Evolution Question About Dinosaurs

[one.opinion]

21 minutes ago, ARGOSY said:

Love you buddy. Don't want a battle of wills. I just thought we could have a decent chat.

Grace and peace, my brother!

[ARGOSY]

On 4/6/2019 at 5:57 PM, one.opinion said:

If you are under the impression that a single mutation is going to nullify the entire process, then you have a fundamental misunderstanding. Expression still occurs and is population-wide, rather than only in single individuals where a single mutation could possibly represent a roadblock.

If we could avoid the side issues and semantics, maybe we could try once more to continue this chat. It is one of my favorite subjects.

The reason I pointed out single point mutations is because of the very logic you affirm in this post. I agree a damaging mutation in one organism definitely will not add to fitness and then become population-wide.  My point was if one small change can sometimes be so damaging to an organism this reveals a certain precision required when a gene expresses itself. 

How was that required precision gained when non-transcribed regions of the genome become active? In the very few instances they have proved that non-transcibed regions can become active, they proudly prove that they are active by noting that this process is lethal to the organism: 

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003860    "Here, we show that RNAi of several Drosophila de novo genes causes lethality – in fact, a higher proportion of de novo genes cause lethality than was found in a similar screen of other young and novel genes"

Edited April 8, 2019 by ARGOSY

[ARGOSY]

On 4/6/2019 at 6:01 PM, one.opinion said:

Why do you think the explanation is weak. Can you provide evidence that refutes it?

Acceptance of a near-spherical earth hasn’t gained universal acceptance, either. Does that mean it isn’t true?

Neither the small shelly fossils of the late Ediacaran, nor the species of the Cambrian Explosion have convincing fossil precursors.  The explanation that the intermediates were soft bodied and therefore did not easily fossilize is negated by the existence of soft bodied fossils ever since. Why the complete absence of these intermediates? 

[ARGOSY]

On 4/6/2019 at 1:43 PM, one.opinion said:

An alternative is that hundreds to thousands of genes were active in humans and other primates, but they all “broke” in the lineages of the other primates and only remained active in humans. Although mutations frequently disrupt the final product, selection of functional genes prevents too many mutations from accumulating because they would lead to overall loss of fitness for the population. The gain of function in a single species is a much more probable event than the coordinated loss of function in many species over the last 6000 or so years (if you believe living organisms have only been on the planet for that long).

Can you show me where in that study, that there were "hundreds to thousands of genes" active in humans, and  inactive in other primates?  Please quote the relevant section. The study's focus was on genes "lacking homologues in any other species", yet you are referring to matching homologues but inactive in some species. 

[one.opinion]

5 hours ago, ARGOSY said:

Can you show me where in that study, that there were "hundreds to thousands of genes" active in humans, and  inactive in other primates?  Please quote the relevant section. The study's focus was on genes "lacking homologues in any other species", yet you are referring to matching homologues but inactive in some species. 

Here is a quote from the Author Summary portion of the paper:

Quote

This is the largest-scale project to date that tries to address this scientific question. We have found thousands of transcripts that are human and/or chimpanzee-specific and which are likely to have originated de novo from previously non-transcribed regions of the genome. We have observed an enrichment in transcription factor binding sites in the promoter regions of these genes when compared to other species; this is consistent with the idea that the gain of new regulatory motifs results in de novo gene expression. We also show that some of the genes encode new functional proteins expressed in brain or testis, which may have contributed to phenotypic novelties in human evolution.

(emphasis mine)

These coding regions lack protein homologues, not DNA homologues. This evidence strongly supports the idea that random changes at the DNA level can lead to new DNA sequences that can be transcribed, and may even lead to new, novel proteins.

While there is no guarantee that these hypothetical new proteins have a positive function for the organism (as your linked article in another post shows), there are examples like an antifreeze protein that appears to have recently developed in certain flies. https://www.pnas.org/content/112/3/737

[ARGOSY]

42 minutes ago, one.opinion said:

Here is a quote from the Author Summary portion of the paper:

(emphasis mine)

These coding regions lack protein homologues, not DNA homologues. This evidence strongly supports the idea that random changes at the DNA level can lead to new DNA sequences that can be transcribed, and may even lead to new, novel proteins.

While there is no guarantee that these hypothetical new proteins have a positive function for the organism (as your linked article in another post shows), there are examples like an antifreeze protein that appears to have recently developed in certain flies. https://www.pnas.org/content/112/3/737

 

You say  ""These coding regions lack protein homologues, not DNA homologues"". You claim these "hundreds to thousands" of genes contain DNA homologues.  This is not right,  de novo genes are specifically genes that contain no homologues.  Your claim is neither logical nor found in the study that you use to support your position. 

The study says  " This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species  "

(yet you say they are observed in the dna)

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005721 ""For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues in any other species. How have these genes originated?""

Let me remind you of your original claim:    

""There are many scientific papers written about the origin of "taxonomically restricted genes". Essentially, many genes have been identified that are very close in DNA sequence to non-coding regions in other, related organisms.""

The study you posted is about de novo genes, not "taxonomically restricted genes". You are yet to support your original claim. 

 

 

 

 

Edited April 8, 2019 by ARGOSY

[one.opinion]

1 hour ago, ARGOSY said:

The study says  " This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species  "

Let's start with some basics. Take a moment to think about what this sentence actually says. It is referring to five thousand "new multiexonic transcriptional events". Do you understand the difference between non-transcribed DNA and transcribed DNA? It is the transcriptional event that is not observed in other species, there is nothing that states that homologous DNA is not present. Let me know when you understand what this means, and then we can proceed.

Did you happen to look at the paper for the antifreeze protein?

[ARGOSY]

45 minutes ago, one.opinion said:

Let's start with some basics. Take a moment to think about what this sentence actually says. It is referring to five thousand "new multiexonic transcriptional events". Do you understand the difference between non-transcribed DNA and transcribed DNA? It is the transcriptional event that is not observed in other species, there is nothing that states that homologous DNA is not present. Let me know when you understand what this means, and then we can proceed.

Yes I understand exactly what the study is referring to, but you are proving again and again that you do not follow it. Yes I understand the difference between non-transcribed and transcribed DNA, I told you I enjoy this subject, and have been studying it before. Let me quote this part again:

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005721 ""For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues in any other species. How have these genes originated?""

The study is precisely trying to establish a database of  genes that are "de novo" in humans and chimps , not matching in any manner to genes in other species, to be able to study these de novo genes further. Yet despite this you still claim there are dna homologues there, yet they are focussing on the GENES  (genes contain dna) which have no homologues. You are missing the whole point of the study. 

[one.opinion]

2 minutes ago, ARGOSY said:

The study is precisely trying to establish a database of  genes that are "de novo" in humans and chimps , not matching in any manner to genes in other species

The reason a very large proportion of these genes do not match other genes isn't because homologous DNA is not present, it is because in other organisms, the homologous DNA regions are not transcribed - and therefore, do not fit the definition of a gene.

6 minutes ago, ARGOSY said:

"For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues in any other species. How have these genes originated?"

Look again - these genes lack homologues - which means that other organisms do not have transcribed DNA that matches. By definition, a gene is required to be transcribed. A very large proportion of these genes do indeed have homology with non-coding DNA in other organisms.

Let me try to illustrate this with an analogy. If I have chocolate chip cookies at my house, but you don't, I cannot conclude that you do not have butter, flour, eggs, sugar, and chocolate chips. All I can say is that you don't have chocolate chip cookies.

P. S. Granted, there are a few genes (much smaller number) that do not even have homology to non-coding DNA sequences, but that's a different story. These are hypothesized to be derived from events that shuffle DNA sequences - very much like the DNA shuffling that occurred in the LTEE that allowed aerobic metabolism of citrate.

[ARGOSY]

4 minutes ago, one.opinion said:

The reason a very large proportion of these genes do not match other genes isn't because homologous DNA is not present, it is because in other organisms, the homologous DNA regions are not transcribed - and therefore, do not fit the definition of a gene.

Look again - these genes lack homologues - which means that other organisms do not have transcribed DNA that matches. By definition, a gene is required to be transcribed. A very large proportion of these genes do indeed have homology with non-coding DNA in other organisms.

Let me try to illustrate this with an analogy. If I have chocolate chip cookies at my house, but you don't, I cannot conclude that you do not have butter, flour, eggs, sugar, and chocolate chips. All I can say is that you don't have chocolate chip cookies.

P. S. Granted, there are a few genes (much smaller number) that do not even have homology to non-coding DNA sequences, but that's a different story. These are hypothesized to be derived from events that shuffle DNA sequences - very much like the DNA shuffling that occurred in the LTEE that allowed aerobic metabolism of citrate.

Where in the study does it indicate that these de novo genes have homology to non-transcribed regions in other organisms?

I rather see comments like these:     Many genes that are annotated as long non-coding RNAs (lncRNAs) are lineage-specific and display high transcriptional turnover 

Lineage specific.