Evolution Question About Dinosaurs

[one.opinion]

1 minute ago, ARGOSY said:

Lineage specific.

Yes, the genes - those DNA sequences that are actually transcribed - are lineage specific. They are not referring to the DNA sequences themselves.

The paper contains many references to syntenic regions - these are regions characterized by shared DNA sequence. This particular study focused on transcripts, not on the DNA sequence of entire genomes - perhaps not the best example of what I am attempting to show.

Here is an article that is a better example, but done in rice and not humans/primates.

https://www.nature.com/articles/s41559-019-0822-5

Quote

New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality genomes of 13 closely related Oryza species provide unprecedented opportunities to understand de novo origination events. Here, we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of translation.

I've explained this about 4 times now. Unless you have evidence to the contrary, I think it's about time we either moved on or take a break from this tangent.

[ARGOSY]

On 4/8/2019 at 11:42 PM, one.opinion said:

Yes, the genes - those DNA sequences that are actually transcribed - are lineage specific. They are not referring to the DNA sequences themselves.

The paper contains many references to syntenic regions - these are regions characterized by shared DNA sequence. This particular study focused on transcripts, not on the DNA sequence of entire genomes - perhaps not the best example of what I am attempting to show.

Here is an article that is a better example, but done in rice and not humans/primates.

https://www.nature.com/articles/s41559-019-0822-5

I've explained this about 4 times now. Unless you have evidence to the contrary, I think it's about time we either moved on or take a break from this tangent.

What is the use of "explaining things", if you do not quote the relevant section of the paper that supports your claim that:

""these de novo genes have homology to non-transcribed regions in other organisms""   

Sure we can move on, but it has been noted that you make claims about the paper that you do not show exist in the paper, otherwise you would merely quote the relevant section that supports your claim. 

Regarding your next link, yes that is a better example which brings to mind my original point that genes are particular in their expression. Genes are so particular in their expression, they are like the bytes in computer code, located in a precise order to produce software. If you move these about randomly you mess with the precision of the software.  To believe that workable DNA code lies dormant in a species, just waiting to be activated is to believe in a higher power that pre-designed that code. It is impossible for non-coding dna to evolve in a positive direction without previous expression, that is unrealistic to any logical mind, because it cannot just appear in workable form. That is like throwing randomly generated bytes into an order and expecting beneficial functioning software.  It's impossible for a section of DNA that has NEVER BEEN CODING, to then suddenly add any benefit/fitness when expressing itself.  Randomly expressed proteins cause damage or are neutral.  There are only two other options then, the non-coding DNA was supernaturally designed, waiting for an opportunity to express itself. Or the non-coding DNA had in the past been coding, and became dormant. 

https://www.nature.com/articles/s41559-019-0822-5

 

Edited April 10, 2019 by ARGOSY

[one.opinion]

6 hours ago, ARGOSY said:

Sure we can move on, but it has been noted that you make claims about the paper that you do not show exist in the paper, otherwise you would merely quote the relevant section that supports your claim. 

You are correct. As I mentioned, this turns out to not be the best example of what I was trying to show. That's why I brought in the Oryza paper.

 

6 hours ago, ARGOSY said:

It's impossible for a section of DNA that has NEVER BEEN CODING, to then suddenly add any benefit/fitness when expressing itself. 

It is not impossible. Changes to DNA sequences occur all the time. Occasionally, those changes can even lead a non-coding sequence to become a coding sequence. Even more rarely, those new coding sequences even have enough benefit to the organism to be retained in the gene pool. Here is a more concrete example:

https://www.pnas.org/content/116/10/4400

Quote

Our paper presents clear evidence that the antifreeze glycoprotein gene of the northern codfish originated from a noncoding region. We further describe the detailed mechanism of its evolutionary transformation into a full-fledged crucial life-saving gene. This paper is a concrete dissection of the process of a de novo gene birth that has conferred a vital adaptive function directly linked to natural selection.

 

[ARGOSY]

34 minutes ago, one.opinion said:

You are correct. As I mentioned, this turns out to not be the best example of what I was trying to show. That's why I brought in the Oryza paper.

 

It is not impossible. Changes to DNA sequences occur all the time. Occasionally, those changes can even lead a non-coding sequence to become a coding sequence. Even more rarely, those new coding sequences even have enough benefit to the organism to be retained in the gene pool. Here is a more concrete example:

https://www.pnas.org/content/116/10/4400

 

Cool, I also didn't think that study was the best example of what you are trying to illustrate.

I was fascinated by the anti-freeze study, but I remain committed to the concept that highly complex beneficial sequences cannot just spontaneously occur. Evolutionists are required to be committed to that process because you have nothing else to explain the spontaneous appearance of precision programming in the genome. 

I claim that the non-coding regions are not merely random sequences, but contain bits and pieces that indicate previous usefulness. They have start codons, stop codons, ATGs, and useful sequences when activated. Obviously these bits and pieces are not in the correct order, but just like the e-coli  example on the nitrates, these sequences can be re-activated if the atg and start codons are mutated into the approximately correct positions. 

In historical global warming periods, there would be natural selection towards non coding and reduced size of those anti-freeze genes. These non coding regions could then re-activate upon random mutations that join the anti-freeze sections with start codons and ATGs of other part genes. Even if there is some excess proteins produced through combining gene sections, the net effect adds to fitness because the anti-freeze is needed in new colder conditions.

I find the concept of dormant genes regaining their coding ability through the mutational transfer of dna switches (eg start codons) far more intellectually feasible than nature spontaneously creating long sequences of well functioning code. 

[one.opinion]

51 minutes ago, ARGOSY said:

Evolutionists are required to be committed to that process because you have nothing else to explain the spontaneous appearance of precision programming in the genome.

Not necessarily - I am a follower of Jesus Christ, and with God, all things are possible. I just believe that the evidence that is available supports my opinion that God used evolution in His creation process. Could God have created all life in a 144-hour period about 6000 years ago in such a manner that it only appears that organisms evolved over hundreds of millions of years? Yes, I absolutely believe He could. Could he cause alterations in DNA sequences to allow antifreeze proteins to stop working, and then start working again? Yes, absolutely. However, these are not the conclusions that fit the observed evidence best.

1 hour ago, ARGOSY said:

I find the concept of dormant genes regaining their coding ability through the mutational transfer of dna switches (eg start codons) far more intellectually feasible than nature spontaneously creating long sequences of well functioning code.

Please read the paper to determine what is actually being hypothesized before considering a competing hypothesis. I'll then be very happy to look at the evidence supporting the competing hypothesis.

[ARGOSY]

8 minutes ago, one.opinion said:

Not necessarily - I am a follower of Jesus Christ, and with God, all things are possible. I just believe that the evidence that is available supports my opinion that God used evolution in His creation process. Could God have created all life in a 144-hour period about 6000 years ago in such a manner that it only appears that organisms evolved over hundreds of millions of years? Yes, I absolutely believe He could. Could he cause alterations in DNA sequences to allow antifreeze proteins to stop working, and then start working again? Yes, absolutely. However, these are not the conclusions that fit the observed evidence best.

Please read the paper to determine what is actually being hypothesized before considering a competing hypothesis. I'll then be very happy to look at the evidence supporting the competing hypothesis.

Nothing in the genome appears like it has evolved. It is the assumption of evolution that creates its own necessity to observe differences between two similar organisms and then try to resolve how those differences evolved.

The genome reveals some mutation events, but nothing in the genome points to evolution in the genome nor in the fossil record. Phenotype adaptability within a clade is observed, combined with some mutational "devolution" events. 

I wasnt proposing the antifreeze gene was supernaturally switched off and on, but via natural mutations that can duplicate commonly found switches (start codons and ATGs). This can occur over short periods. This would explain the findings of that study without the need for nature just to spontaneously create intricate functional sequences. 

[one.opinion]

3 minutes ago, ARGOSY said:

I wasnt proposing the antifreeze gene was supernaturally switched off and on, but via natural mutations that can duplicate commonly found switches (start codons and ATGs).

So your competing hypothesis is that all a DNA sequence needs to change from a non-coding region to an active gene is a change from another codon to an ATG? And that organisms can adapt to changing environmental conditions just by the alteration from ATG to another codon and vice-versa?

[ARGOSY]

46 minutes ago, one.opinion said:

So your competing hypothesis is that all a DNA sequence needs to change from a non-coding region to an active gene is a change from another codon to an ATG? And that organisms can adapt to changing environmental conditions just by the alteration from ATG to another codon and vice-versa?

In some cases a re-activated switch is all that is required. A start codon is required to be re-activated if a dormant gene went dormant through the loss of that codons function. These losses can improve fitness and spread when that species no longer needs that function. But when the need arises, a mutation event that re-inserts a similar start codon can re-activate a lost function and also spread through the population.

 

This is what occurred in the e-coli example, when exposed to nitrates. It's a lot more intellectually feasible than the thought that without evolutionary pressures a non coding sequence can just form in a beneficial manner. As I've said before, these sequences in DNA are very precise and even a minor change can be highly damaging. Being so precise the chance of them being beneficial even though in a random order is statistically negligible.

Edited April 10, 2019 by ARGOSY

[one.opinion]

1 hour ago, ARGOSY said:

In some cases a re-activated switch is all that is required. A start codon is required to be re-activated if a dormant gene went dormant through the loss of that codons function.

Are you aware that to go from non-coding to protein-coding, that more than a new start codon would be required? See if you can ponder why this is true and explain what else would be necessary.

1 hour ago, ARGOSY said:

This is what occurred in the e-coli example, when exposed to nitrates.

No, this is not what happened. It wasn't even nitrates. Do some reading and see if you can figure out what actually DID happen.

[ARGOSY]

14 hours ago, one.opinion said:

Are you aware that to go from non-coding to protein-coding, that more than a new start codon would be required? See if you can ponder why this is true and explain what else would be necessary.

It all depends what de-activated the gene in the first place. Maybe it was a start codon, maybe a promoter region.  If the missing section gets re-inserted it can activate again. This doesn't mean that complex sequences were spontaneously created by chance (an unlikely scenario) , it means that complex sequences were re-activated by a minor mutation (always occurring). 

Quote

No, this is not what happened. It wasn't even nitrates. Do some reading and see if you can figure out what actually DID happen.

 

When e-coli were exposed to nitrates in aerobic conditions, the mutation of a promoter region enabled the re-activation of an old function. 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC107412/