DNA points to reptilian ancestry of birds

As I discussed in the previous post, the fossil record tells a story that at first seems implausible: birds are descendants of dinosaurs. Part of what’s surprising about this idea is that dinosaurs typically appeared very reptilian, whereas birds do not.

Without providing a formal definition of “reptile”, you probably have a general image in your head. This is because reptiles possess a suite of characteristics that intuitively unite them into a group. For instance, reptiles are covered in scales, walk around on all fours, have tails, typically have simple conical teeth and warm up by basking in the sun.

Birds, by contrast, are covered in feathers, walk around on just their hind legs and/or fly, lack tails, have no teeth whatsoever, and are able to generate their own heat, similar to mammals.

Anybody that is at least vaguely aware of animal diversity probably would never mistake a bird for a reptile. So besides a pattern in the fossil record and remnants of tooth genes in their genomes, is there any other evidence that birds are descended from dinosaurs and, ultimately, other reptiles?

One line of evidence comes from comparisons of DNA. When researchers have compared the genes of birds, reptiles, and other animals, they find something that perfectly fits the conclusion of the fossil record: birds are genetically nested within reptiles. In fact, crocodilians are more genetically similar to birds than they are are to turtles or lizards. As just one example of a study that demonstrates this, Chiari et al. [1] compared 248 genes, with a total of 187,026 letters of DNA, among multiple species of reptiles, birds and other vertebrates and found this very pattern:

12915_2011_Article_592_Fig1_HTML

The green branches on this phylogenetic tree indicate lizards, red are turtles, blue are crocodilians and purple are birds.

The link between crocs and birds isn’t entirely surprising to anatomists, who have long remarked that modern and ancient crocodilians share a number of traits with dinosaurs, including teeth set in sockets (thecodonty), holes in the skull in front of the eyes and in the lower jaw (antorbital and mandibular fenestrae), and an extra ridge (trochanter) on the femur. However, birds no longer have most of these traits, and the one trait that they do have (antorbital fenestrae) is not found in modern crocodilians. As such, this conclusion was not always intuitively obvious.

Nonetheless, here we have an excellent example of where DNA and fossils tell the same story. Fossils appear to document a transition from large reptilian progenitors to modern birds and DNA suggests that birds are not only relatives of reptiles, but are descendants of reptilian ancestors shared with crocodilians, turtles and lizards..

Questions for Creationists

Why do birds have DNA more similar to crocodilians than crocodilians do to turtles and lizards? Is it just a coincidence that bird DNA and the fossil record seem to be telling the same story, that birds are descended from reptiles? What kinds of evidence might overturn this hypothesis?

References

1. Chiari, Y., Cahais, V., Galtier, N., & Delsuc, F. (2012). Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). Bmc Biology10(1), 65.

Photo credit

Alligator, caiman lizard, terrapin, tuatara, nightjar, cranes, sandgrouse, sunbird

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28 thoughts on “DNA points to reptilian ancestry of birds

  1. g

    so it’s basically the argument for common similarity as evidence for common descent. but the same can be evidence for a common designer too. for instance: lets say that we will have a self replicating car (with dna). can such a car will evolve into something like airplane in milions of years? another question: is such a car with dna is evidence for design or a natural process?

    1. Thank you for your comment, g!

      It’s not an argument for common similarity as evidence for descent. In fact, it’s the opposite.

      To restate, crocodilians, turtles and lizards all have so many similarities that they have been classified as “reptiles” for many years. Historically, taxonomists grouped them together in Class Reptilia, whereas birds had their own distinct Class Aves.

      This distinct classification was because birds are quite different from “reptiles”, such that it probably wasn’t until the discovery of Archaeopteryx that the bird-reptile connection became really convincing to some scientists.

      Which raises the questions: if birds look so different from reptiles, why are they genetically nested within reptiles? If the Designer created the DNA of these organisms, and similar DNA leads to similar physical traits (phenotypes), why is it that when we compare DNA that reptiles don’t group together separately from birds?

      1. g

        hey christopher. you said:

        “if birds look so different from reptiles, why are they genetically nested within reptiles?”-

        good question. there are 2 options under the creation model:

        a) it’s because internal morphology and not just external.

        b) they were created in a similar geological time. so the difference is only about neutral mutations that doesnt effect the morphology.

        and in the other hand: how evolution explain this? if morphology means nothing then any fossil or morhpological classification is meaningless.

        by the way: i have read several other interesting articles in your site. i think that i can answer many other questions from an id perspective.

        1. Hi g:

          “a) it’s because internal morphology and not just external.”

          So you point out something that is relatively difficult to quantify, but is certainly doable. I’ll mention a few internal features that distinguish birds from reptiles.

          (1) The first is a four chambered heart. This is shared in common with mammals, but genetically birds are nowhere near mammals. Crocodilians appear to have the beginnings of a four chambered heart, whereas turtles and lizards have a pretty typical three-chambered heart.

          (2) The skeletons of birds are very very different from those of reptiles, including the fusion of some leg and arm bones, reduction/fusion of the tail, large keel in the sternum, hollowed out bones, three forward and one backward facing toe (fifth toe lost), loss of several fingers, etc.

          (3) Birds have reproductive organs that are shrunk/absent most of the time, but grow back during the reproductive season.

          (4) The bird digestive tract includes a crop and a gizzard, features not found in reptiles.

          (5) Bird lungs are not anything like that of reptiles, consisting of sacs that create a unidirectional flow of air.

          (6) Bird brains have major differences from typical reptiles, including a large cerebellum for coordination, and tiny olfactory (smell) lobes.

          These are just some features that come to my mind, but the point is that a lot of both the external and internal anatomy of reptiles is relatively similar, whereas birds tend to stand out as being rather distinct. Regardless of the specific organs that are similar or dissimilar, you’ll get the same results if you compare the DNA from vision genes, bone genes, heart genes, nervous system genes, etc. So the gross morphology/DNA connection doesn’t always match up.

          “b) they were created in a similar geological time. so the difference is only about neutral mutations that doesnt effect the morphology.”

          I assume what you’re referring to is that over time neutral mutations may accumulate randomly, and just due to chance birds, may appear genetically nested within reptiles. Is this what you’re referring to?

          If I’m understanding you correctly, what you can do (and researchers often do) is eliminate all of the DNA sites that are prone to neutral mutations (usually nucleotides at the 3rd codon position) and just perform the analyses with sites that are typically important functionally (e.g., 1st and 2nd codon positions). What you’ll find is that you’ll get the same result, probably with even stronger support since neutral mutations indeed due cause problems with these sorts of analyses.

          “and in the other hand: how evolution explain this? if morphology means nothing then any fossil or morhpological classification is meaningless.”

          I’m going to give you a two-sided answer to this:

          Yes, you’re right to question morphological classifications. In fact, this has been a major point of contention among molecular biologists and paleontologists ever since DNA began to be used for these sorts of analyses. In many cases, DNA overturned the classifications created by paleontologists and morphologists, such that “reptiles” are no longer considered a real group because birds are placed within them, artiodactyls or even-toed hoofed mammals (deer, cows, pigs, etc.) are no longer considered real thanks to whales plopping down right in the middle of them, and snakes are simply considered lizards that have lost their legs.

          However, the vast majority of morphological classifications have held up. Carnivores are all considered a single group, both by morphology and DNA. Within carnvores, cats, bears and dogs are all still considered real groups. Bats, odd-toed hoofed mammals (horses, tapirs, rhinos), falcons, parrots, snakes, sharks, etc. are all united by both DNA and morphology.

          So morphological classifications aren’t meaningless. Rather, these results seem to be suggesting that some researchers have in many cases been fooled by evolution (e.g., convergent evolution of anatomy, where different lineages evolve different features) or have let their biases in choosing traits to compare influence their results. This is the beauty of DNA: you compare lots and lots of characters (we’re now doing analyses comparing millions of letters of DNA), removing most of the statistical error coming from choosing too few characters, and taking away almost all of the biases that come from comparing characters discerned by human judgment, since a particular position in a string of DNA is largely, objectively discernible.

          But I should also point out that morphological classifications were originally based on comparing features between species from the present era. For example a bird looks almost nothing morphologically like a reptile, whereas reptiles all have many similarities. Therefore, researchers reasoned, birds should be classified as one group (Aves) whereas reptiles as another (Reptilia). However, comparisons between organisms originally lacked the element of time implicit in evolution. So as we go back in the fossil record, birds look a little more like reptiles, a little less like birds. You go back further and we see birds that look even more like reptiles, and less like birds. You go all the way back to Archaeopteryx and you find that calling it a bird or a reptile becomes an intractable issue of semantics. Then we go back further and see reptiles that sort of look like birds, but don’t have wings, and we call those dinosaurs. And so on.

          So the general picture conveyed by evolutionary theory is one where several lineages of organisms generally retained a certain body plan (reptiles), whereas one lineage (birds) changed drastically relative to their ancestors. This was largely, it is assumed, due to the functional demands associated with flight. So while birds today look very little like most reptiles, past or present, their DNA seems to be pointing to a shared ancestry with their reptile kin.

          “by the way: i have read several other interesting articles in your site. i think that i can answer many other questions from an id perspective.”

          I would love to read your thoughts if you would like to discuss them! 🙂 Since you identity as a subscriber to ID, I assume some of my posts aren’t points of contention for you the way they might be for young earth creationists.

          1. g

            hi again. first; thanks for that imformation. secondly: i meant that maybe the genetics only reflect the geological time that this creature appeared on earth. so this could explain why a whale is more similar (in the genetic level) to a cow then then say to a whale shark (because they both appeared closer to each other in the fossil record). i also doesnt understand if you accept that the internal morphology could explain it too (whale is more similar to a cow then to a shark in it’s internal morphology). by the way: it’s also important to note this interesting finding:

            https://www.newscientist.com/article/dn9402-bats-and-horses-get-strangely-chummy/

            “I would love to read your thoughts if you would like to discuss them!”-

            of course:). please chose your best evidence for a common descent and i will try to explain it by a common design. on the other hand: do you think that if we will find a self replicaiting robot with DNA it will be evidence for design or evolution in this case?

            by the way; english isnt my native. so sorry if i doesnt understand some of your words.

            1. “secondly: i meant that maybe the genetics only reflect the geological time that this creature appeared on earth. so this could explain why a whale is more similar (in the genetic level) to a cow then then say to a whale shark (because they both appeared closer to each other in the fossil record).”

              Oh okay, I think I understand. But again, you’ll get the same results if you eliminate the DNA letters that are typically associated with neutrality and just kept the functional ones (i.e., first and/or second codon positions). Or you could simply do the analyses with amino acids (which are functional elements), and you’ll still get the same results with birds being found within reptiles.

              Regardless, what you’re proposing is something that I’m not sure would be easy to test. Perhaps help me think this through: what you’re saying is that many kinds of organisms were created at the same point in time. Given enough time, they might appear more similar to each other genetically due to chance via the accumulation of neutral mutations. Correct?

              But it wouldn’t necessarily be that appearing at the same time is what matters. It’s simply having been around long enough to have accumulated enough random/neutral mutations to group with another organism by chance. So perhaps organisms that appeared at 20 million years ago or 400 million years ago have each had enough time to ‘shuffle’ their DNA, so to speak, to allow them to appear genetically similar. Or even the organism that appeared just 5 million years ago may be genetically similar to the one that appeared 400 million years ago, because over those 400 million years there have been a ton of genetic changes that could randomly group it with the 5 million year old organism.

              But perhaps I’m not entirely understanding the context of what you’re saying. I’m guessing you accept a sort of model of Intelligent Design where the Creator created different groups of organisms in intervals over millions of years, but didn’t cause certain groups to go extinct? That way some organisms appeared 50 million years ago, others appeared 10 million years ago, and they coexist today? Or they have descendants that coexist today?

              “i also doesnt understand if you accept that the internal morphology could explain it too (whale is more similar to a cow then to a shark in it’s internal morphology).”

              No, you’re right, in theory I would agree with the idea of external morphology being dissimilar and internal morphology being similar, and somehow that being reflected in the genetic code. But then this raises the question: if reptiles look more similar to each other both internally and externally than they do to birds, why is it that analyses of DNA put birds right there in the middle of reptiles? And again, if you looked at genes encoding internal functions or external functions, you would get the same results: birds will come out within reptiles.

              Plus, I’d like to point out that the external/internal morphology idea definitely does not work for certain organisms. Just one that comes to mind is African golden moles and ‘true’ moles: https://evolutionforskeptics.wordpress.com/2016/04/15/molecular-phylogenetics-not-all-moles-are-moles/

              Golden moles and true moles look extremely similar externally, and are probably pretty similar internally too (at least for their skeletons they are). Yet golden moles are much more genetically similar to elephants and manatees, and true moles are much more genetically similar to horses and whales. I assure you that the internal anatomy of a golden mole looks hardly like that of an elephant, and the internal anatomy of a true mole looks almost nothing like the insides of a whale.

              “by the way: it’s also important to note this interesting finding: https://www.newscientist.com/article/dn9402-bats-and-horses-get-strangely-chummy/

              I wouldn’t put too much stock in that particular result, as those of us who have analyzed the genetic similarities between bats, horses and other mammals have found that a few of those relationships change depending on the data and the analyses used.

              So we call the group of animals that bats (Chiroptera) and horses, tapirs and rhinos (Perissodactyla) belong to “Laurasiatheria”. It also includes cows, pigs, camels, whales and relatives (Cetartiodactyla), dogs, cats, bears and relatives (Carnivora), pangolins (Pholidota) and ‘true’ moles’, shrews, hedgehogs and relatives (Eulipotyphla). Whenever we analyze enough DNA of mammals, these six groups always come out together pretty much regardless of the specific genes or analyses used. Eulipotyphla always branches of first, with the remaining five clustering together. Among these five, Carnivora and Pholidota always come out together. But the relationships of Perissodactyla, Cetartiodactyla, Chiroptera and Carnivora+Pholidota shuffle around depending on what you do. While the study you mentioned got Perissodactyla + Chiroptera, an analysis my colleagues and I did got something else (you can see it here: https://www.researchgate.net/publication/284185545_Spectral_shifts_of_mammalian_ultravioletsensitive_pigments_Short_wavelengthsensitive_opsin_1_are_associated_with_eye_length_and_photic_niche_evolution). So whenever someone confidently says they figured it out, people like me just sort of roll our eyes and move on. I personally think it’s unlikely to ever be solved.

              So why are they genetically similar? Well, they aren’t that genetically similar, truth be told, just more genetically similar to each other than they are to, say, humans or armadillos. Just like a lungfish isn’t that genetically similar to a human, but it’s more similar to a human than it is to an earthworm.

              Just for a moment, assume that evolution is true. After those lineages split some 75 million years ago (that’s around the estimate we got in our analysis), they started living in isolation and adapting to different things. They changed, they evolved, and eventually they looked very little alike. Running on the plains and eating grasses would lead to very different adaptations than flying around and eating insects. But, thanks to DNA, we think we have a sort of record of their ultimate relatedness. Analogously, Icelandic people and New Guinea pygmies are pretty different, as far as humans go, but they’re more genetically similar to each other than they are to gorillas. Think of the horse + bat example as just a more extreme case of that.

              “of course:). please chose your best evidence for a common descent and i will try to explain it by a common design.”

              Well, I’m not positive that it’s the best, but my favorite to talk about would be the case of the whales. I’ll point you to a series of posts I did on them. I’ll leave it up to you to decide what you care to read and address:

              There’s the fossil record pointing to whales transitioning from land to water and from toothed whales to toothless whales: https://evolutionforskeptics.wordpress.com/2014/05/18/transitional-fossils-3-through-11-from-land-mammals-to-the-ancestor-of-whales/

              DNA showing whales genetically nested within hoofed mammals pointing to a land to water transition:
              https://evolutionforskeptics.wordpress.com/2014/07/20/molecular-phylogenetics-whales-are-hoofed-mammals/

              The distribution of the whale-like fossils seemingly pointing to a transition from land to water:
              https://evolutionforskeptics.wordpress.com/2014/07/20/biogeography-whales-began-in-pakistan-2/

              Developmental evidence of teeth forming in toothless whales before disappearing:
              https://evolutionforskeptics.wordpress.com/2014/10/10/ontogeny-recapitulates-phylogeny-baby-baleen-whales-have-teeth-before-they-lose-them/

              Developmental evidence of hindlimbs forming in whales before they disappear:
              https://evolutionforskeptics.wordpress.com/2017/01/22/ontogeny-recapitulates-phylogeny-fetal-whales-have-hindlimb-buds/

              Genetic remnants of color vision genes in whales, which live in a relatively colorless environment: https://evolutionforskeptics.wordpress.com/2014/08/25/pseudogenes-whales-have-lost-the-ability-to-discern-colors/

              Genetic remnants of vomeronasal organ genes in whales, which lack a vomeronasal organ:
              https://evolutionforskeptics.wordpress.com/2014/09/10/pseudogenes-whales-have-lost-their-vomeronasal-organ-and-associated-genes/

              Genetic remnants of taste receptor genes in whales, which lack taste buds:
              https://evolutionforskeptics.wordpress.com/2014/09/17/pseudogenes-whales-can-only-taste-salt/

              Genetic remnants of tooth genes in toothless whales:
              https://evolutionforskeptics.wordpress.com/2014/10/05/pseudogenes-whales-have-remnants-of-tooth-genes/

              I have more posts to write on whales, but this is just what I’ve gotten to so far. Also, keep in mind, it’s important not just to explain each point individually, but to take all of the data into consideration and think about what story they’re telling together.

              “on the other hand: do you think that if we will find a self replicaiting robot with DNA it will be evidence for design or evolution in this case?”

              This is a tricky analogy, because we know that humans have created robots and we can see it happen perhaps every day of the year. By contrast, we don’t know that a Creator has ever created life.

              “by the way; english isnt my native. so sorry if i doesnt understand some of your words.”

              No apologies needed! Please let me know if I need me to clarify anything I’m saying. As someone currently living in a foreign country, I understand how difficult the language barrier can be. Thank goodness for things like google translate!

  2. g

    hi

    you said:

    “Oh okay, I think I understand. But again, you’ll get the same results if you eliminate the DNA letters that are typically associated with neutrality and just kept the functional ones (i.e., first and/or second codon positions).”

    yep. the result can be same since those mutations can be semi- neutral. so it’s not such a big different.

    “Perhaps help me think this through: what you’re saying is that many kinds of organisms were created at the same point in time. Given enough time, they might appear more similar to each other genetically due to chance via the accumulation of neutral mutations. Correct?”-

    true. but as far as we go back in time they actually need to be more different from each other (since they get more mutations). so if we will check 2 animals that appeared in the fossil record about 10 my ago, they should be more similar to each other then say 2 animals that appeared about 100 my ago (since they get far more mutations in 100 my).

    “Or even the organism that appeared just 5 million years ago may be genetically similar to the one that appeared 400 million years ago, because over those 400 million years there have been a ton of genetic changes that could randomly group it with the 5 million year old organism.”-

    it’s an interesting possibility.

    “, but didn’t cause certain groups to go extinct? That way some organisms appeared 50 million years ago, others appeared 10 million years ago, and they coexist today? Or they have descendants that coexist today?”-

    it’s possible that some of them indeed extincted. but it’s also possible that some of them still alive today. such as the lungfish or the horseshoe crabs.

    now let’s discuss the evidence for whale evolution.

    lets start with the first one about transitional fossils. i think that any series of fossils cant prove a common descent since we can arrange also objects that were designed in such hierarchy. see this figure for instance:

    https://imgur.com/a/OoZln

    and yet it doesnt prove any evolution. even if those vehicles were able to reproduce.

    another problem is this finding:

    http://news.nationalgeographic.com/news/2011/11/111116-antarctica-whales-oldest-evolution-animals-science/

    and if it’s true then it doesnt fit well with the fossil hierarchy.

    the second post may be explain by our discussion above about neutral mutations:)

    you also point out that whale has a vestigial flipper. but it may only prove that the dolphin ancestor may had an extra flippers. so this can be explain by the creation scenario too.

    “This is a tricky analogy, because we know that humans have created robots and we can see it happen perhaps every day of the year. By contrast, we don’t know that a Creator has ever created life.”-

    ok. but even if we will find such a robot in a far planet, we can conclude that this robot were designed, since we know that a robot cant evolve naturally.

    1. Hi g:

      “true. but as far as we go back in time they actually need to be more different from each other (since they get more mutations). so if we will check 2 animals that appeared in the fossil record about 10 my ago, they should be more similar to each other then say 2 animals that appeared about 100 my ago (since they get far more mutations in 100 my).”

      So the only way I can think that this works is that there needs to be a combination of some similarity due to design AND being created at the same time and existing through to the present to accumulate, by chance, similar neutral mutations, leading to the appearance of genetic similarity due to common descent.

      Do you have any examples that would fit this description? Is this is a scientifically testable hypothesis?

      “it’s possible that some of them indeed extincted. but it’s also possible that some of them still alive today. such as the lungfish or the horseshoe crabs.”

      So as an IDist, what is the typical explanation for why the Designer allowed for some organisms to go extinct, and then It created new organisms at later geological intervals? Or is it simply treated as a mystery?

      “lets start with the first one about transitional fossils. i think that any series of fossils cant prove a common descent since we can arrange also objects that were designed in such hierarchy. see this figure for instance: https://imgur.com/a/OoZln and yet it doesnt prove any evolution. even if those vehicles were able to reproduce.”

      Let’s be clear: science is never about proving anything, including common descent. Indeed, as an IDist, you would claim that a Designer created the organisms in a historical sequence (e.g., reptiles, dinosaurs, birds), just like engineers designed vehicles in a historical sequence (e.g., car, jet, space shuttle), correct? To be clear, we’re not just creating hierarchies here, we’re creating hierarchies that are consistent with estimates of time (i.e., geological dating). So a hierarchy over time could point to evolution or design, assuming the designer likes to tinker with it’s creation rather than just invent new organisms altogether.

      What’s important is looking at the fossil temporal hierarchies, seeing the same pattern in inferred DNA relationships, finding remnants of genes (pseudogenes) associated with novel adaptations consistent with the fossil and DNA relationships, finding developmental features consistent with a former lifestyle, and seeing patterns of geographical distribution consistent with all of the above.

      It’s common to point to human engineering feats as a way to dismiss evolution, but if vehicles and other designed things fit the criteria listed above, and we had (1) a mechanism for how vehicles could evolve on their own, and (2) we had no clear evidence of humans designing vehicles, then I would say that vehicles may indeed have evolved and are evolving. The problem is that vehicles, and other human designed things, don’t have the same properties as life, and so the analogy can only go so far.

      “another problem is this finding: http://news.nationalgeographic.com/news/2011/11/111116-antarctica-whales-oldest-evolution-animals-science/ and if it’s true then it doesnt fit well with the fossil hierarchy.”

      So a few things to note:

      (1) I can’t tell if this has been scientifically reviewed and published. That was announced at a symposium, and symposia aren’t generally subjected to scientific review. I’m not doubting the credibility of the authors (I don’t know them). It does appear that it has since been published here: http://www.bioone.org/doi/10.5710/AMGH.02.02.2016.2922 though what’s interesting is that the date of 53 million years no longer appears to be reported, and it has been adjusted to 47.8 million years (“Early Middle Eocene”). It’s possible their chronostratigraphy was refined and/or they made a incorrect inference initially. This can happen when reported research isn’t peer-reviewed as the initial report from the symposium.

      (2) With the date change, this seems potentially resolved as is, but I would also like to point out that this fossil is only a jaw bone. It doesn’t say much about the skeletal anatomy of the animal, and so there is always the possibility that the animal had functional legs, normal nostrils, etc.

      (3) Even if the original date was correct, and the animal was indeed a full-swimming whale, there are always presumed missing data in the fossil record. Once upon a time, Pakicetus and Ambulocetus were unknown, and then they were discovered. Sometimes fossils are discovered in younger rocks, and then they are found in older rocks, as this project purported to do. So in theory, the animals that are expected to predate whales like this described fossil could still predate them, but we just have yet to find them in the older rocks (or haven’t looked in the right ones). Of course the opposite could be true, and this is always therefore unknowable, but it’s a logical hypothesis and once that has been validated many times.

      (4) Let’s say this fossil was indeed confirmed to be at the date attributed to it (53 million years), and it really was a fully aquatic whale, and we never find fossils that date that much older than it. The article you refer to still says it isn’t the earliest whale-like fossil, but squishes the transition from land to water to a very short interval. It’s possible the evolutionary transition could have still happened in that interval, although I admit that I’d have trouble believing it. The point is that there are still fossils that predate it that look more land-dwelling than this one is thought to be. But beyond this, the group this whale is attributed to (probably Basilosauridae, based on the publication that I linked above) still appears to be a transitional fossil. For example, modern whales don’t have teeth like basilosaurids did (they’re simpler now or completely replaced with baleen), basilosaurids didn’t have blowholes like modern whales, and they still retained complete hindlimbs, even though they probably didn’t use them.

      “the second post may be explain by our discussion above about neutral mutations”

      Again, you can’t dismiss this in isolation. You have to consider it will all of the additional information. So let’s take your scenarios: a Designer designs some whales to exist at the same time as some hoofed mammals (you need to clarify this by the way, because modern whales didn’t exist back then; did modern whales evolve from these whale precursors?), they evolve neutrally for millions of years alongside they hoofed mammals and just happen to, by chance, accumulate enough mutations to be grouped genetically within the hoofed mammals. But why do we also see fossils that show a transition from land to water, gene remnants pointing to a former life on land, developmental features suggestive of a former life on land, etc.?

      “you also point out that whale has a vestigial flipper. but it may only prove that the dolphin ancestor may had an extra flippers. so this can be explain by the creation scenario too.”

      Sure! The point is that modern whales do not have two pairs of flippers, they only have 2. But if they evolved from animals with four flippers to two, we shouldn’t be surprised to see this in their development. So in your beliefs about design, evolving from four flippered whales to two flippered whales is okay?

      “ok. but even if we will find such a robot in a far planet, we can conclude that this robot were designed, since we know that a robot cant evolve naturally.”

      Not true. We don’t know that a robot can’t evolve naturally. Perhaps they can! But what is this robot like? Is it like C3P0 in Star Wars? Is it like the robots that exist in factories? Again, the problem is that human designed things and living organisms are not perfect analogs. Life does things that human designed things simply can’,t or at least currently do not, do. When there are similarities, it’s often because humans are using inspiration from living organisms.

      1. g

        hi again christopher.

        you said:

        “So the only way I can think that this works is that there needs to be a combination of some similarity due to design AND being created at the same time and existing through to the present to accumulate, by chance, similar neutral mutations, leading to the appearance of genetic similarity due to common descent. Do you have any examples that would fit this deion? Is this is a scientifically testable hypothesis?”-

        I thought about it again and again and im not sure i found a clear answer (too many options). so lets put it aside for a moment. i do find those findings interesting and may related to this discussion:

        .http://news.cornell.edu/stories/2013/12/shark-human-proteins-are-surprisingly-similar

        http://news.psu.edu/story/336611/2014/12/02/research/turn-back-molecular-clock-say-argentinas-plant-fossils

        what do you think about those findings?

        you said:

        “So as an IDist, what is the typical explanation for why the Designer allowed for some organisms to go extinct, and then It created new organisms at later geological intervals? Or is it simply treated as a mystery”-

        we realy cant know. id model is only about detecting design in nature. so this question is interesting but dont have a real connection to id.

        you said:

        “Whats important is looking at the fossil temporal hierarchies, seeing the same pattern in inferred DNA relationships, finding remnants of genes (pseudogenes) associated with novel adaptations consistent with the fossil and DNA relationships, finding developmental features consistent with a former lifestyle, and seeing patterns of geographical distribution consistent with all of the above”

        and again: i think that we can explain it without a common descent. so we dont need the explanation of common descent to explain it . if you have a specific evidence that a
        only a common descent can explain- i would like to discuss about it

        you said:

        “Its common to point to human engineering feats as a way to dismiss evolution, but if vehicles and other designed things fit the criteria listed above, and we had (1) a mechanism for how vehicles could evolve on their own, and (2) we had no clear evidence of humans designing vehicles, then I would say that vehicles may indeed have evolved and are evolving. The problem is that vehicles, and other human designed things, dont have the same properties as life, and so the analogy can only go so far”

        so lets say that we are dealing with self replicating vehicles that can reproduce and appeared in an hierarchy in the (“fossil”) record. i think that even in this case the most logical conclusion will be a design rather then a common descent..

        you said:

        “So in theory, the animals that are expected to predate whales like this described fossil could still predate them, but we just have yet to find them in the older rocks “-

        true. the problem is that it doesn’t fit well with the claim about hierarchy. so if example of hierarchy suppose to be evidence for evolution then exmaple of non hierarchy suppose be evidence against it.

        you said:

        “. You have to consider it will all of the additional information. So let’s take your scenarios: a Designer designs some whales to exist at the same time as some hoofed mammals (you need to clarify this by the way, because modern whales didnt exist back then; did modern whales evolve from these whale precursors?), they evolve neutrally for millions of years alongside they hoofed mammals and just happen to, by chance, accumulate enough mutations to be grouped genetically within the hoofed mammals”-

        ok. first: do they check the entire genome or just a group of genes?

        second: i open to the possibility that some modern whales share a common descent with some older whale. but it will not be evolution, rather then variation.

        you said:
        .
        “But why do we also see fossils that show a transition from land to water, gene remnants pointing to a former life on land, developmental features suggestive of a former life on land, etc.?”-

        ok. the first point about transition i already explained. even if we will find such hiearchy in vehicles it will not prove a common descent. the second point about pseudogenes can be explain too. or by the fact that many pseudogenes are now know to be functional, or by the fact that some genes can be miltifunctional and therefore cant represent their suppose old function. but you need to be specific in this case to tell you what i think.

        you said:

        “So in your beliefs about design, evolving from four flippered whales to two flippered whales is okay?”-

        sure. why not? it’s only a degeneration.

        you said:

        “Not true. We dont know that a robot cant evolve naturally. Perhaps they can! But what is this robot like? Is it like C3P0 in Star Wars?”

        i talking about a robot that made from organic components and has a self replicating system. like a living thing. what is more likely: that such a robot need a designer or such a robot evolved by a natural process?

        1. Hello again g!

          “I thought about it again and again and im not sure i found a clear answer (too many options). so lets put it aside for a moment.”

          Okay, no worries! Let me know if you want to re-engage with that point some time.

          “http://news.cornell.edu/stories/2013/12/shark-human-proteins-are-surprisingly-similar”

          So for this Cornell article, what they’re describing is not the same kind of phenomenon as what my post here is discussing (as well as other posts in my blog). What I’m talking about is similarity in gene, and usually ultimately protein, composition, i.e., DNA/amino acid sequence similarity.

          What this is Cornell shark is describing is a similarity in the types of genes being expressed or turned on in tissues, specifically the heart. So our genomes contain all of our genes, but not all of them are turned on at the same time and in the same tissues. For instance, there are genes that are turned on in the eye that aren’t turned on in the heart, and there are genes turned on in the heart that aren’t turned on in the brain.

          So from this article, it appears that this study is showing that for at least one organ (the heart) sharks and humans have more overlap in which genes are turned on than sharks do with zebrafish. The authors speculate that this is due to similar metabolism between sharks and humans (or mammals in general rather) regarding internal maintenance of a constant metabolism (i.e., independent of environmental factors).

          So in terms of evolution vs. design, I can see this fitting both paradigms. Design in that different animals with organs that have similar functions were designed to have similar patterns of gene expression. Evolution in that mammals and sharks independently evolved a similar metabolism and accordingly need to turn on similar sets of genes to have that metabolism function appropriately. Does that make sense?

          “http://news.psu.edu/story/336611/2014/12/02/research/turn-back-molecular-clock-say-argentinas-plant-fossils”

          Regarding the above article and molecular clocks, this is a really difficult issue that has a lot of uncertainty around it. The idea of using rates of DNA evolution to project splits between species over millions of years is a really exciting one, but it’s one that is hampered by a ton of uncertainty. For one, the original assumption was that the ‘clock’, i.e. the accumulation of DNA substitutions over time, was uniform across species. However, we now know that this is almost certainly not true. Different organisms have their DNA evolve at different speeds due to, for instance, how good their DNA copying machinery is (some organisms make more mistakes than others) and how quickly an organism reproduces (whales reproduce much more slowly than mice, so they accumulate fewer mutations over time). I’m not a population geneticist, but I’m fairly certain population size plays an important role too, given that mutations get fixed more quickly in small populations than large ones.

          So given that we know that different organisms tick at different speeds, and we think that this ticking speed can change (i.e., evolve) we don’t know how fast these hypothetical ancestors were evolving. We’re using species in the present to infer times in the past, but we can’t sample from a species living 10 million years ago or 20 million years ago to see how fast their clocks were ticking.

          We think fossils help with this given that in many case they give a minimum time for divergence of two lineages, but we don’t have an objective way to measure a maximum time for divergence.

          This, of course, has no bearing on the validity of evolution anymore than it does for the validity of design. The reality is, these methods (like many) assume evolution to get at time estimates, but they can’t be used to objectively support it.

          “we realy cant know. id model is only about detecting design in nature. so this question is interesting but dont have a real connection to id.”

          Okay, fair enough.

          “and again: i think that we can explain it without a common descent. so we dont need the explanation of common descent to explain it . if you have a specific evidence that a

          only a common descent can explain- i would like to discuss about it”

          As I discussed, I believe all of those topics I discussed specifically support common descent. I think they become incoherent and misleading if they were the result of design.

          “so lets say that we are dealing with self replicating vehicles that can reproduce and appeared in an hierarchy in the (“fossil”) record. i think that even in this case the most logical conclusion will be a design rather then a common descent..”

          Again, this is difficult because we know humans make vehicles, so the logical conclusion is that they were designed. But if we discovered vehicles on another planet (and we had nothing like them on earth), and they had all of the properties of life (e.g., self replicating, have a metabolism, consume things from their planet to be sustained, develop, etc.), and we saw a vehicular fossil record showing transitions, and remnants of their vehicular genetic code equivalent showing changes over time, etc. then I would conclude that they evolved.

          Life is nothing like anything we as humans have ever designed. Of course an all-powerful designer could design things that we as humans could not, but we know that life evolves and we have all of this evidence that it has been evolving for a long time. Hence a designer isn’t invalidated completely, since you can image a lot of versions of a designer (e.g., one that actively causes evolution), but we have very good reason to believe life evolved and descended from common ancestors regardless of whether a designer had some sort of impact. By contrast, we don’t have any direct evidence that a designer has ever designed any living organism because we have never observed it.

          “true. the problem is that it doesn’t fit well with the claim about hierarchy. so if example of hierarchy suppose to be evidence for evolution then exmaple of non hierarchy suppose be evidence against it.”

          No, it does still fit the claim of hierarchy for some of the fossils. Poor fossil sampling, an incomplete fossil record and fast evolution allows for some issues with hierarchy. But if all of the fossils were found at the exact same time despite the alleged hierarchy, I would throw myself in with the IDists/creationists. But the reality is this: we’ve never found modern whales with any of the ancient fully aquatic whales (e.g., Basilosaurus, Dorudon), and we’ve never found modern whales or ancient fully aquatic whales alongside the terrestrial/semi-aquatic whales. The hierarchy exists through time, even if it doesn’t provide the ideal scenario dreamed of by evolutionary biologists (i.e., one fossil followed by another followed by another etc.).

          This is the case for all of the putative transitional fossils described in this blog, including this one about birds and dinosaurs. We don’t have any chickadees sitting next to Archaeopteryx, or Archaeopteryx next to the earliest dinosaurs.

          “ok. first: do they check the entire genome or just a group of genes?”

          Researchers are working their way up to whole genomes, but from the earliest studies that looked at a few genes, to those that looked at dozens and those that looked at hundreds/thousands, we keep getting the same results.

          “the second point about pseudogenes can be explain too. or by the fact that many pseudogenes are now know to be functional, or by the fact that some genes can be miltifunctional and therefore cant represent their suppose old function. but you need to be specific in this case to tell you what i think.”

          I wouldn’t go so far as to say “many” are known to be functional, but to be fair, we’re still learning. But what’s important isn’t that some pseudogenes are functional, rather some species that have certain pseudogenes are special and point point to common descent. One of the links I provided to you involves vomeronasal organ pseudogenes. The vomeronasal organ is sort of like a second way to ‘smell’ your environment. All of the whale vomeronasal genes are now pseudogenes. This prediction follows from the fact that the putative early whale fossils had a vomeronasal organ which then disappeared. What’s particularly important is that whales, and only whales among mammals, are the only species we know of that have these vomeronasal pseudogenes. Or actually, now that i think of it, Primates might also have them, as they don’t have a functional vomeronasal organ either. If pseudogenes are functional, why do whales (and maybe Primates), have these genes as pseudogenes but all other mammals have them as protein coding genes? It works well for evolutionary theory, but it’s just a sort of “Eh, who knows? Mystery” for ID.

          “sure. why not? it’s only a degeneration.”

          So my impression from IDists/Creationists is that “degenerations” (i.e., the loss of a character) is always okay, even if it’s adaptive. Is that what you generally hear/believe too?

          “i talking about a robot that made from organic components and has a self replicating system. like a living thing. what is more likely: that such a robot need a designer or such a robot evolved by a natural process?”

          Again, I don’t think we can talk in likelihoods like this. I think you can’t conceive of such a thing, and I can, but I accept evolution and you don’t. It’s like telling a religious person and atheist that something miraculous happened. One thinks “sure, why not?” the other thinks “impossible”. So again, if this robot made from organic components acted just like life (and humans didn’t know how to make them), then yes I think evolution is extremely plausible.

          How it originated is another issue, and I don’t have a strong opinion on any of the hypotheses for how life arose.

          1. g

            hi again christopher!

            you said:

            “Evolution in that mammals and sharks independently evolved a similar metabolism and accordingly need to turn on similar sets of genes to have that metabolism function appropriately. Does that make sense?”-

            yes, but you have made another interesting point: how this regulation evolve stepwise? for instance: if a gene for making a milk evolved in the first time, how it evolved without any correct regulation that turn it on in the mammary gland and turn it off in the rest of the body?

            you said:

            “But if we discovered vehicles on another planet (and we had nothing like them on earth), and they had all of the properties of life (e.g., self replicating, have a metabolism, consume things from their planet to be sustained, develop, etc.), and we saw a vehicular fossil record showing transitions, and remnants of their vehicular genetic code equivalent showing changes over time, etc. then I would conclude that they evolved.”-

            here is at least one problem with this. we know that a car cant evolve stepwise, since a minimal car will need at least several parts: wheels, an engine and a chassis. so this minimal car cant evolve stepwise and therefore cant be the result of evolution. the same can be true for a living thing, since both creatures and cars need at least several parts for some of their systems.

            you said:

            .”and weve never found modern whales or ancient fully aquatic whales alongside the “-
            terrestrial/semi-aquatic whales”

            but we do find such an example as we have seen with the suppose 49 my whale
            fossil. of course that we can explain it by many ways but the point is that if example of hierarchy is evidence for evolution then why an example of non -hierarchy should not be evidence against it? (and by the way i can bring you several other cases too)

            you said:

            “Researchers are working their way up to whole genomes, but from the earliest studies that looked at a few genes, to those that looked at dozens and those that looked at hundreds/thousands, we keep getting the same results.”-

            not every time. as you can see here:

            https://www.sciencedaily.com/releases/1999/02/990217075533.htm

            “Turtles turned out to be not where they were supposed to be on the family tree whenever their genes were included in a research study”

            and here is another interesting finding that may be similar to an example of human that is closer to mouse then to chimp:

            https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981516/

            “Distributions of sponge trans according to the count of the highest similarity homologs are shown in figure 4. The majority of sponge proteins most closely match the sea anemone proteome, whereas only slightly fewer are, again surprisingly, most similar to human proteins. The sea urchin is ranked third, whereas the sea squirt, fruit fly, and especially nematode are drastically underrepresented in terms of best-matching homologs.”

            you said:

            “. Whats particularly important is that whales, and only whales among mammals, are the only species we know of that have these vomeronasal pseudogenes.”-

            im not sure. see this figure for instance:

            https://www.researchgate.net/figure/251878334_fig3_The-vomeronasal-receptor-gene-repertoires-of-mammals-The-species-represented-are-limited

            you said:

            “So my impression from IDists/Creationists is that ;degenerations; (i.e., the loss of a character) is always okay, even if its adaptive. Is that what you generally hear/believe too?”-

            yep. it’s seems logical.

            you said:

            So again, if this robot made from organic components acted just like life (and humans didn’t know how to make them), then yes I think evolution is extremely plausible.

            ok. fair enough. but do you agree that we will need a good evidence for such evolution and not just a belief?

            1. Hello again, g!

              “yes, but you have made another interesting point: how this regulation evolve stepwise? for instance: if a gene for making a milk evolved in the first time, how it evolved without any correct regulation that turn it on in the mammary gland and turn it off in the rest of the body?”

              Excellent question. So it partially depends on how the gene evolves. Usually we would imagine something like gene duplication occurring, due to poor DNA recombination during meiosis (DNA replication during the formation of sperm and eggs). Since the original gene is still doing its original function, the new gene has the potential to evolve and take on a new function. To go off your example, we’ll say it involves the production of milk.

              If the mutation that produced the second gene was close to the original on the genome, then they would likely have similar regulatory DNA regions, things like promoters and enhancers. These regulatory regions largely determine when and where a gene is turned on, so if the original gene is turned on in the mammary glands and only the mammary glands, then it isn’t difficult for the new milk gene to have the same expression pattern.

              Another possibility is that the original gene is expressed elsewhere, say the brain, but during the gene duplication the new gene ended up somewhere else. If where it ended up was near mammary gland regulatory DNA, then it could be expressed there.

              A third possibility is that the original gene and the new gene don’t have any regulatory DNA near them that has anything to do with mammary gland tissue. The regulatory DNA itself can possibly get inserted near the new gene, through perhaps reverse transcriptase action or again DNA replication errors during meiosis.

              So essentially, in theory, you just need the right regulatory DNA near the new gene, which can happen from putting the gene in the right place or putting the regulatory DNA in the right place. I’m not sure how much this has been studied, but I did read a recent paper that demonstrated evidence of such a mechanism in mice. Specifically, it appears that a immune gene was duplicated and put near genes expressed in a sensory organ called the vomeronasal organ. So even though these immune genes are normally expressed in cells that fight off bacteria and viruses, this one is expressed in the vomeronasal organ of mice, and from what I recall, it appears to be contributing to vomeronasal function (which is kind of like our sense of smell).

              There are probably other mechanisms for changing expression patterns that I’m not aware of (known or theorized), and I’m not sure if we think genes ever start off being expressed ‘everywhere’ and then get localized to a tissue, or if it always starts localized and then spreads elsewhere. If I had to guess, these kinds of questions are still in their infancy and are probably mostly limited to yeast and perhaps fruit flies. I got the impression that the mouse study I read was somewhat ground breaking, and that was just this year.

              “here is at least one problem with this. we know that a car cant evolve stepwise, since a minimal car will need at least several parts: wheels, an engine and a chassis. so this minimal car cant evolve stepwise and therefore cant be the result of evolution. the same can be true for a living thing, since both creatures and cars need at least several parts for some of their systems.”

              So, again, analogies aren’t perfect since cars are operated by people, but I’d argue that they could evolve stepwise (and I’m pretty sure that I’m not the first to think so). Imagine vehicles started off as just a single wheel, relying on gravity and wind to disperse around the world. Then, perhaps, multiple wheels with axels are added for stability, followed by a steering mechanism, followed by a self propelled mechanism (maybe more like a bicycle than an engine), then an engine, etc. Perhaps there are different ways to evolve this too, so you can imagine starting as one wheel, then turning into a unicycle (i.e., self propelled but still one wheel), then to a bicycle, a car, etc.

              Same thing with living systems. There are incredibly simplistic organisms and incredibly complex ones. Some have very simple nervous systems (e.g., jellyfish), some have very complex ones (e.g., vertebrates). Some have very simple digestive systems (e.g., flatworms), some have very complex ones (e.g., cows, sloths). So there is a ton of potential to evolve stepwise from simplistic organisms to complex ones just from studying comparative biology. Showing that it can and does happen, is another matter, of course…

              “but we do find such an example as we have seen with the suppose 49 my whale
              fossil. of course that we can explain it by many ways but the point is that if example of hierarchy is evidence for evolution then why an example of non -hierarchy should not be evidence against it? (and by the way i can bring you several other cases too)”

              Hmm, I should rephrase what I said. The earliest appearance of terrestrial whale like mammals predates the appearance of the first aquatic whales, and the first appearance of aquatic whales predates the first appearance of modern-looking whales. Once a type of organism appears does not necessitate that it goes extinct. Reptiles appeared before birds did in the fossil record, but reptiles also still exist today. They are different kinds of reptiles than the ones that first appeared in the fossil record, but they are reptiles nonetheless.

              So again, we have never, ever found a blue whale, a dolphin, a porpoise, a narwhal, a sperm whale, etc. (all species alive today) in the same rocks as the first terrestrial whale-like fossils (e.g., pakicetus, indohyus), or the first semi-aquatic (e.g, ambulocetus, rodhocetus) or the first fully aquatic whales (basilosaurus, dorudon). We also don’t find the first fully aquatic whales appearing at the same time as the first semi-aquatic ones or terrestrial ones. We also don’t first the first semi-aquatic ones appearing when the first terrestrial ones appear.

              So the first appearances are in a sequence that coincides with the hierarchy of morphology/anatomy. Does that make sense?

              If we found blue whales, basilosaurus, ambulocetus, and indohyus all in the same rocks, and then found ducks, ichthyornis, and archaeopteryx in the same rocks, and humans, the first monkeys and the first primates all in the same rocks, I think evolutionary theory would be in big trouble. Or alternatively, if blue whales predated all the others, or humans predated all the others, etc.

              “Turtles turned out to be not where they were supposed to be on the family tree whenever their genes were included in a research study””

              Again, my comments were not as precise as they should have been, so I apologize. When you go back far enough, the first molecular phylogenetic studies did come up with some surprising relationships, but these have changed as we have increased our sample sizes. For instance, there is an infamous example in mammals where guinea pigs (a type of rodent) came out in early phylogenies not as a rodent at all! What we have learned since then is that sample size matters a lot, just like in normal statistical methods. So as we add additional genes and we add genes from additional species, the results become more and more consistent, no matter what combination of genes you use. So once we got the first genetic result for whales being nested within hoofed mammals (e.g., pigs, camels, deer), we’ve kept getting the same result for larger and larger datasets. As an example, my PhD advisor in 2011 did a paper with 26 genes and 169 species and found whales right in the middle of hoofed mammals. I followed it up in 2015 with a study of 38 genes and 388 species and got the same results.

              So the example you used above for turtles and crocodilians was back in 1999, during the advent of molecular phylogenetics, with a relatively small dataset. I can’t access the paper right now since I’m not at work, so I can’t see how many species were in the dataset, how many letters of DNA, etc. (though it looks like they had an impressive number of genes for back then). Either way, since then, modern analyses, which tend to include more species and many many more genes have repeatedly come to the same conclusion: crocs are more genetically similar to birds. Here’s a very recent study that looked at 100 species of vertebrates and almost 7200 genes, which robustly supports (100% statistical confidence) crocs being closest to birds (you can see it in figure 2): https://www.researchgate.net/profile/Iker_Irisarri/publication/318660128_Phylotranscriptomic_consolidation_of_the_jawed_vertebrate_timetree/links/598084b00f7e9bd660eb4b38/Phylotranscriptomic-consolidation-of-the-jawed-vertebrate-timetree.pdf

              Smaller data sets, just like in traditional statistics, can lead to spurious results.

              “and here is another interesting finding that may be similar to an example of human that is closer to mouse then to chimp: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981516/

              Did you paste the correct article? I don’t see mouse of chimpanzee mentioned in the analyses or the figures.

              “im not sure. see this figure for instance: https://www.researchgate.net/figure/251878334_fig3_The-vomeronasal-receptor-gene-repertoires-of-mammals-The-species-represented-are-limited

              So the vomeronasal pseudogenes referenced in this paper are vomeronasal receptor genes. These are expressed in the vomeronasal organ and bind certain molecules as a way of sensing the environment (this is what I was referring to earlier for the immune gene being turned on in the vomeronasal organ). Most if not all mammals have some vomeronasal receptor pseudogenes and nearly all of them retain some functional ones. It’s the same thing for olfactory (nose/smell) receptors and bitter taste receptors. Essentially we think the numbers of these genes expand and contract depending on the number of different molecules (i.e., ‘smells’, odorants) the organism interacts with, though my personal impression is that we don’t have a very good idea of how this works, only that the number of functional and pseudogenic copies varies.

              Anyway, back to whales: what’s important is that whales have a pseudogenic gene (TRPC2) that’s involved in taking the signals from the vomeronasal receptors and transmitting it to the brain. My memory was correct and apes and old world monkeys (including humans) also have a pseudogenic TRPC2 as well, an important finding in that they are not thought to have a functional vomeronasal organ either: http://www.pnas.org/content/100/14/8337.short

              At some point I will go back to the original paper to verify, but I believe whales only have pseudogenes for the vomeronasal receptor genes too, as opposed to a mixture of functional and pseudogenic copies.

              So that’s why it’s significant. Why were the only mammals without vomeronasal organs created with TRPC2 pseudogenes but no functional TRPC2, whereas mammals that have vomeronasal organs have a functional TRPC2 but not TRPC2 pseudogenes? And is it just a coincidence that whales have these vomeronasal pseudogenes and we have fossil evidence that whales descended from mammals that had vomeronasal organs?

              “ok. fair enough. but do you agree that we will need a good evidence for such evolution and not just a belief?”

              Yes, of course! My first thought would definitely be: “Robots on another planet? Must have been intelligently designed.” But if we learn enough about them to question this, and find a growing amount of evidence to suggest they evolved, at some point I’m likely to tip in that direction.

              1. g

                hi again christopher!. first: thanks for the explanation. i will try to focus in my main points

                you said:

                “, so you can imagine starting as one wheel, then turning into a unicycle (i.e., self propelled but still one wheel), then to a bicycle, a car, etc.”-

                ok. lets assume that those first steps are possible somehow. what about the engine itself? any minimal car engine will need at least several parts to its minimal function. we cant just add one part to get an engine from non engine. so we will stuck at this point.

                you said:

                “Same thing with living systems. There are incredibly simplistic organisms and incredibly complex ones. Some have very simple nervous systems (e.g., jellyfish), some have very complex ones (e.g., vertebrates). Some have very simple digestive systems (e.g., flatworms), some have very complex ones”

                good point. but the real question is how any minimal system of those kinds evolved at the first place. you can call it “minimal complexity”. think about a cell-phone. some are complex and some are less complex. but even the simplest cell-phone required at least several parts to its minimal function. so it cant evolve stepwise from a self replicating matter.

                you said:

                “So the first appearances are in a sequence that coincides with the hierarchy of morphology/anatomy. Does that make sense?”-

                actually yes. we can find such hierarchy in vehicles for instance. cars appeared first, then a commercial vehicle and then a truck. now, even if vehicles were able to reproduce i dont think that it will prove evolution rather then design in this case. so i dont think that the whale case is different.

                you said:

                . “Or alternatively, if blue whales predated all the others, or humans predated all the others, etc.”

                if we will find a monkey fossil date to about 70my we can claim for convergent evolution (monkeys evolve twice) or just push back the evolution of monkeys in the geologic time.

                you said:

                “Why were the only mammals without vomeronasal organs created with TRPC2 pseudogenes but no functional TRPC2, whereas mammals that have vomeronasal organs have a functional TRPC2 but not TRPC2 pseudogenes?”

                ok. even if its true then its just a degeneration rather then evolution.

                you said:

                ;”Robots on another planet? Must have been intelligently designed. But if we learn enough about them to question this, and find a growing amount of evidence to suggest they evolved, at some point Im likely to tip in that direction.”-

                but again; we will need hard proof rather then belief. and evolution (as far as i aware about) is indeed a belief rather then a fact.

                have a nice day.

  3. g

    by the way christopher, i find it interesting that even fish that lack a vns system have those genes:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727394/

    “Interestingly, despite the fact that the morphological traits of the VNS are found only in tetrapods, VNS-specific genes are present in teleost fish and exhibit expression patterns consistent with their involvement in a distinct teleost olfactory system ”

    here is another interesting finding about the trpc2 gene:

    http://jeb.biologists.org/content/217/13/2235

    “Here we examined the localization of TRPC2 in an aquatic amphibian and cloned the Xenopus laevis trpc2 gene. We show that it is expressed in both the MOE and the vomeronasal epithelium.”

    so this gene isnt a vns specific.

    1. Hi g!

      “ok. lets assume that those first steps are possible somehow. what about the engine itself? any minimal car engine will need at least several parts to its minimal function. we cant just add one part to get an engine from non engine. so we will stuck at this point.”

      Maybe it doesn’t start off as an engine the way we envision an engine. Perhaps it starts with wind power, where a simple addition of a structure creates a sail that just allows the wheels to be pushed along in a simple manner. Then maybe this gets elaborated on by the wind getting channeled through pipes or it starts pushing an internal wheel crank that resembles a minimal engine. How does it evolve into an internal combustion engine? I have no idea, but i don’t know very much about cars so I can only stretch this analogy so far.

      But in natural systems, we are increasingly learning how new structures can evolve through changes in how gene expression occurs. The early fruit fly experiments which showed that through mutations eyes can start developing on wings or antennae can replace eyes show just how easy it can be to radically change one’s morphology. Turn on a gene in a new place or take away gene expression from another place, or extend how long you turn on a gene, and you can get some very novel (and frequently bizarre) traits. Of course everyone agrees that most such mutants would not do exceedingly well in nature, but given enough time, rare ones can of course conceivably be adaptive and lead to major evolutionary transitions.

      Think of this in the context of what what IDists and Creationists frequently criticize in terms of evolution: birds couldn’t have evolved from dinosaurs, land dwelling vertebrates couldn’t have evolved from fishes, whales couldn’t have evolved from hoofed mammals. These are rather rare and exceptional instances, aren’t they? We think that we descended from a single group of fishes that came onto land, not that fishes repeatedly came onto land leading to reptiles in one case, amphibians in another, birds in another, etc. Most of the rest of evolution is totally acceptable by creationists and IDist. Getting bigger is fine, changing color is fine, reshaping bones is okay, losing teeth and eyes is okay.

      So this is a way of saying: evolving an engine may seem improbable considering that there are so many evolutionary dead ends, but the natural equivalents of engines evolving are things that we think are extremely rare anyway. Given the plasticity of how changes in gene expression can radically change morphology, these things should not be discounted outright as impossible, even if they are improbable.

      “good point. but the real question is how any minimal system of those kinds evolved at the first place. you can call it “minimal complexity”. think about a cell-phone. some are complex and some are less complex. but even the simplest cell-phone required at least several parts to its minimal function. so it cant evolve stepwise from a self replicating matter.”

      I guess the question is how far back one needs to go to insist on minimal complexity. The vertebrate eye is probably a good example. Vision doesn’t work properly unless you have a pupil to change how much light enters the eye, a cornea and lens to focus the image, something to maintain the internal pressure of the eye to keep the round shape (vitreous humor), cells that absorb light (photoreceptors) and cells to electrically transmit that light (retinal neurons, optic nerve, etc.), and a neural region to process the light information (visual cortex, plus other brain regions). Take one of those away and the system is gone, right? Except you could lose literally every single one of those features and just have photoreceptors cells and you’ll still have a system to quantify light, which is of course a very simplistic but still useful type of information to capture for an organism. Heck, you don’t even need photoreceptor cells, as many unicellular organisms show: you just need some sort of protein that absorbs light and chemically transmits that information to the animal.

      So in this case, there’s a spectrum. Minimal light absorption (presence/absence of light) vs. complex light absorption and processing (presence/absence of light, relative brightness, color, depth, location, motion, etc.). In other words, the vertebrate eye is just adding extra features to the original model. This is not to exaggeratedly make it seem like evolving the vertebrate eye is no big deal. Again, we think it happened once (though octopods and their relatives have a strikingly similar eye), and researchers are working hard to understand how such a complex organ could have evolved. But the point is that every organ/system that I can think of has a minimal example in nature and logically allows for evolutionary elaborations to improve upon these simple systems.

      “actually yes. we can find such hierarchy in vehicles for instance. cars appeared first, then a commercial vehicle and then a truck. now, even if vehicles were able to reproduce i dont think that it will prove evolution rather then design in this case. so i dont think that the whale case is different.”

      I hope to make this clear in case it hasn’t been: I don’t think a temporal sequence (fossil record) appearance of hierarchy proves evolution. It is evidence consistent with evolution that is made stronger by other types of evidence (e.g., DNA, development, etc.). Proof deals with certainty, and I always try to emphasize that science never proves anything. I could die tomorrow and the Creator could tell me, “Dude, Chris, I created these organisms from scratch. The order of the fossils was just a coincidence.”

      But as scientists, just like a crime scene investigators, we are trying to piece together what happened and based on known mechanisms of evolution and the sum of all of the evidence, we (almost exclusively) think that evolution explains this the best.

      “if we will find a monkey fossil date to about 70my we can claim for convergent evolution (monkeys evolve twice) or just push back the evolution of monkeys in the geologic time.”

      If that monkey looked like a modern monkey, had all of the diagnostic features of monkeys, and the rocks and rock dates were validated with near certainty, I think that would put a serious monkey wrench (had to do the pun!) in evolution.

      Some people would just dismiss it as a hoax and ignore it. Perhaps most evolutionary biologists. I would take it very seriously and want to investigate it more. Just chalking up to convergent evolution would be ridiculous if it had all of the diagnostic features, and just saying that monkeys arose that early would also be problematic. The latter would be more realistic, but it would go against a century plus of research so it can’t be dismissed out of hand.

      But it’s important to state that in your example, only a single monkey was found. If we have found a monkey, a walrus, a blue whale, a skunk, a kangaroo, a kangaroo rat, a manatee, etc. and many if not most or all modern organisms all at 70 myr, holy cow that would be such a fascinating and exciting discovery. I would love to publish it, I would love to upend what we think about evolution, and it would certainly sway things into the Creationist camp.

      Unfortunately for this scenario (I legitimately got excited thinking about it!), that’s not what we find at all. Groups of organisms are clearly separated by geological strata, and those geological strata correlate with different periods of time based on isotopic dating methods (and other things). This suggests massive faunal turnovers and our understanding of evolution makes a lot of sense to explain it.

      “ok. even if its true then its just a degeneration rather then evolution.”

      But it’s not as simple as calling it a degeneration. What it suggests is that (1) toothed whales (dolphins, belugas, sperm whales) and baleen whales share a common ancestor, and (2) one of their ancestors had a vomeronasal organ. So if these mammals all share a common ancestor, then that suggests that there was some major evolutionary change that led to things looking as different as a vaquita and a bowhead whale. It also raises the question of why their common ancestor had a vomeronasal organ but modern species do not. If they were created with a vomeronasal organ, why wouldn’t the Creator realize “Oh hey, these animals are not going to be able to use their vomeronasal organ in water. Maybe I should create them without it.” Alternatively, the Creator created them on land and they transitioned into water, which, again, implies major evolutionary changes.

      “but again; we will need hard proof rather then belief. and evolution (as far as i aware about) is indeed a belief rather then a fact.”

      So depending on the semantic definition of fact, evolution is both a fact and a theory (the latter of which is slightly more complicated than a belief). It’s a fact in that we can observe it in natural populations, including humans, but this is the sort of “microevolution” that Creationists/IDists are almost universally okay with. It’s a scientific theory in that we cannot observe things that happened in the past, but we “believe” that it did based on the evidence supporting the theory.

      To make a simple example: let’s say you believe you are your mother’s child. That’s a belief, and it can be as simple as having been told at a young age that you are, and you never questioned it.

      A scientific theory involves questioning that belief by testing it rigorously. So let’s say you go and look at your birth certificate, you interview the doctor who delivered you and the nurses that helped, you ask your dad, your siblings who were young (but present) at your birth, you quantify physical traits to see which of your traits are similar to your mom’s, and then you do DNA testing. If all of those are consistent with the theory of you being your mother’s child, then you’ll probably accept it.

      Could it still be a lie and a cover-up? Yes, it absolutely could. Does it seem likely? Presumably not, but crazier things have happened in this world.

      So in that sense, evolution is both a fact and a theory, and theories are essentially rigorously tested forms of belief. ID isn’t a scientific theory essentially because it’s presumably impossible to test whether a Creator created life. Since we cannot seem to directly observe the Creator, the Creator does not seem to be creating life today, and presumably the Creator would not be available for us to directly analyze Itself, ID remains a non-scientific theory. Could it still be true though? Absolutely.

      As a quick note, your birth mother example is more of a scientific hypothesis whereas a theory encompasses many hypotheses (e.g., gravity, plate tectonics), but it’s basically the same thing but at a different scale.

      “by the way christopher, i find it interesting that even fish that lack a vns system have those genes. so this gene isnt a vns specific.”

      Thank you for finding those! This is still completely consistent with evolution, however. Fish don’t have a vomeronasal organ and they live in water, the same as whales and manatees. The difference is that we think land mammals evolved from an aquatic ancestor shared with fish (which undoubtedly looked fish-y), whereas whales and manatees evolved from land mammals that evolved from the fishy ancestor. So whales and manatees can be thought of as a reversion back to the water.

      So the vomeronasal organ might not be present in fish, but I believe it’s present in most land vertebrates. This would suggest that as vertebrates came onto land, they eventually evolved a vomeronasal organ. TRPC2 and other genes associated with this function had to have come from somewhere, and much of evolution of new structures is thought to come from a process known as co-option. Co-option is a process where a gene is expressed in certain tissues in an ancestor, but in a descendant the gene expression changes to new tissues. So in this scenario, TRPC2 had some other function in early aquatic vertebrates, and by some fortuitous event turned on in some sensory tissue in land vertebrates. Since then, it appears that it has been of incredible importance in functioning in the vomeronasal organ of land vertebrates.

      Now perhaps TRPC2 started out as an olfactory (nose, smell) gene, which is consistent with its being present in both the olfactory and vomeronasal of the frog Xenopus. This wouldn’t be terribly surprising since the vomeronasal organ is very similar to the nose. Or perhaps that expression profile is unique to frogs. TRPC2 could still be co-opted into other functions and that doesn’t negate its special important to the vomeronasal organ.

      So back to whales and other mammals that don’t have a vomeronasal organ. Regardless of whether fishes lack a vomeronasal, or frogs have TRPC2 in both, in mammals TRPC2 appears to be tightly linked to vomeronasal function. Not only does knocking out the gene in mice disrupt the function of the vomeronasal organ, but whales, manatees, old world monkeys and apes (including humans), and many bats both lack a vomeronasal organ and a functional TRPC2 whereas species that have a vomeronasal organ also have a functional TRPC2. This correlation should not be taken to be meaningless, even in light of the fish and frog observations. To add to this, whales, manatees, old world monkeys and apes, and many bats not only lack a functional TRPC2 but they have a TRPC2 pseudogene, suggesting that the gene was formerly functional, and by extension these animals used to have a functional vomeronasal organ.

      If you’re interested, I actually updated this post last weekend which includes links to TRPC2 results in these other mammals: https://evolutionforskeptics.wordpress.com/2014/09/10/pseudogenes-whales-have-lost-their-vomeronasal-organ-and-associated-genes/

      As a side note, I just wanted to say that I really admire your effort in looking into the research on the topics we discuss. Many people just quote a website or a book on ID/Creationism (which is totally okay), but you’re actually challenging me by looking into what the research says. I think that speaks to your sincerity, and I really appreciate it (plus you teach me a lot too!).

      I hope you’re having a wonderful weekend!

      1. g

        hi again christopher!

        you said:

        “So in this case, theres a spectrum. Minimal light absorption (presence/absence of light) vs. complex light absorption and processing (presence/absence of light, relative brightness, color, depth, location, motion, etc.). In other words, the vertebrate eye is just adding extra features to the original model.”

        ok. take a look at this image:

        https://www.google.co.il/search?q=camera+evolution&client=firefox-b&dcr=0&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjUiMLj9qLYAhWBmLQKHd77COoQ_AUICigB&biw=1366&bih=656#imgrc=THXKd6iGHaoyLM:

        as you can see: its very similar to the eye case. but still we have 2 problems:

        1) the first camera need at least several parts to begin with (and therefore cant evolve stepwise)
        2) there is no stepwise way from some simple cameras into the more complex once

        so i dont think its solve the eye evolution. we still need several parts at once in some steps.

        you said:

        “But its important to state that in your example, only a single monkey was found. If we have found a monkey, a walrus, a blue whale, a skunk, a kangaroo, a kangaroo rat, a manatee, etc. and many if not most or all modern organisms all at 70 myr, holy cow that would be such a fascinating and exciting discovery”

        i dont think it will be a problem for evolution. we can argue for rapid evolution or a geological catastrophe (a flood?). its very similar to the cambrian explosion case were many creature suppose to evolve very fast (in geological perspective). or we can claim even for several origins for life or many other scenarios.

        you said:

        “But its not as simple as calling it a degeneration. What it suggests is that (1) toothed whales (dolphins, belugas, sperm whales) and baleen whales share a common ancestor, and (2) one of their ancestors had a vomeronasal organ.”-

        about 1) it may be possible (but again it will be a degeneration rather then evolution)

        as for 2) the suppose ancestor is a land mammal. so its only a belief that the whale ancestor had a vomeronasal organ. we need to prove that whale evolved from such a
        creature and we cant. so we cant claim that whale ancestor had a vomeronasal organ.

        and you continued:

        “If they were created with a vomeronasal organ, why wouldn’t the Creator realize ,Oh hey, these animals are not going to be able to use their vomeronasal organ in water. Maybe I should create them without it.”

        but as we have seen with the fish case: those genes can function underwater too (for other functions). so again we can explain it under the design model without any use of evolution

        you said:

        “So in that sense, evolution is both a fact and a theory, and theories are essentially rigorously tested forms of belief. ID isn’t a scientific theory essentially because it’s presumably impossible to test whether a Creator created life.”

        ok. i still think that the best explanation for the existance of a self replicating robot is a design rather then a natural process. but fair enough:)

        you said:

        “To add to this, whales, manatees, old world monkeys and apes, and many bats not only lack a functional TRPC2 but they have a TRPC2 pseudogene, suggesting that the gene was formerly functional, and by extension these animals used to have a “-
        functional vomeronasal organ”

        even if whale had a vgs system it just means a degeneration. very similar event happened to their olfactory system. do you agree that its very similar case?

        you said:

        “.As a side note, I just wanted to say that I really admire your effort in looking into the research on the topics we discuss. Many people just quote a website or a book on ID/Creationism (which is totally okay), but you’re actually challenging me by looking into what the research says. I think that speaks to your sincerity, and I really appreciate it (plus you teach me a lot too!).”

        thanks christopher. although i do use sometimes id\creation source, especially if they back up their claims by a scientific reference. have a good day (and holyday?).

        1. Hi g,

          Sorry for the very slow reply, I have been inundated with work, family, etc. Just barely getting back into the swing of things.

          “as you can see: its very similar to the eye case. but still we have 2 problems:

          1) the first camera need at least several parts to begin with (and therefore cant evolve stepwise)
          2) there is no stepwise way from some simple cameras into the more complex once

          so i dont think its solve the eye evolution. we still need several parts at once in some steps.”

          Cameras are not the same as photosensitive structures in nature, though they are very similar to the vertebrate eye. As I stated before (I think), photosensitive structures at their simplest are proteins, followed by pigmented spots, pigmented spots with some sort of focusing structure (e.g., lens), etc. So we don’t think the eye started out as complex as a camera, such as that suggested by the camera evolution photos you linked to.

          “i dont think it will be a problem for evolution. we can argue for rapid evolution or a geological catastrophe (a flood?). its very similar to the cambrian explosion case were many creature suppose to evolve very fast (in geological perspective). or we can claim even for several origins for life or many other scenarios.””

          I completely disagree. This is a huge problem for evolution, at least how we understand it. It would require major rewrites of textbooks, reexamination of experiments, etc. I think in such a scenario, creationism would be taken very very seriously.

          “as for 2) the suppose ancestor is a land mammal. so its only a belief that the whale ancestor had a vomeronasal organ. we need to prove that whale evolved from such a
          creature and we cant. so we cant claim that whale ancestor had a vomeronasal organ.”

          You most certainly can claim that, but yes, you cannot prove it. You can only say that there is evidence to suggest it.

          “but as we have seen with the fish case: those genes can function underwater too (for other functions). so again we can explain it under the design model without any use of evolution”

          They do function underwater in fish, but then why did whales lose them? And why do fossil whale-like animals show evidence of having a vomeronasal organ?

          “even if whale had a vgs system it just means a degeneration. very similar event happened to their olfactory system. do you agree that its very similar case?”

          Yes, I agree that it’s similar.

  4. g

    hi christhoper!

    “Sorry for the very slow reply, I have been inundated with work, family, etc. Just barely getting back into the swing of things.”

    sure. take your time!

    you said:

    “Cameras are not the same as photosensitive structures in nature, though they are very similar to the vertebrate eye. As I stated before (I think), photosensitive structures at their simplest are proteins, followed by pigmented spots, pigmented spots with some sort of focusing structure (e.g., lens), etc. So we don’t think the eye started out as complex as a camera, such as that suggested by the camera evolution photos you linked to.”

    but even at the minimal level a light detector require at least several parts (or sites if you want). so its still means a big jump in the first step. we need not just the part that can detect light but also the part that is able to translate it into the creature or do with that something useful.

    you said:

    “Yes, I agree that it’s similar.”

    then its only a degeneration rather then evolution. so a creation can explain it just fine as evolution can.

    by the way: i find this paper interesting since its talking about one of your evidence for a common descent (shared nonsense mutations):

    https://utexas.influuent.utsystem.edu/en/publications/parallel-molecular-evolution-of-deletions-and-nonsense-mutations-

    the conclusion of the paper (as far as i aware) is that shared deletions arent good evidence for a common descent since its not rare to find shared deletions without a common descent. and we also find that some genes with stop codon are functional:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197733/

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164928/

    so we cant be sure that even a nonsense mutation point to a real pseudogene.

    yours sincerely.

    1. Hi g:

      “but even at the minimal level a light detector require at least several parts (or sites if you want). so its still means a big jump in the first step. we need not just the part that can detect light but also the part that is able to translate it into the creature or do with that something useful.”

      Actually, it probably isn’t that difficult. Light detecting proteins are almost always (always?) a family of proteins called G protein-coupled receptors, signaling molecules present in the membranes of cells. Once you have a protein that can absorb light, it would likely already be linked to intracellular proteins that can transmit the light signal, since G protein-coupled receptors are always linked to such proteins. If you had enough interest and time to research this, I think you would find out that such a possibility is not nearly as farfetched as you seem to think.

      “then its only a degeneration rather then evolution. so a creation can explain it just fine as evolution can.”

      A “degeneration” as you call it, is still evolution. We call it regressive evolution, whereby the loss of a trait becomes fixed in a population. Creation would be consistent with it IF a model of Creation allows for evolution to occur AND there is sufficient time for it to take place.

      So many Creationists believe that the earth is 6000-10000 years old. The accumulation of these mutations and lost of these traits would require mutation rates and/or population sizes that are probably very unrealistic based on what we know about these modern species. For instance, whales evolve very slowly because they take so long to grow and become sexually mature and they only have one baby at a time. It therefore becomes extremely difficult to accumulate as many mutations as they have and lose as many organs/tissues as they have via such an evolutionary “degeneration” in only a few thousand years.

      Now, if you’re fine with Creation having taken place tens of millions of years ago, then this isn’t really a problem. Most creationists, however, don’t believe this is consistent with their reading of the Bible, however.

      “the conclusion of the paper (as far as i aware) is that shared deletions arent good evidence for a common descent since its not rare to find shared deletions without a common descent.”

      I would say that this is a generous interpretation of this paper. This would probably be true indeed in bacteriophages, because these are viruses, which involves at extremely rapid rates and have tiny amounts of DNA. Compared to my whale example above (which take man years to reproduce), I believe some viruses replicate within hours. Also, I’m not virus expert, but I do not believe viruses are capable of correcting for mutations, whereas animals and plants have machinery to do this. Therefore, mutations are going to accumulate with far far less frequency. Plus, there is much much more DNA in animals and plants, etc. which means that there are far more types of mutational events, whereas virus mutations are restricted to their tiny stretch of DNA, and therefore can happen with more frequency in the exact same location.

      Nonetheless, stop codons and other inactivating mutations CAN happen in parallel, and we do find evidence of this, but it’s extremely rare. Shared mutations are, on average, much more likely to occur in the species that have other evidence suggesting their common descent.

      ” and we also find that some genes with stop codon are functional”

      Absolutely, but in those instances the stop codon occurs in olfactory receptors which, if insect ones are the same as mammal ones, only consist of a single exon (portion of the gene involved in coding for a protein). This probably isn’t nearly as troublesome as multiexon genes (most genes) in which a premature stop codon occurs in an earlier exon. The reason is that there are mechanisms to prevent these genes from being translated (called nonsense mediated decay). In single exon genes, like olfactory receptors, this is almost certainly does not trigger nonsense mediated decay and the protein can likely be functional more often than not. We are actually interested in this question right now in our lab for single exon genes, as I’m skeptical whether many of the so-called single-exon “pseudogenes” are actually indeed nonfunctional as previously assumed by scientists.

  5. g

    hi christopher!.

    you said:

    “Actually, it probably isn’t that difficult. Light detecting proteins are almost always (always?) a family of proteins called G protein-coupled receptors, signaling molecules present in the membranes of cells. Once you have a protein that can absorb light, it would likely already be linked to intracellular proteins that can transmit the light signal, since G protein-coupled receptors are always linked to such proteins. If you had enough interest and time to research this, I think you would find out that such a possibility is not nearly as farfetched as you seem to think.”-

    but we will need at least another part that can use the signal and translate it for the creature. if we want to add such a minimal sense to a robot, we cant just add a single part and make the robot to sense light and response to it.

    you said:

    .” It therefore becomes extremely difficult to accumulate as many mutations as they have and lose as many organs/tissues as they have via such an evolutionary “degeneration” in only a few thousand years.”-

    just for the sake of the argument lets check this claim. in about 10,000 years we can add to the genome about 100,000 mutations (100 new mutations per generation* 1000 (number of generations in 10,000 years). so a 3 billion genome\100,000 give us about 1 mutation almost per gene. also consider hot spots.

    you said:

    “Nonetheless, stop codons and other inactivating mutations CAN happen in parallel, and we do find evidence of this, but it’s extremely rare.”-

    as far as i aware the author suggest the opposite:

    “This study provides a compelling reason to avoid the assumption that parallel evolution of deletions is rare”

    so its an interesting finding.

    1. Hi g:

      “but we will need at least another part that can use the signal and translate it for the creature. if we want to add such a minimal sense to a robot, we cant just add a single part and make the robot to sense light and response to it.”

      Well, rather than go on with this, let’s put our thinking into two camps: (1) you believe that this is impossible and therefore points to a creator, (2) I believe that it’s premature to say it’s impossible and will venture to guess people are working on this and have better explanations than I. What we know about evolution suggests that it may be uncommon, but I do not think it as unachievable as you seem to. And that’s fine, we can leave it at that!

      “just for the sake of the argument lets check this claim. in about 10,000 years we can add to the genome about 100,000 mutations (100 new mutations per generation* 1000 (number of generations in 10,000 years). so a 3 billion genome\100,000 give us about 1 mutation almost per gene. also consider hot spots.”

      So of course this is simplifying things given that the generation times and mutation rates are going to vary for different species. In addition, of all of those mutations, how many of them would disrupt the function of a gene? Also, of all of those genes, some are huge some are very small, so they would have different rates of mutation accumulation. Finally, a mutation in a gene does not mean fixation in a species. The mutation has to be either neutral (or nearly so) or adaptive and then spread throughout the entire species/population to fixation.

      Then, you have shared mutations between multiple species, so in our whale example, you have to accumulate all of these mutations BEFORE they split into the various species that exist today.

      This seems like it would be relatively straightforward to model (given some gratuitous assumptions), and it would be interesting to see some Creation scientists tackle it.

      “as far as i aware the author suggest the opposite:

      “This study provides a compelling reason to avoid the assumption that parallel evolution of deletions is rare””

      This author was making a common on a single study, and the study was on bacteria, which have tiny genomes, faster rates of mutation and fixation, etc. which makes it far more probably. Comparing that to your 3 billion letter genome example, this becomes far, far less likely.

      My comment is based on my own experience, as I have been working on pseudogenes pretty much exclusively for about 6 years or so (I was even working on some today!). Off the top of my head, I can think of maybe five or so examples of parallel inactivating mutations in the many genes/species I’ve studies, which might mean that there are another five or so that I cannot remember. As far I know, nobody has done a study on how common such parallel mutations might be, but my experience suggests that it’s very rare (though it is far more common for some mutational types than others, since they are probably ‘easier’ DNA copying mistakes to make).

  6. g

    hi again.

    you said:

    “Well, rather than go on with this, let’s put our thinking into two camps: (1) you believe that this is impossible and therefore points to a creator, (2) I believe that it’s premature to say it’s impossible and will venture to guess people are working on this and have better explanations than I. What we know about evolution suggests that it may be uncommon, but I do not think it as unachievable as you seem to. And that’s fine, we can leave it at that!”

    fine with me!

    you said:

    “So of course this is simplifying things given that the generation times and mutation rates are going to vary for different species. In addition, of all of those mutations, how many of them would disrupt the function of a gene?”-

    any deletion or insertion or stop codon. i not sure about their rate but i think they quite common.

    and…

    “Finally, a mutation in a gene does not mean fixation in a species. The mutation has to be either neutral (or nearly so) or adaptive and then spread throughout the entire species/population to fixation.”-

    true. but remember that most mutations suppose to be neutral so there is no problem here. its also possible that a degenerative mutation will be beneficial. so we dont need so much time for fixation.

    and…

    “Then, you have shared mutations between multiple species, so in our whale example, you have to accumulate all of these mutations BEFORE they split “-

    remember again hot spots or beneficial loss, or we can just agree that those whales shared a common whale. depend in the situation.

    you said:

    “My comment is based on my own experience, as I have been working on pseudogenes pretty much exclusively for about 6 years or so (I was even working on some today!). Off the top of my head, I can think of maybe five or so examples of parallel inactivating mutations in the many genes/species I’ve studies, which might mean that there are another five or so that I cannot remember. “-

    can you give references for those examples? it will be interesting to check them out. i aware about 2-3 example too.

    thanks christopher.

    1. Hi G:

      “true. but remember that most mutations suppose to be neutral so there is no problem here. its also possible that a degenerative mutation will be beneficial. so we dont need so much time for fixation.”

      Again, I’m not sure what timescale you’re thinking of for life. 6,000 years? 10,000 years? Millions? Billions? But anyway, if you’re thinking 6,000 or 10,000 years, fixation would probably take much longer than you’re thinking. It would depend on the organism of course, but whales evolve very, very slowly, so for a mutation in the right spot to be fixed in whales prior to diversifying in their many forms today (that is, much less than 6,000-10,000 years) is not particularly likely, especially with multiple genes.

      “can you give references for those examples? it will be interesting to check them out. i aware about 2-3 example too.”

      The only one that comes to mind in a publication is in the following paper, which I’m fairly certain we referred to explicitly in the text: https://www.researchgate.net/publication/270054689_Genomic_evidence_for_rod_monochromacy_in_sloths_and_armadillos_suggests_early_subterranean_history_for_Xenarthra

      It’s for a gene called PDE6C, which is involved in vision. There’s is a stop codon shared by sloths and the nine-banded armadillo, and genetics and anatomy shows consistent evidence of them being related to each other, so we thought maybe it was shared in their common ancestor. When we looked at other armadillos, we found that they didn’t have the stop codon, suggesting that the stop was convergent.

      The other two examples involve genes I’m working on right now but they are not yet published. One is for a tooth-related gene called ODAM where, again, we found a stop shared between an armadillo and two-toed sloths, but other sloths and armadillos don’t share it. I can’t recall what the other gene is, but it’s another tooth gene I’m working on with, again, some species sharing a mutation and others not.

            1. Hi g: ah, yes, ILS could potentially explain something like this. Introgression could as well, and I’m of the opinion that this is more common than ILS in explaining such divergent signals.

              So in the examples I listed, that would mean that sloths and the nine-banded armadillo would have had a common ancestor and either ILS or introgression occurred, leading to the same stop codon. If this was a long time of divergence, however, both ILS and introgression seem less likely to be responsible for something like this, but its at least theoretically possible.

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