DNA of wingless insects points to evolution

Perhaps you haven’t thought of it much before, but relatively few species of insects completely lack wings. One kind of wingless insect is known as a silverfish, an animal that perhaps you have discovered crawling in your home or hanging out in your pantry.

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Typical of insects, they possess six legs, a chitinous exoskeleton, compound eyes and a pair of antennae. Unlike most other insects, they are wingless and have three filaments that jut out from the tail portion of their bodies. The latter traits are typical of multiple species of insects beyond silverfish, including the firebrat and bristletails, a group that I was taught was called Thysanura growing up.

Despite thysanurans seemingly being united by these distinctive characteristics, when scientists began comparing insect DNA, they found that thysanurans didn’t group together. Instead, the results from DNA suggest that they represent two distinct lineages of insects that just happen to look very similar. Below is a molecular phylogeny that included 1478 genes from 144 species of insects and insect-like animals (arthropods) [1]:

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You can see the thysanuran species at the top of the phylogeny. One lineage of thysanurans is now called Archaeognatha, which includes the animals below:

The next group is called Zygentoma, which includes the silverfish and others, such as some oddball species that are blind, lack color and live exclusively with ants and termites:

Despite their striking similarities to one another, zygentomans are actually more genetically similar to winged insects, with forms as diverse as praying mantises, butterflies and beetles. This might seem surprising, but it’s quite plausible if evolution is true.

One scenario in which this is possible is if Archaeognatha and Zygentoma independently evolved a very similar body form, known as convergent evolution. Evolutionary biologists typically expect this to occur when different organisms adapt to very similar lifestyles. However, since these lineages split off in relatively rapid succession, it’s more likely that the earliest insects looked like thysanurans, and archaeognathans and zygentomans retained this ancestral body type.

Questions for Creationists

If God created archaeognathans and zygentomans, as well as the DNA that determines how they look, why is it that their DNA is so different? Shouldn’t animals that look similar have more similar DNA?

References

1. Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., … & Niehuis, O. (2014). Phylogenomics resolves the timing and pattern of insect evolution. Science346(6210), 763-767.

Photo credit

Silverfish 1Archaeognatha 1Archaeognatha 2, Archaeognatha 3, Archaeognatha 4, Silverfish 2, Zygentoma 2Zygentoma 3

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25 thoughts on “DNA of wingless insects points to evolution

  1. TFBW

    Shouldn’t animals that look similar have more similar DNA?

    I realise that the question is largely rhetorical, as you employ exactly the same kind of “questions for creationists” rhetoric on every post, but I find this question oddly incongruous if I take it as a sincere question. Let me be up-front and say that I am a creationist: it saves time, and we can quibble about stereotyping later. I’m also a computer scientist, not a biologist. With that disclosure out of the way, I have an answer to your question: “not necessarily”. I also have a question about your question, which may serve to clarify the answer.

    What makes you think that, on creation, animals that look similar should have similar DNA?

    Clearly you don’t think that similar appearances necessitate similar DNA, because you are pointing out real-world genetic differences in similar-looking organisms (and, for the sake of argument, I assume all your reporting on the subject is factually accurate). As such, you seem to be implying that a creator ought to take the (unnecessary) step of making the genetic code similar to reflect the external similarities. Why do you expect that? It seems quite an arbitrary thing to me.

    Have you considered the possible counter-idea that a creator might design a number of similar-looking things with strikingly different implementation details specifically to make it look like it was not a product of an evolutionary process? If similar-looking things had similar internal workings, it would be strongly suggestive of common descent, right? But if similar-looking things have strikingly different internal workings, it suggests that the things are not closely related, despite superficial appearances. Now, if things with different internal workings have different external appearances, that comes as no surprise to anybody. Superficial similarities hiding deep internal differences, on the other hand, cause eyebrows to be raised. If you were a designer trying to make life look not evolved, this would be a good way to drop the hint.

    1. Thanks for your comment, TFBW! Replies below:

      “What makes you think that, on creation, animals that look similar should have similar DNA?”

      As you point out later, I clearly don’t entirely believe this, though I largely do as I’ll explain below. The origin for this specific type of question posed to creationists is in response to a typical argument I’ve seen creationists make.

      Specifically, evolutionary biologists have long asserted that the fact that DNA is similar between certain species shows evidence of common descent. By sharing some DNA in common, while also showing species-specific differences in this DNA, our genes seem to point to common ancestors that have given rise to multiple species. So when you look at the DNA of a tiger, a leopard and a jaguar and see that their DNA is similar, it points to their shared heritage, the same way that highly similar DNA between two humans points to their common ancestry (e.g. same parents, grandparents, or great-grandparents, etc.).

      A common creationist counter argument is that the reason DNA looks similar between such organisms is because (1) DNA provides a body’s instructions for making anatomy and (2) God created DNA, therefore we shouldn’t be surprised that animals that look similar have similar DNA. I think this is a logical assumption to make if Creationism is true.

      The reality is: most of the time similar looking organisms have similar looking DNA, but there are plenty of exceptions. Cats all are more genetically similar to each other than they are to dogs. Dogs are all more genetically similar to each other than they are to squirrels. But there are also quite a few examples of organisms that look very similar to each other but are not similar genetically, some of which I’ve tried to highlight in this blog. This is the motivation behind posting on this particular topic.

      “Superficial similarities hiding deep internal differences, on the other hand, cause eyebrows to be raised. If you were a designer trying to make life look not evolved, this would be a good way to drop the hint.”

      I’ll have to give this some more thought, because at the moment this isn’t quite making sense to me, though that’s part of what’s difficult about thinking about testable hypotheses for Creationism. How can one know what the Creator would or wouldn’t have done?

      I suppose I would say the following:

      (1) if all similar looking things had very different DNA, this would be very hard to explain from evolutionary theory, and would potentially refute it. I think your point on this is apt.

      (2) if all similar looking things had very similar DNA, this would be consistent with evolutionary theory (similar DNA = shared ancestry) as well as Creationism (similar instructions for anatomy = similar anatomy)

      (3) But the fact that there is a mix of the two I think points to evolutionary theory as the more plausible of the two. Evolutionary theory suggests that organisms can appear similar because of shared ancestry or independent adaptations to the same lifestyle. Shared ancestry is consistent with similar DNA, whereas independent adaptations to the same lifestyle is likely to lead to very different DNA. The reason for this latter point is that two independent lineages already have very different DNA due to the long period of time that has elapsed since their most recent common ancestor. There may be some similar changes in DNA leading to the same adaptations, but the signal will be overwhelmed by their distinct, separate pasts.

      A simple example of this: blonde hair appears in Northern Europeans and Melanesians. Same appearance, but they are genetically very different solutions to coming up with blonde hair. If you were to look at the genes for making hair color in Melanesians and Northern Europeans, you would find that they (relatively speaking) aren’t similar at all, due to their very different human histories.

      It’s of course plausible that a Creator could create some things that look similar with different DNA and some things that look similar with similar DNA, because, of course, the Creator can do whatever the Creator wants. If true, this becomes one of those typical acknowledgements of how the Creator’s methods are unknowable (echoes of Isaiah 55:8). But at least from our human perspective, as limited as it may be, it does seem a bit illogical, don’t you think?

      Creationists frequently use the analogy of cars to explain why animals have similarities: same engineer, same materials, variations on similar ideas. Arguably that same logic would apply to DNA. Would an engineer use steel, rubber and plastic to make one car and plasma, antimatter and superglue to make another? Why would the Creator create most animals with highly similar DNA and then create batches of other animals with completely different DNA?

      So in addressing your very thoughtful question, it seems that both your and my points at least call into question the model of a Creator that is typically invoked by creationists. In the meantime, I’ll have to give this all some more thought.

      1. TFBW

        I’ll have to give this some more thought, because at the moment this isn’t quite making sense to me, though that’s part of what’s difficult about thinking about testable hypotheses for Creationism. How can one know what the Creator would or wouldn’t have done?

        While you’re giving things more thought, let me draw your attention to this little wrinkle. If it’s difficult thinking about testable hypotheses for creation, then isn’t it also difficult to think about testable hypotheses for not-creation? After all, if you have a testable hypothesis for not-creation, and that turns out to be confirmed, then you’ve effectively come up with a testable hypothesis for creation and found it to be disconfirmed. That is to say, if you’re testing for not-creation, then, as a matter of logic, your test can only be distinguishing it from its alternative, which is creation.

        The upshot of that is this: if any of your evidence for evolution is also evidence against creation, then it can only be so on the basis that creation is a testable hypothesis. Either creation is a testable hypothesis, or nothing you have pointed out is evidence against creation. So, to be clear, does anything you present here count as evidence against creation, or is the question of creation/not-creation not decidable on the basis of evidence?

        It seems that you think creation is a testable hypothesis, since you also say the following.

        But the fact that there is a mix of the two I think points to evolutionary theory as the more plausible of the two.

        … where “creation” is the other of the two. Let’s tentatively hold that creation is decidable on evidence, then, and look at the specifics of the argument.

        Evolutionary theory suggests that organisms can appear similar because of shared ancestry or independent adaptations to the same lifestyle. Shared ancestry is consistent with similar DNA, whereas independent adaptations to the same lifestyle is likely to lead to very different DNA.

        The trouble with independent adaptations is their independence. The whole of evolution is a fight against probability: random change is mostly detrimental, and one must obtain it in small enough quantities not to be burdensome (let alone lethal), yet in large enough quantities such that evolution as we envisage it can actually occur in the limited number of generations available to it. I don’t know if you are well-versed in the mathematics of this from a biological perspective: if you are, perhaps you can bring some additional data to the table. I’m well versed in probability, but not in the latest theories of population genetics, or whatever the appropriate speciality is.

        In any case, from a purely probabilistic perspective, it’s one thing to have a mutation rate which is capable of supporting adaptive evolution along one lineage, but exponentially harder for the same adaptations to occur by chance along multiple lineages independently. Independent probabilities multiply. If probability means anything, then the appearance of convergent evolution as a somewhat ubiquitous feature of biology should count as strong evidence against the theory.

        When I think of this issue, my thoughts are drawn to Richard Dawkins and his computer simulations of eye evolution. His general outlook on the issue is that the evolution of eyes must be much easier than Darwin imagined, since it’s happened so often. And yet, of course, he would appeal to “lack of time” to cover for our complete and utter lack of real-world observations relating to gain by evolution of any new organs (let alone eyes). I don’t think the exponential curve in question allows him to have it both ways: if the evolution of eyes has happened often, then it must be so easy as to be reproducible (in part, at least) in a relatively small time frame using fast-reproducing organisms. Conversely, if it’s not even remotely reproducible in a small time frame, then it can’t be easy, and should be rare in nature. It is neither reproducible, nor rare.

        This whole issue was far less of a problem for Darwin, despite his misgivings about the eye, because he envisaged a purpose-driven mechanism for change: the giraffe stretching its neck, and so on. If that kind of mechanism were in operation, then convergence would be no surprise at all. The modern synthesis, however, admits no teleological mechanism for generating desirable mutations — only one for preferring the preservation those that happen by accident.

        It’s of course plausible that a Creator could create some things that look similar with different DNA and some things that look similar with similar DNA, because, of course, the Creator can do whatever the Creator wants. If true, this becomes one of those typical acknowledgements of how the Creator’s methods are unknowable (echoes of Isaiah 55:8). But at least from our human perspective, as limited as it may be, it does seem a bit illogical, don’t you think?

        As I’ve said, it makes sense to me from the perspective of a creator trying to leave evidence of creation, which hardly seems like a deeply mysterious or illogical motivation, particularly when the creation involves creatures capable of doing science. If a creator followed your pattern of making all externally similar things internally similar, then it would look more like evolution, since it’s much easier to explain similarity through common descent than through convergence.

        It is, of course, conceivable that a creator might not care to be obvious in this way, but it’s behaviour that’s easily understandable in terms of ordinary human motives, I think.

        Creationists frequently use the analogy of cars to explain why animals have similarities: same engineer, same materials, variations on similar ideas. Arguably that same logic would apply to DNA. Would an engineer use steel, rubber and plastic to make one car and plasma, antimatter and superglue to make another? Why would the Creator create most animals with highly similar DNA and then create batches of other animals with completely different DNA?

        Hmm, well I don’t think highly of this analogy. I could just as easily point out that DNA is primarily an information storage mechanism, so it’s more like software differences than hardware differences. After all, the DNA code is very nearly universal, even if the software it contains varies in some conspicuous ways, and the lower-level components of life (e.g. amino acids) are similarly nigh-universal.

        Even if I were to accept the analogy, though, I could make a similar point about people using such vastly different storage mechanisms for data as flash memory, magnetic tape, and optical discs. Why use such vastly different technologies for the same purpose? It’s a question which can be asked with as incredulous a tone as you can muster, but that doesn’t make it a big problem.

        And then there’s the converse question: you may find it incredible that a creator may want to construct such similarly-functioning objects out of such vastly different material sets, but we have to weigh it up against your proposal that these things all happened by natural processes, independently, and yet managed to be structurally and functionally similar despite the unrelated materials. Are the laws of the universe construed in such a way that such outcomes are favoured? We’ve seen nothing in physics to suggest it’s so, and it would surely be another argument for cosmic fine-tuning if we did.

    1. Not sure why I can’t reply directly to your comment above, so I’ll do it here:

      “If it’s difficult thinking about testable hypotheses for creation, then isn’t it also difficult to think about testable hypotheses for not-creation?”

      No, quite the opposite! We understand a lot about evolution from observations in nature, which leads to hypotheses with testable predictions. For instance, we know that organisms have DNA, that they pass this DNA on to their offspring, that this DNA can mutate, some of these DNA mutations are beneficial but most of them are probably neutral or harmful, we know separation of populations leads to divergence in DNA over time but reconnection between those populations can erase some or all of those differences, and we know that populations can become reproductive isolated from one another and prevent interbreeding between populations leading to (presumably) permanent isolation.

      This sets up expectations of how species might form and diverge genetically over time, and would lead us to think that similar looking organisms will tend to have similar looking DNA due to this shared ancestry. Just like you probably look similar to your siblings, a little less similar to your 1st cousins, even less similar to your 3rd and 12th cousins, your DNA is most similar to your siblings, followed by your 1st, 2nd, 3rd, etc. cousins. This leads to numerous hypotheses for numerous organisms regarding external similarity and genetic similarity, which have generally turn out to be supported.

      But we also know that by tinkering with the same gene in different ways, or tinkering with different genes that tend to be part of similar pathways, you can generate similar external traits. This leads to the expectation that, given similar ecological conditions, unrelated organisms can converge upon a similar external appearance through identical or (more likely) different means. Again, many individual hypotheses are generated from this and have been supported.

      “After all, if you have a testable hypothesis for not-creation, and that turns out to be confirmed, then you’ve effectively come up with a testable hypothesis for creation and found it to be disconfirmed. That is to say, if you’re testing for not-creation, then, as a matter of logic, your test can only be distinguishing it from its alternative, which is creation.”

      Not necessarily! As I pointed before, many scenarios are consistent with both evolutionary theory and certain models of creationism. Again: the Creator could have created some organisms that look similar with similar DNA, AND It could have created organisms that look similar with very different DNA. Why not?

      The Creator could have created a bunch of fossils of organisms that never existed and just hid them in the rocks. The Creator could have thrown most of the marsupials in Australia and all the ostrich-like birds in the southern hemisphere just because. The Creator, for all intensive purposes, presumably could have done whatever It wanted however It wanted because It presumably doesn’t operate within the bounds of times and space.

      This is the reason that Creationism, in its purest form, is not science. Since there are presumably an infinite number of scenarios that the Creator could have let unfold, we can’t really invalidate the Creation hypothesis. We can however test specific models of Creationism, including the models most prominent in the consciousness of religious communities, which ultimately is what this blog is addressing.

      “In any case, from a purely probabilistic perspective, it’s one thing to have a mutation rate which is capable of supporting adaptive evolution along one lineage, but exponentially harder for the same adaptations to occur by chance along multiple lineages independently. Independent probabilities multiply. If probability means anything, then the appearance of convergent evolution as a somewhat ubiquitous feature of biology should count as strong evidence against the theory.”

      As I’m sure you’re aware, part of this is a numbers game. Given enough time and enough generations, certain mutations can arise that lead to convergence in the same trait. As described above, that’s not the only thing that matters. Part of it comes down to the fact that there are frequently numerous ways to achieve the same outcome.

      As an example from my own research: there are at least six proteins whose only job appears to be to facilitate vision in the cells devoted to bright light and color vision (cones), and each of these proteins is encoded by a different gene. Some animals have lost cones, including some whales and some mole-like animals. What’s interesting is that we know from humans that lack cones due to a genetic disease and mice whose cones are genetically knocked that if you have a defunct version of any of these genes, you completely lose cone function. This means if there is some adaptation to losing cones (say, living in dark environments), you can knockout GNAT2, CNGA3, PDE6C or any of the other genes to achieve the same effect. And though the type of mutation has to be one of several specific types (inserting an extra DNA letter, taking away a DNA letter, among others), there are many ways these mutations can manifest and they can occur almost anywhere along the gene, meaning that it’s not as difficult probabilistically to envision that knockout mutations could occur in different animals. And sure enough, when we look at these whales and mole-like animals, we see that there is overlap in what genes are knocked out, but there are also differences (e.g., one whale has PDE6C knocked out and another doesn’t, but the latter has GNAT2 knocked out but the former doesn’t). Plus the specific knockout mutations that occur in the same genes are different the overwhelming majority of the time.

      So it shouldn’t be difficult to imagine that since there are many solutions to the same problem, given enough time, enough lineages and similar ecological pressures, convergence should arise.

      “I don’t think the exponential curve in question allows him to have it both ways: if the evolution of eyes has happened often, then it must be so easy as to be reproducible (in part, at least) in a relatively small time frame using fast-reproducing organisms.”

      I think part of what’s important here is that while eyes may have evolved repeatedly, photosensitivity in general may have evolved only a few times and has been retained in nearly every organism. Given this shared basis for photosensitivity, it’s not surprising that photosensitive organs have developed and been elaborated on. However, eyes have evolved in generally very different ways, and most of them are pretty rudimentary (if they can even be called eyes). So it may be ‘easy’ to evolve eyes, but not necessarily de novo, and not necessarily to the complexity that we see in vertebrates.

      I think an interesting counter-example comes from flight. Flight presumably is advantageous for many reasons, given it vastly increases your ability to disperse, thereby avoiding predators and finding food. However, we think it has only evolved perhaps four or so times in the entire history of life: insects, birds, bats and pterosaurs. An insect wing is in no way similar to those of birds, bats and pterosaurs, and even within those latter three, despite having far more similarities, they invented wings in completely novel ways.

      “As I’ve said, it makes sense to me from the perspective of a creator trying to leave evidence of creation, which hardly seems like a deeply mysterious or illogical motivation, particularly when the creation involves creatures capable of doing science.”

      Assuming the Creator wants to be discovered, and specifically wants to be discovered through those means. The Creator could have been way more obvious if that was the goal, but perhaps It relishes in making it tricky for us? But again, it’s obviously difficult to fathom the motivations of a Creator, so perhaps you’re right.

      “If a creator followed your pattern of making all externally similar things internally similar, then it would look more like evolution, since it’s much easier to explain similarity through common descent than through convergence.”

      I’m going to disagree with you here and agree with the standard creationist assumption by thinking about the analogy to human creators. Humans design cars and computers and many more things using similar building blocks and ideas, with various elaborations on these same foundational concepts. Nobody (I assume) thinks of designing cars with a chassis made of potatoes and an engine that runs on ketchup.

      It may be fallacious to conceive of a Creator as being like humans in Its thought processes, but it’s arguably the best we have to go off of. Alternatively, you can just speculate about the infinite number of ways the Creator could have done things, and I’m not entirely sure that’s a worthwhile discussion.

  2. TFBW

    I tried posting the same comment again, and it said I’d already posted it. You’ll have to go fishing in the administrative interface if you want to find it. Nothing I can do.

  3. TFBW

    This is the reason that Creationism, in its purest form, is not science. Since there are presumably an infinite number of scenarios that the Creator could have let unfold, we can’t really invalidate the Creation hypothesis. We can however test specific models of Creationism …

    So long as you appreciate that this is symmetrical, in the sense that Natrualism (not-Creationism) is not science either, but specific Natrualistic theories can be testable, then I doubt we have much to argue about.

    As I’m sure you’re aware, part of this is a numbers game. Given enough time and enough generations, certain mutations can arise that lead to convergence in the same trait. As described above, that’s not the only thing that matters. Part of it comes down to the fact that there are frequently numerous ways to achieve the same outcome.

    It’s the numbers which are important. Where exponential combinations are involved, then you run out of “enough time and enough generations” very quickly. It’s that very question of whether we have enough time that I’m raising.

    Look, suppose you were able to be rigorously mathematical enough to say that the probability of a particular evolutionary development happening once (given the available time) is ten percent, and that this measure takes into account all possible paths by which it could occur. If you’re asking me to believe that this development did happen by chance, once, then you’re asking me to believe one in ten odds. No big deal. If you’re asking me to believe that it happened twice, independently, then you’re asking me to believe one in one hundred odds. Slim, but possible. If you’re asking me to believe that it happened three times, independently, then you’re asking me to believe one in a thousand odds — and that’s just to believe that this one particular feature evolved three times independently — never mind every other evolutionary development which has ever happened by chance independently of those.

    Conversely, if we wanted to maintain the odds at ten percent, we would need about ten times as much (i.e. an order of magnitude more) time in which to achieve it per independent development. Billions of years may sound like a lot, but they don’t offer very many orders of magnitude to play with: there’s only nine between one and a billion.

    What’s interesting is that we know from humans that lack cones due to a genetic disease and mice whose cones are genetically knocked that if you have a defunct version of any of these genes, you completely lose cone function.

    Sounds like a textbook example of irreducible complexity. It means that a loss-of-function change like this is particularly easy to achieve, because several simple one-step mutations are capable of producing it. It is therefore easily reproduced (by someone with the necessary skills) in limited time.

    So it shouldn’t be difficult to imagine that since there are many solutions to the same problem, given enough time, enough lineages and similar ecological pressures, convergence should arise.

    Only if the solutions can be arrived at easily (i.e. they have a high probability of arising naturally). And if they have such a high probability, then they should be reproducible experimentally. Imagining that there are many easy solutions to the same problem is a far cry from experimentally demonstrating that claim, and it’s a claim which has to be tested on a case by case basis: demonstrating that a loss-of-function mutation is easy does not translate to demonstrating that gain of the same function is just as easy.

    Convergence is possible if the experimental numbers support it, but infeasible for highly improbable developments. How many proposed instances of convergence have experimental support?

    I think part of what’s important here is that while eyes may have evolved repeatedly, photosensitivity in general may have evolved only a few times and has been retained in nearly every organism. Given this shared basis for photosensitivity, it’s not surprising that photosensitive organs have developed and been elaborated on.

    I reiterate my earlier statement: if the evolution of eyes has happened often, then it must be so easy as to be reproducible (in part, at least) in a relatively small time frame using fast-reproducing organisms. Is there any experimental support for eye evolution? Have any of the speculated intermediate steps been reproduced experimentally like the loss-of-function experiments you mention? How much empirical support does this scenario really have? If it can’t be reproduced experimentally, then how do we know what time frame it actually takes?

    Assuming the Creator wants to be discovered, and specifically wants to be discovered through those means. The Creator could have been way more obvious if that was the goal …

    No, no, no. Don’t run away with the idea — keep your attention on the question which was being asked. A creator has a binary choice along the lines of “make all externally similar things likewise similar internally” (as per your requirement), or “don’t do that” (i.e. make some things which are externally similar but not internally similar). If one of the design goals is to make the result not look like descent from a common ancestor, then which of these two (comprehensive, mutually exclusive) alternatives do you take? The latter, yes? You suggested that the former was what you would expect. I’m providing you with a simple, plausible design criterion as to why the latter might be preferred, and therefore why your prescription for the former might be presumptuous.

    If you want to disagree with me on this, please disagree within the scope of the answer that I’ve offered; otherwise concede that it’s reasonable, as far as it goes. I’d be happy to discuss the broader issues some other time, but I can’t afford to let you broaden the scope without conceding the point. That style of argument does not scale.

    Nobody (I assume) thinks of designing cars with a chassis made of potatoes and an engine that runs on ketchup.

    Of course not — it wouldn’t work. I’m sorry, but is this car made out of potatoes and ketchup meant to be analogous to anything in the real world? Is some organism the equivalent of a car made out of potatoes and ketchup? I don’t see how it can be. It just seems like a deliberately wild and incredible analogy, the badness of which is supposed to rub off on the thing for which it was being used as an analogy.

    Perhaps it would be best if you dropped the rhetoric of analogy and expressed your objection in more precise, technical terms — or at least do that before providing an analogy.

    1. “So long as you appreciate that this is symmetrical, in the sense that Natrualism (not-Creationism) is not science either, but specific Natrualistic theories can be testable, then I doubt we have much to argue about.”

      Agreed!

      “It’s the numbers which are important. Where exponential combinations are involved, then you run out of “enough time and enough generations” very quickly. It’s that very question of whether we have enough time that I’m raising.”

      This is an issue that I take at face value because it makes sense to me (much like your disbelief in it makes sense to you), so it sounds like I’ll have to read up on this sometime to see what has been done in this arena. I know there are examples of this experimentally in bacteria and yeast where they’re able to convergently evolve the same traits relatively easily, sometimes through similar genetic mutations and sometimes through completely different ones, but bacteria and yeast have much shorter generation times and much smaller genomes than, say, an elephant.

      “Imagining that there are many easy solutions to the same problem is a far cry from experimentally demonstrating that claim, and it’s a claim which has to be tested on a case by case basis: demonstrating that a loss-of-function mutation is easy does not translate to demonstrating that gain of the same function is just as easy.”

      Yup, and my general feel of the field is that loss-of-function mutations probably occur at a higher frequencies than gain-of-function mutations. I agree that much, much more experimentation is warranted to understand how such gain-of-function mutations come about, so molecular biologists have a lot of work ahead of them.

      “How many proposed instances of convergence have experimental support?”

      Part of the difficulty with this is you can’t ethically and practically do most of the experiments that would need to be done to demonstrate this with near complete confidence. For instance, we think that whales evolved from a deer-like ancestor and that manatees and their kin convergently evolved aquatic adaptations from an obscure elephant-ish (maybe) ancestor. We can’t ethically and practically mutate deer and elephant embryos at random and see if, given the right conditions, they’ll evolve aquatic adaptations.

      However, given the development of gene editing technologies, such as CRISPR, people are beginning to do this in some detail in mice. For instance, there’s some experimental support for how snakes may have begun to lose their legs from a lizard ancestor thanks to gene editing work on mouse embryos. Keep in mind, this is targeted editing, not random mutations, but it gives some insight into how it may have happened.

      Now let me step back and say that I’m partial to the idea that adaptive gain-of-function mutations aren’t actually completely random. We know that mutations aren’t truly random due to biases of certain types of mutations and where they can happen, but I think it’s possible that adaptive mutations may actually come about somehow due to how an individual experiences stresses in its own life and passes that to its offspring. In other words, I speculate that Lamarckian evolution could have some truth to it. Let me be clear though: I have zero evidence to back this up, but given what we’ve begun to learn about epigenetics (how activities in one’s life influences one’s offspring), I can very easily imagine a mechanism whereby epigenetic effects somehow induce mutations to occur. Maybe scientists have already tested and falsified this (I doubt it, but I don’t know), but it seems reasonable to me that such guided mutations could come about.

      “Is there any experimental support for eye evolution? Have any of the speculated intermediate steps been reproduced experimentally like the loss-of-function experiments you mention? How much empirical support does this scenario really have?”

      I’m not sure! I’ve never looked into this research, but I’m sure people are working on this question.

      “If you want to disagree with me on this, please disagree within the scope of the answer that I’ve offered; otherwise concede that it’s reasonable, as far as it goes. I’d be happy to discuss the broader issues some other time, but I can’t afford to let you broaden the scope without conceding the point. That style of argument does not scale.”

      Don’t take what I said the wrong way. I wasn’t trying to sidetrack you or deflect the question. I genuinely thought I was getting at the issue, though perhaps I misunderstood you or vice versa.

      “If one of the design goals is to make the result not look like descent from a common ancestor, then which of these two (comprehensive, mutually exclusive) alternatives do you take? The latter, yes?”

      So to answer this directly: no, I don’t think either of the two are more consistent with a designer. I can see it both ways, and it’s difficult for me to favor one more strongly than the other.

      “Of course not — it wouldn’t work. I’m sorry, but is this car made out of potatoes and ketchup meant to be analogous to anything in the real world? Is some organism the equivalent of a car made out of potatoes and ketchup? I don’t see how it can be. It just seems like a deliberately wild and incredible analogy, the badness of which is supposed to rub off on the thing for which it was being used as an analogy.

      Perhaps it would be best if you dropped the rhetoric of analogy and expressed your objection in more precise, technical terms — or at least do that before providing an analogy.”

      Again, I think you’re taking me the wrong way. I apologize if I wasn’t as clear as I could have been. I don’t proofread these more than once, and sometimes what I think makes perfect sense does not come off that way to others. As an example, I’ve had to read and re-read some of your comments multiple times to make sense of them, and it doesn’t mean I fully understand them even as I reply!

      So to get back to the analogy: First, I’d bet quite a bit of money that you could indeed make a car out of potatoes and ketchup. Purely potatoes? Probably not, but you could reinforce it with some sort of matrix. Heck, to sell you on the idea: it would be environmentally sustainable (renewable, biodegradable, less toxic) and perhaps more fuel efficient because of the lighter chassis. I also bet the car could run on ketchup because ketchup has stored energy that can be liberated. Don’t doubt engineers being put up to a challenge: they’re smart and I bet you they can figure out a way to create a car out of potatoes and ketchup!

      Now that’s just to establish that one theoretically could design such a car. Of course one wouldn’t because of the precedent set by previous engineers that have tested different materials, fuels, designs, etc. But you could. By extension, a Creator could have created life as we know it AND life largely composed of cyanide AND life largely composed of silica and presumably any sort of material that the Creator decided to create with. But, as the typical creationist analogy goes, the Creator, like an engineer, decided to compose life of similar building materials. So using similar building materials, it shouldn’t be surprising that organisms that look similar have similar DNA. Again: this is the analogy that I’ve seen creationists make. Clearly it doesn’t mean you agree with your fellow creationists! (nor does it mean that all other creationists agree on this issue)

  4. TFBW

    This is an issue that I take at face value because it makes sense to me (much like your disbelief in it makes sense to you), so it sounds like I’ll have to read up on this sometime to see what has been done in this arena.

    By all means do that. The mathematics isn’t a matter of gut feeling, though: it’s quite basic probability. The main problem is the lack of quantifiable anything to plug into the equations as relates to evolution. For a theory which presumes to be a fact, it’s pretty thin on the kind of numeric detail which could reality-check its mathematical feasibility. It’s a pretty poor state of affairs when notable work in the field consists primarily of Dawkins and his “methinks it is like a weasel” trivia.

    Such lack of detail and precision is cause for scepticism.

    Yup, and my general feel of the field is that loss-of-function mutations probably occur at a higher frequencies than gain-of-function mutations. I agree that much, much more experimentation is warranted to understand how such gain-of-function mutations come about, so molecular biologists have a lot of work ahead of them.

    Oh, it’s trivially certain that loss-of-function mutations occur at higher frequencies. Aside from the empirical data, which is quite plain, it’s intuitively obvious that it’s easier to break things than make them. After all, you can break a working protein with a point mutation easily enough, but it takes a large number of highly specific instructions to create a working protein from scratch. That’s why experiments which demonstrate evolution in action (e.g. antibiotic resistance) invariably produce their changes through loss of existing mechanisms, not generation of new ones.

    What’s more surprising is the apparent prevalence of loss-of-function in evolutionary history. Your next post on loss of taste receptors is a case in point. One would expect natural selection to preserve a hard-won feature like that, but evidently not. If evolution can effectively regress like this, with natural selection complicit in the act, then why should we expect that progress will happen naturally? If loss of function is easy, and loss of function can be advantageous, that’s a worrying source of retro-evolutionary influence in an environment where we struggle to identify a positive influence.

    Good luck with the research, but the status quo is cause for scepticism.

    We can’t ethically and practically mutate deer and elephant embryos at random and see if, given the right conditions, they’ll evolve aquatic adaptations.

    Do you honestly think that this line of research would be fruitful if it were permissible? I mean, it’s ethical to experiment with fruit flies, and they have short generation times, but they’ve never shown any indication of becoming anything other than malformed fruit flies, have they? Why would deer be different?

    Surely the empirical data we do have on this kind of research is cause for scepticism?

    For instance, there’s some experimental support for how snakes may have begun to lose their legs from a lizard ancestor thanks to gene editing work on mouse embryos.

    Okay, but that’s more loss of function. The pattern which emerges is, “evolution works primarily by loss of function” — a concept which isn’t going to make an evolution sceptic any less sceptical.

    … I speculate that Lamarckian evolution could have some truth to it. Let me be clear though: I have zero evidence to back this up …

    Well, that’s admirably open-minded of you, but I think there’s good cause to be sceptical of that speculation, especially given the complete lack of evidence.

    I’m not sure! I’ve never looked into this research, but I’m sure people are working on this question.

    Probably — and if they’d produced some results, I’m sure I would have heard Richard Dawkins crowing about it from the rooftops by now. In the absence of concrete results, though, I think scepticism is warranted. Some say that extraordinary claims require extraordinary evidence, but even some fairly ordinary evidence would be helpful — it doesn’t have to be a whole working eye, just some unambiguous forwards progress in terms of novel structures and functional proteins.

    So to answer this directly: no, I don’t think either of the two are more consistent with a designer.

    I didn’t ask which was more consistent with a designer: I asked which was more consistent with the design goal of not looking evolved. I am prepared to accept that both of these possibilities look equally suggestive of evolution to you, however. Paradigms shape perceptions.

    As a matter of curiosity, what would it take for life to look not-evolved to you?

    First, I’d bet quite a bit of money that you could indeed make a car out of potatoes and ketchup.

    If, in the next 30 days, you can find anyone with some relevant qualifications (e.g. automotive engineering or materials science) willing to state on the record that this is a plausible idea (and briefly outline how it might be done), I’ll send you $10 — no need for you to stake anything.

    Now that’s just to establish that one theoretically could design such a car.

    “Theoretically”, no, but I can work with “hypothetically”, so onwards we go.

    By extension, a Creator could have created life as we know it AND life largely composed of cyanide AND life largely composed of silica and presumably any sort of material that the Creator decided to create with. But, as the typical creationist analogy goes, the Creator, like an engineer, decided to compose life of similar building materials.

    Okay … an oversimplified design decision phase, but I’m still with you.

    So using similar building materials, it shouldn’t be surprising that organisms that look similar have similar DNA.

    And … you lost me. It doesn’t surprise me that organisms with similar proteins have similar DNA, because coding for protein is one of the things that DNA does. I am rather less sure that gross structural similarities have much impact on DNA, though. If they did, you wouldn’t be pointing out these differences. As such, it seems like you’d need to make DNA artificially similar, rather than the similarity being a simple consequence of the design decisions you hinted at.

    Thing is, you’ve yet to cite any identifiable reason as to why a designer would impose such unnecessary similarities on the information content of the cell. It just seems like some weird OCD tic on your part, like colour-coding clothes-pegs to match articles of clothing, only in this case you’d be fighting with the natural purpose of DNA (to hold functional information) in order to obtain non-functional similarity. Either that, or you’d need to come up with a really inefficient encoding scheme for physical structure, so that it dominated the DNA content.

    Sorry, your explanation makes no sense to me no matter how clearly you put it. Have you ever obtained an independent second opinion about it from someone whose criticism you would respect?

    1. Since we resolved the DNA-creation misunderstanding, I’ll respond to some of the content from your March 15th comment:

      ” For a theory which presumes to be a fact, it’s pretty thin on the kind of numeric detail which could reality-check its mathematical feasibility. It’s a pretty poor state of affairs when notable work in the field consists primarily of Dawkins and his “methinks it is like a weasel” trivia”

      There’s a ton of mathematical modeling on evolution. People devote their entire careers to this topic and certain scientific journals deal heavily in this topic.

      “That’s why experiments which demonstrate evolution in action (e.g. antibiotic resistance) invariably produce their changes through loss of existing mechanisms, not generation of new ones.”

      Not true. There are quite a few examples of gain of function out there. Perhaps thousands, though I don’t have a list to confirm this the extent of it. The number might depend on how you define evolution in action, however, i.e., whether you just mean laboratory conditions or include observations of evolution in natural populations.

      “What’s more surprising is the apparent prevalence of loss-of-function in evolutionary history. Your next post on loss of taste receptors is a case in point. One would expect natural selection to preserve a hard-won feature like that, but evidently not. If evolution can effectively regress like this, with natural selection complicit in the act, then why should we expect that progress will happen naturally? If loss of function is easy, and loss of function can be advantageous, that’s a worrying source of retro-evolutionary influence in an environment where we struggle to identify a positive influence.”

      I’m not sure how this is a problem. It merely means that loss-of-function can occur frequently and if it’s adaptive or neutral then it can also be fixed in a population with high frequency.

      What do you mean by “progress”.

      Also, I think it’s worth pointing out that loss of function of a gene does not necessarily lead to loss of function of a phenotypic trait. The loss of one gene might lead to the gain-of-function of something or an enhancement of function. For instance, color vision starts with little pigments encoded by multiple genes. The more classes of pigments you have, the better your color discrimination. So if you lose one or more of these genes (something that appears to have occurred repeatedly during the history of animals), you see fewer colors. All loss of function, right? Well, not quite: it appears that people and monkeys that have only two kinds of color vision pigments (humans usually have three, some monkeys do too) sacrifice better color discrimination for a greater ability to detect camouflaged items. Another thing to consider: organisms that live in nearly complete darkness wouldn’t benefit from having the color vision system (since it’s only sensitive at high light levels), so by losing color vision pigments, it makes the retina more abundant in dim light vision pigments. So by losing the color vision genes, it makes the eye more sensitive in dark conditions. So both of these examples are suggestive of gain of trait functions (or enhancement of previous functions) through the loss of genes.

      “Do you honestly think that this line of research would be fruitful if it were permissible? I mean, it’s ethical to experiment with fruit flies, and they have short generation times, but they’ve never shown any indication of becoming anything other than malformed fruit flies, have they? Why would deer be different?

      Surely the empirical data we do have on this kind of research is cause for scepticism?”

      To remind you, this was in response to me suggesting that you could do gene editing on deer, but it would probably not be considered ethical.

      Yes, absolutely this would be fruitful! There’s a ton of research on this now given the development of the CRISPR-Cas9 technology. In my deer example, you could toy around with the DNA and see how you can change cusp morphology of the teeth and see how deer got their specialized teeth for browsing, you could try to influence antler shape and see how you get from a mule deer set of antlers to a moose-like set of antlers, you could see if you could change the number of stomach compartments from four to three or one, etc. One professor at my university gave a talk on how they changed the kinds of limbs present in crustaceans using CRISPR. If you look at a typical crustacean, you’ll see that they have different limbs for things like grabbing, walking, sensation and/or swimming. The species they were working on had, say, 3 pairs for walking and 6 pairs for swimming. They mutated some developmental control region in embryos and changed some of the swimming legs walking legs and vice versa (or something like that; the specifics evade me). This is particularly relevant because we think that crustaceans have evolved such that they’ve modified different pairs of limbs, changed the number of different limbs, etc. In my lab, they’re hoping to replicate evolutionary trends in mice that they see in the wild. They have candidate regions that they’d like to toy with and see if it changes how much fat they deposit, how quickly they metabolize food, alter their nest-building behavior, etc. You’re going to start seeing tons of work using CRISPR in the next 10 years and beyond. They’ll probably get a Nobel prize for developing this technology given the wide range of applications to medicine, evolution, and other fields of biology.

      “Okay, but that’s more loss of function. The pattern which emerges is, “evolution works primarily by loss of function” — a concept which isn’t going to make an evolution sceptic any less sceptical.”

      This was in response to modifications to snake genomes that lead to loss of limb development. Returning to what I said earlier, this could be seen as a gain of function: the removal of limbs provides for a more serpentine body that can easily locomote through grass, crevices, burrows, etc. And the gene wasn’t lost. The deletion was to a regulatory region, meaning the gene just don’t turn on in limbs anymore. It still turns on elsewhere.

      “Well, that’s admirably open-minded of you, but I think there’s good cause to be sceptical of that speculation, especially given the complete lack of evidence.”

      Haha, of course I’m skeptical of my speculation…it’s a speculation!

      “Probably — and if they’d produced some results, I’m sure I would have heard Richard Dawkins crowing about it from the rooftops by now. In the absence of concrete results, though, I think scepticism is warranted. Some say that extraordinary claims require extraordinary evidence, but even some fairly ordinary evidence would be helpful — it doesn’t have to be a whole working eye, just some unambiguous forwards progress in terms of novel structures and functional proteins.”

      You may be right, given that the eye is a topic that goes back to Darwin. But who knows? Dawkins isn’t in the field anymore, so he probably doesn’t read much beyond the two journals Science and Nature. If he looked at vision science and molecular evolution journal, there might be a lot more that he hasn’t seen.

      “I didn’t ask which was more consistent with a designer: I asked which was more consistent with the design goal of not looking evolved. I am prepared to accept that both of these possibilities look equally suggestive of evolution to you, however. Paradigms shape perceptions.

      As a matter of curiosity, what would it take for life to look not-evolved to you?”

      This is a good question and one that these conversations with you have made me increasingly thoughtful about. I’ll hit on a few topics, but keeping in mind that there may be other things that would do it:

      (1) If we started to regularly find fossils of modern species in rocks that are supposed to be hundreds of millions of years old.

      (2) If DNA and protein sequence solely reflected function rather than recapitulating the same relationships regardless of their gross anatomical/physiological differences

      (3) If organisms developed completely differently or when they developed they didn’t have little oddities like tails in human embryos, tooth buds in baleen whale embryos and limb buds in legless lizard embryos.

      (4) If organisms were distributed randomly across the earth, rather than having groups of organisms that share similar DNA being restricted to the same location (e.g., Australasian marsupials, the Australian gecko families, the American xenarthran mammals).

      (5) If pseudogenes didn’t share the same inactivating mutations across multiple species, e.g., sloths and anteaters, despite looking quite different, are more genetically similar to each other than they are to other animals. Anteaters don’t have teeth and sloths don’t have enamel, yet their genomes have remnants of enamel genes. Anteaters and sloths, at least in three of the genes we’ve looked at, share multiple inactivating mutations at the exact same spots. Based on our conversations, I’m increasingly okay with the idea of species adapting post-creation via loss of genes, sharing mutations implies shared history, whereas completely different mutations (occasional false positives aside) would indicate no shared history.

  5. TFBW

    I’d bet quite a bit of money that you could indeed make a car out of potatoes and ketchup.

    Well, I offered you $10 against no outlay on your part, and gave you a month to come up with some qualified testimony to back up this assertion, and you haven’t done so. Do you want to concede, or just ignore me and pretend it never happened?

      1. The lack of response was due to me thinking that a previous comment of yours was unkind, but I’ll address this now: as you can imagine, I don’t have a ton of time to track down an engineer and ask them this directly. Either way, whether I could get a single engineer to agree with me, it’s not relevant to the original point: one could create cars in a different way than we do now, but we don’t because of the precedent of previous engineering, trial and error of other mechanisms, etc. My spaghetti car was indeed extreme, so instead you can imagine a car with a wooden chassis that uses potatoes as a battery, or one that’s made of platinum and runs on the burning of wood.

        Either way, I’m not prone to defending a creationist conception of why a Creator should design things one way or another, since I think there’s no rhyme or reason why a Creator would have to do anything like what humans do. At the same time, I understand why some (most?) creationists believe that it makes sense for the Creator to use the same materials over and over, with little innovations here and there, just like human engineers do. Presumably its the most natural analogy we have to go off of, and/or maybe it’s a logical theological extension of being created in the same image as the Creator (i.e., we create this way, maybe the Creator did it the same way too).

        I’m all for you disagreeing with this conception of Creationism, but since you seem to think that this is a straw man that I conceived of, see below for quotes from relevant websites.

        From christiananswers.net (http://www.christiananswers.net/q-aig/aig-c018.html):

        “Similarity (“homology”) is not an absolute indication of common ancestry (Evolution) but certainly points to a common designer (creation). Think about a Porsche and Volkswagen “beetle” car. They both have air-cooled, flat, horizontally-opposed, 4-cylinder engines in the rear, independent suspension, two doors, boot (trunk) in the front, and many other similarities (‘homologies’). Why do these two very different cars have so many similarities? Because they had the same designer! Whether similarity is morphological (appearance), or biochemical, is of no consequence to the lack of logic in this argument for evolution.”

        “We know that DNA in cells contains much of the information necessary for the development of an organism. In other words, if two organisms look similar, we would expect there to be some similarity also in their DNA. The DNA of a cow and a whale, two mammals, should be more alike than the DNA of a cow and a bacterium. If it were not so, then the whole idea of DNA being the information carrier in living things would have to be questioned. Likewise, humans and apes have a lot of morphological similarities, so we would expect there would be similarities in their DNA. Of all the animals, chimps are most like humans[1], so we would expect that their DNA would be most like human DNA.”

        From gotquestions.org (https://www.gotquestions.org/human-chimp-DNA.html):

        “In conclusion, as interesting as genetic similarities between chimpanzees and humans are, they are not evidence for Darwinism. Design is also able to explain them. Designers often make different products by utilization of similar parts, materials and arrangements. The common percentage pertains to the regions of our DNA that result in proteins. It makes more sense of the data for the Designer of nature to have used the same proteins to perform the same function in a variety of organisms.”

        From defendingthechristianfaith.org (http://www.defendingthechristianfaith.org/dna-and-structural-homology-studies-that-argue-against-evolution.html):

        “From a design perspective one can compare structures and their functions and even behaviors between animal groups. But from a Creationist perspective this does not have anything to with a common genetic ancestry only a common designer.”

        From creationrevolution.com (http://creationrevolution.com/common-ancestor-or-common-designer/):

        “The Bible tells us that God created all things in the beginning. If a common designer made everything to coexist in the same universe and follow the same natural laws, you’d expect to find many similarities among the things He created.

        After all, even human designers use similar parts in different things they design.

        Architects start with the same basic plans that have a foundation, plumbing, electrical, support structures, walls, ceiling, windows, doors and a roof. Even though there are so many different sizes and shapes of buildings, virtually every building designed by them has these basic features.

        There are many different types and styles of cars, but they all have the same basic design and parts – engine, frame, doors, windows and wheels.

        All computers, whether a PC or Mac all have a power source, cooling system, central processing unit, monitor and keyboard.

        Likewise, God used the similar chemicals, genetic codes and systems found in living organisms.”

        The argument is common enough that the evowiki has a page devoted to it: http://evolutionwiki.org/wiki/Similarities_in_DNA_and_anatomy_are_due_to_common_design

        1. TFBW

          I’m all for you disagreeing with this conception of Creationism, but since you seem to think that this is a straw man that I conceived of, see below for quotes from relevant websites.

          Um, no, I don’t really disagree with the quotes you’ve mentioned, which mostly boil down to, “common descent isn’t the only possible explanation for similarity.” I just fail to see how your bizarre analogies about implausible spaghetti or potato-and-ketchup cars address the issue. It would help if you responded to the actual content of my Mach 15 comment.

          1. This is another jerk-ish comment. Saying “Um, no” and calling my analogy “bizarre” is not conducive to discussion. Just because you didn’t understand my point is not a reason to belittle it; it means I need to do a better job of communicating what I’m trying to say to you. But if you care to understand what I’m trying to say, you need to be patient and use friendly words to do it. Treat me like a friend, not like an enemy, and I’ll be happy to continue to this line of discussion. Otherwise, I’m cutting it off.

            1. TFBW

              Then let me rephrase. I don’t understand how your comment addresses anything I said in my March 15 comment. I don’t even understand why you are presenting me with this collection of quotations. I do agree with them, I guess, but how are they relevant?

              1. My series of quotations was the provide clarification for the entire context of this post and my comments. In the beginning (Genesis pun!) you responded to a question in my blog post, which stated:

                “Shouldn’t animals that look similar have more similar DNA?”

                You then followed up with this comment:

                “What makes you think that, on creation, animals that look similar should have similar DNA?

                …you seem to be implying that a creator ought to take the (unnecessary) step of making the genetic code similar to reflect the external similarities. Why do you expect that? It seems quite an arbitrary thing to me.”

                I responded as so:

                “The origin for this specific type of question posed to creationists is in response to a typical argument I’ve seen creationists make.

                Specifically, evolutionary biologists have long asserted that the fact that DNA is similar between certain species shows evidence of common descent…A common creationist counter argument is that the reason DNA looks similar between such organisms is because (1) DNA provides a body’s instructions for making anatomy and (2) God created DNA, therefore we shouldn’t be surprised that animals that look similar have similar DNA….Creationists frequently use the analogy of cars to explain why animals have similarities: same engineer, same materials, variations on similar ideas. Arguably that same logic would apply to DNA. Would an engineer use steel, rubber and plastic to make one car and plasma, antimatter and superglue to make another? Why would the Creator create most animals with highly similar DNA and then create batches of other animals with completely different DNA?”

                You replied:

                “Hmm, well I don’t think highly of this analogy”

                Then I brought up my ketchup and potatoes comments, you dismissed it, and I brought it back to this point:

                “Now that’s just to establish that one theoretically could design such a car [out of potatoes and ketchup]. Of course one wouldn’t because of the precedent set by previous engineers that have tested different materials, fuels, designs, etc. But you could. By extension, a Creator could have created life as we know it AND life largely composed of cyanide AND life largely composed of silica and presumably any sort of material that the Creator decided to create with. But, as the typical creationist analogy goes, the Creator, like an engineer, decided to compose life of similar building materials. So using similar building materials, it shouldn’t be surprising that organisms that look similar have similar DNA. Again: this is the analogy that I’ve seen creationists make. Clearly it doesn’t mean you agree with your fellow creationists! (nor does it mean that all other creationists agree on this issue)”

                Then you continued:

                “And … you lost me. It doesn’t surprise me that organisms with similar proteins have similar DNA, because coding for protein is one of the things that DNA does. I am rather less sure that gross structural similarities have much impact on DNA, though…Thing is, you’ve yet to cite any identifiable reason as to why a designer would impose such unnecessary similarities on the information content of the cell. It just seems like some weird OCD tic on your part…Sorry, your explanation makes no sense to me no matter how clearly you put it. Have you ever obtained an independent second opinion about it from someone whose criticism you would respect?”

                So to repeat, throughout my posts (including this one) and throughout the comments on this particular post, I’ve been addressing a common Creationist claim: (1) similar looking organisms have similar looking DNA because a Creator designed every organism’s DNA, and (2) since DNA encodes the phenotypic characteristics of an organism, whenever It created similar DNA in various organism, naturally there is a similar phenotypic product (i.e., physical characteristics of the organism). E.g., the reason humans, chimpanzees, gorillas and orangutans look so similar to each other is because the Creator created their DNA to be similar.

                Everything that you’ve said suggests that you think that this idea is illogical and/or arbitrary. Which is fine! I don’t care if you think it’s illogical and/or arbitrary. It’s a common creationist belief. As I told you elsewhere in previous comments, my goal is to address common creationist beliefs in this blog.

                I then proceed to quote various Christian/Creationist websites that profess to believe this very concept. After I presented the quotes, trying to help you to understand where I was getting this idea from you said:

                “Um, no, I don’t really disagree with the quotes you’ve mentioned, which mostly boil down to, “common descent isn’t the only possible explanation for similarity.” I just fail to see how your bizarre analogies about implausible spaghetti or potato-and-ketchup cars address the issue.”

                and followed up with a nicer comment:

                “I don’t even understand why you are presenting me with this collection of quotations. I do agree with them, I guess, but how are they relevant?”

                How does this not seem relevant?

  6. TFBW

    I’m still struggling to comprehend the nature of your objection. Your initial question, as you say, was, “shouldn’t animals that look similar have more similar DNA?” You then offered the following clarification:

    But there are also quite a few examples of organisms that look very similar to each other but are not similar genetically, some of which I’ve tried to highlight in this blog. This is the motivation behind posting on this particular topic.

    You then quote a bunch of creationists who say that similarity can be explained by common design as well as common descent. I agree with them. None of them say that structural similarities necessitate genetic similarities, however. Is that how you interpreted them? If so, I think you’ve missed the point they were trying to make, which is simply this: one possible explanation for structural and genetic similarity is common descent; another is common design. You’re highlighting cases where there is structural similarity without the genetic similarity as though this contradicted the common design explanation. It doesn’t — unless you can explain why it does.

    1. I had this wonderful, elegant response written out over a week ago, and then my computer ran out of its battery. I swear it was the perfect reply, one that would have made you swoon, but since I forgot exactly what I wrote, this will merely be a shadow of its brilliance 😉

      Okay, after all of that back and forth, I think you figured out where the miscommunication is.

      “None of them say that structural similarities necessitate genetic similarities, however. Is that how you interpreted them? If so, I think you’ve missed the point they were trying to make, which is simply this: one possible explanation for structural and genetic similarity is common descent; another is common design.”

      Yes, that’s how I understood them, and I’m going to disagree with you and say that they almost certainly meant exactly how I interpreted it. This is not to say that there aren’t creationists that think like you, i.e., common DNA and common design are possible, and different DNA and common design are also possible. Most casual creationists, however, probably have no idea that there are such things as anatomically similar organisms with extremely different DNA. At least some of these websites are probably in the casual creationist category, not the ICR or AiG crowd.

      Regardless, it’s still an issue that needs an explanation. The examples of putative convergent evolution and similar examples that I highlight in my blog are in the far minority. The vast majority of things that look like each other have more similar DNA. All apes (which includes us) have more similar DNA to each other than they do to anything else. All cats have more similar DNA to each other than other animals. When comparing DNA from different organisms, bats always group together, rodents always group together, snakes always group together, etc. So this fits the creationist concept that I’ve been addressing: similar looking organisms have similar looking DNA because the Creator created their DNA to be similar and therefore their bodies look similar.

      The weirdo exceptions are the ones that need more explanation, including the one I discussed in this post. Another example: almost all hoofed mammals, particularly those that have toes in multiples of two (and have various other characteristics in common, including a special ankle bone, multi chambered stomachs, etc) are more genetically similar to each other than to anything else. So llamas, cows, giraffes, deer, etc. comes out as most similar when comparing their DNA. But what’s weird is that whales come out right in the middle of them! In fact, it suggests that whales are more similar genetically to cows, deer and giraffes than camels and pigs are. https://evolutionforskeptics.wordpress.com/2014/07/20/molecular-phylogenetics-whales-are-hoofed-mammals/

      Given that camels and pigs have a lot of similarities to deer and cows but whales have basically nothing in common, why the heck does their DNA look like these hoofed mammals? And you know what’s interesting? It doesn’t matter what genes you look at: they group whales right in the middle of hoofed mammals (provided the genes are large enough and you include enough species; there are statistical limitations for lower gene sizes and species numbers that group species in inconsistent patterns). Look at some vision genes, some taste genes, developmental genes, bone genes, osmoregulation genes, and you’ll get whales as hoofed mammals. This is despite the fact that they have very different vision, very different taste reception (lacking entirely, probably), very different development, very different bone densities, and very different osmoregulation requirements. You can use one gene, different combination of genes or all of the genes in the genomes of these animals: whales come out as being genetically similar to hoofed mammals.

      If they evolved from hoofed mammals, then this would make a lot of sense. Just like you share similar DNA with your cousins since you share grandparents or great-grandparents, etc., maybe whales share similar DNA with cows and deer because they share a hoofed mammal ancestor that walked on land. What’s further interesting about this hypothesis is that whale embryos have hindlimb buds that disappear during development (https://evolutionforskeptics.wordpress.com/2017/01/22/ontogeny-recapitulates-phylogeny-fetal-whales-have-hindlimb-buds/), they have remnants of taste genes that are found in hoofed mammals but are presumably not important for their narrow diets in the ocean (https://evolutionforskeptics.wordpress.com/2014/09/17/pseudogenes-whales-can-only-taste-salt/), they have remnants of vomeronasal organ genes (a chemosensory organ) which are still present in hoofed mammals and even though they lack the organ themselves (https://evolutionforskeptics.wordpress.com/2014/09/10/pseudogenes-whales-have-lost-their-vomeronasal-organ-and-associated-genes/), they have remnants of color vision genes that aren’t likely useful in the monochromatic color palette of the open ocean but are retained in hoofed mammals (https://evolutionforskeptics.wordpress.com/2014/08/25/pseudogenes-whales-have-lost-the-ability-to-discern-colors/), and there are fossils that seem to document a sequence of hoofed mammals transitioning into whales (https://evolutionforskeptics.wordpress.com/2014/05/18/transitional-fossils-3-through-11-from-land-mammals-to-the-ancestor-of-whales/).

      I think your creation hypothesis for DNA being sometimes similar sometimes different is plausible in principle, in that a creator could do all sorts of things to create similar looking organisms. In fact, if the DNA signal was seemingly extremely random, I think I’d tend towards thinking evolution was bunk. If humans were more genetically similar to whales, chimps more genetically similar to squirrels and orangutans more genetically similar to fruit bats, I think it would be too hard to fathom that evolution could produce such a pattern, i.e. a creator seems more reasonable. But that’s not what we see. Instead it is only very rarely true that similar looking organisms have very different DNA. Plus, the signal shown by DNA can’t be considered in a vacuum, but also in the context of other bits of data, some of which I highlighted here.

  7. TFBW

    Yes, that’s how I understood them, and I’m going to disagree with you and say that they almost certainly meant exactly how I interpreted it. This is not to say that there aren’t creationists that think like you, i.e., common DNA and common design are possible, and different DNA and common design are also possible. Most casual creationists, however, probably have no idea that there are such things as anatomically similar organisms with extremely different DNA. At least some of these websites are probably in the casual creationist category, not the ICR or AiG crowd.

    You know that there are different and arguably less-naive creationist positions, but you’re interested in questioning the weakest one you know of — the “casual” creationist. So you’re not attacking a straw-man, just the weakest actual representative you can identify, given the broadest possible selection of targets, and the license of your own interpretation, which you are certain is correct. And you don’t have an agenda, so it’s not like it’s a motivated choice in any case.

    I find this disingenuous. I hope that the reasons become obvious if you consider how it would look if the roles of creationist and evolutionist were reversed here.

    Regardless, it’s still an issue that needs an explanation.

    Convergence is a bigger problem for evolution than for creation or agnostic ID theories. I’ve already defended that point enough here already, and you’ve resisted it because you wanted to focus on the painfully weak argument that you attribute to creationists rather than the arguments that the actual creationist present in the room was offering. I’m not going to repeat myself, and your ongoing lack of engagement with my points has left me with no enthusiasm to engage any more of yours.

    1. Given that you continue to question my integrity, I am going to ask you nicely to no longer comment on my blog. It’s one thing to question and criticize ideas, it’s another thing to assume you understand a person’s motivations and criticize them based on those assumptions.

      For the record, despite disagreeing with you on many points, and being convinced that there are some misunderstandings on others, I have taken some of your thoughts very seriously and am giving a lot of consideration on how to incorporate them into both previous and future posts. I would have been happy to continue to hear your input on things, but your negative attitude towards me is something that I no longer wish to tolerate.

      In the interest of full disclosure, I will be deleting your two recent comments on my other two posts. This is simply so as to not give the impression that I am willfully ignoring arguments for future readers.

      I wish you the best of luck and happiness in your future endeavors!

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