Pete's Quite Thread post

[jnhofzinser]

I never once made any [positive claims]...

Yes, I've noticed it is a tactic of yours -- it is vastly easier to attack others' positive claims than make any oneself, leaving oneself open to attack, isn't it?

But since you asked, try reading this. Note, among other things, that the author is (partly) responsible for the erroneous popular information that human and chimp DNA is 98% similar, and is seeking to correct that error. Note also the cataloguing of at least six insertions longer than 1000 nucleotides(!) And once again, I quote:

One interesting observation is that the sequence divergence between chimp and human is quite large, in excess of 20% for a few regions. Some of the larger gaps are broken by regions within them that align with appropriate segments of the other species

’ DNA sequence but only have distant similarity. These observations suggest that complex processes, presumably involving repeated sequences and possible conversion events, may occur that will require detailed study to understand. The uncertainty in the estimate of 3.4% indels on Table 1 cannot be directly evaluated. In the first place, the sample of 779 kb is small, and the variation between the different BACs is large. Further, there may be large gaps that were missed as part of chimpanzee BAC sequences that could not be aligned with the human genome.

Finally, please note that when Britten concludes with

It is the result of a major evolutionary process.

What he means by the highlighted phrase is that it appears to be more complex than the traditional evolutionary process, namely natural selection+mutation.

 

[jnhofzinser]

This is quite the double standard.

How so? I have given no indication here or elsewhere that I have any other standard but complete scientific honesty. Try to match it

 

[mikeynov]

Yes, I've noticed it is a tactic of yours -- it is vastly easier to attack others' positive claims than make any oneself, leaving oneself open to attack, isn't it?

Not really. I correct a lot of people on this board because they make outrageous claims they can't possibly support. And I do try to meaningfully add to conversations where relevent. If you're talking about this specific thread, I don't think you've been at this board long enough to know either my "tactics" or how many times Mark has created a functionally identical thread to this.

But since you asked, try reading this. Note, among other things, that the author is (partly) responsible for the erroneous popular information that human and chimp DNA is 98% similar, and is seeking to correct that error. Note also the cataloguing of at least six insertions longer than 1000 nucleotides(!) And once again, I quote:

I'll look it over.

Finally, please note that when Britten concludes with

What he means by the highlighted phrase is that it appears to be more complex than the traditional evolutionary process, namely natural selection+mutation.

Your last statement is curious - do you really think the author is suggesting that current evolutionary mechanisms are inadequate to explain this data? I'll have to read this to see whether your claim here is on-target.

 

[mikeynov]

What he means by the highlighted phrase is that it appears to be more complex than the traditional evolutionary process, namely natural selection+mutation.

How is the author saying this in the slightest?

Firstly, the paper is an analysis of the nature of the divergence, not the particulars of the selective factors that would have lead to them.

Secondly, the author himself suggests that:

. These observations suggest that complex processes, presumably involving repeated sequences and possible conversion events, may occur that will require detailed study to understand.

So, the author is waiting for bigger samples to compare and makes note that the nature of the divergence requires further study.

This, to you, reads "classical evolutionary mechanisms are inadequate, and these sequences poofed into existence?"

 

[jnhofzinser]

This, to you, reads "classical evolutionary mechanisms are inadequate, and these sequences poofed into existence?"

There is a world of difference between "classical evolutionary mechanisms are inadequate" and "these sequences poofed into existence".

Even the NCSE admits that:

Is there healthy scientific debate about the role natural selection [i.e., your "classical evolutionary mechanisms"] plays in evolution? Absolutely, and this is widely recognized.

When Britten says:

These observations suggest that complex processes, presumably involving repeated sequences and possible conversion events, may occur that will require detailed study to understand.

he is meaning exactly what he says. If it was clear that "classical evolutionary mechanisms" were responsible, do you really think that he would hesitate to say so?

 

[mikeynov]

Full text of NCSE quoted:

We believe that the Discovery Institute intentionally modified the sentence and thereby changed its meaning. The original PBS sentence focused on evolution - the thesis that living things have common ancestors. It would not be equivalent to say that "all known scientific evidence supports Darwinian evolution"; by adding "Darwinian", the meaning of the quotation is changed. Is there healthy scientific debate about the role natural selection plays in evolution? Absolutely, and this is widely recognized. The discoveries of genetics have led to a better understanding of the sources for variation, and the latter half of the 20th century has witnessed a vigorous debate about the roles of proposed additional mechanisms - including genetic drift, gene flow, and developmental processes. These are some of the most interesting topics in modern evolutionary science. But arguments within the scientific community about how evolution occurs should not be confused with arguments - conspicuously absent from the scientific community - about whether evolution occurred.

No offense, but you seem to have a habit of putting words into people's mouths that they're not really saying. In the above, they go on to say that the diversity of life is undoubtedly NOT limited to natural selection alone, but other factors discovered (which form the modern synthesis, which, afaik, was what was under discussion) as well.

But that evolution is some combination of these factors is, itself, not seriously doubted. Could there be other factors we're not aware of? Sure.

But most of the debates I've witnessed deal with the relative emphasis of particulars, including drift vs. selection, allopatry vs. sympatry in respect to speciation and so forth. You don't often hear biologists say "we have no idea how to account for this diversity, mechanistically speaking, and our current model doesn't work."

Note that this IS what you are suggesting - that the standard evolutionary paradigm is incapable of explaining large degrees of divergence, and that extrapolations of the current model observed within short time frames are inapplicable to longer time frames. Do you think the NCSE or most geneticists would stand behind your statements?

When Britten says:

These observations suggest that complex processes, presumably involving repeated sequences and possible conversion events, may occur that will require detailed study to understand.

he is meaning exactly what he says. If it was clear that "classical evolutionary mechanisms" were responsible, do you really think that he would hesitate to say so?

I seriously don't understand where you're coming from. All the author suggested is that the study, while elucidating a better view of the divergence between chimps and people, was only a small piece in gaining a better understanding of the nature of the divergence between the two lineages. Not once did the author suggest that evolutionary mechanics at present were inadequate to explain this divergence.

Again, stop putting words into people's mouths. I even have a suggestion - why don't you email the author and ask them if your interpretation, that modern evolutionary mechanics are inadequate to explain the divergence, are on target in respect to this author's conclusion? If you're going to put words into this person's mouth, that only seems fair of you to do.

 

[jnhofzinser]

I seriously don't understand where you're coming from.

That much is clear.

But why don't you answer the question: 'If it was clear that "classical evolutionary mechanisms" were responsible, do you really think that he would hesitate to say so?'

Then reconsider your:

Not once did the author suggest that evolutionary mechanics at present were inadequate to explain this divergence.

You seem so hung-up on interpretation. I am just looking at the evidence. Funny, really: agnosticism only ever seems to irritate "true believers"

 

[Tomk80]

But since you asked, try reading this. Note, among other things, that the author is (partly) responsible for the erroneous popular information that human and chimp DNA is 98% similar, and is seeking to correct that error. Note also the cataloguing of at least six insertions longer than 1000 nucleotides(!) And once again, I quote:

One interesting observation is that the sequence divergence between chimp and human is quite large, in excess of 20% for a few regions. Some of the larger gaps are broken by regions within them that align with appropriate segments of the other species</FONT>’ DNA sequence but only have distant similarity. These observations suggest that complex processes, presumably involving repeated sequences and possible conversion events, may occur that will require detailed study to understand. The uncertainty in the estimate of 3.4% indels on Table 1 cannot be directly evaluated. In the first place, the sample of 779 kb is small, and the variation between the different BACs is large. Further, there may be large gaps that were missed as part of chimpanzee BAC sequences that could not be aligned with the human genome.

I'm not sure what you are trying to tell us with this. It is very hard to tell what to do with the data. I can't tell whether these sequences are part of coding regions, regulatory regions or non-coding regions, so it is very hard to estimate the impact of the mutations. Furthermore, a lot of the mutations seem to have occurred in repetitive, and often homopolymeric regions. Again, it is very hard to see what the impact of these mutations would be.

Also, we can't draw conclusions on this with respect to common ancestry yet, because, as far as I'm aware, other genomic sequences haven't yet been researched in the same way (taking into account indels). It will be very interesting when that is done, since there is a clear cut prediction from this. If common ancestry is true, patterns from indels have to match patterns we see from genomic sequencing done earlier.

What I did find interesting is the conclusion that, although the indels make up a large part of the genomic difference with respect to size, they only make up 10% of the number of events. Which is the number Pete worked with in post #170.

Finally, please note that when Britten concludes with

It is the result of a major evolutionary process.

What he means by the highlighted phrase is that it appears to be more complex than the traditional evolutionary process, namely natural selection+mutation.
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I disagree. When reading the preceding sentence:

Nevertheless, the conclusion is clear that comparison of the DNA sequences of closely related species reflects many events of insertion and deletion.

and combining that with the paragraph on rearrangement events, it seems to me that Britten is stating that these events are part of the major evolutionary process he is talking about. Nowhere does he allude that mutation is not sufficient to explain these differences, as he specifically names the mutation events he thinks are responsible for the events (namely, insertion, deletion and rearrangment). He only states that it was a major process, not that current mechanisms are unable to explain the process.

 

[mikeynov]

But why don't you answer the question: 'If it was clear that "classical evolutionary mechanisms" were responsible, do you really think that he would hesitate to say so?'

But he named the factors he felt were responsible preceding the statement in question: insertions, deletions, rearrangements.

In terms of selection/drift's impact on this reality, the author didn't say anything, because it appears to be out of scope for the paper. The scope was the nature of the divergence in terms of sequence correspondance. That's it.

Why would he come out and have to say "but accepted evolutionary mechanisms are certainly responsible for this?" Your question is irrational.

You seem so hung-up on interpretation. I am just looking at the evidence. Funny, really: agnosticism only ever seems to irritate "true believers"

My how things get personal when you have no apparent point to make. And are you referring to yourself as agnostic in terms of accepting evolutionary mechanisms (you half-implied accepting common descent)? Or are you conflating this debate with a polar battle between atheists/theists (ie "true believers")?

But in all seriousness, okay, we're looking at data. What now?

Let me remind you of your own words:

(for example, huge genomic insertions that don't appear to "come from" anywhere)

That's your interpretation, and how this isn't "poofing out of nowhere," I don't know. But that certainly isn't what the author said or even hinted at.

Further, you went on to suggest the the author's admission of uncertainty regarding the exact nature of divergence between chimps and humans (and said author emphasizes the fact that a larger genomic comparison is necessary to draw better analysis) was tantamount to that author denying evolutionary mechanisms as adequate to address this divergence. But the author never said that.

And your only rebuttal to that is a rhetorical question about why the author didn't say the OPPOSITE, that evolutionary mechanisms WOULD be adequate?

This conversation is surreal. I feel like I'm talking to Mark Kennedy #2 (hey, you got personal first).

 

[jnhofzinser]

So Tom seems to be saying that insertions of ABOVE 4000 NUCLEOTIDES (which could, incidentally, be responsible for human musical ability, or some such non-ape phenomenon) can be accounted for by a SINGLE MUTATION??? Talk about leaps of faith.

And no Mikey, when I say that authors of peer-reviewed papers admit to being uncertain about a mechanism (requiring "detailed study to understand"), I am not saying that they are denying evolutionary mechanisms (stop reading nonsense into what I write). I am saying that they are doubting the well-known evolutionary mechanisms.

My position is in complete concord with

the diversity of life is undoubtedly NOT limited to natural selection alone, but other factors ... as well. ... Could there be other factors we're not aware of? Sure.

The difference is that I am willing to defer judgement until the evidence is conclusive, rather than claiming things without basis. Mark is entirely correct that we have, at present, no demonstrable mechanism for the evolution of human-kind from its predecessor.

 

[mikeynov]

So Tom seems to be saying that insertions of ABOVE 4000 NUCLEOTIDES (which could, incidentally, be responsible for human musical ability, or some such non-ape phenomenon) can be accounted for by a SINGLE MUTATION??? Talk about leaps of faith.

Where did Tom say this?

And no Mikey, when I say that authors of peer-reviewed papers admit to being uncertain about a mechanism (requiring "detailed study to understand"), I am not saying that they are denying evolutionary mechanisms (stop reading nonsense into what I write). I am saying that they are doubting the well-known evolutionary mechanisms.

But they didn't even hint at that doubt. The author just admitted that, until more data is in, there's only so much he/she can say on the particulars of the divergence. And that's a consideration that doesn't even pretend to take into account the selective forces which account for this divergence.

If your point is we're not sure what selective forces caused this divergence, and what the exact divergence represents - then okay. But you're making this into something it's not - namely, that it suggests doubt as to the veracity of evolutionary mechanisms.

But, as I said previously, your only defense of this point is that the author didn't say the opposite, without indicating why it'd be even relevent to state it.

Absence of knowledge of particulars accounting for this divergence != lack of confidence that modern evolutionary theory is ultimately capable of accounting for this divergence via known mechanisms.

My position is in complete concord withThe difference is that I am willing to defer judgement until the evidence is conclusive, rather than claiming things without basis. Mark is entirely correct that we have, at present, no demonstrable mechanism for the evolution of human-kind from its predecessor.

But you are claiming things without basis by putting words into the author's mouth.

Further, your last line is misleading - we don't know what particular mechanisms account for this divergence because we don't know the exact nature of this divergence yet (with more to come when we compare bigger segments of the genome). This lack of knowledge has nothing to do with "doubting well-known evolutionary mechanisms."

All you're pointing to is a gap in our present knowledge in terms of what SPECIFIC factors lead to this divergence as well as the specifics of the divergence (due to limited genome comparison). But you haven't presented any reason whatsoever to doubt evolutionary mechanisms, which, as far as I know, is supposed to be your point.

 

[jnhofzinser]

Where did Tom say this?

He said

he specifically names the mutation events he thinks are responsible for the events (namely, insertion, deletion and rearrangment)

In other words, Tom is misinterpreting Britten as saying that an insertion is a "mutation event".

The rest of Mikey's post is mostly misrepresentation, and not particularly on topic. So let's cut to the chase: tell us, Mikey, what traditional evolutionary mechanism accounts for insertions of up to more than 4500 nucleotides? (Please keep in mind that these accumulated insertions, as well as a gazillion differences that can be accounted for via mutation, are responsible for our ability to debate this point)

If you have no answer, then you prove my point.
If you say "mutation" I will laugh all weekend.
If you have another solution, I'm all ears.

 

[Tomk80]

So Tom seems to be saying that insertions of ABOVE 4000 NUCLEOTIDES (which could, incidentally, be responsible for human musical ability, or some such non-ape phenomenon) can be accounted for by a SINGLE MUTATION??? Talk about leaps of faith.

I didn't state that. I stated that the total divergence in number of base pairs is high, but that it is low (10%) when looking at the number of events. And that is not my conclusion, that is a conclusion drawn by Britten in the very article you gave (although based on the paper, I see no reason to disagree with that conclusion). I never stated that insertions of over 4000 nucleotides were the result of a single event, and neither did Britten.

And no Mikey, when I say that authors of peer-reviewed papers admit to being uncertain about a mechanism (requiring "detailed study to understand"), I am not saying that they are denying evolutionary mechanisms (stop reading nonsense into what I write). I am saying that they are doubting the well-known evolutionary mechanisms.

And no, the author did not state that he is doubting well-known mechanisms. He states that there has been a large impact on the genome, and names possible mechanisms for that. He further states that, to assign particular mechanisms to particular insertions and deletions requires further study. He doesn not state anywhere in the article that he doubts the mechanisms currently thought to be responsible, or that we cannot explain the data with those mechanisms.

My position is in complete concord with

the diversity of life is undoubtedly NOT limited to natural selection alone, but other factors ... as well. ... Could there be other factors we're not aware of? Sure.

The difference is that I am willing to defer judgement until the evidence is conclusive, rather than claiming things without basis. Mark is entirely correct that we have, at present, no demonstrable mechanism for the evolution of human-kind from its predecessor.

But you can't draw that conclusion from the paper you presented, and neither does the author of the paper in state in any way that we have to find other mechanisms to explain the divergence. I'm fine with you claiming that we haven't found all mechanisms yet, although at present I see no justification for that claim. But you cannot make that claim on the basis of the paper by Britten, because his paper does not support that claim.

 

[Tomk80]

He saidIn other words, Tom is misinterpreting Britten as saying that an insertion is a "mutation event".

An insertion is a 'mutation event'. You have different kinds of mutations. Insertions and deletions are among those.

The rest of Mikey's post is mostly misrepresentation, and not particularly on topic. So let's cut to the chase: tell us, Mikey, what traditional evolutionary mechanism accounts for insertions of up to more than 4500 nucleotides? (Please keep in mind that these accumulated insertions, as well as a gazillion differences that can be accounted for via mutation, are responsible for our ability to debate this point)

If you have no answer, then you prove my point.
If you say "mutation" I will laugh all weekend.
If you have another solution, I'm all ears.

Insertions. Insertions can, and have been observed to insert large stretches of nucleotides. Insertions can occur in different ways, for example through copying, were a stretch of DNA is copied twice. Insertions are mutations, at least according to the definition of mutation that all biologists and geneticists use (at least, according to my books on biology, my books on genetics, my books on cellular functioning and every other document I've ever read by professional biologists on mutations). If you think they all are in error, be my guest. But I think you're quite alone in your assertion.

And please read up on what mutations are.

 

[mikeynov]

The rest of Mikey's post is mostly misrepresentation, and not particularly on topic.

How is it a misrepresentation in the least? I quoted your own words and gave my own understanding of their implications. The least you could do is clarify what it is you're trying to say by presenting this data, rather than handwaving it away.

But whatever.

So let's cut to the chase: tell us, Mikey, what traditional evolutionary mechanism accounts for insertions of up to more than 4500 nucleotides? (Please keep in mind that these accumulated insertions, as well as a gazillion differences that can be accounted for via mutation, are responsible for our ability to debate this point)

If you have no answer, then you prove my point.
If you say "mutation" I will laugh all weekend.
If you have another solution, I'm all ears.

I'm confused what you think this paper means.

If we're talking about divergence (from two different lineages starting from a point ~10 mya) and what accounts for for 4500 nucleotides worth of insertion, why ISN'T mutation an acceptable answer? That these insertions accumulated and were preserved in the genome probably suggests some obvious degree of positive selection (not sure how drift would figure in per se without knowing what these stretches represent, but drift can account for accumulated insertions if the regions they occur in face no selective pressure). I'm open to other suggestions if you have any in that respect.

But you've already framed the question such that you've eliminated the obvious answer - mutations which have accumulated over the past 10 million years. Why is 10 million years not enough to account for that many nucleotides? It obviously didn't happen in a single generation, and nobody ever said it did.

Your attitude in this is a little strange, and to be honest, you remind me a lot of Mark Kennedy in that you point to research which says something to the effect of "the degree of divergence between humans and <whatever> is X." And then proclaim evolutionary mechanisms to be wanting. Just because.

Sure, we're unsure of A) what exactly the divergence is until we can perform genomic comparisons using larger stretches and B) what natural forces in particular were responsible. But why that implies, in any way, that we should doubt established evolutionary mechanisms is sincerely beyond me. Why would I make any statement about doubting evolutionary mechanisms when the author himself made no such statements?

What is it about this degree of divergence you feel is so radical? How many nucleotides worth of insertions are allowed in 10 million years?

 

[Tomk80]

Also, to go on a little bit of a tangent here, there is plenty of literature on insertion and deletion mutations and the mechanisms behind them. Now, not all mechanisms are completely clear, but even in the article itself slippage and the crossing of a chromosome inversion location are already mentioned as possible mechanisms. Other mechanisms include copying (which in some cases can be actively done by the cell itself) and unequal crossing over (see the Chen et al paper).

Also, Jnhofzinser states that an insertion of over 4000 base pairs would amount to a leap of faith and I would almost have agreed, were it not for the fact that when I went looking through the literature, mention of such large insertions is indeed made. To give an example, Chen at al in their paper on gross insertions causing human disease describe insertions up to 10,000 base pairs in length. Saedler and Heiss observed 8 copies of DNA sequence IS1 (1,400 base pairs in length) and 4 copies of DNA sequence IS2 (800 base pairs in length) in the chromosome of E.coli K-12. Now, the mechanism on how these copies had entered the genome precisely are unknown (or at least, they couldn't find out in their article). However, to suggest that these identical strings of DNA would be anything other than copies of an original DNA sequence would stretch credibility a little too much in my opinion.

So, for me at least, the statement that the differences between human and chimpanzee genome would have been caused by insertion mutations seems valid. We know of several mechanisms how these could have occurred, and we know that in rare instances these mechanisms can even produce insertions of up to 10,000 base pairs. I don't even mean with this that the indels of over 4,000 nucleotides are the result of a single insertion or deletion event, only that I see no reason to conclude that this could not have happened.

 

[yossarian]

both insertions and deletions of >4000 bp can occur in a single event - and we know of mechanisms that can cause these

you'd be wise to ignore mark -he's terminally incapable of drawing accurate conclusions from scientific papers

 

[gluadys]

And once again, I quote:

Finally, please note that when Britten concludes with

What he means by the highlighted phrase is that it appears to be more complex than the traditional evolutionary process, namely natural selection+mutation.
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How so? Indels are mutations.

 

[gluadys]

Mark is entirely correct that we have, at present, no demonstrable mechanism for the evolution of human-kind from its predecessor.

Mark also makes a much bigger claim: that we have no demonstrable mechanism for positive natural selection.

I disagree that we have no demonstrable mechanism for the evolution of modern humans. We have, in fact, several demonstrable mechanisms.

On the selection side we have adaptive selection, sexual selection, genetic drift, gene flow. On the mutation side we have substitutions, transpositions, duplications, insertions, deletions, reversals, chromosomal rearrangements, etc.

What we don't have, and won't have without much more research, is which of these (and perhaps other) mechanisms were applicable in specific instances of genomic change.

 

[jnhofzinser]

How so? Indels are mutations.

Let me respond to this as if it encompassed everyone's objection.

First, let me agree to some facts:
Can mutations cause indels? yes.
Can mutations cause large indels? yes.
Does this mean all large indels are mutations? according to Darwin, yes. But I seriously doubt it:

For the sake of discussion, let's ignore the non-indels (as they represent far fewer nt, but far more events, this shouldn't be a problem for anyone). So, for the sake of discussion, the accumulation of indels represents the difference between a non-human ancestor and human-kind. Clearly, they did not all happen at once. However, just as clearly, these indels are characterized NOT by simple repetition of existing genetic material (if they were, this would be observed in the alignment process, incidentally). As (I think?) Tom says:

to suggest that these [insertions?] would be anything other than copies of an original DNA sequence would stretch credibility a little too much

But in the case under discussion we were NOT talking about some random 4000nt insertion or some 4000nt replication. We were talking about 4000nt hunks of NEW CODE. 4000nt that, for all we know, is critical, in its entirety, to construct the creature we know as "man". As Gluadys quotes Dawkins, "Jumping gaps is not what evolution [by which we can probably agree that Dawkins means natural selection] does." 4knt hunks of new code are most certainly gaps. To blythely wave our hand at such an insertion and say "it is just a mutation" is preposterous. As Mikey correctly says:

It obviously didn't happen in a single generation

But the option that such an insertion happened as a series of mutations has its own difficulties: it is one thing for mutations to happen randomly, it is quite another for those mutations to happen "in the right place". And as Gluadys correctly says:

What we don't have, and won't have without much more research, is which of these (and perhaps other) mechanisms were applicable in specific instances [in particular, large insertions of new code] of genomic change.