What counts as evidence for evolution?

A couple of reviewers of WEIT (and some of my friends and colleagues) have pointed out the book’s dearth of molecular evidence for evolution.  For example, why didn’t I stress that organisms thought to be related based on morphological similarities also show similar relationships in their DNA sequences?  That is, DNA phylogenies generally match morphologically-based phylogenies — doesn’t that count as evidence for evolution?  To my mind, not very strongly, and for two reasons.  First, at least for protein-coding genes, morphology and DNA are not independent: the genes are blueprints for the organism’s appearance, so the coincidence of trees is not independent evidence for evolution.

My strategy here was to use as evidence for evolution only those data that rule out the most widely-accepted alternative scenario, i.e., some form of creationism.  Similarities of molecular and morphological trees don’t necessarily rule out the action of a celestial designer.  He/She/It could have used similar genes to make similar organisms.

Well,  you ask, what about those parts of the DNA that are “neutral”?  (E.g., the third positions of codons, in which a mutation doesn’t necessarily change the structure of the protein made by that gene.)  Well, yes, those could count provided that they really are neutral.  As molecular evolutionists examine genomes more thoroughly, they often find that “neutral positions” aren’t really neutral, but could play some role in the fitness of the organism.  In such cases, their phylogenetic match to appearance-based phylogenies again fails to rule out creationism.

The one type of molecular evidence that does absolutely rule out creationism, I think, involves pseudogenes: those genes that were once active in ancestors but have become inactivated. I describe several cases in chapter 3 of WEIT; they include olfactory receptor genes in humans, many of which have become inactivated in the human lineage as we gradually lost reliance on our sense of smell and became more vision-oriented.  DNA changes in pseudogenes can hardly be subject to natural selection, so pseudogenes change in a purely time-dependent manner as those dead genes accumulate mutations over time.  Thus, the match between phylogenetic trees based on pseudogene DNA sequences (reflecting only the passage of time) with phylogenetic trees based on organisms’ appearance are expected under an evolutionary scenario but not a creationist one.  Creationists largely deny common ancestry (and don’t accept that organisms change with the passage of time). They wouldn’t, then, predict a phylogenetic match between features that simply mark the passage of time and features that independently reflect ancestry (e.g., the placenta of placental mammals that is not found in marsupials).  This is why I concentrated on pseudogenes in my book.  I’ve never seen a creationist explanation for why DNA trees based on pseudogenes match traditional trees based on morphology.

Similarly, people often cite Hox (“homeobox”) genes as evidence for evolution (these are the genes that demarcate different segments of animal bodies). It turns out that in organisms which are very dissimilar, such as humans and my beloved fruit flies, Hox genes nevertheless play similar roles in building bodies.  Why don’t I count this as evidence for evolution? Because it doesn’t rule out the alternative of a celestial designer.   Such a designer could have used the same genes in different species as His/Her/Its way of building bodies.  There’s no reason why a designer couldn’t hit on certain fundamental ways of making bodies, and then use them over and over again.

This, then, was my strategy throughout the entire book: to use only that evidence that could not easily be explained by creationism or other alternatives to evolutionary theory.  This, of course, is precisely the strategy that Darwin used in The Origin, since he had to convince readers that his theory was superior to the reigning creationist paradigm of the day.  I guess you can say that, given prevailing opinions in the US and some other countries, I adopted the same evidence-based strategy.

20 Comments

  1. newenglandbob
    Posted April 4, 2009 at 6:08 pm | Permalink

    Great essay, informative. Write a second book that includes this kind of evidence also. To (their) hell with creationists and their attempt to co-opt the evidence.

  2. Posted April 4, 2009 at 6:19 pm | Permalink

    I agree with your approach. But, I think some of the ideas could use a closer look. It is true that it is a creationist claim that matching trees are consistent with creationism, but are they really? First, the fact that we can get a tree (on morphology) at all is necessary for and predicted by evolution. On creationism the fact isn’t explained. Then that a molecular tree matches is first a confirmation of the morphological tree – but that it matches for each molecule is above and beyond that. Cytochrome c functions the same way in every organism. On creationism, the “best” molecule would be ubiquitous – on evolution, the cytochrome tree will follow the morphological/fossil tree.

    I find it that for virtually any of the foundational evidence for evolution, the creationist interpretation carries needless flaws, while evolution is a parsimonious, predictive and falsifiable explanation.

  3. Richard
    Posted April 5, 2009 at 2:56 am | Permalink

    “Similarities of molecular and morphological trees don’t necessarily rule out the action of a celestial designer. He/She/It could have used similar genes to make similar organisms.”

    An omnipotent, inscrutable being could have done anything at all. So no observation rules out the action of such a designer. It’s an unfalsifiable hypothesis.

    A good scientific theory explains why we see X and not Y. Evolutionary theory does this. The creationist hypothesis doesn’t. God could have used similar genes to make similar organisms, but he also could have used different ones. The creationist hypothesis doesn’t explain why he used similar ones.

  4. whyevolutionistrue
    Posted April 5, 2009 at 6:01 am | Permalink

    Richard,

    Good point; I just think that people have some idea that their designer is indeed “intelligent”, and so it constitutes some refutation of creationism to show that evolution does stuff that an “intelligent” designer wouldn’t do. I think in general it’s more effective to say “Evolution predicts X and creationism doesn’t, and we see X,” rather than saying “Evolution predicts X and we see X.” That’s because, in the back of many peoples’ minds, they could say
    “Well, maybe God could have ALSO done X.”

  5. Posted April 7, 2009 at 10:43 am | Permalink

    If I’m understanding your post correctly, the evidence that you accept (because it doesn’t fit the creationist model) is that evolution is true because we have genes that we no longer use/need. How is that evolution? Isn’t evolution supposed to add information to the genome and therefore add changes in form/ability to the organism? How does having nonfunctional genes prove evolution? That sounds much more like the Biblical view that things are getting worse because of sin in the world, things are breaking down. From a Biblical perspective we would expect things to be getting worse, i.e. humans used to be able to smell better but now they can’t because these genes are no longer functional.

    I don’t find this evidence convincing since it presents the opposite of what evolution is supposed to produce. What else can you present?

    Also, a Biblical perspective supposes that God is unchanging, normative and rational so it would make sense (though not necessitate) that God would use similar materials to accomplish similar functions in organisms. I do think that the “God of the gaps” idea is thrown around too much by believers sometimes but there are many things that science can not yet explain as well. Science can’t explain everything and Christians can’t always explain why God did the things in the way He did them. I’d love to continue dialoguing in these areas.

    • JoH
      Posted November 5, 2009 at 7:48 am | Permalink

      Dave,

      the *existence* itself of the no-longer-used genes is not the main argument here. Their role in this particular reasoning is that they create regions in the DNA that are not under pressure of selection. Since they are non-functional, mutations in these regions have no consequences, will not be selected against, and will freely build up and become inherited over the generations.

      When we map the existing mutations in these pseudogenes in different species, a phylogenetic tree appears that happens to perfectly match the trees created on the basis of functional genes and/or morphology. But while those two latter trees could invoke common design as a possible underlying cause(i.e. in order to result in a particular phenotype, the genes HAD to look this way), this would make no sense at all for the tree based on non-functional pseudogenes. In the absence of common descent, one would expect mutations to be *randomly* distributed between the same pseudogenes in different species. Common descent is the only reasonable (and in fact crystal-clear) explanation for a relationship that matches other phylogenetic trees.

      • Posted November 5, 2009 at 8:08 pm | Permalink

        “In the absence of common descent, one would expect mutations to be *randomly* distributed between the same pseudogenes in different species.”

        One would only “expect” that if they assume that there is not a transcendent, intelligent creator. In the Biblical worldview, nothing is really random. There are no coincidences. God has a plan that He is working out through history.

        If our genes have evidence of traits that no longer express themselves (but used to), where do we get the new information that evolution requires? Where is the evidence for positive mutations that add information? The evidence for this should be overwhelming if evolution is true! The Biblical prediction is that we will find lots of evidence of things breaking down (traits that used to express that don’t anymore) but no evidence of new information being added. Isn’t that what we see?

      • NewEnglandBob
        Posted November 5, 2009 at 9:26 pm | Permalink

        Dave:

        No that is not what we see. Whole sequences can be copied. Entire chromosomes can be duplicated. New sequences can be added by meiosis.

    • Caroline52
      Posted May 30, 2012 at 2:12 pm | Permalink

      Dave,
      You ask, “Isn’t evolution supposed to add information to the genome?”

      That’s not exactly right. Natural selection preserves any change to the genome that make organisms more likely to survive in their particular environment.

      An adaptive change can be one that:

      -adds information (an eye that sees a little bettter), or one that

      –reduces information (for example, causes a feature that’s no longer useful to stop developing fully), or one that

      –exchanges one piece of information for another, adding one thing but dropping another, leaving the total amount of “information” in the genome the same.

      Not all organisms evolve to be more complex.

      Some organisms stay simple because more complexity won’t help them survive better in their particular environment.

      And some organisms, like parasites, adapt by becoming simpler, like tapeworms, for example. They rely on the host to digest their food for them so they no longer have the digestive systems their ancestors had.

      (Biologists, please correct me if I got any of that wrong.)

  6. scaryreasoner
    Posted April 9, 2009 at 10:26 pm | Permalink

    The fact that the genome codes morphology may be true, but consider the audience — how well do people know this?

    I think a bit more material on the molecular DNA evidence for evolution would have been good, even if not “independent” evidence for evolution.

    Esp. I think more than one paragraph should have been devoted to ERVs.

    Take a look at this, for example:

    http://scienceblogs.com/erv/2009/04/abbie_vs_charles_jackson.php#comments

    It’s 3.5 hours of debate betwen Abbie Smith aka “ERV” and Charles Jackson (YEC) about the molecular evidence for evolution.

    Granted, there’s a limited amount of paper the publishers are willing to put in a book, and I don’t know what the tradeoffs were, but I would have liked to see a bit more about the molecular and genetic evidence.

    Criticisms aside (and who am I to criticize? Joe Random blogger, is all) I really liked the book a lot.

  7. Posted November 5, 2009 at 9:32 pm | Permalink

    I don’t see another “reply” button so I’ll continue down here.

    “Whole sequences can be copied. Entire chromosomes can be duplicated. New sequences can be added by meiosis.”

    All of those examples duplicate existing information not add new information. You’ll never get from an amoeba to an elephant by copying, duplicating, or dividing by meiosis. Give an example of *new* information being introduced via mutation (or any other source). This is necessary for evolution and we don’t see it.

    • NewEnglandBob
      Posted November 5, 2009 at 9:38 pm | Permalink

      No one goes from an amoeba to an elephant. That is a nonsense argument.

      How else would you expect to get new information besides copying and recombination via meiosis? You apparently do not understand the processes.

      Do you think a god adds new information? There are only 4 basic elements in all of DNA. Copying and recombining those 4 have trillions of trillions of possibilities.

      If you still don’t see it, then open your eyes and learn the science behind it.

      • Posted November 5, 2009 at 9:52 pm | Permalink

        Obviously no one believes that an amoeba transitions right to an elephant. If evolution is true, there were thousands upon thousands of transitional forms in between.

        Can you give me an example of an experiment or observation where a population was seen to have evolved new genetic information (a new trait) that didn’t previously exist in that population? Evolution hinges on this process (new information being produced, selected, and passed on to future generations). Science is based on experimentation and observation so this is crucial. If no evidence has been found then evolution is based on faith (or lack of it) and is religious, not scientific.

      • whyevolutionistrue
        Posted November 5, 2009 at 10:08 pm | Permalink

        o.k. Dave, that’s enough. You are spouting intelligent-design arguments without having done your homework. Go read Dawkins on the acquisition of new information, or, if you want a more specific reference, see Ken Miller’s discussion of the evoution of nylonase in his book Only a Theory. And don’t post any more on this topic until you do that reading.

  8. Posted November 6, 2009 at 9:53 am | Permalink

    Respectfully, I’m familiar with Miller and the nylonase discovery (which doesn’t prove new information because the bacteria wasn’t under observation before the discovery was made) and Dawkins is more faith-based and fundamentalist than most Christians. I’m asking for scientific evidence that new traits have been observed in organisms that didn’t exist before. Isn’t this evolution? Why is it so hard to find an example? Please understand, I’m not trying to win an argument, I’d just like to know what evidence people have for believing (knowing) that this (production of new traits) has happened billions of times throughout history.

    • JoH
      Posted November 12, 2009 at 5:59 am | Permalink

      Richard Lenski experiments for you: http://www.newscientist.com/article/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

      Try to imagine a trillion times as many colonies of bacteria being subjected to millions of different selective pressures for billions of years in an open-ended environment.

      Waiting for your goalpost to move…

      Now, the thing you need to understand most here is that you should drop the “I want to see THE SINGLE ALL-DEFEATING piece of evidence for evolution!”. The confidence in common descent is based on a NUMBER of SEPERATE lines of evidence that all “miraculously” point in the same direction(molecular genetics, geographic distribution of species, vestigal features, fossile record etc. etc. etc.). To such a degree that it requires a significant level of preoccupation to keep denying the obvious. Yes, evidence CAN point in a wrong direction. If all those “wrong” directions nicely line up though, it might be time to consider the possibility that it might possibly be RIGHT instead.

  9. Patrick
    Posted July 21, 2012 at 4:36 pm | Permalink

    Hello Prof. Coyne: I have read Dr. Douglas Theobald’s 29+ Evidences for Macroevolution for years now, and I was just reading it again to refresh my memory before I stumbled across this post. Anyway, I have always been astounded by the logic expressed by Dr. Theobald regarding the convergence of traditional morphological phylogenies with that of the more recent trees informed by molecular biology. You disagree with this assumption on the grounds that, “First, at least for protein-coding genes, morphology and DNA are not independent: the genes are blueprints for the organism’s appearance, so the coincidence of trees is not independent evidence for evolution.”

    This is a very interesting position indeed, but is this clearly not the reason why biologists utilize genes that code for proteins that are universal or nearly so among various organisms(e.g., cytochrome c found among taxa as diverse as bacteria, bees, fish, ants, whales, humans, etc.) when constructing evolutionary relationships? Clearly a protein that functions in bacteria would not affect the anatomical traits of chimpanzees and gorillas. So a cytochrome c protein sequence that is, for example,(identical) among humans and chimpanzees is certainly significant and confirms what biologists have contended for decades: chimpanzees are the closest relative of humans.

    Also, and more significantly, Dr. Theobald quotes Dr. Hubert Yockey’s calculation that there are 2.3 x 10^23 possible cytochrome c sequences! That is one big number! Out of this (literally countless) galaxy of possible cytochrome c sequences, it is very, very unlikely that humans and chimpanzees would just randomly possess the same sequence——a sequence that just so happens to confirm traditional projections of evolutionary relationships among apes.

    This post is not to inflame, but rather to perhaps stoke some insights from the great Prof. Coyne. Perhaps and I am missing something? Thanks…

    http://www.talkorigins.org/faqs/comdesc/section4.html

  10. Patrick
    Posted July 24, 2012 at 7:20 am | Permalink

    I have read Why Evolution is True and all I have to say is that it is many orders of magnitude superior to Richard Dawkins’ book “The Greatest Show on Earth.” No offense to the latter, I just believe the former is more academic and less pretentious in content. So buy it!

  11. newenglandbob
    Posted November 12, 2009 at 11:45 am | Permalink

    Actually the opposite of evolution took place. The E. Coli strains lost the ability to catabolize ribose.

    This is yet another example of someone who does not understand evolution. There is no direction to evolution. Changes are seen due to stresses in the environments that natural selection selects for. Some character can be added or it can be removed. It can go back and forth as the environment changes.

    Once again, copying and moving around IS the way information is added. The question by Dave is a straw man, an argument from ignorance.

  12. whyevolutionistrue
    Posted November 12, 2009 at 2:52 pm | Permalink

    Dave, you don’t have the slightest idea of what you’re talking about. Evolution has no directionality, unless you’re talking about how organisms had to start simple and now SOME are more complex. If you knew anything about evolution, you’d know that some organisms, like parasites, become simpler over time.

    You are here to troll, not to learn or contribute new information or ideas. Please find a creationist website that is to your liking.


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