Genetics

[USincognito]

I'd like to open up this thread by posting a bunch of letters and numbers I've come across recently and in the past and see if that alone can foster a discussion. I've also found a very interesting page on globin gene duplication and mutation that I'm hoping someone with more skin in the game can translate into layman.

FoxP2
BMP2
HAR1
LRP5
MCM6

Globin evolution


Gonna toss this in too:
GNN - Quick Guide to Sequenced Genomes

 

[sfs]

Random comments about the ones I know something about:

FoxP2

If I recall correctly, the original paper arguing for selection at FoxP2 was somewhat inconsistent, since the signature of selection suggested very recent selection but the presence of the putative selected alleles in all modern humans (and, IIRC, now Neandertals as well) suggests much older selection. So this might be a complex story.

HAR1

Probably not selection, but GC-biased gene conversion instead. (Many of the other HAR regions probably do represent positive selection, however.)

MCM6

I had to look this one up -- I didn't realize the putative functional change controlling lactase expression was in another gene. An old, well-established case of strong positive selection.

 

[Loudmouth]

I'd like to open up this thread by posting a bunch of letters and numbers I've come across recently and in the past and see if that alone can foster a discussion. I've also found a very interesting page on globin gene duplication and mutation that I'm hoping someone with more skin in the game can translate into layman.

FoxP2
BMP2
HAR1
LRP5
MCM6

Globin evolution


Gonna toss this in too:
GNN - Quick Guide to Sequenced Genomes

That's a nice list. I don't want to distract from those genes, but one of my favorites is the MC1R gene in pocket mice.

The genetic basis of adaptive melanism in pocket mice

It is similar to selection of melanism in peppered moths, but a much more complete and compelling case.

 

[USincognito]

Probably not selection, but GC-biased gene conversion instead. (Many of the other HAR regions probably do represent positive selection, however.)

I need to read up on biasd gene conversion will Galtier and Duret's 2007 paper give me the basics?

 

[sfs]

I need to read up on biasd gene conversion will Galtier and Duret's 2007 paper give me the basics?

Probably -- I don't remember if I've read that article, but TiG generally has good review articles. For specifics on biased GC and the HARs, see Kostka et al.

 

[USincognito]

That's a nice list. I don't want to distract from those genes, but one of my favorites is the MC1R gene in pocket mice.

The genetic basis of adaptive melanism in pocket mice

It is similar to selection of melanism in peppered moths, but a much more complete and compelling case.

That's exactly the sort of thing I'm looking for - genes, areas or molecular functions that represent an outright qualitative benefit, a positive selection or mutations over time that replicate morphological nested hierarchies (like the duplication and mutation in globin genes).

If anyone has any others to add, please do so. I'm trying to put together a simple list I can drop on Creationists when they make some of the cockamamie claims they do about genetics.

 

[USincognito]

Probably -- I don't remember if I've read that article, but TiG generally has good review articles. For specifics on biased GC and the HARs, see Kostka et al.

That's a slog of a read, but very interesting. Let me see if I'm getting the gist.

When mutations happen in areas subject to gBGC the substitution trend is for G and C to replace A and T. Those substitutions occur without any regard to fitness, and thus aren't subject to selective pressure (or at least not positive selection). An analysis of HARs showed that ~80% of them were subject to selection while ~20% resulted from gBGC and HAR1 fell within that 20%.

Or am I off base? (pun intended)

eta - Scanning back over the paper again I noticed a direct reference to HAR1 where they note it was particularly subject to gBGC.

Pollard, Salama, King, et al. (2006) found a positive correlation between acceleration level and the proportion of inferred human substitutions that were weak-to-strong across the 202 HARs, with the most striking evidence of gBGC in extremely accelerated HARs (HAR1–HAR5).​

The supplemental data table is mostly gibberish to me, but I can see that HAR1 has a delta GC of .132 (which is more than a third as much as HAR2) while almost all of the others are in the hundredths or thousandths and many of them are negative.

 

[sfs]

That's a slog of a read, but very interesting. Let me see if I'm getting the gist.

When mutations happen in areas subject to gBGC the substitution trend is for G and C to replace A and T. Those substitutions occur without any regard to fitness, and thus aren't subject to selective pressure (or at least not positive selection). An analysis of HARs showed that ~80% of them were subject to selection while ~20% resulted from gBGC and HAR1 fell within that 20%.

Or am I off base? (pun intended)

eta - Scanning back over the paper again I noticed a direct reference to HAR1 where they note it was particularly subject to gBGC.

Pollard, Salama, King, et al. (2006) found a positive correlation between acceleration level and the proportion of inferred human substitutions that were weak-to-strong across the 202 HARs, with the most striking evidence of gBGC in extremely accelerated HARs (HAR1–HAR5).​

The supplemental data table is mostly gibberish to me, but I can see that HAR1 has a delta GC of .132 (which is more than a third as much as HAR2) while almost all of the others are in the hundredths or thousandths and many of them are negative.

You've pretty much got it. The alleles are still subject to selection, but the bias toward GC will favor their fixation unless there is strong selection against it.

The RHA produced by HAR1 is clearly functional, and has been conserved for a long time, and yet it has had multiple changes in the human lineage. The original HAR paper suggested that this was because the changes were positively selected, perhaps for some new function. The strong bias in the actual base-pair changes in the human lineage, however, suggest that they occurred because of gene conversion, which accompanies recombination. Probably this happened because a recombination hotspot developed at that locus, dramatically increasing the frequency of recombination there. The fact that several of the changes to HAR1 have compensating changes(*) suggests that the RNA is still functional in humans.

(*) Based on the predicted structure of the final RNA. This has a hairpin shape, with two parts of the RNA pairing to form locally double-stranded RNA; there are several places where both sides of the pair have been changed in the human lineage, one by gene conversion and the other by a random mutation that restored the structure.

(Note: this is from memory, so it's a bit vague in spots, but I'm too lazy, er, efficient, to look up the details.)

 

[Redheadedstepchild]

Mod Hat

I have cleaned this thread. The OP requested discussion about specific genomes. Please take care to make sure that your responses are also specific. Broad statements about the genetic code are really not on topic.

 

[Justatruthseeker]

You've pretty much got it. The alleles are still subject to selection, but the bias toward GC will favor their fixation unless there is strong selection against it.

The RHA produced by HAR1 is clearly functional, and has been conserved for a long time, and yet it has had multiple changes in the human lineage. The original HAR paper suggested that this was because the changes were positively selected, perhaps for some new function. The strong bias in the actual base-pair changes in the human lineage, however, suggest that they occurred because of gene conversion, which accompanies recombination. Probably this happened because a recombination hotspot developed at that locus, dramatically increasing the frequency of recombination there. The fact that several of the changes to HAR1 have compensating changes(*) suggests that the RNA is still functional in humans.

(*) Based on the predicted structure of the final RNA. This has a hairpin shape, with two parts of the RNA pairing to form locally double-stranded RNA; there are several places where both sides of the pair have been changed in the human lineage, one by gene conversion and the other by a random mutation that restored the structure.

(Note: this is from memory, so it's a bit vague in spots, but I'm too lazy, er, efficient, to look up the details.)

Yet all the process leading up to the assumption have been inferred from other assumptions inferred from other assumptions.

"found a positive correlation between acceleration level and the proportion of inferred human substitutions..."

So once again we find it is not science fact that backs up evolutionary theory, but inferences based upon assumptions. So they found a correlation between an observed aspect, and one that is only inferred to reach their assumption.

We observe this, but actually believe something else happened without any proof, just mere assumption that substitutions were involved. Yet if the inferred substitutions did in fact not ocurr, which has never been shown, nor can be, being far, far in the past, where does that leave you?

A theory based upon speculation, not matching observations. Once again, the genome has never been seen to become more complex or less for that matter. It simply turns on or off pre-existing sequences.

Why do evolutionists insist the genetic code evolves when geneticists know full well it is merely dominate or repressive traits passed down from generation to generation? It i9s always the same genomes, human genomes that are passed down from generation to generation. They have never once been observed to become anything but what they originally were.

 

[sfs]

Yet all the process leading up to the assumption have been inferred from other assumptions inferred from other assumptions.

"found a positive correlation between acceleration level and the proportion of inferred human substitutions..."

So once again we find it is not science fact that backs up evolutionary theory, but inferences based upon assumptions. So they found a correlation between an observed aspect, and one that is only inferred to reach their assumption.

We observe this, but actually believe something else happened without any proof, just mere assumption that substitutions were involved. Yet if the inferred substitutions did in fact not ocurr, which has never been shown, nor can be, being far, far in the past, where does that leave you?

A theory based upon speculation, not matching observations. Once again, the genome has never been seen to become more complex or less for that matter. It simply turns on or off pre-existing sequences.

Why do evolutionists insist the genetic code evolves when geneticists know full well it is merely dominate or repressive traits passed down from generation to generation? It i9s always the same genomes, human genomes that are passed down from generation to generation. They have never once been observed to become anything but what they originally were.

One simple suggestion: learn what the words "genetic code" mean. Hint (I've given you one before): they don't mean what you think they mean.

One simple question: what is the creationist explanation for the fact that, at so many places where the human version of HAR1 differs from that of other genomes, the human version has a G/C allele?

 

[Loudmouth]

Yet all the process leading up to the assumption have been inferred from other assumptions inferred from other assumptions.

"found a positive correlation between acceleration level and the proportion of inferred human substitutions..."

An inferrence is not an assumption. An inferrence is made from evidence. Perhaps you could actually point to the assumptions instead of making vague and baseless accusations.

 

[Justatruthseeker]

An inferrence is not an assumption. An inferrence is made from evidence. Perhaps you could actually point to the assumptions instead of making vague and baseless accusations.

Just pointed to the assumptions. The assumptions that substitutions must have taken place. There exists not one single piece of scientific evidence to even make that assumption. They then "infer" that based upon the assumption that substitutions happened, that the acceleration levels correlate the assumptions.

You are attempting to prove an inferred correlation based upon an assumption, then claim it as fact.

Just as you once declared as a positive fact that dinosaurs were reptile.

Just as you once declared that the young of some dinosaur were separate species, with complete and detailed hierarchy trees separate from their own parents.

Just as you always change the story paragraph by paragraph, while never once looking at the first assumptions that lead to those incorrect hypotheses. You can change the ending of the book all you want, rewrite it in all the flowery words you like, but it won't help as it is the beginning were the error lies.

Your very basic concepts are what is flawed, yet never do you question them when over and over and over, observations and experimentation show theory to be wrong. Instead you rewrite the last chapter written, not once considering that chapter is in error because the one before it is, and the one before it, all the way back to the beginning.

Assumption based upon assumption based upon inference upon assumptions.

Your entire carbon dating theory is useless as well, based upon Fermi's theory of the electroweak force, yet his theory was shown to be incorrect almost 50 years ago, is no longer used in the atomic structure, yet radiocarbon dating has never changed. Still based upon the theory shown to be incorrect.

But better to fake your way through it than to admit you have no valid theory to reliably date anything (without which geology would still be the philosophy it was before radiocarbon dating "legitimized" it into a science.) But then relying on a theory known to be incorrect is really just a guess anyways.

Just don't expect me to accept your guesses as facts, and all will be well. Especially when the facts seem to require you to do a major revision every few years as new technology proves the last theory wrong. But let's pretend the base assumptions are correct, that it is just everything else observation always falsifies.

 

[CabVet]

Just pointed to the assumptions. The assumptions that substitutions must have taken place. There exists not one single piece of scientific evidence to even make that assumption.

Are you out of your mind? We can sequence people's genomes, you know, we can sequence your genome and your offspring genome's and pinpoint exactly where the substitutions are. We can sequence a bacterial genome, than sequence the next generation and show exactly where the substitutions are. We can even induce substitutions by using mutagenic agents. It is an observable fact.

 

[Justatruthseeker]

Are you out of your mind? We can sequence people's genomes, you know, we can sequence your genome and your offspring genome's and pinpoint exactly where the substitutions are. We can sequence a bacterial genome, than sequence the next generation and show exactly where the substitutions are. We can even induce substitutions by using mutagenic agents. It is an observable fact.

Sure you can, and in all those gene sequencing you have NEVER observed those inferred substitutions you are assuming, or they would not be inferred assumptions, now would they? You are infering this happened long, long ago, and as I said before, might as well be in a galaxy far, far away as well.

Really? show me a single substitution. You would not need to infer them if you had one single laboratory experiment that showed substitutions actually took place. You do however know that gene sequences turn off or on. That some come from each parent, combine, and turn traits on or off.

But substitutions, no, that has NEVER been observed, that is why it is an assumption.

 

[CabVet]

Sure you can, and in all those gene sequencing you have NEVER observed those inferred substitutions you are assuming, or they would not be inferred assumptions, now would they? You are infering this happened long, long ago, and as I said before, might as well be in a galaxy far, far away as well.

Really? show me a single substitution. You would not need to infer them if you had one single laboratory experiment that showed substitutions actually took place. You do however know that gene sequences turn off or on. That some come from each parent, combine, and turn traits on or off.

But substitutions, no, that has NEVER been observed, that is why it is an assumption.

Yes, they have been observed and are observed all the time, you have no idea what you are talking about. You can take a lab mouse, blast radiation at a certain portion of the genome and cause a substitution to happen.

How do you think courts do DNA tests? Or paternity tests? The only reason those tests are possible is because of substitutions. They are so predictable, that we can say with very high confidence how related two people are.

Here are a few of thousands of examples of substitutions happening:

APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells : Scientific Reports : Nature Publishing Group

DNA alteration induced by ultraviolet light in human metaphase chromosomes substituted with 5′-bromodeoxy uridine: monitoring by monoclonal antibodies to double-stranded and single stranded DNA - Springer

Vitamin B-12 Deficiency Induces Anomalies of Base Substitution and Methylation in the DNA of Rat Colonic Epithelium

I just cannot believe I am arguing such a basic concept, this is evidence from 1981:

Radiation-induced base substitution mutagenesis in single-stranded DNA phage M13

 

[EternalDragon]

Yes, they have been observed and are observed all the time, you have no idea what you are talking about. You can take a lab mouse, blast radiation at a certain portion of the genome and cause a substitution to happen.

How do you think courts do DNA tests? Or paternity tests? The only reason those tests are possible is because of substitutions. They are so predictable, that we can say with very high confidence how related two people are.

Here are a few of thousands of examples of substitutions happening:

APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells : Scientific Reports : Nature Publishing Group

DNA alteration induced by ultraviolet light in human metaphase chromosomes substituted with 5′-bromodeoxy uridine: monitoring by monoclonal antibodies to double-stranded and single stranded DNA - Springer

Vitamin B-12 Deficiency Induces Anomalies of Base Substitution and Methylation in the DNA of Rat Colonic Epithelium

I just cannot believe I am arguing such a basic concept, this is evidence from 1981:

Radiation-induced base substitution mutagenesis in single-stranded DNA phage M13

Are all these substitutions adding fitness or taking away fitness? What I mean is are they making the organism worse off or better off? It looks like it is making things worse or losing function.

 

[CabVet]

Are all these substitutions adding fitness or taking away fitness? What I mean is are they making the organism worse off or better off? It looks like it is making things worse or losing function.

It does not matter one bit. My point was exclusively to refute Justatruthseeker's statement that "substitutions don't exist and have never been observed".

If you want to talk about beneficial mutations I can give you the same list that I gave you 10 times before in other threads. In fact, I think I will just have that saved as a template somewhere. For the moment, I will refer to a source that I think you trust, Answers in Genesis:

Are There Beneficial Mutations? - Answers in Genesis

In the article above, even they concede that there are beneficial mutations, and that creationists should not say otherwise.

 

[sfs]

Just pointed to the assumptions. The assumptions that substitutions must have taken place. There exists not one single piece of scientific evidence to even make that assumption. They then "infer" that based upon the assumption that substitutions happened, that the acceleration levels correlate the assumptions.

You are attempting to prove an inferred correlation based upon an assumption, then claim it as fact.

Just as you once declared as a positive fact that dinosaurs were reptile.

Just as you once declared that the young of some dinosaur were separate species, with complete and detailed hierarchy trees separate from their own parents.

Just as you always change the story paragraph by paragraph, while never once looking at the first assumptions that lead to those incorrect hypotheses. You can change the ending of the book all you want, rewrite it in all the flowery words you like, but it won't help as it is the beginning were the error lies.

Your very basic concepts are what is flawed, yet never do you question them when over and over and over, observations and experimentation show theory to be wrong. Instead you rewrite the last chapter written, not once considering that chapter is in error because the one before it is, and the one before it, all the way back to the beginning.

Assumption based upon assumption based upon inference upon assumptions.

Your entire carbon dating theory is useless as well, based upon Fermi's theory of the electroweak force, yet his theory was shown to be incorrect almost 50 years ago, is no longer used in the atomic structure, yet radiocarbon dating has never changed. Still based upon the theory shown to be incorrect.

But better to fake your way through it than to admit you have no valid theory to reliably date anything (without which geology would still be the philosophy it was before radiocarbon dating "legitimized" it into a science.) But then relying on a theory known to be incorrect is really just a guess anyways.

Just don't expect me to accept your guesses as facts, and all will be well. Especially when the facts seem to require you to do a major revision every few years as new technology proves the last theory wrong. But let's pretend the base assumptions are correct, that it is just everything else observation always falsifies.

So what was your explanation for the observed differences in the human version of HAR1, again? That, after all, is the subject of this thread -- not the false statements you're making about radioactive dating, not the falsehoods you keep repeating about Fermi, not the complete fabrications you're posting about substitutions -- but HAR1, and the other specific genetic loci. I'd like to hear the creationist explanation for the data.

 

[USincognito]

That's a nice list. I don't want to distract from those genes, but one of my favorites is the MC1R gene in pocket mice.

The genetic basis of adaptive melanism in pocket mice

It is similar to selection of melanism in peppered moths, but a much more complete and compelling case.

Over the weekend I remembered some exchanges in the past where I'd cited melanocytes in roses as a potential falsification for evolution and the golden zebrafish was tossed back at me. Obviously fish =/= rose so their objection fell flat, but it was an interesting find that continues to provide insight into melanin regulation in vertebrates and hair and skin color in humans.
Pmch1 and Pmch2
Characterization of two melanin-concentrating ... [J Comp Neurol. 2009] - PubMed - NCBI

A fish of a different color
SLC24A5
SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans