Intelligent Design

Sean Carroll on Why DNA Proves Evolution

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In his book The Making of the Fittest, Sean Carroll writes “the degree of similarity in DNA is an index of the [evolutionary] relatedness of species.” [98] This can only make sense if we first assume evolution is true. But Carroll’s book is a defense of evolution, intended to demonstrate that the theory is true without first assuming it is true. He seeks to prove evolution is true, but he begins with evolutionary reasoning and interpretations. That is circular reasoning. Unfortunately such circular reasoning is a common motif in the evolution genre.  Read more

23 Replies to “Sean Carroll on Why DNA Proves Evolution

  1. 1
    Collin says:

    Mr. Hunter,

    You are right. As one physics teacher of mine said to our class, subtly, “DNA proves that species have common origin.” I think he specifically did not say “common descent.” It could be common descent, but it could also be common design.

  2. 2
    mofi says:

    Great job at revealing the underlying faulty reasoning. I agree with Collin and his physics teaching, this is just evidence for common origins.

    Does anyone know if someone has refuted this ( lame ) video: http://www.youtube.com/watch?v=rtmbcfb_rdc

    There are so many flaws there but there are also many strange assertions that I would like to hear counter arguments for.

  3. 3
    van says:

    Mr Hunter. You are the master. You are one of the few clear, level-headed voices of reason out there….keep up the good work.

  4. 4
    Bilboe says:

    Just waiting for someone to publicly disagree with that nasty, evilutionist,Michael Behe about it.

  5. 5
    bornagain77 says:

    I think Dr. Behe is quite clear that the supposed genetic evidence for common ancestry is not evidence for the mechanism of Neo-Darwinism:

    As well, the evidence of pseudogenes, and other junk DNA, is not nearly as ironclad as evolutionists would like people to believe since “unexpected function” is being discovered at a rapid pace for Junk DNA which undermines the false interpretation that evolutionists put on the supposed useless sequences in the first place.

    Refutation Of Endogenous Retrovirus – ERVs – Richard Sternberg, PhD Evolutionary Biology – video
    http://www.metacafe.com/watch/.....nberg_phd/

    Endogenous Retroviruses (ERVs) – Page up for Pseudo-genes refutation
    http://www.detectingdesign.com.....Endogenous

    How The Junk DNA Hypothesis Has Changed Since 1980 – Richard Sternberg – Oct. 2009 – Excellent Summary
    Excerpt: A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way. http://www.evolutionnews.org/2.....is_ha.html

    Endogenous retroviruses regulate periimplantation placental growth and differentiation
    http://www.pnas.org/content/103/39/14390.abstract

    Junk DNA Found To Have High Level Function – List Of Over 100 Studies
    http://docs.google.com/View?id=dc8z67wz_25gqm4zzfd

    Yet what is really surprising is the fact that DNA doesn’t even encode for body plan morphogenesis in the first place

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/.....ody_plans/

    Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video
    http://www.metacafe.com/watch/.....hur_jones/
    entire video:
    http://edinburghcreationgroup.org/fishfossils.xml

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2.....footnote19

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    As well as “cloning” studies:

    “There is now considerable evidence that genes alone do not control development. For example when an egg’s genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact.”
    The Design of Life – William Dembski, Jonathan Wells Pg. 50

  6. 6
    Seversky says:

    Collin @ 1

    Mr. Hunter,

    You are right. As one physics teacher of mine said to our class, subtly, “DNA proves that species have common origin.” I think he specifically did not say “common descent.” It could be common descent, but it could also be common design.

    Interesting how many physics teachers or physicists or lawyers or mathematicians or philosophers or engineers think they understand biology better than professional biologists.

    Is the case for common descent based solely on the commonality of DNA or might there be other evidence.

    And on the question of evidence I am surprised to hear a science teacher claiming the DNA proved anything. The more scientific formulation would be that DNA provided evidence for common descent.

    Perhaps he was really a creationist?

    1

    Collin

    03/03/2010

    11:24 am

    Mr. Hunter,

    You are right. As one physics teacher of mine said to our class, subtly, “DNA proves that species have common origin.” I think he specifically did not say “common descent.” It could be common descent, but it could also be common design.

  7. 7
    Matteo says:

    Interesting how many physics teachers or physicists or lawyers or mathematicians or philosophers or engineers think they understand biology better than professional biologists.

    I find it equally interesting how many professional biologists think they understand philosophy, probability, rules of evidence, or the nature of designed systems better than philosophers, mathematicians, lawyers, and engineers, respectively.

    Evolutionary biologists show on a continual basis that they have almost no understanding of those areas. Hence their unreflective credulity toward the intellectual abomination that is their “theory”.

  8. 8
    Cabal says:

    What is implied by the words “common design”?

    The way I understand evolutionary theory is that the fact of nested hierarchies is a strong evidence for common descent. If the species diversity should be the result of intentional design – by itself a rather dubious claim, since life is full of exaamples of sloppiness of design that would get any human
    designer instantly fired – it looks most unreasonable a designer would bother with creating evidence for common descent.

    Isn’t it about time ID proponents got around to doing some research so we can get to know how it all happened? What did the designer do, where, and when? Equally important, what did the designer not do, what was nature allowed to do all by itself? Since it has established that the designer is God, why not give credit where credit is due?)

    If God is the designer, I believe he did it by magic. A starting point for ID research might perhaps be to search for evidence that God did not employ magic?

  9. 9
    Clive Hayden says:

    Matteo,

    I find it equally interesting how many professional biologists think they understand philosophy, probability, rules of evidence, or the nature of designed systems better than philosophers, mathematicians, lawyers, and engineers, respectively.

    “That old gentleman with the wild, white beard and the wild, white hat—that venerable humbug was not really a philosopher; but at least he was the cause of philosophy in others. That scientific gentleman with the bald, egg-like head and the bare, bird-like neck had no real right to the airs of science that he assumed. He had not discovered anything new in biology; but what biological creature could he have discovered more singular than himself?”
    G. K. Chesterton, The Man Who Was Thursday.

  10. 10
    Bilboe says:

    Bornagain77: :I think Dr. Behe is quite clear that the supposed genetic evidence for common ancestry is not evidence for the mechanism of Neo-Darwinism:

    Prof. Behe is also quite clear that the supposed genetic evidence for common ancestry is good enough that “there no longer remains any good reason” to doubt it, contra Dr. Hunter.

  11. 11
    bornagain77 says:

    Bilboe,
    If you mean that the evidence points to a common designer, I will agree, but if you are suggesting a natural mechanism for the common ancestry, I will disagree. I believe Dr Behe draws the line for natural descent at the level of species and perhaps genus and family and maybe order, but major class features and above are beyond the reach of natural processes.

    A review of The Edge of Evolution:
    Behe argues very cogently that random mutations and natural selection are capable of very little (hence ‘the edge of evolution’) and cannot explain the major features of living organisms. Natural processes can explain variety at the level of species and perhaps genus and family and maybe order, but major class features and above are beyond the reach of natural processes.
    http://creation.com/review-mic.....-evolution

    (It should be noted that gross molecular differences that suggest special creation are just simply ignored by evolutionist)

    such as:

    Chimps are not like humans – May 2004
    Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that “83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect,” Sakaki said. http://cmbi.bjmu.edu.cn/news/0405/119.htm

    Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:
    http://www.ncbi.nlm.nih.gov/pubmed/15716009

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723

    How in the world did the proteins change by +80% while the genes, which supposedly code for those proteins, remained virtually unchanged? Why is this huge +80% anomaly ignored by materialists and only the biased genetic similarity stressed?

    On top of this huge +80% difference in proteins, the oft quoted 98.8% DNA similarity is not even rigorously true in the first place. Just considering this 1.5% of the genome, other recent comparisons of the protein coding genes, between chimps and man, have yielded a similarity of only 96%. Whereas, the December 2006 issue of PLoS ONE reported that human and chimpanzee gene copy numbers differ by 6.4%, which gives a similarity of only 93.6% (Hahn). Even more realistically, to how we actually should be looking at the genomes from a investigative starting point, Dr. Hugh Ross states the similarity is closer to 85% to 90% when taking into account the chimp genome is about 12% larger than the human genome. A recent, more accurate, human/chimp genome comparison study, by Richard Buggs in 2008, has found when he rigorously compared the recently completed sequences in the genomes of chimpanzees to the genomes of humans side by side, the similarity between chimps and man fell to slightly below 70%! Why is this study ignored since the ENCODE study has now implicated 100% high level functionality across the entire human genome? Finding compelling evidence that implicates 100% high level functionality across the entire genome clearly shows the similarity is not to be limited to the very biased “only 1.5% of the genome” studies of materialists.

    Chimpanzee?
    10-10-2008 – Dr Richard Buggs – research geneticist at the University of Florida
    …Therefore the total similarity of the genomes could be below 70%.
    http://www.refdag.nl/artikel/1.....anzee.html

  12. 12
    Upright BiPed says:

    Bilboe,

    If that is the case, then your comment in #4 makes no sense.

    Perhaps if you hadn’t been in such a rush to say something clever, you might have noticed it.

  13. 13
    bornagain77 says:

    Bilboe cont;

    Moreover, when scientists did a actual Nucleotide by Nucleotide sequence comparison, to find the “real world” difference between the genomes of chimps and Humans, they found the difference was even more profound than Dr. Richard Buggs estimate:

    Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship?
    Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.]
    http://www.apologeticspress.org/articles/2070

    Even this more recent evolution friendly article found the differences in the protein coding genes of the Y chromosome between chimps and Humans to be “surprising”:

    Chimp and human Y chromosomes evolving faster than expected – Jan. 2010
    Excerpt: “The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content.,,, The chimp Y, for example, has lost one third to one half of the human Y chromosome genes.
    http://www.physorg.com/news182605704.html

    The evolutionary scientists of the preceding paper offered some “evolutionary just so” stories of “dramatically sped up evolution” for why there are such significant differences in the Y chromosomes of chimps and humans, yet when the Y chromosome is looked at for its rate of change we find there is no evidence for any change at all, much less the massive changes they are required to explain:

    CHROMOSOME STUDY STUNS EVOLUTIONISTS
    Excerpt: To their great surprise, Dorit and his associates found no nucleotide differences at all in the non-recombinant part of the Y chromosomes of the 38 men. This non-variation suggests no evolution has occurred in male ancestry.
    http://www.reasons.org/interpr.....lutionists

    I find it extremely interesting that the Y chromosome (male chromosome) would have such a pronounced “signature of individuality” in the human genome since it is clearly one of the primary chromosomes directly involved in overseeing human reproduction of males. A “reproductive individuality” for human men which, of course, has direct and severe contradictory implications to the Darwinian scenario since only the “reproductive mutations/variations” that manage to “slip thru” actually count in any Darwinian scenario.

  14. 14
    Joseph says:

    Cabal:

    The way I understand evolutionary theory is that the fact of nested hierarchies is a strong evidence for common descent.

    Nested hierarchies argue against Common Descent.

    Ya see nested hierarchies are based on defined characteristics, not descent.

    And with descent we would expect to see a blend of characteristics in all the transitional forms that must have existed.

    Isn’t it about time ID proponents got around to doing some research so we can get to know how it all happened?

    Not yet- not enough resources.

    But my money is on a targeted search.

    What about your position?

    With all the resources you guys have you still don’t know if mutations can accumulate in such a way as to give rise to new protein machinery, new body parts and new body plans.

    And how many designers that you are aware of use magic to design their products?

    If you don’t know of any do you really think your diatribe means something?

  15. 15
    Joseph says:

    Bilboe,

    I disagree with Dr Behe about Common Descent.

    However his position is that it was guided, so given that I am not totally sure of his PoV.

    Did the designer have to intervene- what was the intervention- etc., etc.

    Does he accept front-loading?

    Does he accept that Common Descent occurs via differential reproduction of heritable variation?

    That part of his position isn’t clear to me.

    That said I disagree with Common Descent because there isn’t anything to account for the physiological and anatomical differences observed.

    There is no way to test the transformations…

  16. 16
    Seversky says:

    “That old gentleman with the wild, white beard and the wild, white hat—that venerable humbug was not really a philosopher; but at least he was the cause of philosophy in others. That scientific gentleman with the bald, egg-like head and the bare, bird-like neck had no real right to the airs of science that he assumed. He had not discovered anything new in biology; but what biological creature could he have discovered more singular than himself?”
    G. K. Chesterton, The Man Who Was Thursday.

    Matthew Harrison Brady: Is it possible that something is holy to the celebrated agnostic?

    Henry Drummond: Yes! The individual human mind. In a child’s power to master the multiplication table, there is more sanctity than in all your shouted “amens” and “holy holies” and “hosannas.” An idea is a greater monument than a cathedral. And the advance of man’s knowledge is a greater miracle than all the sticks turned to snakes or the parting of the waters.

    Inherit The Wind

  17. 17
    Smidlee says:

    Cabel:
    “If the species diversity should be the result of intentional design – by itself a rather dubious claim, since life is full of exaamples of sloppiness of design that would get any human
    designer instantly fired.”
    If a man could design a small nano-machine that can build completely whole robots with high intelligence he wouldn’t have to care if he got fired since he would be a multi-billionaire.

  18. 18
    Timaeus says:

    Bilboe:

    Dr. Behe clarified his position on a couple of things here:

    http://www.evolutionnews.org/2009/11/
    god_design_and_contingency_in.html

    T.

  19. 19
    Clive Hayden says:

    Matthew Harrison Brady: Is it possible that something is holy to the celebrated agnostic?

    Henry Drummond: Yes! The individual human mind. In a child’s power to master the multiplication table, there is more sanctity than in all your shouted “amens” and “holy holies” and “hosannas.” An idea is a greater monument than a cathedral. And the advance of man’s knowledge is a greater miracle than all the sticks turned to snakes or the parting of the waters.

    But the scientific men do muddle their heads, until they imagine a necessary mental connection between an apple leaving the tree and an apple reaching the ground. They do really talk as if they had found not only a set of marvellous facts, but a truth connecting those facts. They do talk as if the connection of two strange things physically connected them philosophically. They feel that because one incomprehensible thing constantly follows another incomprehensible thing the two together somehow make up a comprehensible thing. Two black riddles make a white answer…

    A law implies that we know the nature of the generalisation and enactment; not merely that we have noticed some of the effects. If there is a law that pick-pockets shall go to prison, it implies that there is an imaginable mental connection between the idea of prison and the idea of picking pockets. And we know what the idea is. We can say why we take liberty from a man who takes liberties. But we cannot say why an egg can turn into a chicken any more than we can say why a bear could turn into a fairy prince. As IDEAS, the egg and the chicken are further off from each other than the bear and the prince; for no egg in itself suggests a chicken, whereas some princes do suggest bears. Granted, then, that certain transformations do happen, it is essential that we should regard them in the philosophic manner of fairy tales, not in the unphilosophic manner of science and the “Laws of Nature.”

    It is not a “law,” for we do not understand its general formula. It is not a necessity, for though we can count on it happening practically, we have no right to say that it must always happen. It is no argument for unalterable law (as Huxley fancied) that we count on the ordinary course of things. We do not count on it; we bet on it. We risk the remote possibility of a miracle as we do that of a poisoned pancake or a world-destroying comet. We leave it out of account, not because it is a miracle, and therefore an impossibility, but because it is a miracle, and therefore an exception. All the terms used in the science books, “law,” “necessity,” “order,” “tendency,” and so on, are really unintellectual, because they assume an inner synthesis, which we do not possess.

    I deny altogether that this is fantastic or even mystical. We may have some mysticism later on; but this fairy-tale language about things is simply rational and agnostic. It is the only way I can express in words my clear and definite perception that one thing is quite distinct from another; that there is no logical connection between flying and laying eggs. It is the man who talks about “a law” that he has never seen who is the mystic. Nay, the ordinary scientific man is strictly a sentimentalist. He is a sentimentalist in this essential sense, that he is soaked and swept away by mere associations. He has so often seen birds fly and lay eggs that he feels as if there must be some dreamy, tender connection between the two ideas, whereas there is none. A forlorn lover might be unable to dissociate the moon from lost love; so the materialist is unable to dissociate the moon from the tide. In both cases there is no connection, except that one has seen them together. A sentimentalist might shed tears at the smell of apple-blossom, because, by a dark association of his own, it reminded him of his boyhood. So the materialist professor (though he conceals his tears) is yet a sentimentalist, because, by a dark association of his own, apple-blossoms remind him of apples.

    G. K. Chesterton, Orthodoxy

  20. 20
    Joseph says:

    This is too funny- Seversky quotes a Hollywood movie (Inherit the Wind) known to misrepresent reality.

    You rock Seversky- you are a joke of course, but you rock…

  21. 21
    Timaeus says:

    Joseph, Bilboe:

    My comment 18 above was directed to Joseph @15, not Bilboe. Sorry for the confusion.

    T.

  22. 22
    Seversky says:

    Clive Hayden @ 19

    But the scientific men do muddle their heads, until they imagine a necessary mental connection between an apple leaving the tree and an apple reaching the ground. They do really talk as if they had found not only a set of marvellous facts, but a truth connecting those facts. They do talk as if the connection of two strange things physically connected them philosophically. They feel that because one incomprehensible thing constantly follows another incomprehensible thing the two together somehow make up a comprehensible thing. Two black riddles make a white answer

    I really do not think you want to be advancing this as an argument.

    As I read it, Chesterton is arguing the same case for skepticism about causality as David Hume some 250 years earlier.

    On the one hand, it is a good philosophical point. All we really observe are the conjunction of events. If we see that conjunction happening regularly then we infer a causal relationship. But that is all it is, just an inference, a “dreamy, tender connection between the two ideas”. We lack the “inner synthesis”, the detailed, link-by-link account of the causal chain connecting the two events, assuming it exists.

    On the other hand, one such inference was drawn from the – possibly apocryphal – observation of an apple becoming detached from a branch and falling to the ground. The theory built on that inference has led to extraordinary achievements. For example, a space probe, launched from the surface of a planet that is rotating about its axis at around 1,000 mph at the equator and orbiting its parent star at around 66,000 mph. The probe was not aimed at the target planet where it was at the time of launch. It was steered towards where the planet would be – according to theory – nearly seven years in the future. The journey was not direct but followed a circuitous course which made use of four gravity-assisted flybys of other planets. Both planet and probe reached the rendezvous point with pinpoint accuracy.

    If you want to think of scientific inferences and theories as being no more than “two black riddles” making “a white answer” then that is your choice. But it is hard to imagine better evidence than the Cassini-Huygens mission to Saturn for the case that inferences and theories are a whole lot more than just “dreamy, tender connections”. Whether some here like it or not, they work.

    One further point: if Chesterton is right, it would be catastrophic for the whole enterprise of reason, including StephenB’s “right reason”. Reason depends on the Universe being more than a just collection of discrete and unrelated facts. If there are no causal connections between objects and events, if we can only describe but not explain, then reason itself must fail.

    Chesterton was a clever man and a gifted writer but, on its face, this is a foolish argument.

  23. 23
    Clive Hayden says:

    Seversky,

    Anyone steeped in scientism would feel the way you do, but it is simply the problem of induction in the study of nature. And the argument against Chesterton’s insight is foolish. He is exactly right that we cannot say why anything is connected philosophy when we seem them together physically. We can see the reasonableness of real laws, laws of logic and reason, we can only describe events in nature and arbitrarily call them laws based on some arbitrary criteria such as repeatability. But that repeatability is only a description, and a description doesn’t make an argument against a proscription. We cannot say why anything in nature couldn’t have been otherwise, for we have no insight into the reasonableness of inner synthesis of the connection of any two things. This is devastating to sceintism, which is understandable that you would be offended, but the reasonableness and logic of it is sound. If you want to argue against Chesterton, you should tell me what the philosophical connection between flying and laying eggs is. You take it for granted that it happens, why it must, what the idea is behind it, as if it were a mental necessity, you cannot say, for you have no such knowledge, all you can do is describe. But, as I said before, a description is never an argument against a proscription. Reason is presupposed by any study of nature, we do not reason from nature, but to nature. Chesterton’s position is not catastrophic for reason, but it upholds true reason against a false reason such as is scientism. Reason would exist even if there were a different nature, for reason doesn’t depend on roses being red, or birds flying and laying eggs. The connection of facts doesn’t produce our reason. If we are to be reasonable we cannot say why they must be connected. Whether or not these descriptions work makes absolutely no difference to the truthful point Chesterton made. Pragmatism is not a philosophy of truth because it is pragmatic. I know this is always the argument of scientism, but it is not a good argument. I’m sorry Seversky, I suspect you really do not understand the true implications of Chesterton reading your comment. Nature is a mystery of why, and telling how two things are seen together, as if they must by some mental necessity be together, doesn’t dispute that fact, for we have no such knowledge of its inner synthesis nor enactment.

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