put in this non-functional DNA just to trick us?’. I’ve used it when I’ve been queried about why I believe in evolution as it is far harder to dispute than discussions of fossil evidence.

    I think it will take time for me to digest these findings and responses. As with all things biology is far more complicated beneath the surface, but for those not willing to dig deeper these type of headlines provide an easy way out from having the conversation.

  • John I.

    1. Dawkins has almost made a career out of declaring that non-functional junk DNA is proof of evolution. Ever since the term was coined by evolutionists in the 70s, the lack of any functionality was used by them as a proof of evolution. That is, large amounts of nonfunctional DNA (greater amounts than functional) should be produced by Darwinian evolution. It is a prediction of the theory that this is so. Hence, finding junk DNA confirms evolutionary theory (the fact that the prediction was made after, not before, the “finding” of junk DNA is not exactly rigourous logic or scientific methodology seems to have eluded its proponents).

    2. Given the above, finding functionality for the DNA thus disproves the hypothesis that evolution by additive mutations in DNA will result in large amounts of nonfunctional or junk DNA.

    3. However, since evolution is largely a theory of history (rather like Marxism) and not science (unless historiography is counted as a soft science), it is non-confirmatory / nondisprovable. That is, given that evolution is a “fact” or the “structure of reality”, any event or fact that is found must be part of the theory. So, whether or not we find actual junk DNA is irrelevant: if we find it, then it must be part of evolution; if we don’t find it then that lack is part of evolution.

    4. God is omnipotent and can, and could, do whatever he pleases. He could have used Darwinian evolution or some other method of evolution. He could have intervened over billions of years (he seems to like intervening and interacting with his creation). He could have done it instantaneously (as Augustine believed). He could have done it over six 24 hour days 6 – 8, 000 years ago (as YECs believe). The method is pointless so long as it is God exclusively (which is the point of Genesis 1).

    I’m as interested as the next guy in how things actually work, and in finding out how God actually did it. But the continual triumphalism of evolutionists, and their disparaging of any other theory, is quite annoying. It’s not like scientists never came up with aether or phlogistan as explanations.

    5. Though the continual finding of more and more functions for more and more parts of DNA defeats the old evolutionary hypothesis of the 70s, 80s, 90s and 00s, it’s not like it’s a nail in the coffin. What is more damning is Lenski’s experiment where he follows 10s of thousands of generations of bacteria and finds no significant evolution. If he were following generations of whales, he would have gone from the earliest whales to the present with the exact same creature he started with.

    Evolution: meh
    YEC: meh
    ID: meh
    Jesus: yeah!

  • http://jcarmichael861a@yahoo.com Jim

    The point about the 6-24 hour days is one of hermeneutics. If you don’t take the words literally, as they sit on the page, how do you interpret anything in Scripture? What do you take literally & what don’t you? The Hebrew word ‘yom’ for day, although it can various shades of meanings, e.g., a regular day, a working day, evening and morning, sabbath day, day of Yahweh, a day in someone’s life or plural – days, indefinite number of days, time, today, in the construct before verbs, “the day of” (BDB, ppg. 398-400), as Moses wrote it in Gen. 1 means a 24 hour day. Unless you take it that way, you are open to subjective hermeneutics (you become equal to the Word rather than sitting under it & submitting to it) & that leads to false beliefs such as theistic evolution. Calvin & Luther didn’t have any problem understanding Moses & they took it literally as did the Church Fathers.
    Besides, when did Moses write the Pentateuch? Right after Israel’s release from bondage in Egypt. He wrote Gen. 1 & 2 for theological reasons, not cosmological. In his day, everyone believed in gods/God. There were about 12 extant pagan cosmologies by the time Moses was born. With each day of creation, numerous Egyptian (& later Canaanite gods) were brought under God’s judgment & debunked, so that a mixed multitude left w/ Israel from Egypt. Evangelism was accomplished. Gen. 1 & how one interprets it is an issue of hermeneutics, & I humbly submit that yours is found wanting.

  • Bev Mitchell

    RJS,

    Interesting topic. I am surprised that people reluctant to accept evolution gravitate to the lack of certainty re the function, or lack of function, of various pieces of DNA for presumed evidence against evolution. It’s well established that all complex organisms have functional DNA whose origin is clearly traced to before the beginning of eukaryotic life (cells with a nucleus). For a great example, have a look at Fig. 3 in “Ancient Invasions: From Endosymbionts to Organelles” Dyall, et al. Science 9 April 2004: 253-257.

    This is not my field, but the figure is easily understandable, even for non-scientists. It depicts some of the transport proteins essential to the function of mitochondria (part A) and to chloroplasts (part B), with each protein placed in the location where it does its thing. These proteins are responsible for moving materials from the cell into the organelle. Mitochondria and chloroplasts are two of the most important cellular organelles for the existence of complex life. Just search ‘chloroplast’ or ‘mitochondrion’ on Wikipedia for a refresher.

    For the mitochondrion, the gene sequences show the following origins for the respective genes:

    17 Eukaryotic origin (like the modern cell under study)
    10 Eubacterial origin (originated from some ancient true bacteria)
    3 Partial (domain only) eukaryotic origin

    For the chloroplast, the gene sequences show the following origins for the respective genes:

    4 Eukaryotic origin (like the modern cell under study)
    3 Eubacterial origin
    2 Partial (domain only) eubacterial origin
    8 Cyanobacterial origin

    This is just a snapshot, but a fundamental one. The ancient symbiotic relationships between cells that gave rise to the primary energy production and management (mitochondria) and carbon fixation (chloroplasts) functions of all complex organisms is one of the best one-stop-shopping places to help those who doubt biological evolution. Of course, the details are still being worked out (it’s a complex story of events that began over 1.5 billion years ago (1.5 Ga)). However, progress has been amazing and the generally agreed upon parts of the story are fascinating and revealing

  • Patrick

    Based on this commentary, it seems to me some of the idea of natural selection genus changing is based on what people expect DNA to do based on preliminary observables, more extrapolation than proof of the end product.

    The actual fossil record supporting genus changes is sketchy , IMO.

    Another problem area with me is philology and archaeology do not “see” super ancient humanity like anthropology does. It is difficult for me to believe we cranked up around 200K(or further) back and it took almost 190K( more in philology) to see physical evidence of our lingual and organizational evolutions. That does not make sense to me.

    None of these 3 disciplines knows all there is to know, however, when 2 see a youthful humanity span and 1 sees a super longspan , I can’t help but wonder.
    No theology involved, I see Genesis’ cosmology as Egyptian myth mainly. I just have always questioned this idea.

  • Klasie Kraalogies

    Patrick @ 5, the fact is, would we know 3 million year old tools if we found them? The fact is that distinguishable tools only appear at a certain time. Before that – just another rock/branch.

    What we have then is an acceleration of technological and cultural innovation once a breakthrough has been made. (Soundtrack – 2001: A Space Odyssey :) )

  • AndyM

    junk DNA going the way of the vestigal organs? Who’d have thunk that God might have done it, and had purpose in what He did?

    Once you can explain away the days of genesis as being meaningless, you’ve undermined the authority of scripture to a point that liberalism and making the bible say whatever you want is an easy step.

  • http://jesus.scilla.org.uk/ Chris Jefferies

    There’s a thoroughly interesting page in ‘New Scientist’, (22nd September 2012, p12). The article briefly summarises some impressive links between ancient climate reconstructions and early human migrations from Africa. This fits into the overall picture and is relevant to comments 5 and 6.

    Along with the origins of mitochondria and chloroplasts (comment 4) and RJS’s thoughts in the original post, there does seem to be a long story to be told about the origins and development of life. It’s a story supported by evidence from many fields of study, not just biology. And it’s a story that’s very supportive of the very well-established theory of evolution. (Not some kind of guess, but a synthesis that has proved impossible to disprove over a long period.)

    Writing as a biologist I have to say it’s a cogent and self-consistent story that is most unlikely to be proved wrong even though it will undoubtedly continue to be refined in many of its details.

    Writing as a believer in and follower of Yahshua ha’Mashiach (Jesus the Anointed, Jesus Christ) I have to say that it contradicts nothing that I believe. It fills me with awe at the wonderfully creative and inventive nature of the three-in-one Most High – the Father, Son and Spirit.

    There’s much that I don’t understand, but I know my Lord and Saviour is utterly amazing! HalleluYah!

  • John I.

    1972

    “So much ‘junk’ DNA in our genome,” Brook Haven Symposia in Biology (23:366-370), S. Ohno: “[non-coding DNA] are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”[1]

    1976

    The Selfish Gene, R. Dawkins: “The amount of DNA in organisms is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the ‘purpose’ of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”

    1980

    Nature (284:604), Orgel & Crick: “much DNA in higher organisms is little better than junk”

    1994

    “Life’s Grand Design,” Technology Review (97(2)), K.R. Miller: “In fact, the human genome is littered with pseudogenes, gene fragments, “orphaned” genes, “junk” DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming. In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection to innovate, to test, and to discard what fails in favor of what succeeds. The organisms that remain alive today, ourselves included, are evolution’s great successes.”

    Molecular Biology of the Cell, B. Alberts: “Unlike the sequence of an exon, the exact nucleotide sequence of an intron seems to be unimportant. Thus introns have accumulated mutations rapidly during evolution, and it is often possible to alter most of an intron’s nucleotide sequence without greatly affecting gene function. This has led to the suggestion that intron sequences have no function at all and are largely genetic ‘junk’”.

    1995

    “Talking Trash,” Scientific American (272(3)), P. Yam: “These regions have traditionally been regarded as useless accumulations of material from millions of years of evolution. … In fact, the vast majority of genetic material in organisms from bacteria to mammals consists of noncoding DNA … In humans, about 97 percent of the genome is junk.”

    1996

    Vital Dust: Life as a Cosmic Imperative, C. de Duve wrote: “The simplest way to explain the surplus DNA is to suppose that it is a parasite or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”

    1998

    Refuge of Spandrels, Current Biology (8(19), S. Brenner: “The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it.”

    2004

    A Devil’s Chaplain, Dawkins: “[the genome] consists of multiple copies of junk, ‘tandem repeats,’ and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.”

    2005

    Molecular Biology: Understanding the Genetic Revolution, D. Clark: “Some of these integrated DNA segments are able to move around from site to site within host DNA molecules and are known as transposable elements or transposons. Other stretches of parasitic DNA are stuck permanently where they are and are probably the remains of once mobile gene creatures. They have degenerated into junk DNA. Much of the large human genome is comprised of these types of junk DNA that are no longer active.”

    2006

    The Language of God, F. Collins: “Mammalian genomes are littered with such AREs [ancient repetitive elements]“, “with roughly 45 percent of the human genome made up of such genetic flotsam and jetsam.”

    “Unless one is willing to take the position that God has placed these decapitated AREs in these precise positions to confuse and mislead us, the conclusion of a common ancestor for humans and mice is virtually inescapable.”

    Why Darwin Matters: The Case Against Intelligent Design, M. Shermer: “Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution.”

    2009

    The Greatest Show on Earth, Dawkins: “the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.”

    2010

    Inside the Human Genome: A Case for Non-Intelligent Design, J. Avise: “noncoding repetitive sequences — ‘junk DNA’ — comprise the vast bulk (at least 50%, and probably much more) of the human genome.”

    ***

    So, when it was believed that junk DNA was a fact, evolution was consistent with that fact, predicted that fact, and that fact was a supporting proof for evolution. In addition, that fact was held to be inconssitent with creation by an omnipotent God, and so disproved any theory of creation by an intelligent being.

    Now that junk DNA does have functions, this new fact (which contradicts the old fact) is held to be consistent with evolution, predicted by evolution, and a proof of evolution.

    Since it is a premise that evolution is ture, it necessarily is consistent with all discovered facts and so it explains anything discovered and everything discovered. There is no possibility of ever finding a disconfirming fact. As a theory, it assumes the truth of its premises and so belongs to the class of logical fallacies called “begging the question”.

    Furthermore, “evolution” is a term both vague and ambiguous because there are severa variant theories of evolution, some of which are inconsistent with each other. Consequently, whenever the bare term “evolution” is used it is never clear which theory is being referred to and the result is often equivocation on the term.

    Perhaps just as important is the fact that this incorrect postulate of evolution (all theories of) misdirected research for decades. Hence evolution, rather than being a useful theory that pushed research in a correct direction, moved it in a wrong direction. The correction to our scientific understanding of the genome came not from doing evolutionary research, but from doing basic genetic research–research that would be carried out the same way even under an 18th century paradigm of “God created the world, God is regular and created a rule governed universe, and we can understand that universe by investigating the regularities.”

  • RJS

    John I,

    You have to look as well at what the functions are – not just that there are “functions.”

    We can come up with many possible functions – structural, binding, signaling, spacers, encoding, acting as a statistical “soup” reducing the probability of damage to important units, …

    These different functions have different consequences for the DNA sequence. Some require very specific sequences, some don’t. The evidence for evolution is in the sequence – in sections that require high specificity, but also in sections that don’t require high sequence specificity.

    The argument for evolution from segments that require high sequence specificity is dismissed by some who argue for special creation through the idea that God used the same template and framework in different situations.

    The argument for evolution from segments that don’t require high sequence specificity is harder to dismiss. But nothing in the current discussion of functions for “junk” DNA counters this at all.

    And – don’t cite Dawkins as an authority, please. Yes he knows biology, but he is more of a polemicist than a reasoned discussant these days.

    (Oh – and note that it is the “evolutionists” who are continuing to explore functions for the “junk” – there is no dogma that is sacrosanct. This is an ongoing discussion and discovery.)

  • Bev Mitchell

    RJS,

    I had a chance to take a quick look at the ENCODE papers in the recent Nature. The data re how much DNA is “junk” or not are overshadowed by the extremely strong support for the importance of gene regulation in our thinking. Even the concept of the gene is likely in for a big change. This is completely in line with those who are calling for a much greater systems level orientation to our thinking in biology. The upstream, higher level events (above the DNA code itself) have much to say about how life, and evolution, work. The case for more systems level thinking in biology is elegantly made by Denis Noble in his easy to read and very informative “The Music of Life.”

    There is no support in any of this for the static creationist model so often championed in evangelical circles. Also, there is nothing here that would suggest we can do away with a loving God.

    Here are a few quotes from selected abstracts and conclusions.

    “Overall, the project provides new insights into the organization and regulation of our genes and genome,….” Encode Consortium Nature 489: 57-73 (2012).

    “….top-level transcription factors more strongly influence expression and middle-level ones co-regulate targets to mitigate information-flow bottlenecks.” Mark B. Gerstein (and 55 other authors) “Architecture of the human regulatory
    network derived from ENCODE data.” Nature 489: 91-100 (2012)

    “three-quarters of the human genome is capable of being transcribed,…” (see Djebali, below).

    “…..we would propose that the transcript be considered as the basic atomic unit of inheritance. Concomitantly, the term gene would then denote a higher-order concept intended to capture all those transcripts (eventually divorced from their genomic locations) that contribute to a given phenotypic trait.” Sarah Djebali (and 84 other authors) “Landscape of transcription in human cells” Nature 489: 101-108 (2012)

  • AHH

    Bev @11 said regarding ENCODE,
    There is no support in any of this for the static creationist model so often championed in evangelical circles. Also, there is nothing here that would suggest we can do away with a loving God.

    And, important to recognize, nothing that undermines in any significant way the genetic evidence for common descent as a correct description of how God’s creation of life has unfolded. I feared the anti-evolution propagandists would jump on this (some of the fault comes from careless ways scientists and others have talked about “junk DNA” in the past), and alas it is happening.

  • Patrick

    Klassie,

    I assumed archaeologists can date stuff within some reasonable parameters. I know as little about their techniques as I do the DNA crew or the fossil searching crew.

  • John I.

    I didn’t just quote Dawkins, and the early quote from him was before he became a polemicist. And even though he is a polemicist, on junk DNA he is just repeating what has been said by evolutionist for 40 years.

    As for evolutionists research function, if any of them are doing it as part of a research program then great. However, the research to date has been by genetic researchers who are trying to understand genes, not the process or progress per se of evolution. Yeah, notionally one could say that they are researching evolution because the science establishment works under the evolutionary paradigm, but that is trite. No one thought to research “junk” DNA because they thought that finding functions would support the theory of evolution. Indeed, research for that purpose was discouraged in the literature.

    So, when there were no functions for the junk DNA, that “fact” was held to support the theory of evolution. Now that functions are being found, this new “fact” is held to support the theory of evolution. Contrary facts, which if either are true would provide inconsistent support for the theory of evolution, but evolution can’t lose because it is de facto true. No matter what we find, evolution cannot be disproved as all new facts will be absorbed into the theory. “Temporary” conflict between “facts”, and between facts and theories, is tolerated because materialism and evolutionary theory are fully promissory: in the future we will resolve the conflict and sort out which theory of evolution is more correct.

    As far as the authors quoted (and they are not the only ones), it is the bare fact of there being any function at all that was the issue, not the type of function.

    Non-evolutionary creationists may be overpressing their case, but it is certainly true, and obvious, that both theistic and materialist and atheistic evolutionists pressed the case very hard that junk DNA was a “fact” that “proved” that creationists were wrong. So now evolutionists have to backpedal from that assertion.

  • RJS

    John,

    No, this it the point I am trying to make. It isn’t back-pedaling. Nothing – absolutely nothing – in this requires back-pedaling on the arguments for evolution from the non-coding DNA sequences. It doesn’t require back-pedaling from the argument Collins made in his book, or Falk in his book, or that Dennis makes on the BioLogos site.

    The sequences in non-coding DNA are the most potent argument for evolution out there and this argument is only bolstered by all the other evidence, nothing contradicts it. For that matter the sequences in coding DNA are also powerful evidence for evolution – but this argument tends to be dismissed on the basis that God reused the same motif. That dismissal doesn’t work for a variety of reasons, but is a little more involved to make the argument.

  • RJS

    John,

    By the way – I don’t expect you to take my word for my opinion here. This post was an attempt to start to make my point about this issue. Dennis’s posts are an attempt to start to make the argument about this issue.

    I view my job as “to convince” not “to decree.”

    I’ll come back to it again in the future I expect.

  • John I.

    I fail to see how the current statements about so-called junk DNA do not constitute backpedalling. As is evident from the quotes that I provided (and there are more like them), the new understanding of “junk DNA”, and the concomitant argument that function in the junk DNA supports evolution, requires a wholesale repudiation of the former commitments in regard to junk DNA. The new understanding is directly contrary to prior assertions by scientists. here is considerable whitewashing going on in some of the quotes from scientists who try to pooh-pooh the controversy. There is no reason to give more credibility to their statements over statements by other scientists who talk about the controversy and the former disparagement of junk DNA.

    The Washington Post article, rather than being hype, is spot on. So-called junk DNA was almost without exception disparaged for decades and evolutionary theory never posited possible functionality for junk DNA as a hypothesis of the theory. Moreover, to the extent that any evolutionist bothered to consider any non-materialist theory of biological origins and evolution, the uselessness of junk DNA was used as evidence that demonstrated that materialist evolution was a superior and true theory in comparison to the inferior and obviously false non-materialist theories (i.e., any sort of process that involved a supernatural person at any point in time).

    Furthermore the reanalysis of junk DNA by evolutionists clearly demonstrates that there is no such thing as an empirical finding that could disprove evolution as a theory of biological change over great time. Anything that is discovered by empirical research will be held to be confirmatory of materialist evolution from a common ancestor. However, it would be just as accurate to state that every such empirical finding supports the ID theory of evolution over time. Either way, the theorist merely has to make a promissory claim that inconsistencies or apparent contradictions will be resolved with further research.

    In this world of competing promissory paradigms, it remains a fact that there does not currently exist any empirical research that demonstrates a process by which gross biological change occurs over time, or which provides a chain of event causation for even one significant series of genetic changes that corresponds to an observable morphological change in an organism (i.e., one detectable in fossils), wherein significant refers to a change that leads to non-interbreedable speciation. The last is neologism, but one that seems necessary given that there is no agreed definition of species.

    RE Venema’s articles – The do not address the controversy but explain how genes, DNA, transposons, etc. function. Nothing controversial in his explanation, though he makes claims that go beyond the data vis a vis the debate between “evolution” and “creation”.

    As I never indicated that I thought you were decreeing anything, I’m not sure about the relevance of your comment on that. However, your assumption is the same as mine: you are trying to convince or persuade your readers.

    John.

  • RJS

    John,

    The fact that the NIH poured millions of dollars into ENCODE and other projects over the last decade calls into question the premise of your comment. Many scientists thought this was a valuable search – well worth a large chunk of the pot.

    Do you really think all of these scientist, all those involved in peer review of the projects, and the papers would have channeled so much money in this direction if they had all been convinced that “junk” as in totally without purpose and function was the appropriate designation?

    There is a continuing development in understanding of the DNA – this is the way the scientific process works.

    Nothing in the ENCODE findings calls into question the evolutionary mechanism.

    I added the second comment – about decreeing because I thought I came on a little strong in the prior comment and I wanted to clarify a bit.

  • John I.

    re my “never posited possible functionality for junk DNA as a hypothesis of the theory” – I do realize that I use terms that are undefined and ambiguous, and that more recent works by evolutionists have discussed evolution of junk DNA (e.g., 2006, Evolutionary Genetics: Concepts and Case Studies, see the stuff on the eukaryotic genome). However, these are post-fact discussions of junk DNA, and the authors discuss various competing theories as well as the relevant operations in the cell. Hence these are not hypotheses that preceded the discovery of junk DNA.


CLOSE | X

HIDE | X