Your reply. Read the sentence again (“self-correcting science in action”) but this time, with sarcasm.
The point @CrisprCAS9 is making (I believe) is that Dawkins’ statements should not be construed as “science”. This is a guy that does not hold a great deal of scientific respect, talking about things outside of his field of expertise. This is NOT a leading scientist getting something wrong in his particular field. The sarcasm missed it’s mark.
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Yes, that is one of the chief ploys of the ID Creationists. They try portray evolution as an atheistic ideology rather than a scientific theory, and one strategy they use is refer to it with eponyms like “Darwinism” or now “Dawkinsism.”. The parallel with a term like “Marxism” is decidedly NOT coincidental.
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The only person Creationists are fixated on more than Dawkins is Charles Darwin himself. I suspect it’s because they only recognize arguments from authority. To them the Bible is the ultimate authority so they reason evolutionists must have an ultimate authority too. Things like the consilience of evidence no matter who provided the evidence seem beyond their ken.
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Neither the statement by Dawkins nor the blog post by Buggs constitute ‘science’, so your comment is pointless. A condition not helped by the childishness of its delivery.
If science had to correct every non-scientific statement with no basis in reality made by people operating outside their depth and/or field, the journals would just be clogged with responses to the Discovery Institute. Instead, the irrelevant are ignored and progress is made.
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I know. I’m sure the authors know too.
But that’s not “other words” of saying the same thing unless you first define exactly what you mean by an ancestor. If you’re going to here respond that if it isn’t a cell then it isn’t an ancestor by definition, then your argument is just an appeal to a personal definition fallacy. You don’t establish what is true about the world by insisting on a particular meaning for a word.
For a contrary perspective consider that polymers of ribonucleotides can serve as templates for the next “generation” of ribonucleotides. They do so in cells today of course. That fact is employed in PCR. Or in directed evolution of enzymes, where each round of synthesis, screening, and selection of improved mutants is considered a generation. Viruses aren’t cells, yet have generations, genealogies, and ancestors.
A chain of ribonucleotides produced over many rounds of PCR amplification thus clearly has a genealogy of ancestral templates going back through all those rounds of amplification.
So there can, in principle, be a genealogy of molecular replication extending back far before cells. It seems to me a genealogy of replications of DNA (or some other genetic polymer) is very sensibly a form of ancestry.
Now if in your world this idea of pre-cellular genealogical ancestry of replicating genetic polymers(or even some pre-genetic system of interacting molecules) is intolerable, so be it.
Try PCR. No cells involved, yet you clearly can have generations of replication of the DNA.
They just don’t think it was a cell, they still think all extant cells share ancestry. It’s right there Figure 1.
From a common pre-cellular entity, that is a population of progenotes, that evolved. The first progenote was, in their view, the first universal common ancestor.
Your reference there just doesn’t appear to support your argument. Of course, one could argue about the reasoning employed in the paper regarding the cellular nature of the last universal common ancestor and whether that is the most reasonable inference to draw from the available evidence, but that would really be besides the point here. And just to emphasize, the point is you haven’t brought an article that argues against using consilience of independent phylogenies to infer common descent.
The main argument employed by the authors against inferring a cellular luca is the lack of universally conserved biosynthetic pathway for membrane lipids.
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Well, most IDcreationists appear to be more than 60 years behind the abiogenesis literature, given their obsession with Miller & Urey.
I suspect that acknowledging the existence of metabolism-first hypotheses is just too much trouble.
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I didn’t intend to. If you look back in this thread, the question originally raised by evograd was (my paraphrase) how much difference between living things would justify rejecting common ancestry from LUCA? Lack of congruence among molecular phylogenies might represent one such line of evidence. Another would be differing pathways for membrane synthesis, or the structures of the membranes themselves, or differences in DNA replication proteins, all of which de Farias et al. 2021 mention.
Evolutionary biologists – Joe Felsenstein, in this thread, provides a perfect example – tend not to take seriously the question “If common descent from LUCA were false, how would we know it?” Their flippant answers indicate that not only does the question seem to them pointless, it should be regarded as being posed in bad faith by bad actors (e.g., me). In one respect, this response is entirely to be expected. Every science has its core commitments, which to question invites ridicule.
In another respect, however, mocking a question indicates that one hasn’t thought about it, maybe ever, so jokes and ridicule are the best one can do. What I like about the de Farias et al. 2021 paper is they are taking the question seriously. And the editors and referees of BioSystems are as well, which is good. The question isn’t going away.
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“Centuwion, why do they titter so?”
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So this is all about universal common descent, specifically, and you are in no way questioning common descent among, for example, all eukaryotes? It didn’t sound like that. You have cited papers that cover much narrower ground.
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I am interested in how inferences to common ancestry work, logically and evidentially. At the moment, doubt about LUCA’s real existence is growing, but that is permissible within the discipline, given that life has to start somehow. If it started once, it might well have started many times, in spatiotemporally distinct theaters, and some of those independent abiogenesis events may have left offspring in the current biosphere. All this, if not strictly mainstream, is still kosher, and publishable (witness the de Farias et al. 2021 paper).
Inferences to common (versus separate) ancestry higher up in the Tree of Life face an additional constraint, however – the Law of Biogenesis. That changes, fundamentally, how evidence of discontinuity is evaluated. No more starting from scratch independently, once the abiogenesis window has closed irreversibly. Now, if you exist as a cell, you need an ancestor, all the way back.
None of this has anything to do with ID, and everything to do with the structure of evolutionary theory.
Richard Buggs, btw, is a Professor of Evolutionary Genomics at Queen Mary University of London. He does phylogenetic inference as his day job. 
Not opposed to the methods in the least.
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Really? Is there a sort of survey of the state of the field somewhere?
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Hey Paul, I see you completely ignored the main part of my response concerning your unexplained and unreasonably restrictive views on the concept of ancestry.
No, he’s talking about the degree of incongruence between phylogenetic trees. So is the article you linked in the post that spawned this very thread, to which he is responding.
An incongruence between two gene-trees is not a difference between living things, it’s a difference in inferred patterns in the data.
The paper you reference is not using the lack of a homologous structure between two domains to argue against their common ancestry, but rather the lack of homologous genes in the pathways for it’s biosynthesis to argue against the existence of the products of those genes(a cell membrane).
And they’re still not arguing against common ancestry. They’re arguing that it would not have been a cell.
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I’m considering leaving this comment on the blog site, and my main hesitation is that I really don’t think the piece deserves attention. I note also that the blog site used to be explicitly linked to the journal (Nature Ecology and Evolution) but now seems to be completely absent from the journal site.
This piece gives the appearance of being about “public understanding of phylogenomics.” I’m not so sure. The author is right that a simplistic view of how genetic sequences map onto trees is a potential problem when that view is exaggerated as the author claims it is, and when it is being used as an argument that evolution has happened. This, of course, is true of any discussion of any kind with laypeople: when creating models and metaphors, there are dangers in oversimplification and overfreighting, and these dangers are magnified in the presence of institutions and organizations devoted to the discrediting of science itself. Yes, let’s do better when it comes to talking about phylogenomics to the lay public.
But look again at the piece. That’s not what it’s about. It’s about 11-year-old comments by one specific science popularizer. There is no attempt to show that the oversimplification has led to significant misunderstanding or to harm in the ongoing project of defending evolution from the aforementioned institutions nor is there any explanation of how this harm would come about. There is no attempt to show that the popularizer’s oversimplification has grown or spread or been repeated in the ensuring decade. It may be that such harm exists, but it’s hard to imagine that the comments of this one popularizer have wrought the destruction of minds, especially because the oversimplification is contained within words like “approximate” and “consistency of agreement.”
Moreover, the inherent simplification of the tree of life (TOL) has been deeply explored by others in the last few years, most notably in the work of W. Ford Dolittle. He, too, worried about oversimplification embedded in that metaphor, and five years ago listed exactly the same phylogenetic phenomena discussed by our author. In fact Doolittle headlined a whole collection of papers on “How microbes ‘jeopardize’ the modern synthesis” and explicitly emphasized the uses and risks of biological metaphors.
Why then do we have this odd piece about one guy, fawning over the guy, lamenting the guy’s exaggerations, and then–tragically oblivious to the irony–exaggerating them (“Gloriously and utterly wrong”)? Why a piece about old YouTube videos by this guy and not, say, a conversation about uses and risks of metaphors and simplification? I don’t know, but I think it matters that our author refers to “this teaching” as he attacks a person best known not as an evolutionary biologist but as a popularizer of evolution and now much more as a critic of religion. Spend a little time around Christian believers talking about evolution, and you’ll read/hear the phrase “this teaching” while watching them pulverize a voodoo doll named Dawkins. You will hear them link this powerful malevolent being with whole systems of thought, as you see in the title of our author’s post.
Caveat lector.
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Maybe you should wait ten years and then make the comment.
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Are you unacquainted with the literature, then? True, we never test common ancestry vs. a null model of separate ancestry, but the effective null model, of “we can’t resolve the relationships”, would seem a reasonable substitute. Treelike structure in the data implies common descent. Absence of such structure can have multiple explanations, only one of which is separate descent, but that should be good enough. Since there’s treelike structure within eukaryotes, and certainly within metazoans and within vertebrates, that tells us that there is common descent within those groups. That doesn’t mean there aren’t exceptions — perhaps some highly divergent species that can’t be resolved were separately created — but there’s ample evidence for the general case.
In that case I apologize for several things I said. His admiration for Dawkins may be sincere. And perhaps he used extreme language to make a point, though I strongly disagree with his wording. Perhaps you could ask him about phylogenetics.
I see he has a video on why phylogenetics is hard, but again that’s an exaggeration. Sometimes it’s hard, and other times it’s childishly easy. Primate phylogeny, for example, mostly falls into the latter bin. It all depends on what data you can get, how long the terminal branches are, and how short the internal branches are. And of course on whether there’s been much of non-treelike behavior on the part of the genome; plants have that annoying habit of forming hybrid species. Still, it doesn’t seem to prevent plant phylogeny from being worked out.
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Given Buggs’ frequent association with the DI and ID, I find that somewhat doubtful. Buggs is (or was) in fact a member of the DI’s UK offshoot ‘Truth in Science’.
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Several tests of common versus separate ancestry have been tried recently:
https://onlinelibrary.wiley.com/doi/abs/10.1111/evo.12934
The really interesting question, in each case, concerns the model of separate ancestry (SA). I’ll be helping to run an online ID journal club discussion next week (April 8) on the Baum et al. 2016 study. They model SA as random draws from a character distribution. Is that reasonable? I have my doubts. Cuvier and Agassiz would not have agreed that characters fall into a hodgepodge of this and that.
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I agree with you here. I’ve stated for years that an old earth model that has special creation by modification of existing creatures would be indistinguishable from common descent.
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Do you have a hypothesis?
You have doubts, OK, but what’s your alternative hypothesis?
Why do you say that while using the first-person plural? Who is “we” in that sentence? Is there some reason (or do you have a hypothesis?) why early life had to have been cellular?
They wouldn’t and couldn’t exist today given the ubiquity and stability of ribonuclease. However, that stability is consistent with the hypothesis that early cellular life, after the RNA World, evolved an incredibly stable (you can boil it without killing it) ribonuclease to secrete and clobber any open-system, self-replicating ribonucleoproteins in the environment.
That explanation for the stability of ribonuclease is a hypothesis that you can take seriously. Do you have an alternative ID hypothesis of your own to offer?
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