Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

5,163 thoughts on “Common Design vs. Common Descent

  1. Corneel,

    Corneel: I am feeling very accommodating today, so I will grant you your argument and see where that leads us.

    J-mac: It is very much appreciated… Me too, therefore I’m going to drive an extra nail into the coffin… 😉

    Corneel: So you are saying that nobody here can fathom why the Designer created a nested hierarchy, until we create living cells ourselves?

    J-mac: I can’t speak for others …
    But one can make the same argument for common design… So, if you can’t recreate life and actually test that nested hierarchies make sense from the prospective of evolution, your assumption is just as good as mine or Sal’s…

    Coreel: First: How do you know that? Can’t we discover those reasons through careful study? Not even devote students like Sal? Why not?

    J-mac: You don’t know that either and as I mentioned above, your speculation is just as good as ours…though yours is clearly bs and has more holes than my grandmother’s strainer, such as the lack of hollow bones in ratites is a big blow you are willing to ignore…

    Corneel: Second: Most creationists here claim that certain designed characters of species are best understood as adaptations to their envirnonment. So what exactly is preventing us from learning why some adaptations must be nested within others?
    J-mac: Why should I care what other people claim here? Give me one reason! I follow the evidence and NOT claims…

    Coreel: Please enlighten me.
    With pleasure!

    What evidence for nested hierarchies are you actually talking about? You mean the evidence as you see it? The Harshman delusions?
    Well, don’t you think that before you can make the nested hierarchies assumptions you need to resolve some of the major fundamental issues, like the miraculous gene insertions into the tree of life?
    How about the assumptions in endosymbiosis theory flop? Or the orphan features or whole systems?
    Do you think that those issues can be just ignored because you chose to believe in some nested hierarchy nonsense?

    Since I am feeling very accommodating today, so I will grant you your argument and see where that leads us.
    Let’s go even deeper…
    How does the nested hierarchy apply to the origins of the first cell and its essential components that are necessary for the cell to function?
    Let’s just use few examples, so that we don’t get too much of the overwhelming evidence here…
    How does the nested hierarchy apply to ATP, Proteins, DNA and Enzymes within a cell? What’s the evidence for nested hierarchies here or the order of nature (my kids are reading it)?

    Enlighten me! 😉

  2. John Harshman,

    Yes, because none of those are problems for common descent. They are at most problems for the natural origin of certain features of some organisms. That isn’t relevant to the question of common descent. How many times has this been brought to your attention?

    I think getting a definition of common descent is in order. Maybe we are all in agreement and don’t know it. Is it possible common design and common descent could both be valid?

  3. John Harshman:

    That isn’t relevant to the question of common descent.

    Yes it is, because if some creature is mechanisitically precluded from evolving to another creature, common descent won’t happen except by a miracle.

    How can there be common descent by natural means if one creature can’t evolve to be another?

    How many times has this been brought to your attention?

    You mean how many times have you repeated a fallacy and I refused to accept the fallacy.

  4. Sal’s back to blathering about constraint, yet his argument still essentially boils down to a classic appeal to ignorance fallacy. He can’t himself imagine how something can evolve with all these levels of constraint, so therefore it can’t.

    Proteins are poly functional and need constraints for binding sites and sites for post translational modification and glycol conjugation, etc.

    It boggles the mind how these levels of constraint are simultaneously achieved!

    And there we have it. This is the essence of Sal’s argument. It boggles his mind, so he thinks it can’t happen. The real world shows that it did.

    Anyway, people don’t seem to appreciate DNA’s Brownian motion can shepard molecular machines and components with pin-point accuracy. This is partly due to binding site specificity, but then maybe stuff we’re only beginning to appreciate. All this to say, we can’t just assume stuff is free to mutate merely because functionally similar proteins between species may only have 12% sequence similarity.

    Nobody “assumes” anything. The empirical evidence says it can mutate due to epistasis between different residues. A residue might initially look strongly deleterious if mutated, but if another mutation in a different location which is neutral happens first, the one that previously was strongly deleterious is now free to change.

    The very fact that there is a diversity of sequence for all these elements is itself an indication that it has changed imcrementally over deep time. The very same phylogenetic methods used to detect species relationships can also be used to elucidate the evolutionary relationships of these different regulatory molecules.

    Often times scientists can even bridge the sequence “gaps” between very distantly related molecules, such as the only 12% similar ones you mention.

    For example, if A is 90% similar to B is 90% similar to C is 90% similar to D is 90% similar to E is 90% similar to F and so on. Until we get to J, which is only 10% similar to A.
    This exact phenomenon is true for the steroid hormone-controlled family of transcription factors I linked articles to earlier. Some of the most divergent members are around 10-12% similar. Yet the entire range can be bridged by families of molecules that are >95% similar, all the way down to those 10-12% similar ones. An entire phylogeny of steroid hormone gene-regulators. And they evolved by simple duplication and accumulation of point mutations in different copies.

  5. colewd:
    John Harshman,

    I think getting a definition of common descent is in order.Maybe we are all in agreement and don’t know it.Is it possible common design and common descent could both be valid?

    It isn’t the definition of common descent that’s your problem here. A group of species has common descent if they are all descended from a single ancestral species. It’s common design that’s the problem; it’s generally understood to be an alternative to common descent as an explanation for similarities among species. It’s possible to combine common descent and intelligent design, but common design is something else.

  6. stcordova: How can there be common descent by natural means if one creature can’t evolve to be another?

    There’s your problem: you have added “by natural means” without noticing the modification. Once more, you are talking about the origin of adaptations and perhaps other innovations. That isn’t what common descent is about. Whether the origin of innovations is natural or miraculous is irrelevant to common descent. Why not adopt Michael Behe’s position on this matter? Then we could stop arguing about common descent and start arguing about what you actually want to talk about. Of course you would have to give up young earth creationism, or creationism at all. But your reasons for keeping it are religious, not scientific.

  7. John Harshman: What prokaryote clade? If there’s a prokaryote clade, aren’t eukaryotes part of it?

    Since prokaryotes are defined by the absense of a nucleus, and the absense of the mitochondrial and plastid endosymbionts, I don’t see how they could be. Meh, I see your point, a clade is defined by the common ancestor and all it’s descendants. Which would make eukaryotes belong to prokaryotes, which would contradict the definition of prokaryotes.

    Okay, but then we can basically just define a clade that contains bacteria and archaea (and all their descendants) by their shared characteristics, and give it a name. The clade that contain all replicating cells with lipid-based membranes, ribosomal protein translation and D-DNA-based genomes. Eukaryotes would then also belong to this clade of course.

  8. John Harshman,

    It isn’t the definition of common descent that’s your problem here. A group of species has common descent if they are all descended from a single ancestral species. It’s common design that’s the problem; it’s generally understood to be an alternative to common descent as an explanation for similarities among species. It’s possible to combine common descent and intelligent design, but common design is something else.

    How would you define descended in this case?

  9. stcordova: Yes it is, because if some creature is mechanisitically precluded from evolving to another creature

    If common descent is impossible, then common descent is impossible. Great Sal, what a truly insightful conclusion.

    Is common descent impossible? Doesn’t look like it at all. In fact, if common descent was impossible, one has to wonder why we observe the exact kind of evidence we would expect to find if common descent took place in actual history.

    … common descent won’t happen except by a miracle.

    Why a miracle? Why does it have to be “miraculous” rather than some other thing? By miraculous I presume you mean divine intervention, right? Why can’t an intelligent species like aliens have done the designing?

    How can there be common descent by natural means if one creature can’t evolve to be another?

    How can there be divine intervention if there is no creator-God?

    You get nowhere by these hypotheticals based on unsubstantiated premises. Such as “one creature can’t evolve to be another”. That’s an unsubstantiated premise. The fact that we find the very pattern that common descent predicts, should lead you to STRONGLY suspect that one creature CAN and actually DID evolve to be another.

  10. GlenDavidson: Life?

    Glen Davidson

    No. We could find extraterrestrial life unrelated to bacteria and archaea, without lipid-based membranes, ribosomal protein translation or D-DNA based genomes. It would be a bad idea to define a clade by those properties and call it “life”, as then we’d have to conclude cells on another planet, replicating, evolving, with a different type of genetic material and protein translation system, shouldn’t be called life.

    Maybe earthkaryota? 🙂

  11. stcordova: Yes it is, because if some creature is mechanisitically precluded from evolving to another creature, common descent won’t happen except by a miracle.

    Do we have evidence of common descent by miracle?

    How about evidence of miracles doing anything at all? Basic facts underlying your worldview are notably lacking.

    Glen Davidson

  12. Sal’s back to blathering about constraint, yet his argument still essentially boils down to a classic appeal to ignorance fallacy. He can’t himself imagine how something can evolve with all these levels of constraint, so therefore it can’t.

    I can’t imagine how perpetual motion machines can work because they won’t work.

    With respect to the few among the buzzillions of gaps I’ve commented on, there are problems with physics, chemistry, and probability.

    But the problem is evolutionists can’t imagine in clear mechanistic detail how some of the gaps I’ve described can be bridged.

    So, essentially the same question I posed to John Harshman: “is there a gap of mechanistic difficulty big enough that would persuade you a miracle was needed?” If you say, “yes”, then suggest why the gaps I described are too small. If you say, “no”, then even if God worked a miracle, you’d never be able to realize it given your epistemological policy.

    I realized something about 15 years ago, unless we are God, we can’t absolutely know something is true (except maybe the existence of our own pain). Therefore, some amount of faith is always needed for us to accept what is true because of necessity, we lack exhaustive information.

    The real world shows that it did.

    Correction, you’re imagined world, and an imagined world that lacks mechanistic details to boot. You believe it without sufficient mechanistic detail. If you claim evolution is mechanistically feasible, it’s not to much to ask to try to provide mechanistic details. The mechanistic details should follow an outline like:

    0. Initial state
    1. event that creates next state
    ….
    N. Final state

    Common descent theories don’t have mechanistic descriptions when they can’t even describe the ancestor (state 0) of orphan systems, much less the intermediates connecting the ancestor to the final descendant (state N).

    Theories invoking miracles don’t require mechanistic explanations. But the claim of common descent without miracles is a claim a creature like a lungfish like fish can evolve into a giraffe naturally requires mechanistic description if it is to be elevated to the level of other mechanistic theories like Celestial Mechanics. I’ve provided lines of reasoning not based on incredulity, but on improbability. You could of course say, “we don’t know, but we believe despite lack of direct observation.” That’s more acceptable than saying universal common descent is “fact fact fact”, so much so you call your imagination “the real world”.

    argument still essentially boils down to a classic appeal to ignorance fallacy

    Wrong, proof by contradiction (loosely speaking).

    If someone said a tornado passed through a junk yard and created a 747 and I didn’t believe him, would you say that lack of belief on my part is from ignorance or understanding?

    You all have been given numerous opportunities to provide mechanistic details of some of the gaps described. You all sound to me like people claiming 747s can be made by tornados passing through a junkyard, and your lack of detailed responses doesn’t persuade me you have a credible case, in fact quite the opposite.

  13. colewd:
    John Harshman,

    How would you define descended in this case?

    In the ordinary way. Individuals reproduce, DNA undergoes semi-conservative replication and replicated genomes are inherited by daughter cells. As opposed to poofing of organisms out of thin air, or perhaps assembly from raw materials in a lab. Tinkering by Jesus would presumably not interfere with the process of common descent any more than any other sort of mutation would.

  14. In any case, after I met Nathaniel Jeason this Fall at the Lipscomb University conference, I realized he came to some of the same conclusions I did about the evidence of the recency of MRCA of so many creatures, but he did so in a far more rigorous way. Jeanson’s a smart guy, PhD in stem cell research at Harvard. He dedicated his career to studying creation.

    If all the MRCA’s are relatively recent relative to geological time, then the timeline of LUCA will look rather questionable, and maybe even LUCA itself, and thus also common descent.

    That’s why I put on the table the problem of MRCA.

  15. stcordova: Common descent theories don’t have mechanistic descriptions

    Actually, common descent theories have mechanistic descriptions of exactly what they’re proposed to explain: that nested hierarchy I keep bringing up. Common descent does not explain the causes of mutations or other transformations. It’s not intended to explain them. Nobody thinks common descent is the cause of mutations or other transformations. The only connection between them is that common descent provides evidence that such transformations occurred. In order to know how or why you have to get into other sorts of theories and evidence. Common descent’s mechanistic explanation for the nested hierarchy is simple enough that I can imagine even you understanding it: inheritance.

    Why can’t you understand these simple facts?

  16. stcordova: But the problem is evolutionists can’t imagine in clear mechanistic detail how some of the gaps I’ve described can be bridged.

    Yet you have no problem imagining how a supremely intelligent God would make rigid bird wings by fusing ancestrally-articulated bones into single structures. Or how this supremely intelligent being would choose to make (most) mammalian testes develop in essentially their ancestral positions then design for them to descend to the scrotum, rather than simply adopting the high-temperature avian testes.

    IOW, evolution explains, you just stonewall, looking for something that evolution supposedly can’t do. Meanwhile, you explain nothing about design, and nothing about the Designer’s mind that somehow follows evolutionary pathways. Not understanding life appears to be your goal, and you seem to be there already.

    Glen Davidson

  17. stcordova:
    In any case, after I met Nathaniel Jeason this Fall at the Lipscomb University conference, I realized he came to some of the same conclusions I did about the evidence of the recency of MRCA of so many creatures, but he did so in a far more rigorous way.Jeanson’s a smart guy, PhD in stem cell research at Harvard.He dedicated his career to studying creation.

    Hey, Harvard is a prestigious university, and you forgot to mention that. When will you realize that name-dropping is not an argument?
    Incidentally, the name appears to be “Jeanson”.

    If all the MRCA’s are relatively recent relative to geological time, then the timeline of LUCA will look rather questionable, and maybe even LUCA itself, and thus also common descent.

    Why? Please show your work. Why would we expect MRCA’s within a species to date back to the beginning of geological time? Do different genes within a species date back to the same time? What about alleles that transcend species, like the HLA alleles I mentioned? What, for that matter, about paralogs within a species? If you want to talk about this notion of yours, you first need to explain it coherently.

  18. stcordova,

    But why do you even invoke coalescence? Most stuff drifts out of populations if the population size is constricted.

    What you’re describing there is coalescence. If an allele drifts out of a population – or is lost through selection for that matter – and only one version remains, everyone is descended from one ancestral sequence – the coalescent – at that locus.

  19. colewd,

    Deleterious mutations are a problem for the theory. Especially mutations that can stop a proper birth from occurring.

    Deleterious mutations that stop a birth from occurring trouble evolution not one whit. I should not have to explain why.

  20. stcordova,

    If all the MRCA’s are relatively recent relative to geological time, then the timeline of LUCA will look rather questionable, and maybe even LUCA itself, and thus also common descent.

    You’d think someone would have noticed.

  21. Allan Miller,

    Deleterious mutations that stop a birth from occurring trouble evolution not one whit. I should not have to explain why.

    Please don’t be impervious to evidence that is contradictory to the TOE. This statement is categorically false. If not you are claiming that no amount of delirious mutations that stop embryo development can affect the TOE.

    As I said, they are mine fields. If we find enough mines then it becomes virtually impossible to walk through the field randomly and not get blown up.

    Again, we are talking about delirious mutations that terminate embryo development.

  22. stcordova: I can’t imagine how perpetual motion machines can work because they won’t work.

    We know why perpetual motion machines won’t work by deductive entialment from basic physical laws.

    You have not done any entailments for evolution. You have tried to argue by vaguely hinting in the direct of “constraints”. But nowhere have you shown that these constraints deductively entail immutability.

    With respect to the few among the buzzillions of gaps I’ve commented on, there are problems with physics, chemistry, and probability.

    No, there isn’t at all any such problem. If there was such a problem, you would have shown there was, rather than just wave your hands vaguely in the direction of constraints.

    You have no deductive arguments, or mathematical calculations, from which it logically follows these things can’t evolve. You just have a list of things that constrain evolution, and then your subjective feeling that these constraints amount to immutability. But that is just it, a subjective feeling. You have not shown using proper logic how it actually follows. You never give any numbers or produce a valid logical syllogism.

    But the problem is evolutionists can’t imagine in clear mechanistic detail how some of the gaps I’ve described can be bridged.

    What a silly thing to say. Anyone can imagine everything. And you’d be the first one to complain if someone just imagined something. Which makes your demand for some arbitrary level of detail you can’t even meet yourself, extremely hypocritical.

    So, essentially the same question I posed to John Harshman: “is there a gap of mechanistic difficulty big enough that would persuade you a miracle was needed? If you say, “yes”, then suggest why the gaps I described are too small.

    Yes. A life form that defies the laws of physics.

    None of the gaps you speak about are between a form of life that obeys the laws of physics, and one that doesn’t.

    I realized something about 15 years ago, unless we are God, we can’t absolutely know something is true (except maybe the existence of our own pain).Therefore, some amount of faith is always needed for us to accept what is true because of necessity, we lack exhaustive information.

    We don’t have to know things to an absolute certainty to have enough evidence that we can be extremely confident in some conclusion.

    Correction, you’re imagined world, and an imagined world that lacks mechanistic details to boot.

    Excuse me, I’ve linked several articles in this very thread that shows how and when an entire family of steroid hormone-controlled gene regulatory elements evolved. You’ve refused to even comment on a single one of them. You keep pretending this evidence doesn’t exists and just try to speak in vague generalities about “constraints” and then pretend your job is done.

    I could give another twenty such articles on a diverse range of reconstructed evolutionary histories for entire families of enzymes and other genes. All of it evidence that shouldn’t exist, and inferences that shouldn’t be possible if the data didn’t indicate it to an extreme level of significance.

    You believe it without sufficient mechanistic detail.

    I believe it with a mindbogglingly high level of detail we could not even have imagined was possible to possess a hundred years ago.

    The complete evolutionary histories of entire families of many hundreds of different transcription factors (not to mention all sorts of metabolic enzymes and countless other forms of genes and their products) are in many cases known to the single-mutation level from their origins billions of years ago and subsequent divergence into the total diversity of known cellular life.

    The “sufficent mechanistic detail” you ask for betrays you having a FANTASTIC level of hypocritical double-standard wrt evidence, when you yourself can give NONE AT ALL for the vacuous place-holder answer you wish to supplant evolution with.

  23. colewd: we are talking about delirious mutations that terminate embryo development

    Yes, and the obvious point that Allan is desperately hinting at is that such mutations never attain a frequency greater than 1/(2n), nor does any dominant lethal, and so they never matter in evolution. Now what you’re claiming is perhaps that lethal mutations are such a high percentage of all mutations that if mutations actually happened we would all be dead. And yet if that’s true you can’t account for the standing genetic diversity within species, heterozygosity within individuals, or the hundred or so new mutations in every human individual.

  24. Rumraket, to Sal:

    The fact that we find the very pattern that common descent predicts, should lead you to STRONGLY suspect that one creature CAN and actually DID evolve to be another.

    And not just strongly, but overwhelmingly. Sal thinks his personal incredulity is enough to outweigh odds of 10^38 to 1. He’s not a very smart gambler.

  25. stcordova: If you claim evolution is mechanistically feasible, it’s not to much to ask to try to provide mechanistic details. The mechanistic details should follow an outline like:

    0.Initial state
    1.event that creates next state
    ….
    N.Final state

    First of all, it’s YOUR job to account for the nested hiearchy of life with an actual predictively falsifiable theory. No amount of us lacking your hypocritically demanded level of detail is going to make YOU be in possession of a coherent explanation for the pattern you are asked to account for.

    But since you’re asking, I’ve already posted this, you completely ignored it:

    McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW.
    Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module.
    Cell. 2014 Sep 25;159(1):58-68. doi: 10.1016/j.cell.2014.09.003

    Summary
    Complex gene regulatory networks require transcription factors (TFs) to bind distinct DNA sequences. To understand how novel TF specificity evolves, we combined phylogenetic, biochemical, and biophysical approaches to interrogate how DNA recognition diversified in the steroid hormone receptor (SR) family. After duplication of the ancestral SR, three mutations in one copy radically weakened binding to the ancestral estrogen response element (ERE) and improved binding to a new set of DNA sequences (steroid response elements, SREs). They did so by establishing unfavorable interactions with ERE and abolishing unfavorable interactions with SRE; also required were numerous permissive substitutions, which nonspecifically improved cooperativity and affinity of DNA binding. Our findings indicate that negative determinants of binding play key roles in TFs’ DNA selectivity and—with our prior work on the evolution of SR ligand specificity during the same interval—show how a specific new gene regulatory module evolved without interfering with the integrity of the ancestral module.

    Introduction
    Transcription Factor Specificity and the Evolution of Gene Regulatory Networks
    Development, homeostasis, and other complex biological functions depend upon the coordinated expression of networks of genes. Thousands of transcription factors (TFs) in eukaryotes play key regulatory roles in these networks because their distinct affinities for DNA binding sites, other proteins, and small molecules allow them to specifically regulate the expression of unique sets of target genes in response to various hormones, kinases, and other upstream molecular stimuli. Most studies of the evolution of gene regulation have focused on how changes in cis-regulatory DNA can bring a new target gene under the influence of an existing TF (Carroll, 2008, Wray, 2007) or on changes in protein-protein interactions among TFs (Brayer et al., 2011, Lynch et al., 2011, Baker et al., 2012). TF specificity for DNA can and does evolve (Baker et al., 2011, Sayou et al., 2014), however, and little is known concerning the molecular mechanisms and evolutionary dynamics by which such changes occur. In turn, it remains unclear how distinct gene regulatory modules—defined as a transcription factor, the molecular stimuli that regulate it, and the DNA target sequences it recognizes—emerge during evolution. If TFs are constrained by selection to conserve essential ancestral functions (Stern and Orgogozo, 2009), how can new regulatory modules ever arise? Do specific modules evolve by partitioning the activities of an ancestral TF that is promiscuous in its interactions with DNA targets and molecular stimuli (Sayou et al., 2014) or by acquiring entirely new interactions (Teichmann and Babu, 2004)? What is the genetic architecture of evolutionary transitions in TF specificity, and what kinds of biophysical mechanisms mediate these changes? Answering these questions requires dissecting evolutionary transitions in TFs’ capacity to interact specifically with DNA and molecular stimuli. Ancestral protein reconstruction, combined with detailed studies of protein function and biochemistry, has the potential to accomplish this goal (Harms and Thornton, 2010).

    The knowledge gap concerning transcription factor evolution mirrors uncertainty about the physical mechanisms that determine TFs’ specificity for their DNA targets. DNA recognition is usually thought to be determined by favorable interactions—especially hydrogen bonds but also van der Waals interactions—between a protein and its preferred DNA sequences (Garvie and Wolberger, 2001, Rohs et al., 2010). Supporting this view, structural studies have established that positive interactions are typically present in high-affinity complexes of protein and DNA. Specificity, however, is determined by the distribution of affinities across DNA sequences, and it is unclear whether positive interactions sufficiently explain TFs’ capacity to discriminate among targets. In principle, negative interactions that reduce affinity to nontarget binding sites—such as steric clashes or the presence of unpaired polar atoms in a protein-DNA complex—could also contribute to specificity (von Hippel and Berg, 1986). Evaluating the role of negative interactions in determining specificity, however, requires analyzing not only high-affinity TF/DNA complexes but also poorly bound ones, which are vast in number and difficult to crystallize. We reasoned that, by focusing on a major evolutionary transition in DNA specificity during the history of a family of related TFs, we could gain direct insight into the genetic and biophysical factors that cause differences in DNA recognition (Harms and Thornton, 2013).

    This is just the summary and introduction. Read the whole paper, it’s open access. No excuses.

    This paper has what you ask for. Reconstructed evolutionary histories of families of transcription factors, some times at the single mutation level.

    How is this possible if the phylogenetic methods used to derive these histories are just fantasies? Why can functional ancestral states be inferred and tested?

    How many such articles do you want, and much more importantly, WHAT DO YOU EVEN HAVE TO SHOW IN THEIR STEAD? Nothing. You have NOTHING. This entire thread is a testament to the complete failure of special creationism at accounting for the nesting hiearchy of life.

    Theories invoking miracles don’t require mechanistic explanations.

    Which would make them not-even-theories. If they can’t be observationally tested even in principle, then it’s not science. It’s just unfalsifiable conjecture. Imagination. Just-so stories. Fables you tell yourself out of comfort and personal desire.

    This is a bug, not a feature. Your asking for ANY detail at all when you yourself neither can nor will even attempt to supply any is the act of a HYPOCRITE.

    Wrong, proof by contradiction (loosely speaking).

    You can’t “losely” prove by contradiction. That’s in the words “proof by contradiction”. Which require actual proof and contradiction.

    So get to work. Derive the contradiction.

    If someone said a tornado passed through a junk yard and created a 747 and I didn’t believe him, would you say that lack of belief on my part is from ignorance or understanding?

    Since nobody has claimed this is what happened, you’re now guilty of both the false analogy and appeal to ignorance fallacy.

    You all have been given numerous opportunities to provide mechanistic details of some of the gaps described.

    And since technically we aren’t required to provide any at all, since we are merely trying to account for the nested hiearchy of life, and we have, your demand for anything else than that is just a red herring fallacy.

    But since we also HAVE provided PLENTY of examples of those mechanistic details being bridged, you’re just engaging in denial.

    You all sound to me like people claiming 747s can be made by tornados passing through a junkyard, and your lack of detailed responses doesn’t persuade me you have a credible case, in fact quite the opposite. LALALALA I CAN’T HEAR YOU

    Fixed it for you.

  26. keiths:

    Sal thinks his personal incredulity is enough to outweigh odds of 10^38 to 1. He’s not a very smart gambler.

    Glen:

    I think he’s gambling on people’s gullibility, although I’m not saying that he does so consciously.

    If so, not such a bad bet.

    Except that he’s also making the same bad bet he’s encouraging them to make.

  27. John Harshman,

    Yes, and the obvious point that Allan is desperately hinting at […]

    Haha! I do find that desperate hinting saves an enormous amount of time in actually formulating a response.

  28. Rumraket, to Sal:

    First of all, it’s YOUR job to account for the nested hiearchy of life with an actual predictively falsifiable theory. No amount of us lacking your hypocritically demanded level of detail is going to make YOU be in possession of a coherent explanation for the pattern you are asked to account for.

    All Sal can honestly say in response is “I assume for no reason that there’s a God Designer, and I assume for no reason that he behaves in a way that precisely mimics unguided evolution.”

    It’s Rain Fairy reasoning.

  29. Sal mentions introns in just about every other post. The point appears to be “‘how do you get from ‘XXXX’ to ‘XiiiiXiiiiXiiiiX'” by point mutation? The answer: you don’t.

  30. John Harshman,

    Yes, and the obvious point that Allan is desperately hinting at is that such mutations never attain a frequency greater than 1/(2n), nor does any dominant lethal, and so they never matter in evolution.

    How do you validate the number 1/2n? Are you claiming they cannot be lethal? This is invalidated by experiment.

    And yet if that’s true you can’t account for the standing genetic diversity within species, heterozygosity within individuals, or the hundred or so new mutations in every human individual.

    Can you support the claim that diversity within species requires random change?

    Now what you’re claiming is perhaps that lethal mutations are such a high percentage of all mutations that if mutations actually happened we would all be dead.

    As the mutations start to accumulate through a family by a random walk that families ability to reproduce gets reduced through loss of fitness. This is another obstacle to the claim that the genetic variation we are observing is through random change.

  31. colewd,

    Please don’t be impervious to evidence that is contradictory to the TOE. This statement is categorically false. If not you are claiming that no amount of delirious mutations that stop embryo development can affect the TOE.

    No, I’m not claiming that. I’m claiming that deleterious mutations that do not reach a significant frequency cannot contribute to evolution. Only if all mutations are deleterious does the ToE have a problem with them.

  32. colewd: Please don’t be impervious to evidence that is contradictory to the TOE.

    We aren’t. It isn’t contradictory. The theory of evolution is ENTIRELY compatible with the existence of both lethal and deleterious mutations. They are PART OF the theory.

    This statement is categorically false.

    No, it is absolutely true. Bill, you need to understand the difference between the distribution of mutations that HAPPEN, and the distribution of mutations that get PASSED ON and FIXED.

    Lethal mutations exist, they happen some times. But rarely. Most mutations are not lethal. The frequency of lethal mutations is so low that cells can go through several divisions without even a single one happening.

    So just because you happen to know of a paper where one such mutation was identified, that doesn’t mean that particular mutation happens often.

    Do you understand this Bill?

    If not you are claiming that no amount of delirious mutations that stop embryo development can affect the TOE.

    Nobody is claiming that NO AMOUNT of deleterious mutations can affect TOE. What they’re claiming is that the amount of deleterious mutations that actually happen isn’t big enough to be a problem. They happen, yes, but not often enough.

    You understand this right? There’s a very big difference between saying “there is no amount of deleterious mutations that can ever be a problem”, and “the amount of deleterious mutations that happen is low enough that it isn’t a problem”.
    We are saying the latter, not the former.

    As I said, they are mine fields. If we find enough mines then it becomes virtually impossible to walk through the field randomly and not get blown up.

    Yes, I agree. So Bill, how many mines are there? I’m asking how many, not for a handful of examples. How many mines are there?

  33. colewd:
    John Harshman,

    How do you validate the number 1/2n?Are you claiming they cannot be lethal?This is invalidated by experiment.

    1/(2n) means once, in one gamete that then forms a zygote. That’s as high a frequency as a lethal mutation can get to. And lower and it wouldn’t have happened at all.

    Can you support the claim that diversity within species requires random change?

    What alternative do you propose? If all mutations are lethal, then there can be no variation, because only one genotype is viable.

    As the mutations start to accumulate through a family by a random walk that families ability to reproduce gets reduced through loss of fitness.This is another obstacle to the claim that the genetic variation we are observing is through random change.

    No, that’s your unsupported claim. I would claim that almost all mutations are neutral (in fact, that’s a requirement for random walk), so there is no loss of fitness. Is it your claim that genetic variation arises through divine intervention?

  34. Not sure I am feeling enlighted yet, but here goes.

    J-Mac: So, if you can’t recreate life and actually test that nested hierarchies make sense from the prospective of evolution, your assumption is just as good as mine or Sal’s…

    Why can’t we just test using existing life forms, like bacteria or viruses? Heck, I can demonstrate that common descent gives rise to a nested hierarchy using a piece of paper and pen. What makes it so much more difficult for common design?

    J-Mac: Coreel: First: How do you know that? Can’t we discover those reasons through careful study? Not even devote students like Sal? Why not?

    J-mac: You don’t know that either and as I mentioned above, your speculation is just as good as ours…

    It was YOU who asserted that we cannot know why the designer created a nested hierarchy. Are you admitting that you were speculating?

    J-Mac: Corneel: Second: Most creationists here claim that certain designed characters of species are best understood as adaptations to their envirnonment. […]
    J-mac: Why should I care what other people claim here? Give me one reason! I follow the evidence and NOT claims…

    Are you saying that adaptations don’t exist? Fins and flippers are not for propulsion in water? Camouflage is not for hiding from prey or predators? Designed characters do not really serve a purpose?

    J-Mac: What evidence for nested hierarchies are you actually talking about? You mean the evidence as you see it? The Harshman delusions?

    Heh, that would be neat. The nested hierarchy of life was established long before my or John’s time. It even predates Charles Darwin. It is an observation predating modern evolutionary biology (though common descent explains it very well).

    J-Mac: Well, don’t you think that before you can make the nested hierarchies assumptions you need to resolve some of the major fundamental issues, like the miraculous gene insertions into the tree of life?
    How about the assumptions in endosymbiosis theory flop? Or the orphan features or whole systems?
    Do you think that those issues can be just ignored because you chose to believe in some nested hierarchy nonsense?

    Nope, they are just irrelevant for the issue at hand so I won’t discuss them here (sorry keiths).

    J-Mac: How does the nested hierarchy apply to the origins of the first cell and its essential components that are necessary for the cell to function?

    It doesn’t.

    J-Mac: How does the nested hierarchy apply to ATP, Proteins, DNA and Enzymes within a cell?

    None of those are taxonomically restricted, so once again: irrelevant

    J-Mac: What’s the evidence for nested hierarchies here or the order of nature (my kids are reading it)?

    I can’t believe you just asked me for evidence of the nested hierarchy. I sure hope your kids are reading this, because I feel silly having to explain it:
    Let’s consider sea snakes again. I hope it is obvious that sea snakes are sharing a number of features with other snakes, like vipers (NOT the absence of limbs, experts use features from the skull and skeleton). But snakes are themselves part of a larger group, the scaled reptiles which includes lizards with which they share certain unique features. So we go up to reptiles, vertebrates, animals, etc. Each group has distinguishing characteristics that are nested within the characteristics of the larger group, but not outside it (For example, there are no snakes with hair).
    Modern taxonomists use molecular data from DNA sequences and get exactly the same thing.

  35. stcordova: You represent common descent as physically feasible through ordinary process. Well, where are the details. You can start with this problem:

    prokaryote
    XXXXXXX

    vs.

    eukaryote
    iiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiii

    Maybe you should start with this problem, since you are so fond of it. What prevented the designer from doing this:

    prokaryote 1: XXXXXXXX
    prokaryote 2: XXiiiiXXXiXXX
    prokaryote 3: iiiiiiiiiiiiXiiiiiiiiiiXiiiiiiiXiiiiiiiiiiXiiiiiiiXiiiiiiiiiXiiXiiiiXiiiiii

    eukaryote 1: XXXXXXXX
    eukaryote 2: XXiXXXiiiiXXX
    eukaryote 3: iiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiii

    Any reason why introns have to co-occur with a nuclear envelope?
    BTW yeah I know about bacterial introns.

  36. Allan:

    Deleterious mutations that stop a birth from occurring trouble evolution not one whit. I should not have to explain why.

    colewd:

    Please don’t be impervious to evidence that is contradictory to the TOE. This statement is categorically false.

    No, Bill, it’s absolutely correct. Lethal mutations don’t accumulate in populations. They get removed by purifying selection. As Allan says, we should not have to explain why.

  37. keiths: Lethal mutations don’t accumulate in populations. They get removed by purifying selection.

    It would depend on when the lethality took effect.

  38. It would depend on when the lethality took effect.

    Reading comprehension, Mung.

    We are talking about “deleterious mutations that stop a birth from occurring”. It’s right there in Allan’s comment.

  39. Corneel: J-Mac: How does the nested hierarchy apply to ATP, Proteins, DNA and Enzymes within a cell?

    None of those are taxonomically restricted, so once again: irrelevant

    Irrelevant??? O’RLY?

    Tell us Mr. science how exactly this is irrelevant because my 12 and 14 year old kids are laughing their heads off at your no doubt “words of wisdom” and point to this very “irrelevant fact”:

    DNA is required to make enzymes, but enzymes are required to make DNA. Some of the proteins can only be made by the cell, but a cell can only be made with proteins. Outside the cell, molecules break down. Inside the cell, they cannot reproduce without the help of other complex molecules that have to be there at the same time

    We didn’t even mention RNA just in case you are a believer of the “RNA World” because id you did RNA is required to make proteins, yet proteins are involved in the production of RNA…

    Can you enlighten my kids about this irrelevancy?

    Because you can only think about one thing:

  40. Rumraket: So you don’t know, which means you don’t have an explanation at all…

    We don’t need no stinking explanations. We reject the PSR.

  41. Rumraket: …yet his argument still essentially boils down to a classic appeal to ignorance fallacy.

    I can’t appeal to what I know! Give me a break.

  42. keiths: We are talking about “deleterious mutations that stop a birth from occurring”. It’s right there in Allan’s comment.

    I wasn’t responding to Allan’s comment. I was responding to your comment:

    Lethal mutations don’t accumulate in populations. They get removed by purifying selection.

  43. Mung: My sentiments exactly.

    Mung,
    How can you read their stuff? They contradict each other every other comment and pretend that nothing is wrong or that the major issues they can’t explain are irrelevant… I lost interest…

  44. Rumraket:

    But since you’re asking, I’ve already posted this, you completely ignored it:

    You ignored the gaps I specifically stated. That’s why your irrelevant paper was ignored.

    But thanks any way for an informative link to an another of your failed attempts to put a mechanistic model for bridging important gaps.

  45. Mung:

    I wasn’t responding to Allan’s comment. I was responding to your comment:

    My comment was in direct response to Allan’s, which I quoted immediately beforehand. You ignored that, of course, because you wanted to score a point, and you couldn’t do that honestly.

    It’s a habit of yours. As Rumraket noted elsewhere in the thread:

    And yes, that one’s on you. There’s no way keiths post could seriously be taken to mean anything other than universal common descent except by a deliberately hostile reading.

    You could have elected simply to respond with “I presume you mean universal common descent when you write ‘common descent’”. But you didn’t do that, you responded as if keiths had made some colossal error that has been “refuted”.

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