Intelligent Design

Two quick questions for Professor Coyne

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Over at Why Evolution Is True, Professor Jerry Coyne is gleefully celebrating the impending demise of the Discovery Institute and of Intelligent Design. But before he pops the champagne, I wonder if he would care to answer two questions I’d like to ask him, in relation to some remarks he made on Casey Luskin’s recent announcement that he would be leaving Discovery Institute to further his studies.

1. Professor Coyne, you wrote that “the early claim that ENCODE showed that 80% of our genome had a function was incorrect, and there remains a huge portion of the human genome that’s nonfunctional,” and you added: “And even if 80% of the human genome were functional, how does that prove the existence of an intelligent designer? What about the other 20%? Did the Great Designer screw up there?”

Before I pose my question, I’m going to make a concession right up-front that will raise a few eyebrows: after reviewing the arguments, I’m inclined to believe that the critics of ENCODE’s bold claim were mostly right, and that the proportion of our genome which is functional is probably between 10 and 20%. (And as you correctly point out, Professor, even ENCODE has now backtracked from its claim.)

I’d now like to draw your attention to a WEIT post titled, DNA: optimised source code?, written by Professor Matthew Cobb, who is a regular contributor to your Website. (I commented on the post here.) The post discussed the following cartoon from xkcd.

Professor Cobb argued that since at least 85% our genome is junk, our DNA should be viewed as the mindless product of a series of historical accidents. But then he made a startling admission (the first bold emphasis is mine – VJT):

On a final note, in some cases, within this amazing noise, there are also astonishing examples of complexity which do indeed appear to be the result of optimisation – and they would boggle the mind of anyone, not just a cocky computer scientist in a hat. In Drosophila there is a gene called Dscam, which is involved in neuronal development and has four clusters of exons (bits of the gene that are expressed – hence exon – in contrast to the apparently inert introns).

Each of these exons can be read by the cell in twelve, forty-eight, thirty-three or two alternative ways. As a result, the single stretch of DNA that we call Dscam can encode 38,016 different proteins. (For the moment, this is the record number of alternative proteins produced by a single gene. I suspect there are many even more extreme examples.)

Evidently Professor Cobb agrees with agnostic Bill Gates, who wrote twenty years ago: “Human DNA is like a computer program but far, far more advanced than any software ever created.” (The Road Ahead, Penguin: London, Revised Edition, 1996, p. 228.)

So my first question is: if (i) Nature contains systems which accomplish a feat (namely, coding for complex structures) in a manner which is far better than what our best computer scientists can do, and (ii) despite diligent searching, scientists have failed to observe any cases in Nature of unguided processes generating a new code from scratch, then why isn’t it reasonable to infer (at least provisionally) that these systems were designed by a super-human Intelligence? You tell me, Professor.

Regarding your remarks on junk DNA, I’d also like to draw your attention to something I wrote on my post in response to Professor Cobb:

Even if Professor Cobb is right about junk DNA – and I’m inclined to think he is (for reasons I’ll discuss in another post) – that’s beside the point. At most, it shows is that DNA which doesn’t code for anything wasn’t designed. But my question is: what about the DNA which does code for proteins, and which does so in a manner that boggles the ingenuity of our brightest minds? Professor Cobb, it seems, is missing the wood for the trees here.

Junk DNA might be described as degenerate code – but there has to be a code in the first place, before it can degenerate. The existence of junk DNA cannot be used as an argument against design: all it establishes is that the designer of our DNA – whether out of benign neglect, laziness, illness, or ignorance that something has gone amiss – doesn’t always fix the code he created, when it becomes corrupted. Accordingly, junk DNA cannot be used as a legitimate argument against the proposition that the DNA in our cells which codes for genes was designed.

My second question, Professor Coyne, relates to your remarks on epigenetics, which Casey Luskin cited in his latest post as his “Exhibit B” of a prediction made by Intelligent Design that had been fulfilled:

Exhibit B: The burgeoning field of epigenetics has also validated ID’s prediction of new layers of information, code, and complex regulatory mechanisms in life. We’ve seen discoveries of new DNA codes (e.g., multiple meanings for synonymous codons), as well as the histone code, the RNA splicing code, the sugar code, and others. It’s a great time to be an ID proponent!

In response, you wrote:

Umm. . . the “new layer of information” that ID predicted was DIVINE information, not epigenetics. And the part of epigenetics that does add “information” — the epigenetic modifications of DNA already encoded in the genome — have been known for a long time. As for those “Lamarckian” modifications induced by the environment, well, that “information” is erased after a couple of generations, and so has no evolutionary import.

May I point out for the record that epigenetics can be defined as “the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself,” and that the use of the term “epigenetic” to describe processes that are not heritable is highly controversial. But let that pass.

I’d now like to draw your attention to a passage from Dr. Stephen Meyer’s book, Darwin’s Doubt (HarperOne, New York, 2013), concerning the role of epigenetic information in embryonic body-plan formation:

These different sources of epigenetic information in embryonic cells pose an enormous challenge to the sufficiency of the neo-Darwinian mechanism. According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy — within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops — for body-plan morphogenesis — then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand.

Even in a best-case scenario — one that ignores the immense improbability of generating new genes by mutation and selection — mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information — information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion. (pp. 281-282.)

So my second question for you is: will you concede that neo-Darwinism is unable to account for the origin of the epigenetic information needed to create novel body-plans (which must have occurred before the Cambrian explosion took place), and that natural selection therefore doesn’t explain all cases of apparent design in nature, falsifying your previous claim that it’s the “only game in town” for producing adaptations?

Incidentally, are you aware of any good evidence that epigenetic information is not divine in origin? If so, please elaborate.

Best wishes for your retirement,

Vincent Torley

33 Replies to “Two quick questions for Professor Coyne

  1. 1

    After following Coyne’s blog for several years, I came to the conclusion that Coyne abandoned his scientific career (probably for good reasons, given that a fruit fly is still a fruit fly) and instead became a professional Atheist.

  2. 2
    Jim Smith says:

    Does Coyne really think that if 80-90% of the DNA was deleted, the remaining DNA could produce a fully viable organism that is identical to the original?

    But, the presence or absence of junk DNA is not a good argument for anything. It works both ways, natural selection produces things that have the appearance of design, except when it doesn’t? Natural selection can produce highly efficient engineering marvels like the human eye, except when it produces junk? Similarity of DNA sequences between species is evidence of common descent, and any differences are explained as junk? Such a theory is not falsifiable.

    The existence of junk DNA as an argument against ID is a religious argument because it is based on assumptions about the designer.

    As someone who worked as a software engineer I can say definitely that the presence of junk (obsolete, unmaintained, duplicate) code doesn’t rule out design as an explanation of the origin of an instruction set.

    The debate over junk DNA is a distraction, started by the Darwinists, from much more rigorous arguments for design such as the fine-tuning of the universe to support life and the origin of information, irreducibly complex systems, and semiotic and cybernetic systems in living organisms.

  3. 3
    J-Mac says:

    VJTorley,

    I admire your persistence in trying to provide All the evidence in the world to people like Coyne or Moran to admit what they will never admit, at least publicly.

    When I once tried to be as eager as yourself, one elderly man realized that and asked me a few questions:

    1. Do you you believe what the bible says? I said yes. He asked me “why”. Although it took me a while to gather my thoughts to answer it, I pretty much said that one of the reasons were that it was scientifically sound and that it was like any other book. Their writers wrote stories that were different than other story books.
    2. Then he asked my this question that I will never forget for a long time: “Why did the bible writers write the stories of people who experienced Jesus miracles, such as resurrections, admit to them as being the fact, and then conspire against Jesus to kill him?

    Do you think that if Jesus did today, what he had done 2000 years ago, All people would accept him?

    To me, it is the same struggle. If people saw Jesus performing miracles such as raising people from the dead, what evidence could you possibly have that surpasses Jesus’?

  4. 4
    Robert Byers says:

    i didn’t read that guys stuff on Luskin as I AM BANNED at his free thought/can take competition blog!!!
    Anyways.
    Ouch about Liskin leaving. HE WAS GREAT in intelligence, articulate, entertaining and so how to fill the shoes.
    I understand Gauger is coming in and so thats a great move. I like her stuff.

    Are these evolutionists saying it hELPS their side for Lisskin to go?? That means it was hurting eh?! Logic here.
    Is evolutiondom really threatened by a few fighters of the opponents?
    Its that unsteady in its position?
    Are the great ideas of origins being decided by small tiny groups of people jousting in the field?!
    Evolutionism/anti-creatorism should be as solid as REAL SCIENCEY conclusions.
    It should not even NOTICE personal movements of small organized groups saying they got things wrong!!
    It would make no difference to evolutionists side if anyone or all sudden;t retired to stud.
    Its ideas are the target of goodguy creationism and not personal.
    This is why YEC/YD will prevail. IT really does make its case on evidence and argument and spirit and courage.
    Leaders, like Luskin, are great but not the ultimate source of strength.
    Its being right and smart and down in the dirt dogged persistent.

    i do find evolutionists, in these circles, really do see ID as the result of very confident smart and effective individuals.
    They miss that its the merits of God and christianity and Anglo American western scientific civilization that is the real punishing enemy to evolutiondom and company.
    2015 was a great year for YEC and ID.
    2016 is on a great curve of history here.
    I’m sure mr Luskin welcomes the compliment of being the threat but probably denies its true.

    By the way. Any good evos around with good fighting form.
    anyone compliment, wish well, mr Luskin who they must see as a worthy opponent??
    Any good sportsmanship attributes ?
    If not it will be a reflection on character.
    UD here has complimented many evolutionists in passing or generally.
    I would wish any evo Gods speed or wind in the junktard speed!!

  5. 5
    JGuy says:

    Apparently in response to Casey Luskin leaving the DI for now, Coyne thinks to write up a blog titled:

    “Is the Discovery Institute falling apart?” – Jerry Coyne

    Obviously, his is a dim over-reaction. Especially, given Casey’s clearly written reason that reads, “I am doing so in order to fulfill a lifelong goal of furthering my studies.”

    Given Coyne’s thinking… and given Coyne is retiring from research and his position. I have one question, and seeing that Coyne used this reasoning… it must certainly apply more logically to his own case (even if his use of it wasn’t rational):

    IS THE EVOLUTION INSTITUTION FALLING APART?

    lol! farewell evolution!

  6. 6
    DaRook says:

    J-Mac

    I believe that if Jesus did the same miracles as He did 2000 years ago, people would still not believe. They would react the same way the people did in Luke 8:37 with the healing of the demonic:

    “Those who had seen it reported to them how the man who was demon-possessed had been made well. And all the people of the country of the Gerasenes and the surrounding district asked Him to leave them, for they were gripped with great fear; and He got into a boat and returned.”

    Look at Israel when they experienced the parting of the Red Sea, the quail, the manna and the very presence of God Himself in the form of the cloud and fire. Only a small remnant believed. The heart is desperately wicked, who can know it? ID and General Revelation can only point to a Creator, Special Revelation shows them who that Creator is.

  7. 7
    Dionisio says:

    Had humans stayed in Eden, DNA wouldn’t have any junk at all. But we all know the rest of the story.
    Actually, it’s amazing that DNA doesn’t contain more junk, after screwing it up so badly as we have since then. Also, it’s amazing that it works the way it does with so much junk in it.
    The good news is that all this mess we have made of ourselves will be gone someday. Everything will be new. And there won’t be any junk. Sing hallelujah and rejoice!

  8. 8
    Bob O'H says:

    So my first question is: if (i) Nature contains systems which accomplish a feat (namely, coding for complex structures) in a manner which is far better than what our best computer scientists can do, and (ii) despite diligent searching, scientists have failed to observe any cases in Nature of unguided processes generating a new code from scratch, then why isn’t it reasonable to infer (at least provisionally) that these systems were designed by a super-human Intelligence?

    Isn’t this just a God of the Gaps argument? Doesn’t the response start with asking whether there’s any other evidence for such a super-human Intelligence?

  9. 9
    Mung says:

    Isn’t this just a God of the Gaps argument?

    Doesn’t look like one to me.

  10. 10
    bFast says:

    Jim Smith (2) “As someone who worked as a software engineer I can say definitely that the presence of junk (obsolete, unmaintained, duplicate) code doesn’t rule out design as an explanation of the origin of an instruction set.”

    Amen to that! These days, when I write an ultra-simple “Hello World!” program (you run it, it says on the screen “Hello World!” and is done) the executable is about 1.5 megabytes. 99.99% of the code in this executable is irrelevant — junk.

    I am an old fashioned coder. I love to use “obsolete” commands like sprintf(). No modern coder would use it. Most modern programs don’t contain a single instance of sprintf(), but virtually all executables have the code to implement the thing embedded in them. For that executable it is junk.

  11. 11
    Mung says:

    Is it junk because it once worked and is now broken, or is it junk because it can never be put to good use?

  12. 12
    vjtorley says:

    Hi Bob O’H,

    Thank you for your post. In answer to your question: as mathematician John Lennox points out in his book, Seven Days that Divide the World, there are good gaps and bad gaps. The latter are gaps of ignorance and are closed by advancing scientific knowledge; the former are revealed by the advance of science. The discovery of code in our DNA is an instance of a good gap; thinkers like Robert Boyle, Isaac Newton and even William Paley had no inkling that such a code existed.

    Also, the kind of reasoning I use in my argument is abductive: it’s an inference to the best explanation. At the present time, the best explanation for the existence of a code is an intelligent code-maker.

  13. 13
    J-Mac says:

    DaRook,

    My grandfather who was apparently an atheist up until his death (I fear that he remained atheist until his death) used to say:

    “If Jesus came in to the world today, he would be executed much, much faster than 2000 years ago, but just like in that time by the demands of the most powerfully religious.”

  14. 14
    Bob O'H says:

    vj – how do you distinguish between a good gap and a bad gap? Good gaps are often (usually?) closed by advancing scientific knowledge, and are thus also bad gaps. And until a gap has been filled, you don’t know that it is a bad gap. Thus any lack of knowledge that is currently a gap is, by your definition, a good gap. Whether it is a bad gap or not.

    If you don’t like the last paragraph, you could explain how you define “best” with respect to abductive arguments.

  15. 15
    Zachriel says:

    vjtorley: the former are revealed by the advance of science.

    Every time scientists discover something in the gap, they create two new gaps!

  16. 16
    Mung says:

    Zachriel should be off discovering new gaps rather than wasting his time posting here.

  17. 17
    nkendall says:

    Dr. Torley,

    Regarding your concession that perhaps only 10-20% of the genome is useful…Maybe I am missing something but I don’t think the references at Sandwalk are current or unbiased. Have you read:

    – Carey, Nessa (2015-03-10). Junk DNA: A Journey Through the Dark Matter of the Genome. Columbia University Press.

    – Parrington, John (2015-05-28). The Deeper Genome: Why there is more to the human genome than meets the eye. Oxford University Press.

    – Various articles by James Shapiro.

    – Webcasts by Richard Sternberg and Cornelius Hunter at Discovery?

  18. 18
    bill cole says:

    Hi Bob O’H

    “Also, the kind of reasoning I use in my argument is abductive: it’s an inference to the best explanation. At the present time, the best explanation for the existence of a code is an intelligent code-maker.”

    Inference to the best explanation is also the same reasoning Darwin used building his theory. The alternative is the Scientific Method, but so far no known mechanism for explaining the origin of order inside DNA can stand up to this standard.

  19. 19
    vjtorley says:

    Hi nkendall,

    In answer to your questions: I haven’t read the books you cited. As I’m a sole breadwinner, books are a luxury for me, and I seldom order more than one or two per year via Amazon. Most of my reading on junk DNA has consisted of articles on the Internet, coupled with the lively and vigorous exchanges between Evolution News and Views and Professor Larry Moran’s Sandwalk blog. My overall impression is that Moran seems to have the better of the argument. Time and time again, he has shown up his critics. Any fair-minded referee would say that he’s leading by many points in this match. He seems to have dispatched James Shapiro, as well. Showing that tiny pieces of repetitive DNA have a function isn’t the same as showing that all or most of it is functional.

    Moran’s response to Parrington is here and his response to Carey is here . They’re both pretty devastating.

    Dr. Sternberg’s work intrigues me. He might be onto something.

  20. 20
    vjtorley says:

    Hi Bob O’H,

    You ask how I distinguish between a good gap and a bad gap. Easy. Gaps are seldom static: they tend to widen or narrow with the passage of time. Bad gaps narrow. Good gaps widen. Abiogenesis posed a much bigger riddle for Louis Pasteur’s contemporaries than it did for people in the Middle Ages, and it poses an even greater riddle for people living today than it did for people living in Pasteur’s day. That’s an example of a good gap.

    The reptile-to-mammal fossil transition was very patchy several decades ago. Now it has been pretty much filled. That’s an example of a bad gap.

  21. 21
    Bob O'H says:

    vj – I suspect people working in abiogenesis would argue that the gap has narrowed: even if we don’t have the answer, we have better ideas than pasteur did. Pasteur didn’t even know enough to know how big the gap is.

    Until we either close the gap or demonstrate it is not closable, we can still make progress on trying to close it. Thus we will see them as bad gaps. I certainly think abiogenesis is in this stage: there’s been quite a bit of progress over the last few years (including some amusing theoretical work that uses information theory to suggest that self-organisation may not be so difficult to attain). It may be that people are barking up the wrong tree, but how can we tell? Progress is being made, but we don’t know what the end product is.

  22. 22
    Bob O'H says:

    bill cole – Yes, Darwin built up a lot of evidence to suggest that evolution was the best explanation (and we’ve improved on it since then). The problem with suggesting an intelligent designer is that there is no evidence for the designer: all we are shown is evidence against abiogenesis or evolution (and, of course, most scientists aren’t convinced this evidence is any good).

  23. 23
    Zachriel says:

    vjtorley: Abiogenesis posed a much bigger riddle for Louis Pasteur’s contemporaries than it did for people in the Middle Ages, and it poses an even greater riddle for people living today than it did for people living in Pasteur’s day.

    It did? Evolution provides a great deal of evidence of how life diversified, and there are some inklings about chemical abiogenesis. But even if you reject that, the most you can say is that no one had any idea then, and no one has any idea now.

  24. 24
    Mung says:

    The problem with suggesting an intelligent designer is that there is no evidence for the designer

    And I’ve seen no evidence for Bob O’H.

  25. 25
    Mapou says:

    Bob:

    The problem with suggesting an intelligent designer is that there is no evidence for the designer

    This is the stupidest statement of the year and the year barely started. Everything is evidence for an intelligent designer. Wake up, Bob.

  26. 26
    bill cole says:

    Hi bob
    “The problem with suggesting an intelligent designer is that there is no evidence for the designer”

    Agree with this.

    Do you see any evidence in biology of design? Simply the result of something that was designed.

  27. 27
    bill cole says:

    VJ
    Can you give me any more detail on your belief that the genome is 80% junk.I honestly do not think this sways the evolutionary debate because 4^300million and 4^3billion of sequential space are both essentially infinity for all intents and purposes but it seems premature to say that there is no function especially given the evidence of a dark proteinome. I have read Dr Moran’s arguments and they are centered around counting ncRNAs and other elements. The term junk DNA seems like a buzz word to me that tries to support modern evolutionary theory through spin and as a result seems anti scientific.

  28. 28
    Zachriel says:

    bill cole: The alternative is the Scientific Method, …

    Abduction and the scientific method are not contrary to one another. Abduction is a common way of devising a hypothesis. However, the hypothesis then has to entail empirical observations that can be subject to testing (at least in principle).

    bill cole: … but so far no known mechanism for explaining the origin of order inside DNA can stand up to this standard.

    Then the claim isn’t scientific.

    bill cole: Inference to the best explanation is also the same reasoning Darwin used building his theory.

    Darwin used abduction, but then proposed a testable scientific theory. A good theory generates many testable hypotheses. A great theory spawns entire new fields of study. By this measure, Darwin’s Theory of Evolution is a great theory.

  29. 29
    Virgil Cain says:

    Zachriel:

    Darwin used abduction, but then proposed a testable scientific theory.

    That is incorrect as no one knows how to test Darwin’s concepts. Darwin’s ideas didn’t generate any testable hypothesis.

    Darwin proposed a falsification criteria which demanded opponents prove a negative.

    Zachriel is either lying again or bluffing again.

  30. 30
    Virgil Cain says:

    Bob O’H- bluffing and clueless:

    Yes, Darwin built up a lot of evidence to suggest that evolution was the best explanation (and we’ve improved on it since then).

    That is incorrect as no one knows how to test the claim that natural selection produced anything.

    The problem with suggesting an intelligent designer is that there is no evidence for the designer: all we are shown is evidence against abiogenesis or evolution (and, of course, most scientists aren’t convinced this evidence is any good).

    There is plenty of evidence for a designer, Bob O’H doesn’t know how to assess it. And ID is not anti-evolution, which makes both Bob and zachriel grand equivocators.

    No one knows how to test the claim that natural selection, drift and neutral changes can produce a bacterial flagellum. The concept is vacuous and scientifically sterile.

  31. 31
    vjtorley says:

    Hi bill cole,

    Just for starters, try these references:

    Dan Graur’s SMBE/SESBE Lecture on ENCODE & junk DNA (see slides 21, 30, 32, 33, 34, 35, 36, 39, 55, 73, 78, 79, 80, 82, 83, 88, 89, 92 to 100, 109, 110, 1221, 122, 125, 130, 135, 136, 149, 156)
    The case for junk DNA
    The truth about ENCODE

    I’ll blog on this topic at a later date.

  32. 32
    bill cole says:

    Hi Vj
    Thanks for the links. I read through the slides and the second article and agree the ENCODE statement of 80% is also premature. The issue is the less than 20% statement based on strong experimental data and I do not see strong support here. The onion test does not have credibility because of the continued discovery of alternative splicing that creates protein differences despite similar genes. The origin of the splicing codes is not well understood and may be part of the DNA sequences that are currently not seen as functional. Here is an interesting paper on AS in vertebrates.
    The Evolutionary Landscape of Alternative Splicing in VertebrateDOI: 10.1126/science.1230612

  33. 33
    nkendall says:

    Vtorley @19,

    Hmmm…I see things the other way. I think Shapiro is very careful in his statements and backs them up with many, many references. Moran”s responses are primarily assertions, and from what little interaction I have had or witnesses, is not a credible source. My money is on Shapiro and others who claim that most DNA will prove to have useful function. Time will tell.

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