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.
I gather that according to Sal’s calculations he is much more closely related to chimps than to himself… 😉
It’s not his fault… It’s the evolution that plays tricks on humans by making every chimp genome that was sequenced 99% identical to human… a miracle in itself…
I guess the 1% difference accounts for:
3.5 times larger brain
2.5 times brain to body ratio
4 times higher number of brain neurons-16 billion (horsey has 25% more than chimp, needs it to choose organic hay)
3 times more cerebral cortex neurons.Those neurons count the most, because that’s where higher cognitive functions reside (horsey also has 50% more than chimp). That would explain why my friend’s horse seems to be always thinking abstract thoughts when I ride it…
Sal,
While we on the subject of chimp vs human similarity (seriously this time), do you know or have access to the recent data of what % of human dual coding genes is shared with chimps?
The last data I have only says that about 7-8% human genes are dual coding…which I’m sure evolution predicted…
And that’s all he wrote…
And Bill thinks that I am the one that is creating confusion.
What happened to the TAXONOMY you mentioned at some point in this discussion? Did you somewhere in this thread reject the objective nested hierarchy?
BTW: I am duly impressed though by your ability to examine all the molecules in a creature. Perhaps you could show this work sometime?
Yes it does, it still does. It is still the exact kind of pattern common descent predicts.
Common descent explains both. Common descent is what explains the tree pattern, the various mechanisms of evolution is what explains why there are differences between species (be they mutations in orthologous genes, or novel characters that define clades).
No, it isn’t. You’re still not getting it: There would not be any reason for there to BE convergence of independent phylogenies if common descent didn’t take place. Despite all your imagined difficulties, the pattern persists: There is convergence of independent phylogenies. This alone should tell you that your difficulties are imagined, not real.
If they really were a problem for common descent then there simply shouldn’t be convergence of independent phylogenies.
This isn’t indicative of anything at all that has any bearing on the existence of the exact kind of pattern that only common descent is a good, falsifiable explanation for.
What the heck does any of that crap have to do with evolution? You’re just bullshitting with fancy buzzwords, jargon and rhetorical technobabble again.
This silly crap you constantly make up with evolutionary biology somehow being “out of touch” and “antiquated” is just a rhetorical device you’re trying to prop up. You want concoct this deceptive story that there’s some sort of split between evolutionary and molecular biology. Nothing could be further from the truth. They both inform and support each other, in fact they’re inseperably linked.
Of course you actually know this deep down, which is why you’re forced to make up these bullshit lies to try to camouflage the fact that this five thousand post thread is the most colossal spanking of creationism ever seen on the internet.
I can only repeat myself here:
If your creationist religious beliefs were actually true, why do you have to lie like this to support them?
No it doesn’t.
stcordova,
Where have you been? The crocks may have not needed to go to the ark…
Is John’s molecular analysis still valid?
I replied here:
Here is one class of flightless birds I find fascinating. The Penguins. See this video of them swimming and launching out of the water using bubbles to smooth the fluid flow.
The reporter slipped up when describing their function, “this is what they were DESIGNED to do.”
https://prezi.com/_lsrsadatvzf/why-do-penguins-swim-so-fast/
Also
I think Penguins could be a created kind. I don’t think there is enough time to evolve them from a common ancestor in 6,000 years or so.
Here is more on the Penguin’s trapping air bubbles in their feathers and releasing it for launch. It’s cute to see a few you tube commenters thinking God must have made a penguin after seeing the 4-minute BBC video:
They are truly incredible birds. It’s cute to see a few you tube commenters thinking God must have made a penguin after seeing the 1.5-minute BBC video:
Evolution is amazing… its truly a miracle for natural processes initiated by dumb luck to accomplish it…
How about tardigrades? Do you think they are also a created kind?
So would a couple million years suffice?
So you believe penguins can evolve given sufficient time?
So all it requires is for you to be wrong about the age of the earth for evolution to be a valid explanation for penguins?
But of course, it’s impossible that you are wrong about the age of the earth. The preponderance of the evidence obviously points to a 6000 year old earth…..
Yes it does.
Whereas of course it makes much more sense to attribute the origin of penguins to a god that itself handily does not itself need its origin explained.
It’s a very convenient escape hatch you have there J-Mac. By the state of the hinges I can tell it’s used daily…
OMagain,
Yep. And there are no fossil penguins. Or there are but they are just modern ones. Or something.
There are cave paintings older then how old Sal thinks the earth is.
C’mon, the only acceptable response is
[Took the family to the panto this weekend]
🙂
DNA_Jock,
🙂
In this specific case, I agree with you.
But I have a sneaking suspicion that you didn’t watch the 1.5 minute video from the BBC that I referenced.
OTOH maybe you did. In which case, yikes!
Corneel may have unwittingly given a method for YLC/YECs to identify Baramin with the Phospo Proteome. See, it pays to participate here at TSZ!
So now I might have something to present at the annual Baraminology conference ( which has recently evolved it’s name to Creation Biology Society):
http://www.creationbiology.org/
I don’t see how my statement conflicts with that, the examples I gave are monophyletic traits.
Regarding the claim common descent will result in a branching pattern in genes, does this cover the situation like a bacterium with an aaRS gene that’s been around for a hundred million years. Should we expect the gene to diverge in that bacterium between individuals? I mean you all keep swearing a branching pattern over time is predicted. You aren’t going to go back on it now and plead coalescence, are you?
Why do the gene trees have to parallel the morphology trees for species that have been around hundreds of millions of years. Coalescence is a possibility, but it’s not a necessity, is that right. If we, for example have two isolated populations of sharks for 300 million years, the genes in the population should diverege between the two populations right? Should the morphology necessarily diverge.
Common descent doesn’t predict a NECESSARY congruence of morphology and genes does it?
What evidence do you have that whatever individuals you are talking about have been separated for a hundred million years? I know nothing about this aaRS gene, but feel free to cite some literature.
There are no species that have been around for anywhere near that long.
Yes, genes will necessarily diverge. Morphology probably will too, but perhaps not to a great extent. Depends.
Sure it does. Just not necessarily in rate of evolution.
stcordova,
Some genes are highly conserved. I know you don’t think it’s really conservation, but basically they vary less. If exceptions are found to a rule, it does not invalidate the rule for all cases.
That’s a strange statement. I don’t think a branching pattern and coalescence are at odds.
But third positions are not commonly conserved. If there’s little variation at third positions, conservation seems out as an explanation. But I don’t know what data Sal is talking about.
When Sal says “branching pattern” here, he doesn’t actually mean a branching pattern. He just means “large divergence”.
Yeah I’d like to hear more about this aaRS (aminoacyl-tRNA-synthetase) story too.
John Harshman,
I also think when he says ‘coalescence’ he means ‘convergence’.
I suspect that what Sal is hinting at is that aaRS genes don’t follow ‘vertical’ phylogenies all that well – not in deep branches, at least. The standard explanation would be HGT – it seems more likely that such a gene can be transferred between distant relatives without serious impact, since glueing an amino acid to a tRNA is a fairly standard procedure and readily transferable in principle.
As John says though, silent and chemically conservative substitutions are not prohibited, and I’m willing to stake a mince pie on these following other phylogenies quite closely, the more so as one gets towards twig tips.
Not clear why a given aaRS would actually need to vary at all, on Design.
One clear signal is that there are two different basic aaRSs, dividing the acid set neatly in two, distinguished by the reaction sequence. There’s no obvious ‘design’ constraint there either; I’d say that’s certainly suggestive of evolution of the genetic code itself, along two pathways.
Don’t tell Sal that the common ancestors of both the two classes of aaRS have been inferred using ASR, synthesized in the lab, and tested to be functional.
And that these two common ancestors of class I and II, can be encoded two antiparallel strands of DNA. So the 3′-5′ DNA strand will encode the common ancestor of class I, and the 5′-3′ strand complementary to it can encode the common ancestor of class II.
If these two enzyme classes did not evolve from common ancestors, and if they were not originally encoded by opposite strands of the same gene, why can scientists use phylogenetic methods of inference to elucidate the sequences of these ancient genes, recreate them in the laboratory, and test them to have the functions predicted by phylogeny? Such results should be pretty much impossible if common descent, and a deep history of life, did not take place.
Rumraket,
Really? That would be remarkable.
Yep. An amazing fact.
Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene.
Luis Martinez-Rodriguez, Ozgün Erdogan, Mariel Jimenez-Rodriguez, Katiria Gonzalez-Rivera, Tishan Williams, Li Li, Violetta Weinreb, Martha Collier, Srinivas Niranj Chandrasekaran, Xavier Ambroggio, Brian Kuhlman, and Charles W. Carter, Jr.
From the introduction:
“Introduction
Previous studies, summarized in Fig. 1 (1, 2), established a strong posterior probability of the sense/antisense ancestry hypothesis (3, 4) by verifying biochemical predictions of the hypothesis. Parallel structural evolution of the two families is consistent with a similar hierarchy over a 10^5-fold range in catalytic proficiency. We deconstructed members of both aaRS(4) superfamilies to reveal structurally invariant cores that are relatively free of insertions and deletions that would rule out such coding (5, 6). These “Urzymes” (from Ur = primitive) contain the most highly conserved 120–130-amino acid fragments from the two superfamilies. They contain intact active sites, and they accelerate amino acid activation by 10^8–10^9-fold (7, 8) and tRNA aminoacylation by 10^6-fold (9). Furthermore, they are consistent with the antiparallel sequence alignment implied by the Rodin-Ohno hypothesis. This is not true for the intermediate sized catalytic domains with 200–325 residues, which exhibit somewhat larger catalytic enhancements (1, 10), but in Class I they contain long and variable insertions.
Bioinformatic evidence for sense/antisense ancestry is largely obscured by adaptive radiation of Class I and II genes to generate first a full repertoire of synthetases and then through the ∼3.5 billion years during which phyla speciated. We nonetheless identified statistically significant (34%) codon middle-base pairing between antiparallel sequence alignments excerpted from ∼200 contemporary Class I tryptophanyl- (TrpRS) and Class II histidyl (HisRS)-tRNA synthetases and smaller samples from the closely related tyrosyl- and prolyl-tRNA synthetase sequences. Those percentages increased to 42% as independently reconstructed ancestral sequences approached their respective roots (11).
Despite the strength of these two kinds of indirect evidence, it would be desirable to establish whether peptides translated from opposite strands of one gene can indeed accelerate the appropriate chemistry. We report such a direct experimental test here (Fig. 2), in which we extend the hierarchy in Fig. 1 to structures only 46 residues long.
Our earlier biochemical studies showed that Urzymes from both classes retain ∼60% of the free energies of activation associated with kcat/Km (7,–9) and ∼25% of those associated with specific rejection by fully evolved synthetases of noncognate amino acids (1, 2). The catalytic power of peptides related by consensus phylogeny to contemporary aaRS is thus far greater than was anticipated from the gap between the uncatalyzed rates of amino acid activation and peptide bond formation. Uncatalyzed peptide bond formation (12, 13) is ∼106-fold slower than the rate at which Urzymes produce activated amino acids. This million-fold excess catalytic proficiency argues that Urzymes closely resemble true ancestral forms, that they are highly evolved, and hence had simpler functional ancestors. We show here that such ancestors might now themselves be experimentally accessible, especially in context of the literature on uncatalyzed rates (12,–16), which both motivated this study and helped to shape the methods used.”
This is also pretty substantial evidence of a period of evolution before the universal common ancestor of cellular life, and of an evolutionary history of the translation system.
Rumraket,
Interesting, completely counter-intuitive! It seems weird that a completely different set of acids can have such a similar function.
Not given it much thought, but the pattern may actually reflect, or be due to, the curious symmetry of the code itself. More here, (caveat emptor).
AWESOME. You made my day. Merry Christmas, Rumraket.
The question of the aaRS gene and the other question about two separate shark populations (or lungfish populations, or coelacanth populations, etc.) is worth investigating in detail.
I found one very nice paragraph in Joe Felsenstein’s book that is preliminary for some of the subsequent discussions:
From the paper Rumraket cited:
Wrong, it directly substantiates the design of the Class I and Class I aaRS. The experimenters confirmed the common design, they didn’t confirm common descent. Did they create the 46-mers by random mutation? NO! They created them by DESIGN. Thank you very much.
You mean the genes as a matter of principle are young. Thank you very much too!
Actually, even assuming Class I and II had a common ancestor in the SAME gene, it shows that the ancestor had to be remarkably polyconstrained! Even Allan Miller could see this would be a remarkable feat.
Tracing the references in the Christmas gift Rumraket provided:
https://www.ncbi.nlm.nih.gov/pubmed/7494636
Yeah, and we know what happened the last time I analyzed something by Ohno, don’t we? 🙂
They inferred the common ancestors (about 120 amino acids) of the two classes (which are about 300 amino acids in extant life) and resurrected them in the laboratory and tested them for function.
They also inferred that these two common ancestors had evolved from two even smaller active sites (what they call the “invariant cores”), those are the two 46-mers they designed basically by snipping away a domain from each 120 amino acid ancestral protein. And you still have to actually explain why these would even work in the first place.
You should really read the paper instead of scanning for ways to try to dismiss their results or you will make a fool of yourself again and again. If you’re truly desperate you can of course disregard the 46-mers, since the cutting away of the extra domain from the 120 aa class I and II ancestors is of course a design choice (to test an additional evolutionary hypothesis), but you still have to explain why it was possible to infer the two evolutionary ancestors of two entire families of proteins involved in the translation system, using the phylogenetic method of ancestral sequence reconstruction, recreate the inferred sequences in the laboratory, and test them to be functional. The two 120 aa ancestors weren’t designed. They were implied by phylogeny. The tree effectively constitutes a hypothesis about the past, and the inferred ancestors can be and were created, and tested to be functional in the ways predicted by theory.
All of these are facts you can’t explain. So go ahead, flail around trying to make this about the two 46-mers and you will still not have dealt with the meat of the subject.
How does that even follow? The common ancestors of the two classes of tRNA-synthetases have not existed on Earth for over 3.5 billion years at least. You’re just brainlessly asserting the opposite of demonstrable facts.
If phylogenetic trees are just evolutionary fantasies, why does it successfully infer ancestral nodes that provably work in the ways predicted by theory? These results should be basically impossible if creationism was true.
If they were truly incapable of change, why are they even different between species in the first place? Why can a common evolutionary history of the two classes be inferred by phylogenetic methods, the enzymes recreated in the laboratory, and tested to have the functions predicted by theory? How are all these results possible if the past evolutionary history of life did not take place?
What, exactly, could Allan Miller see?
You’re welcome to see if you can find something wrong with it. But at least try to contain your premature ejaculations this time. 🙂
Agreed, Allan, that would be remarkable. 😉
Tracing the bibliographies in Rumraket’s citation shows his citation is a Christmas gift that keeps on giving:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772232/
BWAHAHA!
and
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082485/#B37
And how did these ancestors appear simultaneously? A comparably improbable POOF, 10 poly constrained UR genes that can be read forward and backward poofed together.
Poofology!
Evolutionists believe in things so vanishingly improbable as to be practically indistinguishable from a miracle. They may as well be miracles.
Thanks for all of you venturing a guess, but I was being coy earlier, and I’ll be more direct…..
We have living fossils do we not? Let’s say hypothetically we had living fossil shark populations that were reproductively isolated from each other 300,000,000 million years ago, maybe even before the era of dinosaurs……
So morphologically they are the same, more or less. A shark is a shark. What do you expect the gene differences to look like between individuals of the two populations. Will the shark genes diverge between other sharks about as much as shark genes from humans? I mean, all this insistence on branching pattern is driven by the assumption of inevitable divergence barring coalescence.
Coalescence may limit the branching pattern to some extent within each population, but between populations what would you expect? Obviously this issue could be extended to the aaRS gene of bacteria that have been around for millions of years and are geographically isolated.
Rurmaket found even a bonus feature of aaRS genes. There 20 aaRS genes in each creature, and 10 have backward reading fragments of the other 10. The researchers involved in this discovery were so astonished, they used this to argue against the RNA world and pointed out for the RNA world to work it would require multiple universes. So, at what point will one accept a miracle of God if one will accept the “miracle” of multiple universes.
Notice how Sal is basically trying to change the subject. Rather than explain why it is possible for ancestor reconstruction based on phylogenetic methods to infer functional molecules predicted by theory if common descent did not take place, he just picks out completely irrelevant sidetracks and to focus on. Such as Eugene Koonins suggestion that a translation system springing up fully formed by chance would be extremely unlikely. Who the hell wouldn’t agree with that?
“BWAHAHA!” indeed.
If you had any idea about how to even begin to answer that question you would be attempting such a thing. This response of yours basically amounts to a concession speech.
Haha oh my god. Sal please read the papers for comprehension. All the papers you find, from which you pick out single sentences to demonstrate your desperation with
The ancestors of the two classes preferentially catalyze amino acid activation for the 10 amino acids in their own class. That means only one of them had to arise, as the DNA strand that encodes it, necessarily implies that the antiparallel strand encodes the ancestor of the complementary class. And by that alone there’d be amino acid activation for both entire classes.
You really need to actually read the paper.
The ancestors are significantly promiscous. The ancestor of the class I family, inferred by maximum likelihood phylogeny, prefentially catalyzes amino acid activation of all ten class I amino acids. And the ancestor of the entire family of class II enzymes, preferentially catalyzes amino acid activation of all ten class II amino acids.
The whole implication of these several papers and their experiments (they do many different tests to verify their results), is that the twenty enzymes that exist today, ultimately derive from one single original gene, which encoded a single, possibly only 46 amino acid long protein, and that it’s antiparallel strand did the same. And these two proteins were capable of promiscously but preferentiallly catalyzing aminoacylation of tRNA with all 20 amino acids.
Sal, how are these results possible? Why is it possible to infer functional ancestral states that do not exist in anything living today, using phylogenetic methods, if the methods are just fantasies? This result should not be possible if your creationism is true.
I’ll believe “ancestor reconstruction” when I see it.
Again with these aaRS genes of bacteria. Please give a reference and explain what your point about them is.
LOL, no they didn’t. They argue against the RNA world hypothesis, but it has nothing to do with the fact that the ancestors of these genes can be encoded by opposite strands of the same gene.
No, they didn’t point this out at all. Rather, the authors of the paper mention that in another paper, Eugene Koonin had argued that for a functional translation system to emerge by chance, it would be incredibly unlikely. Which is why nobody believes the translation system emerged by chance.
At this stage I would consider it miraculous if you started to read for comprehension and did not constantly try to mislead and avoid the thread-subject.
By the way, I’d welcome you (or Mung) to start a thread on miracles. What is a miracle, by definition, and what sets a miracle of God, apart from a miracle of nature? Quantitatively? Qualitatively? You both use this word a lot but it’s never clear what you mean by it.
What are you saying here?
That when the authors claim they do ancestor reconstruction by using phylogenetic methods to infer ancestral nodes in an evolutionary tree, they actually aren’t?
Rumraket,
Do you remember how I intelligently designed sequences that created a phylogenetic tree?
The fact a phylogenetic tree can be built from data that have similarity to each other is no proof of phylogeny, it’s proof of similarity.
I already pointed out how remarkable the ancestor must have been so that its genes could be read two ways.
But since we’re talking about the paper, when we are talking anti-codons, my understanding is “TTT” is the anti codon of “AAA”, “CCC” is the anti codon of “GGG”.
We could also say T is the complement of A, and C the complement of G. Is that right?
So, these UR genes in question, if they are anti-parallel, are we reading one in the reverse complement direction or are we reading them in the forward complement direction? I presume reverse complement, but perhaps you can tell me what you think.
But if the UR-gene is readable simultaneously in the forward way, and then in the reverse complement way, the gene is dual coded by being able to be read one way and create a functional protein and then able to be read upside-down complemented and backward and still create another functional protein!!!! You think random chance can make such POOFs of dual function like this?
Natural selection will have a hard time arriving at such polyconstrained architectures: ref. common sense, even the paper you cited, and (gasp) Montanyez, Fernandez, Marks, Sanford on polyconstrained structures.
So your phylogenetic phantasies rest on the miraculous emergence of a dual coded ancestor gene essential for life, actually about 10 such miracles simultaneously. Like so many of your phylogenetic phantasies, it needs a miracle here and there to make it actually feasible.