Startling Result–90% of Animals Less than 200 kya

_{May 28, 2018

Darwinism, Evolutionary biology, extinction, Intelligent Design, Tree of life}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

From PhysOrg this morning, in a study using “DNA bar-codes” (mitochondrial DNA, using a specific gene COI) and conducted around the world, here’s the verdict:

The study’s most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.

“This conclusion is very surprising, and I fought against it as hard as I could,” Thaler told AFP.

The scientists can’t figure out what might have caused this. They ask:

Was there some catastrophic event 200,000 years ago that nearly wiped the slate clean?

Maybe a “flood”?

About “bar-codes” there’s this:

On the one hand, the COI gene sequence is similar across all animals, making it easy to pick out and compare.

On the other hand, these mitochondrial snippets are different enough to be able to distinguish between each species.

“It coincides almost perfectly with species designations made by specialist experts in each animal domain,” Thaler said.

IOW, this method works, unlike, say, ‘phylogenetic trees’!

Here’s the actual article. I haven’t had time to read it.

Enjoy!

Comments

One way to refresh your memory and move beyond your imagining of what was in the paper would be to read it. The figure you making the most of, 90% of animal species having a mrca for mtDNA btween 100ka and 200ka is simply not supported by any analysis at all. Why you feel the need to defend this paper's authors I do not know. To know if the level of diversity was consistent with the strict neutrality of mtDNA variants you would need some independent estimate of the effective population size of each species. They don't have that. FWIW, the fact mtDNA does not usually recombine means it is unlikely to evolve as if it were neutral, as selection effects the whole molecule and drags neutral variants along with it.Amblyrhynchus_{June 4, 2018
June
06
Jun
4
04
2018
02:15 PM
2
02
15
PM
PDT}

Amby: If you are going to pay attention to the figure shouldn’t it come from data by way of some sort of calculation? If my memory serves me well, they make mention that 'neutral theory' would require that a much higher level of variation of mt-DNA be found that the very low levels GenBank returns. I imagine it's a straightforward calculation, almost trivial.PaV_{June 3, 2018
June
06
Jun
3
03
2018
07:00 AM
7
07
00
AM
PDT}

as to: "If you are going to pay attention to the figure shouldn’t it come from data by way of some sort of calculation?" So the results of Mathematics now matter to Darwinists?
Darwinian Evolution vs Mathematics - video https://www.youtube.com/watch?v=q3gyx70BHvA
Mathematics is not a friend to Darwinian presuppositions in the least. Where Darwinian evolution is based on a materialistic view of reality which denies that anything beyond the physical exists, on the other hand, Mathematics, which provides the backbone for all of science, engineering and technology,,, mathematics exists in a transcendent, beyond space and time, (Platonic) realm which is not reducible any possible material explanation. Simply put, Mathematics itself, contrary to the materialistic presuppositions of Darwinists, does not need the physical world in order to exist. And yet Darwinists, although they deny that anything beyond the physical exists, need this transcendent world of mathematics in order for their theory to be considered scientific in the first place. The predicament that Darwinists find themselves in regards to denying the reality of this transcendent, immaterial, world of mathematics, and yet needing validation from this transcendent, immaterial, world of mathematics in order to be considered scientific, should be the very definition of self-refuting.
What Does It Mean to Say That Science & Religion Conflict? - M. Anthony Mills - April 16, 2018 Excerpt: In fact, more problematic for the materialist than the non-existence of persons is the existence of mathematics. Why? Although a committed materialist might be perfectly willing to accept that you do not really exist, he will have a harder time accepting that numbers do not exist. The trouble is that numbers — along with other mathematical entities such as classes, sets, and functions — are indispensable for modern science. And yet — here’s the rub — these “abstract objects” are not material. Thus, one cannot take science as the only sure guide to reality and at the same time discount disbelief in all immaterial realities. https://www.realclearreligion.org/articles/2018/04/16/what_does_it_mean_to_say_that_science_and_religion_conflict.htm An Interview with David Berlinski - Jonathan Witt Berlinski: There is no argument against religion that is not also an argument against mathematics. Mathematicians are capable of grasping a world of objects that lies beyond space and time…. Interviewer:… Come again(?) … Berlinski: No need to come again: I got to where I was going the first time. The number four, after all, did not come into existence at a particular time, and it is not going to go out of existence at another time. It is neither here nor there. Nonetheless we are in some sense able to grasp the number by a faculty of our minds. Mathematical intuition is utterly mysterious. So for that matter is the fact that mathematical objects such as a Lie Group or a differentiable manifold have the power to interact with elementary particles or accelerating forces. But these are precisely the claims that theologians have always made as well – that human beings are capable by an exercise of their devotional abilities to come to some understanding of the deity; and the deity, although beyond space and time, is capable of interacting with material objects. http://tofspot.blogspot.com/2013/10/found-upon-web-and-reprinted-here.html
bornagain77_{May 30, 2018
May
05
May
30
30
2018
05:02 PM
5
05
02
PM
PDT}

Amb,
If you are going to pay attention to the figure shouldn’t it come from data by way of some sort of calculation?
You must be new here. :).Allan Keith_{May 30, 2018
May
05
May
30
30
2018
03:47 PM
3
03
47
PM
PDT}

Their 90% figure comes, I’m rather sure, from what they see as an almost uniform lack of mt-DNA variation.
If you are going to pay attention to the figure shouldn't it come from data by way of some sort of calculation?Amblyrhynchus_{May 30, 2018
May
05
May
30
30
2018
03:40 PM
3
03
40
PM
PDT}

Ambly: Is it "blunt-nosed," as in 'scissors'; or is it "snub-nosed" as in a 'revolver'?PaV_{May 30, 2018
May
05
May
30
30
2018
03:20 PM
3
03
20
PM
PDT}

Ambly: I think I've followed their argument fairly well. I think it's simply a matter that you don't agree with them. Their 90% figure comes, I'm rather sure, from what they see as an almost uniform lack of mt-DNA variation. They might be onto something. But, I do agree, they haven't presented it as clearly and forcefully as they might have. But, then again, maybe they're afraid to speak their mind, or their article might be published anywhere.PaV_{May 30, 2018
May
05
May
30
30
2018
03:18 PM
3
03
18
PM
PDT}

Origenes, You keep talking about this argument you have presented,but you haven't articulated it at all. Please try to do so in plain English. But bear in mind, we are talking about gene birth, then posts you've linked to are about evolution over 600 million years. Very hard to imagine they are relevant. PaV, This 90% of animals statistics simply isn't supported by anything in the paper. The idea that a recent common ancestor for mtDNA requires a clonal period is simply wrong. These authors are very confused (presumably why this ended up in such an odd little journal), and you're reading of them is only more confused.Amblyrhynchus_{May 30, 2018
May
05
May
30
30
2018
12:51 PM
12
12
51
PM
PDT}

Amblyrhynchus (Blunt-Nose)[Viper?]: This is from Stoeckle and Thaler’s July 2014 paper:P
In contrast, direct measurements of mitochondrial mutation rate per generation are roughly similar in animals analyzed so far including organisms with very different population sizes and generation times such as fruit flies and humans [37]. The ad hoc modifications to neutral theory commonly proposed to account for low variation in individual cases, namely, recurrent bottlenecks or selective sweeps, struggle as general mechanisms. If bottlenecks limit variation, then a universal low ceiling implies recent population crashes for all species. This appears unlikely– almost a Noah’s Ark hypothesis–although perhaps long-term climate cycles might cause widespread periodic bottlenecks [38]. If selective sweeps limit variation, then a universal low ceiling implies a dynamic view of evolution, with all species adapting all the time [39], in contrast to the equilibrium model at the core of neutral theory.
This makes clear that they were struggling with the fact that mt-DNA clusters were showing that ‘neutral theory’ did not apply. This is a starting point for them. You’ll also note they reach the same conclusion in 2014 that I did in reading their paper: a “Noah’s Ark hypothesis.” They were obviously uncomfortable with this. From the Conclusion of the 2014 paper:
COI barcode variation within avian species is uniformly low regardless of census population size. This finding directly contradicts a central prediction of neutral theory and is not readily accounted for by commonly proposed ad hoc modifications. As an alternative model consistent with empirical data including the molecular clock, we propose extreme purifying selection, including at synonymous sites, limits variation within species and continuous adaptive evolution drives the molecular clock.
The obvious solution to neutral theory’s failure in regard to mt-DNA was to look for “extreme purifying selection.” And so they take up this view in their current, 2018, paper:
Codons that end in G are underrepresented by a factor of about ten in animal mitochondria. Previously we interpreted the lack of third position G’s in mitochondrial coding sequences is evidence of a role for extreme purifying selection in determining the COI DNA barcoding gap [20] but we now find this argument flawed. On the one hand there appears to be purifying selection against codons that end in G but this apparent selection is similar in neighboring species. With selection against G-ending codons in all animal species it could not be a source of species-specific adaptive peaks. Further insight into the lack of G in the third position follows from a focused review of the wobble hypothesis in the context of mitochondria.
So, the ‘neutral theory’ won’t explain the clustering of mt-DNA, nor will “purifying selection,” at least not for codons ending in G. So, now what? It appears that the authors look to “bottlenecks” as the answer to “speciation.”
Bottlenecks, founder effects, lineage sorting, and gene sweeps decrease genetic diversity in a population [111]. The question is how widespread these effects are in the context of defining animal species and if it is possible distinguish them in other than a rhetorical manner. Here we emphasize the overlap—in fact the near congruence—in the conditions that favor each of these mechanisms.
They quote Mayr---"(originally 1942, here quoted from a reprise based on interviews in 2004 [136])”:
The reduced variability of small populations is not always due to accidental gene loss, but sometimes to the fact that the entire population was started by a single pair or by a single fertilized female. These “founders” of the population carried with them only a very small proportion of the variability of the parent population. This “founder” principle sometimes explains even the uniformity of rather large populations, particularly if they are well isolated and near the borders of the range of the species.
Then, invoking Gould and Eldridge:
Models of allopatric or peripatetic speciation invoke a bottleneck with an additional feature: What emerges from the bottleneck looks or acts differently, i.e., it is a bona fide new species. It may be more frequent that what emerges from a bottleneck looks and acts like a middling representative of what went in.
So, Stoeckle and Thaler are saying it’s just a ‘winnowing down’ of what exists prior to a ‘bottleneck’ that counts. Immediately, they say:
If mitochondria are considered “honorary prokaryotes” then the dominant mode in prokaryotes of frequent processes that lead to clonal outgrowth either by selection or random processes [138] are not counterintuitive. A number of different processes could lead to the mitochondrial sequence becoming clonal. Candidate processes include bottlenecks and lineage sorting on three different levels: Within organelles, among organelles in the same cells, among cells in an organism (particularly in the germ line) and among organisms. Not certain is whether different processes have led to a similar result throughout the animal kingdom or if a single process operates throughout. Occam’s razor, the principle of parsimony, suggests that a single explanation should be considered.
In conclusion, their hypothesis seems to be that ‘speciation’ isn’t the result of either ‘neutral theory’ or of ‘natural selection (purifying)’, but of a kind of mitochondrial “cloning” wherein the mitochondria act as a kind of a “honorary prokaryote.” Hence, the whole notion that “90 percent of animal life, genetically speaking, is roughly the same age” is for Stoeckle and Thaler, an indication that some severe “bottleneck” event occurred within the past 200,000 years. And the lack of ‘neutrally’ induced variation ‘within species’ might represent a very new way of looking at how “speciation” takes place. Hence, their final paragraph:
Mitochondria drive many important processes of life [160-162]. There is irony but also grandeur in this view that, precisely because they have no phenotype, synonymous codon variations in mitochondria reveal the structure of species and the mechanism of speciation. This vista of evolution is best seen from the passenger seat.
Obviously the “grandeur in this view” phrase harkens to Darwin’s original conclusion in the Origin of Species and that Stoeckle and Thaler feel as though they've discovered a new, perhaps "the", mechanism for evolution.PaV_{May 30, 2018
May
05
May
30
30
2018
11:22 AM
11
11
22
AM
PDT}

Amblyrhynchus @55 In #44 I quoted your idea of how genes can be explained. The arguments I presented show that your proposal is a non-starter as a full explanation of genes. Moreover, in certain cases, under discussion in GPuccio's OP's, the information jump in gene sequence, during the vertebrate transition, is so large and homology with pre-vertebrates so low, that the distinction between "old" and "new" gene becomes arbitrary.Origenes_{May 30, 2018
May
05
May
30
30
2018
06:50 AM
6
06
50
AM
PDT}

In #44 I point out the glaringly obvious, namely that your archetypal fantasy about gene origination is a non-starter due to lack of probabilistic resources and your unwarrented assumption of integrability of new genes.
You'll note this is still not an argument. In 44 you linked to a post about BLAST bitscores and some calculation about the number of mutations occurring in a single population over time. Somehow I'm meant to conclude from this that evolution couldn't happen (?), but even then, none of this has anything to do with the de novo origin of genes. So... yeah. I find it all a little confusing (and, I'll admit, amusing too).Amblyrhynchus_{May 30, 2018
May
05
May
30
30
2018
04:21 AM
4
04
21
AM
PDT}

In 45 Amblyrhynchus claims:
"Often the regulation comes before function, actually."
Because of course, as every Darwinists knows, regulating non-function is essential if you ever want to someday regulate function? :)
No Mere Bike Messenger, RNA Code Surpassing DNA in Complexity - March 21, 2017 Excerpt: In short, RNA has graduated from servant to master. The numerous RNA transcripts floating around in the nucleus, once thought to be genetic “noise,” may actually be the performance, like virtuosos in an orchestra bringing static notes written in DNA to life. This huge shift in thinking appears to be deeply problematic for neo-Darwinism. It sounds like a symphony of intelligent design. https://www.evolutionnews.org/2017/03/no-mere-bike-messenger-rna-code-surpassing-dna-in-complexity/
Amblyrhynchus then states:
"Random transcription makes lots of RNA, a few of them have a function."
Actually, RNA transcriptions are "highly non-random",,,
Toppling Another Evolutionary Icon, ENCODE Suggests Endogenous Retroviruses Are Functional - Casey Luskin - September 7, 2015 Excerpt: ENCODE didn't merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production--patterns which indicate that these vast quantities of RNA transcripts aren't junk.... ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases. Thus, as two pro-ENCODE biochemists explain, "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue-specific transcription in human cells." http://www.evolutionnews.org/2015/09/toppling_anothe099111.html
Moreover many classes of RNA transcripts are now shown to have function of some sort.
Shedding light on the 'dark matter' of the genome - May 19, 2016 - University of Toronto Excerpt: What used to be dismissed by many as “junk DNA” is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) — genome’s messages that do not code for proteins — in development and disease.,, ncRNAs come in multiple flavours: there’s rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA’s place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe’s group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings. https://www.sciencedaily.com/releases/2016/05/160519120935.htm
Moreover, Darwinists certainly did not predict that the vast majority of the genome would be transcribed into functionally important RNA transcripts,.
Junk DNA not as worthless as once thought - 07/24/2014 Excerpt: As early as 2007,, Hackermüller, together with a number of colleagues, was able to demonstrate,, practically the entire genome (is transcribed into RNA—a template which normally serves the production of proteins),,, In their latest study,, Hackermüller and his team,, were able to bridge yet another knowledge gap. The transcription of non-coding regions in the genome is precisely regulated by cellular signaling pathways—and on a grand scale: up to 80% of the RNA copies were non-coding. "We did not expect such a magnitude," says Hackermüller. "This is not indicative of a chance product—it is highly likely that the non-coding RNAs perform a similarly important functions to that of protein-coding RNA." http://www.rdmag.com/news/2014/07/junk-dna-not-worthless-once-thought?et_cid=4064233&et_rid=653535995&location=top
In fact, Darwinists presupposed non-functionality for the vast majority of the genome because it was forced on them by the mathematics of population genetics. That is precisely the reason why Dan Graur said that “if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.”
Dan Graur, Darwin’s Reactionary - June 21, 2017 Excerpt: In 2013, biologist Dan Graur criticized the “evolution-free gospel of ENCODE” and accused its researchers of “playing fast and loose with the term ‘function,’ by divorcing genomic analysis from its evolutionary context.”81 In a lecture at the University of Houston, Graur argued that “if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.” In other words: “If ENCODE is right, then evolution is wrong.” But for Graur, evolution can’t be wrong. His solution to the problem? “Kill ENCODE.”82,,, Lots of evolutionists think that way but only the rare Darwinian atheist materialist is willing to state the matter as nakedly as this. No wonder Dr. Graur is among a list of individuals thanked by Dr. Wells in his Acknowledgments for “making embarrassingly candid or unwittingly humorous statements.” https://evolutionnews.org/2017/06/dan-graur-darwins-reactionary/
Amblyrhynchus then states:
"In general, young genes don’t have especially complex function,"
Actually, many 'young' genes are shown to have essential functions.
Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm
Amblyrhynchus then states:
"many of them make proteins that don’t fold in the way we are used to, for example."
Amblyrhynchus then links to Intrinsically Disordered Proteins (IDPs). IDPs are not as friendly to Darwinian concerns as Amblyrhynchus seems to believe.
Unfolded 'junk' Proteins have function - April 2014 Excerpt: In 2013 functions were identified for many of these (unfolded) “intrinsically disordered proteins” (IDPs), as they are sometimes called. Functions such as crucial roles in regulating ion channels and molecular hubs in intracellular signaling networks. A friend points us to: [1] Bozoky Z, Krzeminski M, Chong PA, Forman-Kay JD (2013) Structural changes of CFTR R region upon phosphorylation: A plastic platform for intramolecular and intermolecular interactions. FEBS J 280:4407-4416. doi:10.1111/febs.12422 [2] Ferreon ACM, Ferreon JC, Wright PE, Deniz AA (2013) Modulation of allostery by protein intrinsic disorder. Nature 498:390-394. doi:10.1038/nature12294 [3] Cumberworth A, Lamour G, Babu MM, Gsponer J (2013) Promiscuity as a functional trait: Intrinsically disordered regions as central players of interactomes. Biochem J 454:361-369. doi:10.1042/BJ20130545 https://uncommondescent.com/intelligent-design/junk-proteins-hit-the-antiques-road-show-and/
Amblyrhynchus said ID was similar to a "Cargo Cult" which is interesting claim for him to make since he is the one that is found to be pretending that he has real evidence of some sort that will fly instead of him actually having any real evidence that will actually fly. https://cdn3.omidoo.com/sites/default/files/imagecache/full/images/bydate/201507/cargo-cult.jpg The shoe is squarely on the other foot, "Cargo Cult", is an extremely apt phrase for the unfalsifiable pseudoscience of Darwinian evolution
Darwin’s Theory vs Falsification https://www.youtube.com/watch?v=8rzw0JkuKuQ
bornagain77_{May 30, 2018
May
05
May
30
30
2018
04:12 AM
4
04
12
AM
PDT}

Amblyrhynchus @ In #44 I point out the glaringly obvious, namely that your archetypal fantasy about gene origination is a non-starter due to lack of probabilistic resources and your unwarrented assumption of integrability of new genes.
Amblyrhynchus: No argument has been presented to me. ...
Well, good for you.
Amblyrhynchus: As I say, it’s an amazing place.
Don't worry, you will be escorted back to where you belong very soon.Origenes_{May 30, 2018
May
05
May
30
30
2018
03:49 AM
3
03
49
AM
PDT}

Amb, no argument has been presented? I suspect, you mean no argument you are willing to take seriously. That reaction on your part is, as they say, interesting. KFkairosfocus_{May 30, 2018
May
05
May
30
30
2018
03:10 AM
3
03
10
AM
PDT}

of related note to the handle "Amblyrhynchus" : It seems that Amblyrhynchus cristatus, which refers to "Galápagos marine iguana", remains "mutually fertile" with land iguanas which it supposedly separated from some 8–10 million years ago.
(Amblyrhynchus cristatus), Galápagos marine iguana, Excerpt: Researchers theorize that land iguanas (genus Conolophus) and marine iguanas evolved from a common ancestor since arriving on the islands from Central or South America, presumably by rafting.[8][9] The land and marine iguanas of the Galápagos form a clade, and the nearest relative of this Galápagos clade are the Ctenosaura iguanas of Mexico and Central America.[5] The marine iguana diverged from the land iguanas some 8–10 million years ago, which is older than any of the extant Galápagos islands.[10][11] It is therefore thought that the ancestral species inhabited parts of the volcanic archipelago that are now submerged. The two species remain mutually fertile in spite of being assigned to distinct genera, and they occasionally hybridize where their ranges overlap, resulting in the so-called hybrid iguana of South Plaza Island.[12]
In other words,the iguana is, like Darwin's finches, a fairly lame example of adaptation that is falsely claimed as proof for 'Darwinian evolution". And here is a picture of our new troll "Amblyrhynchus": https://depositphotos.com/106907528/stock-photo-the-marine-iguana-amblyrhynchus-cristatus.html Handsome little devil isn't he? :)bornagain77_{May 30, 2018
May
05
May
30
30
2018
02:48 AM
2
02
48
AM
PDT}

No argument has been presented to me. PaV took a press release on face value, boranagin pasted a lot of quotes, Rob Sheldon pontificated on... something, jorronet lost the plot, Kaiser strung together a lot of words but produced no meaning and you have linked to giant posts that combine wikipedia-style summaries of particular proteins with some reification of BLAST bit scores to prove... well I'm stilll not sure what they are meant to prove. As I say, it's an amazing place.Amblyrhynchus_{May 30, 2018
May
05
May
30
30
2018
02:44 AM
2
02
44
AM
PDT}

Amblyrhynchus: This place is kind of amazing though.
It must feel uncanny being outside the echo chamber. Meanwhile I note that you have failed to address the arguments presented to you. That is, I take it that you understand that your reference to IDP's is irrelevant to the issue of probabilistic resources. Also IDP's are not in any conceivable way an explanation for huge information jumps as we see in the evolutionary history of e.g. Ubiquitin system.Origenes_{May 30, 2018
May
05
May
30
30
2018
02:30 AM
2
02
30
AM
PDT}

PaV @ 21 -
Was there a ‘flood’ 200 kya? Wouldn’t that be an acceptable hypothesis?
The flood would have to have lasted 100,000 years, so not really.Bob O'H_{May 30, 2018
May
05
May
30
30
2018
01:52 AM
1
01
52
AM
PDT}

when you've seen a cargo cult before it doesn't take long to spot another one. This place is kind of amazing though.Amblyrhynchus_{May 30, 2018
May
05
May
30
30
2018
01:32 AM
1
01
32
AM
PDT}

Amblyrhynchus @ Your "judgement" of two large OP's by GPuccio formed within a time frame of 11 minutes. Do not be offended when I say that your judgement has no value whatsoever.Origenes_{May 30, 2018
May
05
May
30
30
2018
01:25 AM
1
01
25
AM
PDT}

Those linked posts are... really something. Often the regulation comes before function, acutally. Random transcription makes lots of RNA, a few of them have a function. In general, young genes don't have especially complex function, many of them make proteins that don't fold in the way we are used to, for example.Amblyrhynchus_{May 30, 2018
May
05
May
30
30
2018
12:59 AM
12
12
59
AM
PDT}

Amblyrhynchus: So, you have a huge flux in lineage specific transcripts, most of which are doing nothing. Very occasionally, one takes on a biological function and then natural selectio acts to conserve that transcript. When that happen a lineage gains a new gene that will survive into all of its descendants. But the flux is much greatr than the accumulation of new genes.
Wishful thinking. First, we often see information jumps larger than 500 bits, while even the probabilistic resources of bacteria in 4 billion years of natural history, under a hugely optimistic estimate, are well under 140 bits — see here. Second, what are the odds that a new gene sequence can be incorporated by the organism? There are countless biological functions, but any specific organism has no use for the vast majority of them. Moreover, the new sequence needs to be regulated, what is the chance that a functional regulation system just happened to be in place at the advent of the new gene?Origenes_{May 30, 2018
May
05
May
30
30
2018
12:48 AM
12
12
48
AM
PDT}

What?Amblyrhynchus_{May 30, 2018
May
05
May
30
30
2018
12:04 AM
12
12
04
AM
PDT}

Amb, the issue is the informational import joined to the blind search for needles in a haystack. What is before us is evidence of deeply isolated islands of function -- scattered needles with a lot of haystack between. Where, a Hamming distance of just 500 bits is effectively insuperable for blind search mechanisms and the only empirically warranted cause for such is intelligently directed configuration. Where, 500 bits corresponds to a configuration space of 3.27 * 10^150 possibilities. And while I spoke to species above, the far more key cases are OoL and Oo Body Plans. The former requires 100k - 1,000 k bits, more or less and the latter 10 - 100+ M bits. 100 k bits is a space of 9.99*10^30102. Those are vastly beyond the search resources of our solar system or indeed the observed cosmos; which set a threshold at 500 - 1,000 bits. It does not take a lot of singletons to pass that threshold, and in any case the deep isolation of a lot of folds in AA sequence space is also highly relevant. So, while yes some of the phenomenon is explicable on artifacts, that does not credibly explain it away. Likewise, essentially random transcription etc does not escape the search challenge I outlined. KFkairosfocus_{May 29, 2018
May
05
May
29
29
2018
11:58 PM
11
11
58
PM
PDT}

Kaisorfocus, Gene birth and turnover is actually one of my areas of reasarch. The existence of "singleton" genes in newly sequenced genomes is explained by two processes: (a) When we sequence a genome we focus on species that have not close relative already sequenced. The first sea squirt genome had thousands of singletons, but as we have sequanced more of this species relatives we have whittled that number of lineage-specific genes down. So "singleton" genes are partly an artefact of the way we prioritize genome projects, rather than a biologicl result. (b) None the less, there are a suprising (to me) number of totally new genes in some lineages. As we have studies these groups closely, the dynamics of gene birth and death have become clear. There is a lot of essentially random transcription going on in Eukaryotes. As long parrticular sequence motifs are present and chromatin is accessible then transcipts get made. As the sequences underlying these chromatin states and the motifs driving expression drift, the parts of the genome that are randomly transcribed differs among species. So, you have a huge flux in lineage specific transcripts, most of which are doing nothing. Very occasionally, one takes on a biological function and then natural selectio acts to conserve that transcript. When that happen a lineage gains a new gene that will survive into all of its descendants. But the flux is much greatr than the accumulation of new genes. It's a really interesting field at the moment.Amblyrhynchus_{May 29, 2018
May
05
May
29
29
2018
11:29 PM
11
11
29
PM
PDT}

Amb, kindly read this: http://vixra.org/pdf/1105.0025v1.pdf , noting from abstract: "The predominant viewpoint appears incompatible with the finding that the sequenced genome of each species contains hundreds, or even thousands, of unique genes - the genes that are not shared with any other species. These unique genes and proteins, singletons, define the very character of every species." Reflect on the implication of isolated islands of function starting at molecular level and moving up through the diversity of body plans, then down to the requisites of a first living, metabolising, von Neumann self replicator using cell. Especially, on implications of codes and regulated, pretty exact stepwise functional processes. KFkairosfocus_{May 29, 2018
May
05
May
29
29
2018
11:06 PM
11
11
06
PM
PDT}

I said in 25, the general statement that within-species diversity of mtDNA is generally low is well known and not a new result. But, if you actually read the paper, within species diversity varies beteen 0 and 0.8%, with humans at 0.1%. There is still considerable variation in this number. Precisely nothing you have quote about the yeast paper is about mtDNA, the numbers you have cited are not within-species diversity and the comment you made about the paper in 29 is completely unrelated to this point. Just stop.Amblyrhynchus_{May 29, 2018
May
05
May
29
29
2018
10:47 PM
10
10
47
PM
PDT}

1.- For the planet’s 7.6 billion people, 500 million house sparrows, or 100,000 sandpipers, genetic diversity “ is about the same,” he told AFP. 2.- The data is in the paper. 3.- The same as in point 1.jorronet_{May 29, 2018
May
05
May
29
29
2018
09:59 PM
9
09
59
PM
PDT}

What is the author's claim? How is it supported by data in the paper? How is it supported by this yeast paper?Amblyrhynchus_{May 29, 2018
May
05
May
29
29
2018
09:45 PM
9
09
45
PM
PDT}

Not at all, the paper supports the author’s claim and yeast is just another example, you have not presented anything that proves the paper wrong except your disbelief.jorronet_{May 29, 2018
May
05
May
29
29
2018
09:44 PM
9
09
44
PM
PDT}

1 2 3 Next

You must be logged in to post a comment.

Leave a Reply