Posted: Sep 19, 2017 4:46 pm
Wortfish wrote:This paper is not reporting large-scale morphological changes, only changes to hormone receptors.
I know. Which is why I wrote that you bringing up the terms micro and macroevolution to begin with was besides the point.
Wortfish wrote:Macroevolution, strictly understood as "speciation" or "adaptive radiation", is not disputed by either creationists or ID proponents.
Total bullshit.
Wortfish wrote:Rumraket wrote:Third, creationists and ID proponents VEHEMENTLY reject ALL sorts of "blind" evolution (microevolutionary or otherwise). Creationist in particular are taught to stay away from the word 'evolution' entirely. They're taught to call all instances of microevolution (such as the evolution of antibiotic resistance in microbes) for 'adaptation' rather than evolution, and to insist it is just "a pre-existing ability to adapt".
That's just semantics. Creationists accept that mutations occur and that some loss-of-function mutations can be beneficial.
I agree that creationist arguments are just semantics. So too is the labeling of mutations as "loss-of-function" mutation. Just semantics. Actually it's nothing but a rhetorical trick.
Wortfish wrote:Rumraket wrote:ID-Creationists of all stripes pay lip-service to the idea that they accept microevolution, as a rhetorical device, yet in actual fact they utterly reject it. They have all sorts of practiced and rehearsed responses, such as "the information for adaptation was front-loaded/pre-programmed into the genomes and just had to activate first". So no, they don't accept microevolution. They claim they do, they utter the words like you just did "we accept microvoluiton", but in actual fact they don't. They LIE when they say they do.
No. There isn't a single creationist who, for example, denies that bacteria adapt to their environment through mutations: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708842/
Yes there are, we've had some on this site. I've argued with these nutcases before myself. There was one over on talkrational who outright denied that adaptation had anything to do with mutation. And this isn't an unusual phenomenon. I suggest you go to the well-known pro ID blogs like uncommon descent and ask "what kind of evidence is there really that mutations and selection can produce any kind of adaptation?". Then notice how nobody actually answers that question but instead join you in the implication that there is no such evidence. Why would they do that? Because they completely reject all the evidence for anything evolution related. Including the adaptive power of mutation. They're so nuts they think the concep of fitness itself is incoherent and they reject that natural selection takes place. I'm not kidding you.
Wortfish wrote:Rumraket wrote:Fist of all, the paper DOES address the origin and diverging evolutionary histories of two entire classes of transcription factors, from a single ancestor >450 million years ago. And by what standard of measure is the change in specificity from the ancestor, "small"? That's just denialist rhetoric. They prefer DNA sequences that diverge by 33%. How is that a "small" change?
No. It talks about descent from an ancestral gene/protein, and associated changes, not the origin of the ancestor itself.
I don't claim it addresses the origin of the ancestor itself, so there's nothing to say "no" to.
Wortfish wrote:Rumraket wrote:The proteins themselves from their respective classes, differ from each other by as much as ~80% of their total amino acids. The SR protein from Sheep (Q95L13_SHEEP from UniPROT), has an amino acid sequence identity of 19.4% to the orthologous SR protein from american alligators (Q765N5_ALLMI from UniPROT). You can even find this protein in Octopus, an invertebrate. The Octopus protein (Q765N5_ALLMI, UniPROT) has a sequence identity to the American Alligator protein of only 15%. This is so divergent if those were the only two proteins you had, you couldn't infer a homologous relationship without structure-functional data. Then we'd have someone like you sit here and claim they would be entirely different proteins and couldn't possibly have a common evolutionary source. But that massive divergence can be bridged, incrementally, through the orthologous proteins spread out in the diversity of life. So you're fucked.
The SR protein for sheep you cite is an estrogen alpha receptor.
Yes that was a typo, one is an SR and another is an ER. The comparison is still valid however.
Wortfish wrote:A BLAST between the human and the chicken for ESR1 shows a 79% identity, not the low levels you report:
The numbers I report are absolutely correct, but notice how I wrote "as much as ~80%". I didn't say all of them diverge exactly as much. Which should have been obvious since I cite two different numbers for two different comparisons. They were examples I picked from their supplementary materials files where they list all the proteins they used to infer ancestral states with.
Obviously the closer related the species are, the less time there will have been for differences to accumulate. Sheep and Humans are both mammals, and therefore their proteins are much more similar, and for the same class of receptors (SR only) the differences will also be smaller. Octopus is an invertebrate, and is therefore among the most divergent from the vertebrates, and of course much more divergent than the level of differences you will get from within mammals.
Wortfish wrote:But you were comparing an ER for sheep with a PR (progesterone) receptor for the alligator. Apples and oranges.
No, they have a common ancestor protein, which was an ER, that's the point.
Steroid receptors (SR) arose from oestrogen receptors (ER) over 450 million years ago.
But I see now that what you called "a rather small change in the specificity of a transcription factor" up above, you're now calling "apples and oranges". Hoisted by your own petard!
Wortfish wrote:The authors seem to be making the case that the small changes to the daughter gene - three substitutions to be precise - act as a sort of switch between estrogen and androgen specificity. I presume that both androgens and estrogens were produced in the ancestors of vertebrates, so it isn't clear to me if this is an innovation or just a separation of existing functions/specificities.
What they find is that it only takes three specific amino acid substitutions for the functional switch to occur in a duplicate of the ancestral oestrogen receptor (AncSR1), in order to produce the ancestral steroid receptor (AncSR2). The proteins have been further drifting apart ever since.
Wortfish wrote:Rumraket wrote:So what you, random internet nobody, call a "rather small cange in specificity", the authors of the paper call a radical shift in affinity.Second, there used to be only one protein, and now there is two, so one had to actually originate. It originated by duplication and they both subsequently diverged. Furthermore, the study in question PROVES that besides the massive changes in protein sequence and function that has taken place over the last 450 million years of macroevolutionary change, there were STILL MANY MANY MORE functional evolutionary trajectories possible. This thing, the whole thing, in this single paper, properly understood and looked at in context, ROYALLY FUCKS UP THE ASS all IDcreationist arguments ever. Ever.
They can describe it as "radical", but they need to be able to quanitfy what they mean by this.
Funny how the need to make quantifiable statements about the size of the functional shift is now suddenly a requirement when the rhetoric is turned back against you.
But they actually explain that the SR no longer interacts with the ERE (oestrogen response element, AGGTCA), and ER no longer interacts with SRE (steroid response element, AGAACA). They can no longer perform each other's functions. And the ancestral protein AncSR1 that gave rise to both classes (SR and ER) preferred ERE exclusively. So the function for interacting with SRE came after duplication and divergence of the two copies.
Wortfish wrote:As you point out, a copy of an ancestral gene has evolved - through three small changes - differing binding affinity but it is not clear if these mutations simply disabled the ability of the duplicate gene to bind with estrogen-specific DNA sequences.
It is not clear from the small part I quoted above, and the specific work was elucidated in a previous publication of theirs from 2014:
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
In that paper there's this nice figure:
- Fig1.jpg (132.33 KiB) Viewed 2860 times
Accompanied by this text:
Figure 1. Evolution of Novel Specificity Occurred via a Discrete Shift
between AncSR1 and AncSR2
(A) Architecture of SR response elements. All SRs bind to an inverted palindrome of two half-sites (gray arrows) separated by variable bases (n). x indicates sites at which ERE and SREs differ.
(B) SR phylogeny comprises two major clades, which have nonoverlapping specificity for ligands (stars) and REs (boxes). Preferred half-sites for each clade are shown; bases that differ are underlined. Ancestral and extant receptors are colored by RE specificity (purple, ERE; green, SREs; pink, extended monomeric ERE). The orange box indicates evolution of specificity for SREs; number of substitutions on this branch and the total number of DBD residues are indicated. Nodal support is marked by the approximate likelihood ratio statistic (aLRS): unlabeled, aLRS 1 to 10; one solid dot indicates aLRS 10 to 100; two solid dots indicate aLRS > 100. Scale bar is in substitutions per site.
(C) AncSR1 specifically activates reporter gene expression driven by ERE (purple bar) with no activation from SRE1 (light green) or SRE2 (dark green); AncSR2’s specificity is distinct. Bar height indicates fold activation relative to vector-only control with SEM of three experimental replicates.
(D) Ancestral binding affinities reflect distinct specificities for ERE versus SREs. Bars heights indicate the macroscopic affinity (KA,mac) of binding to palindromic DNA response elements, measured using fluorescence polarization; error bars show SEM of three experimental replicates. Colors as in (C).
(E–G) The components of macroscopic binding affinity—affinity for a half-site (K1) and cooperativity of binding (u)—by AncSR1 and AncSR2 were estimated by easuring binding to a half-site and a full palindromic RE and then globally fitting the data to a model containing both parameters. Error bars show SEM of three experimental replicates. See Figure S1 and Tables S1, S2, and S3.
I have highlighted the relevant part in bold.
Wortfish wrote:The ancestral gene may have been, as the authors state, "promiscuous".
They don't write that, where do you get this crap from?
They explicitly reject that inference:
McKeown et al 2014 wrote:The distinct specificities of extant SRs could have evolved by partitioning the activities of a promiscuous ancestor among descendants or by a discrete switch from ancestral to derived forms of specificity. To distinguish among these possibilities, we synthesized coding sequences for the inferred ancestral DBDs and characterized their functions and physical properties. We focused on the capacity to bind ERE, SRE1, and SRE2 because these classical REs differ only at two bases in the half-site and are fully distinct in their responses to the two classes of SR (Zilliacus et al., 1992). Using a dual luciferase reporter assay in cultured cells (Figure 1C), we found that AncSR1 had DNA specificity like that of extant ERs, driving strong activation from ERE but exhibiting no expression above background from SREs. AncSR2, in contrast, specifically activated from both SREs but did not activate from ERE. These results are consistent with the strong sequence similarity between AncSR1 and extant ERs and between AncSR2 and the vertebrate ARs, PRs, GRs, and MRs (Figure 1B). They are further corroborated by the pattern of RE specificities across extant members of the SR family tree: because all known descendants of AncSR2 recognize SREs and all other family members and close outgroups bind ERE-like sequences, the most parsimonious expectation by far is SRE specificity by AncSR2 and ERE specificity by AncSR1 (Eick and Thornton, 2011).
Wortfish wrote:And, of course, it is highly doubtful that all steroid receptors are descended from this hypothetical reconstruction which is more of a template than an actual ancestor.
Thank you for this pile of counterfactual assertions, all of which are contradicted by the results of these papers. Basically what you just did amounts to saying "nya nya didn't happen".
