De-Novo Gene Origination from protogenes.

Incl. intelligent design, belief in divine creation

Moderators: Calilasseia, DarthHelmet86, Onyx8

Re: De-Novo Gene Origination from protogenes.

#81  Postby Rumraket » Apr 16, 2019 10:49 pm

Wortfish wrote:
Rumraket wrote:
Wortfish wrote:
Rumraket wrote:
I would agree that it's a badly worded sentence. What they mean is that additional duplications of the tripeptide repeat also happened after the proto-ORF had ackquired transcriptional regulation. That's why the dark blue part in the figure become significantly longer in the last step F, as they write in the figure legend: "(F) Intragenic (Thr-Ala-Ala)n cds amplification, fulfilling the antifreeze function under natural selection."


Actually, there were 3 duplication events claimed by the authors. Look again at the figure.

Yes, and the one under selection is the last one. Obviously.


The duplication event I am referring to is step C which precedes Step D (the gain of the promoter):

We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred. As the number of AFGP tripeptide-coding repeats increased, the antifreeze function would become augmented.

No, that's not the one. The part you quote is speaking of the last step F. That's the duplications under selective pressure. Obviously.

The other can't be under selective pressure, because at that time there was presumably no expression of the gene, and even if there were, before the association with a signal peptide the protein is unlikely to have found itself in the bloodstream of the fish.

So again, the authors merely expressed themselves badly(and you seem to have got the mistaken impression that they're saying the first duplications were under selection).

They are not actually claiming the gene duplications that happened prior to the locus acquiring a promoter, were evolving under selection before it was expressed. They clearly and obviously only meant to say that the repeat expansions that happened in the last step F were the ones that were happening under selection.

You are making a big deal out of nothing. Get over it already. :roll:
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13215
Age: 40

Print view this post

Ads by Google


Re: De-Novo Gene Origination from protogenes.

#82  Postby Wortfish » Apr 16, 2019 11:21 pm

Rumraket wrote:
No, that's not the one. The part you quote is speaking of the last step F. That's the duplications under selective pressure. Obviously.


No, it isn't. From the figure legend:

(C) A 9-nt in the midst of the four 27-nt duplicates became the three codons for one AFGP Thr-Ala-Ala unit and underwent microsatellitelike duplication forming a proto-ORF.
(D) A proximal upstream regulatory region acquired through a putative translocation event.

They explain in the main text that:

We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred.


This is clearly stage C, and not stage F, that they are referring to.

The other can't be under selective pressure, because at that time there was presumably no expression of the gene, and even if there were, before the association with a signal peptide the protein is unlikely to have found itself in the bloodstream of the fish.


That is precisely my point!

So again, the authors merely expressed themselves badly(and you seem to have got the mistaken impression that they're saying the first duplications were under selection).


Yes. They are claiming that the initial microsatellite repeats of the 3 codon element that make up most of the protein occurred because of selective pressure before the acquisition of the promoter and the frameshift creating a read through ORF with the signal peptide.

They are not actually claiming the gene duplications that happened prior to the locus acquiring a promoter, were evolving under selection before it was expressed. They clearly and obviously only meant to say that the repeat expansions that happened in the last step F were the ones that were happening under selection. You are making a big deal out of nothing. Get over it already. :roll:


Even if you are right - and they did not imply selection was involved with the first two bouts of duplication - the formation of the ORF would have been made possible only through completely chance mutations - but occuring in a very nice order - along with random drift. That is wishful thinking to say the very least.

They also offer no explanation for how parts of the sequence were spliced out as introns.
User avatar
Wortfish
 
Posts: 971

United Kingdom (uk)
Print view this post

Re: De-Novo Gene Origination from protogenes.

#83  Postby Rumraket » Apr 17, 2019 12:01 am

Wortfish wrote:
Rumraket wrote:
No, that's not the one. The part you quote is speaking of the last step F. That's the duplications under selective pressure. Obviously.


No, it isn't.

Yes it is.

From the figure legend:

(C) A 9-nt in the midst of the four 27-nt duplicates became the three codons for one AFGP Thr-Ala-Ala unit and underwent microsatellitelike duplication forming a proto-ORF.
(D) A proximal upstream regulatory region acquired through a putative translocation event.

That doesn't contradict what I said.

They explain in the main text that:
We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred.


This is clearly stage C, and not stage F, that they are referring to.

No, it clearly isn't. The segments being duplicated in stage C and F are the same, the Threonine-Alanine-Alanine tripeptide encoded by a 9-nucleotide repeat.

The other can't be under selective pressure, because at that time there was presumably no expression of the gene, and even if there were, before the association with a signal peptide the protein is unlikely to have found itself in the bloodstream of the fish.

That is precisely my point!

Then all the more reason not to think the authors are somehow stupid and would seriously postulate that selection somehow made duplications happen in a locus not being expressed.

There has to be some sort of limit to how stupid we should allow ourselves to think the authors are. You are familiar with the concepts of strawmanning and steelmanning? Rather than giving their words a deliberately hostile interpretation, try to be at least somewhat charitable and assume they can think.

So again, the authors merely expressed themselves badly(and you seem to have got the mistaken impression that they're saying the first duplications were under selection).

Yes. They are claiming that the initial microsatellite repeats of the 3 codon element that make up most of the protein occurred because of selective pressure before the acquisition of the promoter and the frameshift creating a read through ORF with the signal peptide.

No, there is absolutely zero fucking reason to think they are claiming that, and only a braindead creationist tool with a pseudoscientific political agenda would deliberately ascribe to them this fatuous insinuation.

They are not actually claiming the gene duplications that happened prior to the locus acquiring a promoter, were evolving under selection before it was expressed. They clearly and obviously only meant to say that the repeat expansions that happened in the last step F were the ones that were happening under selection. You are making a big deal out of nothing. Get over it already. :roll:

Even if you are right - and they did not imply selection was involved with the first two bouts of duplication - the formation of the ORF would have been made possible only through completely chance mutations

What's a "completely chance" mutation and how would those be different from mutations happening even if a particular selection pressure is in operation? Natural selection doesn't make particular mutations happen. It instead acts to bias their rate of increase or decrease in frequency in the population when and if they occur, should those mutations have an effect on fitness.

- but occuring in a very nice order - along with random drift. That is wishful thinking to say the very least.

No, it's a completely straightforward explanation of the pattern observed from comparative genetics of the sample of fish taxons being stuided. These are the types of patterns expected to exist if a protein coding gene evolved from non-coding DNA.

They also offer no explanation for how parts of the sequence were spliced out as introns.

What are you even talking about here?
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13215
Age: 40

Print view this post

Re: De-Novo Gene Origination from protogenes.

#84  Postby Wortfish » Apr 17, 2019 3:26 am

Rumraket wrote:
No, it clearly isn't. The segments being duplicated in stage C and F are the same, the Threonine-Alanine-Alanine tripeptide encoded by a 9-nucleotide repeat.


Please read the text and the quotes I provided:

B. "We discovered that the ancestral 9-nt element likely originated within a pair of conserved 27-nt GCA-rich duplicates that now flank each end of the repetitive (Thr-Ala-Ala)n cds in functional AFGPs."

C."We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred."

F."Subsequent intensification of environmental selection pressures likely drove the intragenic (Thr-Ala-Ala)n cds expansion forming large AFGP polyprotein genes (Fig. 4F) as well as additional whole gene duplications."

There are three stages of duplication claimed.

1. Duplication of a GCA-rich stretch of 27 nt ncDNA (Stage B).
2. Duplication of 9 nt elements within the duplicated 27 nt stretches (Stage C).
3. Final intragenic duplications of the TAA tri-codons (Stage F).


Then all the more reason not to think the authors are somehow stupid and would seriously postulate that selection somehow made duplications happen in a locus not being expressed.


Maybe they are stupid....or believe in some sort of Lamarckism where the environment induces mutations to happen.

There has to be some sort of limit to how stupid we should allow ourselves to think the authors are. You are familiar with the concepts of strawmanning and steelmanning? Rather than giving their words a deliberately hostile interpretation, try to be at least somewhat charitable and assume they can think.


We should never assume anything.

No, there is absolutely zero fucking reason to think they are claiming that, and only a braindead creationist tool with a pseudoscientific political agenda would deliberately ascribe to them this fatuous insinuation.


They make that very clear within the text.

What's a "completely chance" mutation and how would those be different from mutations happening even if a particular selection pressure is in operation? Natural selection doesn't make particular mutations happen. It instead acts to bias their rate of increase or decrease in frequency in the population when and if they occur, should those mutations have an effect on fitness.


The repeated bouts of microsatellite-like duplication of just the TAA codons (why not others?) are not just chance mutations but also extremely unlikely to the point of being wishful thinking.

No, it's a completely straightforward explanation of the pattern observed from comparative genetics of the sample of fish taxons being stuided. These are the types of patterns expected to exist if a protein coding gene evolved from non-coding DNA.


It isn't. The whole scenario presented is ridiculous. The worst part is the idea that the proto-sequence was transplanted to a new genomic region and the authors admit they have no idea how it happened:

We propose the possibility that the cis-promoter region was acquired in the most recent common ancestor of the AFGP-bearing clade through a stochastic translocation of the ancestral AFGP founder region to a new genomic site that happened to contain a TATA motif thereby conferring transcriptional capability. Although the specific mechanism of the translocation is currently unclear, cryptic transcriptional initiation sites and regulatory signals are deemed prevalent throughout genomes as increasing evidence suggests large portions of genomes become transcribed at some time.


What are you even talking about here?


Again. Read the paper:

The latent signal peptide (SP)-coding exons were fortuitous noncoding DNA sequence immediately upstream of the 9-nt element, which, when spliced, supplied a typical secretory signal......A functional AFGP consists of three exons and two introns. The first two small exons (E1 and E2) and the first two nts of the large third exon (E3) encode the SP, and the rest of E3 encodes a short propeptide and the long AFGP polyprotein.
User avatar
Wortfish
 
Posts: 971

United Kingdom (uk)
Print view this post

Re: De-Novo Gene Origination from protogenes.

#85  Postby Rumraket » Apr 17, 2019 11:10 am

Wortfish wrote:
Rumraket wrote:
No, it clearly isn't. The segments being duplicated in stage C and F are the same, the Threonine-Alanine-Alanine tripeptide encoded by a 9-nucleotide repeat.


Please read the text and the quotes I provided:

B. "We discovered that the ancestral 9-nt element likely originated within a pair of conserved 27-nt GCA-rich duplicates that now flank each end of the repetitive (Thr-Ala-Ala)n cds in functional AFGPs."

C."We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred."

F."Subsequent intensification of environmental selection pressures likely drove the intragenic (Thr-Ala-Ala)n cds expansion forming large AFGP polyprotein genes (Fig. 4F) as well as additional whole gene duplications."

There are three stages of duplication claimed.

1. Duplication of a GCA-rich stretch of 27 nt ncDNA (Stage B).
2. Duplication of 9 nt elements within the duplicated 27 nt stretches (Stage C).
3. Final intragenic duplications of the TAA tri-codons (Stage F).

None of which contradicts what I said.

Wortfish wrote:
Rumraket wrote:Then all the more reason not to think the authors are somehow stupid and would seriously postulate that selection somehow made duplications happen in a locus not being expressed.


Maybe they are stupid....or believe in some sort of Lamarckism where the environment induces mutations to happen.

Which there is zero reason to think. In fact the authors state the opposite:
Proto-ORF Model of de Novo Evolution of Gadid AFGP.
The deduced evolutionary process of the gadid AFGP gene from non-sense DNA adds valuable insights into how adaptive functional genes could arise “from scratch.” The birth of de novo genes involves two fundamental events: the formation of an ORF and the acquisition of regulatory signals for transcription. In principle, these events could occur in either order. This prompted two major competing models: the protogene versus the proto-ORF model (3, 17, 29⇓–31). The occurrence of a protogene is generally easier to detect as the de novo gene has a noncoding ortholog with demonstrable transcripts in the out-group species. Thus, the model has found ample support in studies that showed transcription preceded the emergence of an ORF (6, 17, 30, 32). The proto-ORF model states that an ORF was present before regulatory signals for expression were acquired. The existence of proto-ORFs is challenging to prove as they likely accumulate mutations that would interrupt the ORF before they could become transcribed for selection to act upon (3, 29, 30, 33).

This shows the authors understand that there could not have been selection operating on the gene before it acquired a transcriptional promoter. So there's no other way to make senes of their words than selection driving the expansion of the Thr-Ala-Ala tripeptide in stage F.

Wortfish wrote:
Rumraket wrote:There has to be some sort of limit to how stupid we should allow ourselves to think the authors are. You are familiar with the concepts of strawmanning and steelmanning? Rather than giving their words a deliberately hostile interpretation, try to be at least somewhat charitable and assume they can think.

We should never assume anything.

Then stop assuming the authors are stupid, or lamarckians, when there's zero evidence to support it, and only evidence against it.
Wortfish wrote:
Rumraket wrote:No, there is absolutely zero fucking reason to think they are claiming that, and only a braindead creationist tool with a pseudoscientific political agenda would deliberately ascribe to them this fatuous insinuation.

They make that very clear within the text.

That there's zero reason to think they're claiming it? I agree.

Wortfish wrote:
Rumraket wrote:What's a "completely chance" mutation and how would those be different from mutations happening even if a particular selection pressure is in operation? Natural selection doesn't make particular mutations happen. It instead acts to bias their rate of increase or decrease in frequency in the population when and if they occur, should those mutations have an effect on fitness.

The repeated bouts of microsatellite-like duplication of just the TAA codons (why not others?) are not just chance mutations but also extremely unlikely to the point of being wishful thinking.

Microsatellite duplications of repetitive DNA is very common. The longer a repetitive sequence is, the more likely it is you get unequal crossover during homologous recombination because you will get stretches of homologus alignment even if the sequences aren't perfectly aligned.

Microsatellite DNA mutations that increase or decrease the number of repeats are so common they are used in DNA profiling and paternity testing, and in forensics because they are so likely to mutate and change in number that they exhibit significant change even over single generations, from one person to it's offspring.

Microsatellite repeat expansions are common drivers of certain neurodegenerative diseases such as Alzheimer's and certain types of frontotemporal dementia caused by CAG repeat expansions (so-called polyglutamine tracts). The more of them you have, the more likely they are to expand further(again, because the longer the repetitive sequence becomes, the more likely it will be misaligned during crossover), causing further and earlier lifetime cognitive decline.

There's nothing unusual or wishful thinking about these duplications. On the contrary, absense of such duplications in a repetitive area of the genome is the unlikely option.

Wortfish wrote:
Rumraket wrote:No, it's a completely straightforward explanation of the pattern observed from comparative genetics of the sample of fish taxons being stuided. These are the types of patterns expected to exist if a protein coding gene evolved from non-coding DNA.

It isn't. The whole scenario presented is ridiculous. The worst part is the idea that the proto-sequence was transplanted to a new genomic region and the authors admit they have no idea how it happened:

Transposition of gene duplicates is an observed fact. It happened in the LTEE when the citrate transporter gene was duplicated into a different area of the E coli genome under control of a completely different promoter. So it's "so miraculously unlikely" that scientists literally watched it happen in a laboratory experiment. That's one of the mutations responsible for the cit+ ability under aerobic conditions, because the previous promoter was inhibited by the presence of oxygen.

There are a myriads of ways known that can facilitate this, of which low levels noisy transcription and subsequent reverse transcription is just one.

We propose the possibility that the cis-promoter region was acquired in the most recent common ancestor of the AFGP-bearing clade through a stochastic translocation of the ancestral AFGP founder region to a new genomic site that happened to contain a TATA motif thereby conferring transcriptional capability. Although the specific mechanism of the translocation is currently unclear, cryptic transcriptional initiation sites and regulatory signals are deemed prevalent throughout genomes as increasing evidence suggests large portions of genomes become transcribed at some time.

Heh, yes. As I were just suggesting.

Wortfish wrote:Again. Read the paper:
The latent signal peptide (SP)-coding exons were fortuitous noncoding DNA sequence immediately upstream of the 9-nt element, which, when spliced, supplied a typical secretory signal......A functional AFGP consists of three exons and two introns. The first two small exons (E1 and E2) and the first two nts of the large third exon (E3) encode the SP, and the rest of E3 encodes a short propeptide and the long AFGP polyprotein.

Yeah what's the problem? Introns are defined by the existence of splice site sequences. These recognition sequences are quite short and can exist many places in noncoding DNA entirely by accident. A whole host of similar and not completely identical sequences can be recognized and spliced.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1522026/
PMC1522026_1471-2105-7-263-4.png
PMC1522026_1471-2105-7-263-4.png (83.55 KiB) Viewed 996 times

Logos of donor and acceptor splice sites. A graphic representation of aligned donor and acceptor splice sites. The relative heights of letters correspond to frequencies of bases at each position. The degree of sequence conservation is reflected in the total height of a stack of letters, measured in bits of information.
Last edited by Rumraket on Apr 17, 2019 12:25 pm, edited 1 time in total.
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13215
Age: 40

Print view this post

Re: De-Novo Gene Origination from protogenes.

#86  Postby Spearthrower » Apr 17, 2019 12:15 pm

Spearthrower wrote:That's clearly not what it says. You've misread it. You should make sure you understand what you are saying before accusing others of dishonesty lest people levy the same charge against you.


:ask:
I'm not an atheist; I just don't believe in gods :- that which I don't belong to isn't a group!
Religion: Mass Stockholm Syndrome

Learn Stuff. Stuff good. https://www.coursera.org/
User avatar
Spearthrower
 
Posts: 27887
Age: 44
Male

Country: Thailand
Print view this post

Re: De-Novo Gene Origination from protogenes.

#87  Postby Wortfish » Apr 18, 2019 1:15 am

Rumraket wrote:
None of which contradicts what I said.


IT DOES. The authors are referring to Stage C, and not Stage F, when they write the following:

"In short, the emergence of a functional AFGP polyprotein cds required only a single nucleotide change in the ancestral 9-nt GCA(Ala)-rich element for it to become the founder codons for one Thr-Ala-Ala tripeptide. Following this, microsatellitelike tandem duplications of the tripeptide cds unit would be required, but both processes could occur with relative ease."


They write later on the following:

Forming proper coding regions of the AFGP gene alone would not lead to a gene product unless a minimal promoter was acquired to activate transcription thereby functionalizing the gene..


In other words, the microsatellite-like repeats of the 3-codon element (Thr-Ala-Ala) preceded the gain on the promoter and the onset of transcriptional activity. And, yet, they still claim that these repeats happened under "selective pressure."

We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred.


That is clearly wrong.
User avatar
Wortfish
 
Posts: 971

United Kingdom (uk)
Print view this post

Ads by Google


Re: De-Novo Gene Origination from protogenes.

#88  Postby Wortfish » Apr 18, 2019 1:15 am

Spearthrower wrote:
Spearthrower wrote:That's clearly not what it says. You've misread it. You should make sure you understand what you are saying before accusing others of dishonesty lest people levy the same charge against you.


:ask:


see above.
User avatar
Wortfish
 
Posts: 971

United Kingdom (uk)
Print view this post

Re: De-Novo Gene Origination from protogenes.

#89  Postby Spearthrower » Apr 18, 2019 1:17 am

Wortfish wrote:
Spearthrower wrote:
Spearthrower wrote:That's clearly not what it says. You've misread it. You should make sure you understand what you are saying before accusing others of dishonesty lest people levy the same charge against you.


:ask:


see above.



Above is you still insisting that your misreading is right.

So...
I'm not an atheist; I just don't believe in gods :- that which I don't belong to isn't a group!
Religion: Mass Stockholm Syndrome

Learn Stuff. Stuff good. https://www.coursera.org/
User avatar
Spearthrower
 
Posts: 27887
Age: 44
Male

Country: Thailand
Print view this post

Re: De-Novo Gene Origination from protogenes.

#90  Postby Wortfish » Jul 01, 2019 10:39 pm

Here is a podcast with two scientists discussing the paper. Note that at 36:16, one of the researchers agrees with me that the authors of the paper seem to imply that the environment induced the mutations: http://www.microbe.tv/twievo/twievo-41/

"I think it is a little misleading, it's like the conditions are causing the mutations..."
Last edited by Wortfish on Jul 01, 2019 10:52 pm, edited 1 time in total.
User avatar
Wortfish
 
Posts: 971

United Kingdom (uk)
Print view this post

Re: De-Novo Gene Origination from protogenes.

#91  Postby Spearthrower » Jul 01, 2019 10:52 pm

Great context there.
I'm not an atheist; I just don't believe in gods :- that which I don't belong to isn't a group!
Religion: Mass Stockholm Syndrome

Learn Stuff. Stuff good. https://www.coursera.org/
User avatar
Spearthrower
 
Posts: 27887
Age: 44
Male

Country: Thailand
Print view this post

Re: De-Novo Gene Origination from protogenes.

#92  Postby Wortfish » Jul 01, 2019 10:53 pm

Spearthrower wrote:Great context there.


Forgot to add the link: http://www.microbe.tv/twievo/twievo-41/ (36:16 onwards)
User avatar
Wortfish
 
Posts: 971

United Kingdom (uk)
Print view this post

Re: De-Novo Gene Origination from protogenes.

#93  Postby Rumraket » Jul 02, 2019 7:02 am

Yeah it's a badly worded sentence, as I initially stated. That's still all it is. They don't make it clear that they're talking about stage F in their later Figure 4, not stage C.
Image
Fig. 4.
Evolutionary mechanism of the gadid AFGP gene from noncoding DNA. The color codes of the sequence components follow Fig. 1. (A) The ancestral noncoding DNA contained latent signal peptide-coding exons with a 5′ Kozak motif, adjacent to a duplication-prone 27-nt GCA-rich sequence. (B) The 27-nt GCA(Ala)-rich sequence duplicated forming four tandem copies. (C) A 9-nt in the midst of the four 27-nt duplicates became the three codons for one AFGP Thr-Ala-Ala unit and underwent microsatellitelike duplication forming a proto-ORF. (D) A proximal upstream regulatory region acquired through a putative translocation event. (E) A 1-nt frameshift led to a contiguous SP, a propeptide, and a Thr-Ala-Ala-like cds in a read-through ORF. (F) Intragenic (Thr-Ala-Ala)n cds amplification, fulfilling the antifreeze function under natural selection.

Natural selection is only mentioned in the final step F.

So here you are confused having found other people confused by the same sentence. Now you're three people who are confused by a badly worded sentence. Great, that's just further evidence it's a badly worded sentence. Yet there's still nothing in the context of the discussion that contains the sentence in question which suggests they must be talking about stage C.

There's no reason to think the authors actually believe selection drove fixation of duplications in an unexpressed noncoding region, that wouldn't make sense and we don't have to assume the authors are so stupid and ignorant they don't know this.

They should have just added this to remove any confusion:
"We hypothesize that, following acquisition of a transcriptional promoter, upon the onset of selective pressure from cold polar marine conditions, additional duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred. As the number of AFGP tripeptide-coding repeats increased, the antifreeze function would become augmented."

That's it, then there would have been no confusion. If you read the legend to figure 4 you will see that natural selection is only mentioned in step F.
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13215
Age: 40

Print view this post

Re: De-Novo Gene Origination from protogenes.

#94  Postby Wortfish » Jul 02, 2019 10:37 am

Rumraket wrote:Yeah it's a badly worded sentence, as I initially stated. That's still all it is. They don't make it clear that they're talking about stage F in their later Figure 4, not stage C.


Let's take a look at the offending sentence again, shall we?

"We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred."

Now, let's look at the descriptions of stages C and F:

(C) A 9-nt in the midst of the four 27-nt duplicates [/b]became the three codons for one AFGP Thr-Ala-Ala unit and underwent microsatellitelike duplication forming a proto-ORF.

(F) Intragenic (Thr-Ala-Ala)n cds amplification, fulfilling the antifreeze function under natural selection.

I think it is fairly obvious that they mean Stage C.

Natural selection is only mentioned in the final step F.


Except that the authors seem to think that there were "selective pressures" at stage C.

So here you are confused having found other people confused by the same sentence. Now you're three people who are confused by a badly worded sentence. Great, that's just further evidence it's a badly worded sentence. Yet there's still nothing in the context of the discussion that contains the sentence in question which suggests they must be talking about stage C.


Read above.

There's no reason to think the authors actually believe selection drove fixation of duplications in an unexpressed noncoding region, that wouldn't make sense and we don't have to assume the authors are so stupid and ignorant they don't know this.


The authors could be confused. In any case, in the absence of selection, there is no reason to think that any of the incremental steps would have been preserved and not lost to subsequent mutations or to random drift.

They should have just added this to remove any confusion:
"We hypothesize that, following acquisition of a transcriptional promoter, upon the onset of selective pressure from cold polar marine conditions, additional duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred. As the number of AFGP tripeptide-coding repeats increased, the antifreeze function would become augmented."


They didn't, because they are referring to Stage C and not F.

That's it, then there would have been no confusion. If you read the legend to figure 4 you will see that natural selection is only mentioned in step F.


But "selective pressures" are referred to earlier.
User avatar
Wortfish
 
Posts: 971

United Kingdom (uk)
Print view this post

Re: De-Novo Gene Origination from protogenes.

#95  Postby Rumraket » Jul 02, 2019 10:50 am

Wortfish wrote:
Rumraket wrote:Yeah it's a badly worded sentence, as I initially stated. That's still all it is. They don't make it clear that they're talking about stage F in their later Figure 4, not stage C.


Let's take a look at the offending sentence again, shall we?

"We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred."

Now, let's look at the descriptions of stages C and F:

(C) A 9-nt in the midst of the four 27-nt duplicates [/b]became the three codons for one AFGP Thr-Ala-Ala unit and underwent microsatellitelike duplication forming a proto-ORF.

(F) Intragenic (Thr-Ala-Ala)n cds amplification, fulfilling the antifreeze function under natural selection.

I think it is fairly obvious that they mean Stage C.

It's fairly obvious that they don't, since natural selection isn't mentioned in stage C, only in stage F.

Done, case closed.

Natural selection is only mentioned in the final step F.


Except that the authors seem to think that there were "selective pressures" at stage C.

Except they don't. Read above.

So here you are confused having found other people confused by the same sentence. Now you're three people who are confused by a badly worded sentence. Great, that's just further evidence it's a badly worded sentence. Yet there's still nothing in the context of the discussion that contains the sentence in question which suggests they must be talking about stage C.


Read above.

Read above.

There's no reason to think the authors actually believe selection drove fixation of duplications in an unexpressed noncoding region, that wouldn't make sense and we don't have to assume the authors are so stupid and ignorant they don't know this.

The authors could be confused.

They could also be unclear. They could be all sorts of things. There's no reason to think they're incompetent, as opposed to just unclear.

In any case, in the absence of selection, there is no reason to think that any of the incremental steps would have been preserved and not lost to subsequent mutations or to random drift.

The incremental steps before F are a chain of mutations happening by random drift.

They should have just added this to remove any confusion:
"We hypothesize that, following acquisition of a transcriptional promoter, upon the onset of selective pressure from cold polar marine conditions, additional duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred. As the number of AFGP tripeptide-coding repeats increased, the antifreeze function would become augmented."

They didn't, because they are referring to Stage C and not F.

No, they're referring to stage F and were just being unclear.

That's it, then there would have been no confusion. If you read the legend to figure 4 you will see that natural selection is only mentioned in step F.

But "selective pressures" are referred to earlier.

Not in the legend to figure 4. When they speak about selective pressure driving fixation of mutations, they're speaking of step F because that's the only point at which selection can operate to fix mutations in the population. There's no reason to think the authors don't know that, and your interpretation is unnecessarily malicious.
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13215
Age: 40

Print view this post

Ads by Google


Re: De-Novo Gene Origination from protogenes.

#96  Postby felltoearth » Jul 02, 2019 11:28 am

Here's an idea Wortfish. Why not contact the authors and ask for clarification?
"Walla Walla Bonga!" — Witticism
User avatar
felltoearth
 
Posts: 14006
Age: 53

Canada (ca)
Print view this post

Re: De-Novo Gene Origination from protogenes.

#97  Postby Rumraket » Jul 02, 2019 11:48 am

Ironic, came back to post that I just emailed them myself, asking for clarification.
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13215
Age: 40

Print view this post

Re: De-Novo Gene Origination from protogenes.

#98  Postby Rumraket » Jul 04, 2019 7:12 am

The authors have responded and I got permission to post the following from our email exchange:

The upshot is, your interpretation is correct.

The initial duplication of the 9-nt (Fig. 4C) was almost certainly random. There were five GCA repeats already at the site embedded within any of the 27-nt sequence copies (Fig. 3D). Short repeats are prone to expansion as we well know.

For expansion of a functional AFGP coding region as depicted in Fig. 4F to occur, it had to be driven by natural selection, which was indicated in the figure legend (and in the main text). This is the context for the sentence in question.

The paper structured the description of the evolutionary process by genic component. The section on the formation of AFGP coding sequence containing the sentence in question preceded the section on functionalization. I can see how the location of that sentence could lead to mis-interpretation if one does not consider the multiple components holistically.

The alternate sentence you suggested indeed would make it more clear.


:cheers:
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13215
Age: 40

Print view this post

De-Novo Gene Origination from protogenes.

#99  Postby felltoearth » Jul 04, 2019 7:47 am

Good stuff! Thanks Rumraket
"Walla Walla Bonga!" — Witticism
User avatar
felltoearth
 
Posts: 14006
Age: 53

Canada (ca)
Print view this post

Re: De-Novo Gene Origination from protogenes.

#100  Postby Animavore » Jul 04, 2019 8:27 am

It's like when Sean Carroll played a vid from Alan Guth at the WLC debate to confirm Craig was misinterpreting BVG.
A most evolved electron.
User avatar
Animavore
 
Name: The Scribbler
Posts: 44680
Age: 42
Male

Ireland (ie)
Print view this post

PreviousNext

Return to Creationism

Who is online

Users viewing this topic: No registered users and 2 guests

cron