Common Descent by ID?

Further to the OP Munging ID it seems that there is still a significant amount of confusion as to whether ID could be, or even is, compatible with common descent… Moreover, Mike Behe has been quoted by Paul Nelson here at TSZ as one of the very few from among the Discovery Institute (DI) who “supports” common descent, common ancestry or descent with modification…

While I doubt we would be able to get Mike Behe to post at TSZ, for the reasons I have already mentioned in the moderation issues in the past, unless his book critics decide to post here and he would be provoked to respond, let’s just watch some of the videos where elaborates on those very issues:


Intelligent Design and Common Ancestry – Michael J. Behe, PhD

Another issue related to common ancestry is the that some members of DI, including Mike Behe and Ann Gauger apparently accept the possibility of “guided evolution”… which in my view would be an oxymoron…I must stress however that I have not seen any real details about that coming from either of them, so I don’t really know what they mean by “guided evolution”…Perhaps Behe’s upcoming book will provide us with some insight on the theme…Have they come to a similar conclusion Jonathan Wells has with the embryo development (cell differentiation) where the information beyond DNA would have to be added in the process? I don’t know at this point…

I have also mentioned it in the past that ID supporters, as well as logically thinking creationists, must accept some sort of “micro-evolution” or descent with modification within “kinds”…

The example of that type of evolution, or rather devolution, is the “evolution” of dogs from wolves by the breaking genes or the decreasing gene functions…

Other possible “evolutionary changes” leading to dog evolution from wolves could be compared to the antibiotic resistance evolution that had already existed in the some genomes before the antibiotics were even developed…

406 thoughts on “Common Descent by ID?

  1. Mung: They are compatible until they are not compatible.

    I don’t think that’s true. ID is 100% compatible with common descent.

    Mung: You may be able to devolve a bicycle from an airplane but you cannot evolve an airplane from a bicycle.

    I am not aware of anything in ID theory that forbids this.

  2. J-Mac: In short,
    ID had no choice but to claim that human genome would be expected to be mainly functional if they were to claim that it was designed…

    WHY did ID have no choice? Now you’re saying the claim doesn’t actually arise from any principle of ID but was just a knee-jerk reaction to criticism?

    ALL SCIENCE SO FAR!

  3. Mung: Yes. So why do we find the profound discontinuities at the beginning of the process rather than at the end of the process?

    We find the deepest branches longest ago. Isn’t that what we’d expect?

  4. Allan Miller: We find the deepest branches longest ago. Isn’t that what we’d expect?

    I’m not sure Mung is actually asking a question at this point. I mean, can anybody write out what you quoted without coming to your conclusion as they type?

    Why is the tree thinnest at the tips of the branches?
    Why does history get more vague the further back you go?
    Why do birds suddenly appear every time you are near?

    etc etc.

  5. J-Mac: ID says the great majority of human genome should be functional…

    Can you put an actual figure on that? Dare you put an actual figure on that?

    What is “great majority”? 90% 99% 99.9? 99.9999999999%

    As right now it seems to me it could be determined to be 51% and you’d claim vindication for your “great majority” claim.

  6. J-Mac,

    J-Mac: ID predicted and still predicts the great majority of human genome will be functional.. I asked Joe Felsenstein to put his career on evolutionary prediction of junk DNA just like Grour..”.if encode is right, evolution is wrong ”
    You have faith, don’t you?

    Then ID has already been falsified since ~90% of the human genome is accumulating mutations at a rate consistent with neutral mutation.

  7. Mung: Yes. So why do we find the profound discontinuities at the beginning of the process rather than at the end of the process?

    For the same reason we have profound discontinuities in human history the farther back we go.

  8. Allan Miller: We find the deepest branches longest ago. Isn’t that what we’d expect?

    The deepest roots of the tree are the ones that extend the farthest into the earth.

    Rumraket’s comment was about the most profound discontinuities.

  9. Mung: The deepest roots of the tree are the ones that extend the farthest into the earth.

    Rumraket’s comment was about the most profound discontinuities.

    Profound: Middle English: from Old French profund, from Latin profundus ‘deep’, from Latin pro ‘before’ + fundus ‘bottom’.

    You should think before playing word games.

  10. “Junk’ DNA reveals vital role
    Inscrutable genetic sequences seem indispensable.

    If you thought we had explored all the important parts of our genome, think again. Scientists are puzzling over a collection of mystery DNA segments that seem to be essential to the survival of virtually all vertebrates. But their function is completely unknown.

    The segments, dubbed ‘ultraconserved elements’, lie in the large parts of the genome that do not code for any protein. Their presence adds to growing evidence that the importance of these areas, often dismissed as junk DNA, could be much more fundamental than anyone suspected.

    David Haussler of the University of California, Santa Cruz, and his team scanned the genome sequences of man, mouse and rat1. They found more than 480 ultraconserved regions that are completely identical across the three species. That is a surprising similarity: gene sequences in mouse and man for example are on average only 85% similar. “It absolutely knocked me off my chair,” says Haussler.

    The regions largely match up with chicken, dog and fish sequences too, but are absent from sea squirt and fruitflies. The fact that the sections have changed so little in the 400 million years of evolution since fish and humans shared a common ancestor implies that they are essential to the descendants of these organisms. But researchers are scratching their heads over what the sequences actually do.

    “It absolutely knocked me off my chair”
    Themost likely scenario is that they control the activity of indispensable genes. Nearly a quarter of the sequences overlap with genes and may be converted into RNA, the intermediate molecule that codes for protein. The sequences may help slice and splice RNA into different forms, Haussler suggests.

    Another set may control embryo growth, which follows a remarkably similar course in animals ranging from fish to humans. One previously identified ultraconserved element, for example, is known to direct a gene involved in the growth of the brain and limbs.

    To solve the conundrum, experts predict a flurry of studies into the enigmatic DNA chunks. “People will be intrigued by this [finding],” says Kelly Frazer who studies genomics at Perlegen Sciences in Mountain View, California. “It is the kind of stuff that blows people away.”
    Hard to believe 🤣

    Geneticists have known for some years that there are critical sections of DNA aside from the much-acclaimed genes. A fair fraction of the mouse and human genomes, aside from protein-coding sequences, show strong similarities.

    But ultraconserved segments are particularly unusual because they are 100% identical in man and mouse. Until now, some thought they were human DNA that had contaminated mouse samples. “People had a hard time believing it,” Frazer says.

    The presence of exact copies in different animals suggests that even tiny changes in the sequence of these segments destroy whatever they do, and have been weeded out during evolution. Non-essential regions of DNA, by contrast, tend to accumulate mutations so that the sequences vary in different organisms.

    Figuring out what the mystery segments do will be difficult. There are few similarities between one region and another, so these cannot be used to provide clues to their function. One laborious technique will be to genetically engineer mice that lack one segment and see how that affects their growth and behaviour.

    Once the function of ultraconserved elements is resolved, researchers will still have to tackle other vast tracts of the genome that are similar in different organisms, says geneticist Kerstin Lindblad-Toh of the Broad Institute in Cambridge, Massachusetts. “This is the tip of the iceberg,” she says. “

    All this was predicted by evolutionary theory and more… 😂
    Who would have known that, but Darwinists?!

    Let’s listen to the excuses now…

  11. J-Mac:
    Inscrutable genetic sequences seem indispensable … ultraconserved … conserved … ultraconserved … conserved …

    All this was predicted by evolutionary theory and more…

    Didn’t you read that the clue to the importance of these segments was their high conservation? Well, that’s because evolutionary theory predicts that important sequences will show high conservation.

    J-Mac:
    Who would have known that, but Darwinists?!

    Any scientist, actually anybody, who understands the notion of purifying selection would have known that. No need to wait for “Darwinists,” whatever that might mean, to tell us.

    J-Mac:
    Let’s listen to the excuses now…

    Excuses for what? You presented a scientific hypothesis that stems directly from evolutionary theory to try and argue against evolution and against junk DNA. IOW, you shot yourself in both feet with a single bullet!

    Do you understand that these segments stand out against a background of poorly conserved sequences? Do you really think that because some previously uncharacterized, highly conserved, segments might be functionally important therefore none of the genome is junk?

    I know you’re clueless, that you won’t understand what your problems is, despite it being so obvious, and that it’s useless to give you any explanations, but your tone makes it really hard to feel compassion for you. I’ll leave you to your fantasies now. You make an excellent job of ridiculing yourself without my help.

  12. Mung: Yes. So why do we find the profound discontinuities at the beginning of the process rather than at the end of the process?

    Allan Miller: We find the deepest branches longest ago. Isn’t that what we’d expect?

    I believe my prediction that Mung is just about to go full retard YEC is close to fulfillment

  13. Rumraket:
    I like how evolution happening even faster is somehow validation of ID and falsification of evolution.

    Reminds me of Robert Beyers back on the old RD.net forums who insisted that it would be impossible for whales to evolve from terrestrial mammals because “there just isn’t enough time” (no work was done to show this of course), and then he instead invoked … hyperspeed evolution following the global flood to explain how whales evolved from terrestrial mammals “according to their kind”.

    You can’t make this shit up. IDcreationists wouldn’t recognize critical thinking if it was injected into their eyeballs.

    Oj yeah the old Richard Dawkins place. They pulled the plug. Some evolutionists there were malicious and even their own side couldn’t stand it.

    Yes its impossible for land critters to evole into water ones by selection on mutations. its unreasonable and not intellectually persuasive.
    Yet thee could be in the glorious complexity of biology innate triggers that, after threshold, switch genes on/off to change bodyplans as needed.
    Human speciation proves this. instant and a whole population at once.

  14. Entropy: Didn’t you read that the clue to the importance of these segments was their high conservation? Well, that’s because evolutionary theory predicts that important sequences will show high conservation.

    Oh baloney, evolution theory never predicted this. They found out that many sequences were highly conserved, then said, well, what do you know…

    Random mutations, and yet tons of sequences with no mutations…nonsense.

  15. dazz:
    I believe my prediction that Mung is just about to go full retard YEC is close to fulfillment

    No less a personage than Stephen Jay Gould makes this error, in Wonderful Life, when he talks about the origination of multiple phyla in the Cambrian…

  16. phoodoo: Oh baloney, evolution theory never predicted this.They found out that many sequences were highly conserved, then said, well, what do you know…

    Evolutionary theory does predict that conserved regions – those varying less in a clade – are more likely to be under selection. It doesn’t predict what proportion of sequence will display this pattern.

  17. Allan Miller: No less a personage than Stephen Jay Gould makes this error, in Wonderful Life, when he talks about the origination of multiple phyla in the Cambrian…

    And Elizabeth picked up Stephen Meyer for the same error in his book, Darwin’s Doubt.

    Meyer’s Mistake

  18. Allan Miller: Evolutionary theory does predict that conserved regions – those varying less in a clade – are more likely to be under selection. It doesn’t predict what proportion of sequence will display this pattern.

    Oh really, when did they make this prediction?

    Around the same time they predicted punctuated equilibrium during the Cambrian?

  19. phoodoo: Oh really, when did they make this prediction?

    Not before the realisation that genes were DNA sequences that encoded biologically active proteins and RNAs (or didn’t). Mid 1960s

    ETA

    This experiment reported in 1961 was a significant milestone.

  20. phoodoo: Oh really, when did they make this prediction?

    This comes up over and over again. There is a difference between the colloquial understanding of ‘prediction’ – a specific event will occur – and the scientific one – given particular circumstances, particular patterns would be expected.

    Differential conservation of selected sequence is an expectation of evolution. Regions under long term selection should differ less than those where selection is relaxed, sampling variation in a clade. So if we find high conservation for a sequence, we infer that the sequence has been under selection. Is that unreasonable?

    What would ID have to say about these differentials?

  21. phoodoo:
    Allan Miller,

    How can something NOT be under selection, going by your accidents are everything theory?

    Because some things are not under selection – it is not a universal. I’m not convinced you fully grasp the subject.

  22. Allan Miller: Because some things are not under selection – it is not a universal. I’m not convinced you fully grasp the subject.

    Sorry, but your theory is that EVERYTHING that exists is because of mutation and selection. If you have a new theory, so be it, I wouldn’t blame you for wanting to change it.

    To say things aren’t under selection is just nonsensical. Almost as nonsensical as your fitness concept, which says some thing are fitness, and some aren’t because, well, because…

  23. phoodoo: Sorry, but your theory is that EVERYTHING that exists is because of mutation and selection.

    You are just wrong. And actually, after arguing on the subject here for at least the last 5 years, it is pitiful that you still cling to your strawman view of the subject, and refuse to learn anything about it.

    To say things aren’t under selection is just nonsensical.

    Some parts of the genome are not under selection. In fact, enormous swathes of the (human) genome are not under selection. If (say) 90% of the genome is junk, then clearly at least 90% of the genome is not subject to selection.

    The problem lies entirely in your head. Are you seriously insisting that evolutionists are simultaneously arguing that 90% of the genome is junk AND 100% of it is under selection?

  24. It’s instructive to read Ohno’s original 1972 paper (hosted, ironically, by an anti-junk enthusiast, Andras Pellionisz, with whom I had a couple of run-ins at Sandwalk till he decided I didn’t have enough PhDs to be worth bothering with!).

    It includes a fair estimate of the number of protein coding genes, 30,000 from theory, which has been borne out, give or take, by modern techniques.

    Ohno’s definition of Junk was ‘cannot suffer a deleterious mutation’, which translates to ‘is not under purifying selection’.

  25. phoodoo,

    Scientists were aware that some parts of the genome were more conserved than other parts in the 1960’s. See, for example, Dubnau et al.
    Then Britten and Davidson (1969) figured out that metazoans carried butt-loads of highly repetitive DNA.

    The widespread, across phyla, data to elucidate these patterns did not start to be generated until DNA sequencing got a whole lot easier in 1977.
    [It is amazing how much people figured out from circular dichroism and CoT values!]
    A word of caution when reading papers about transcription of repetitive DNA from the time period 1969 – 1977: splicing hadn’t been discovered yet…
    Punk Eeek was more of an ’80’s thing.

  26. phoodoo: Then how did they get there?

    One class of DNA sequences that are non-functional and thus neutral to selection are endogenous retroviruses.. Originally, they were the result of viral infection of a germ-line cell that was none-the-less viable. The viral sequence is incorporated in the host genome and its progeny. Mutations result in the viral sequence not being expressed and any further mutations can occur at the background rate, undergoing no selective pressure. This provides useful information regarding phylogeny.

  27. DNA_Jock: Duplication and mutation.
    Seriously, learn some biology.

    So natural selection is irrelevant, is that what you are saying?

    I wonder how you measure fitness then.

  28. phoodoo: I wonder how you measure fitness then.

    It is the organism that is subject to selection by the niche environment. An organism carries a suite of genes that determine the phenotype and contribute to that organism’s fitness and survival. It may also carry sequences that are non-functional and have no bearing on fitness.

  29. Alan Fox: Where DNA sequences are non-functional, yes.

    If the DNA sequences are non-functional, why in the world would they be highly conserved?

  30. phoodoo: So natural selection is irrelevant, is that what you are saying?

    Irrelevant to how they got there, which was what you asked. Specifically, you asked about how sequences that are not under selection got there. Selection, where it is acting, will be a factor in whether the sequences get to hang around.

    I wonder how you measure fitness then.

    You would 😉

  31. phoodoo: If the DNA sequences are non-functional, why in the world would they be highly conserved?

    They wouldn’t. That’s not what he’s saying. There are no highly conserved sequences that anyone thinks are nonfunctional.

  32. phoodoo: So natural selection is irrelevant, is that what you are saying?

    I wonder how you measure fitness then.

    Offspring numbers, as usual. If the alleles of a particular locus are not under selection, then there is no difference in their effect on carriers – the mean offspring numbers are the same between the different classes. Selection, expressed as relative rate of increase due to a locus of interest, is a continuum from zero, rather than a toggle.

  33. phoodoo: Then how did they get there?

    It depends on the sequence. An insertion in the germline genome that comes from a virus infection will not be under selection once it has entered your genome. This sequence will then accumulate mutations because it performs no function your organism depends on. That’s one way a DNA sequence not under selection can get into an organisms genome.

    So when such an insertion happened in the distant past in a common ancestor of some species, it will then be inherited by all the offspring. The common ancestor goes through some speciation event leaving two lineages evolving in parallel. So each lineage is now accumulating mutations independently. Since the viral (now retroviral) insertion is not under selection, it is free to accumulate mutations. Many generations down the line the two species genome sequences can be compared and it can be seen that some DNA sequences are much more like each other. The less changes there are between them, the more conserved it is. The more changes there are between them, the more diverged it is.

    Nonfunctional viral insertions in both species will have diverged more since the time of their last common ancestor, than genes that have remained important for basic cellular functions.

  34. Rumraket,

    But Allan is saying the highly conserved sequences are not under selection!

    So if they are non-functional, there is no reason they would be highly conserved, and if they ARE functional, then you can’t say they aren’t under selection.

  35. phoodoo:
    Oh baloney, evolution theory never predicted this.

    Of course it did. Evolutionary theory includes the notion of purifying selection. I have to know. I’m constantly looking for highly conserved sequences in my own work.

    phoodoo:
    They found out that many sequences were highly conserved, then said, well, what do you know…

    You’ve got it backwards. How could they find highly conserved sequences without looking for them? Without performing comparative analyses?

    phoodoo:
    Random mutations, and yet tons of sequences with no mutations…nonsense.

    It would be nonsense if random mutations was the whole thing, but that’s not how it works. You keep forgetting selection.

  36. phoodoo: But Allan is saying the highly conserved sequences are not under selection!

    I’m pretty sue that if he really said that it was just a case of a badly formulated sentence.

  37. One of the main classes of surplus DNA is formed by various copy-paste transposons – 45% or so. These probably derive from viruses. They have a deleterious effect because they can disrupt important genes, but once established, their fossil remains are hard to shift.

  38. phoodoo: So if they are non-functional, there is no reason they would be highly conserved

    I agree.

    and if they ARE functional, then you can’t say they aren’t under selection.

    Yes, I agree.

  39. phoodoo:
    Allan Miller,

    Alleles don’t have offspring, organisms do…you keep forgetting that.

    No, I’m well aware of that. That’s why we say ‘mean offspring of carriers’, not of the allele itself. Though naturally, if the organism it’s in has offspring, the allele gains a copy.

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