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Messages - Pingu

1
Dave: one of the most common and widely studied type of allelic variation in humans is Single Nucleotide Polymorphisms, or SNPs, Snips to its friends.

SNPs are variants in which just one nucleotide is different.

How do you think that such variants might occur by either HGT or recombination?

And if you can't think of how they might occur other than by what you would call a "copying error", are you of the view that they are extremely unlikely ever to be advantageous?
2
No I'm trying to convince you but I'm afraid that's not possible.

No, it isn't possible to convince us that your utterly confused understanding of genetics and the mechanisms of genetic variation has anything to do with reality.

That's because it doesn't.
3
As it turns out she does believe that errors under my definition are necessary to ensure long lineages. But she's wrong. She, like many evolutionists, believe this on faith alone because there is absolutely no evidence for this whatsoever. In fact the whole Third Way movement got started because many scientists are finally beginning to realize this.


No.  please read my fucking posts.

I said that ERRORS under MY definition, which INCLUDES errors under YOUR definition but ALSO includes mutations caused by OTHER mechanism are necessary for long lineages.

There has to be SOME mechanism for getting variation into the genome.  It doesn't HAVE to be any one of those mechanisms.  It could be ANY of them.
4
Seriously, Dave, this is what we mean when we say that you have no reading comprehension. Pingu explicitly spelled out what she meant in her initial post. You somehow misunderstood what she wrote, ignoring her explicit statement. When people pointed out that she had made that explicit statement, you continued to insist that she had fucked up by not meaning what you wanted her to mean. You have entirely sidestepped the fact that she said exactly what she meant, and you still didn't understand her.

Thanks uncool :)
5
I'll put this to you in another way, Dave.

You say you have already posted lots of evidence that mutations that arise at time time when a genome is copied virtually never give rise to beneficial mutations, while mutations that arise from other processes e.g. recombination and HGT do.

I am not aware of any such evidence.  You may have posted some and I missed it.  Alternatively you may have posted what YOU thought was such evidence but it did not peg my radar as being evidence for any such thing.  Perhaps you thought that link to Shapiro's paper was a link to such evidence.

Is that what you meant?  If not, could you link to what you did mean?
6
I actually think I persisted in that error for only a few hours at which time I corrected it. And that was 12 years ago. And yes I know a lot more now. Apparently I know a lot more than Pingu.

Nope.
7
... But the point is that without some imperfection in the reproduction process, i.e. without most, or at least some, offspring being unique, populations are doomed not to adapt. Which is why small populations tend to be vulnerable to extinction. Which is also why the Ark story is so bloody silly, but I do realise that the subtext here is that somehow you've got to get a lot of extra genetic variance into those animal pairs but you can't bring yourself to call them "errors".  But you won't get them from recombination either.  You need new alleles, which means that at least some of the gene sequences need to split and recombine mid-gene in a manner that will produce a gene different from both parents.  Some would call this an "error" in the recombination process.
This was the crux of the issue back in the "Who says Adam didn't have HUNDREDS of alleles?"  days, and Hawkins seems to have made no progress on it since.

Where DID the tens / hundreds / thousands of alleles per locus in animal genomes come from ?

Hint: Spoiler (click to show/hide)


I'm getting off Pingu's latest stupid merry go-round ...

But this from Voxrat is interesting ...

I will revisit it


So you got nuthin'

you are one transparent weasel Dave Hawkins.
8
I've shown you the evidence for that over the years many times. Don't play dumb. Not gonna dig it up again.

No you have not.

Cite a single paper that provides evidence that mutations that originally arose during a copying event are much less likely to be beneficial than mutations that arose from HGT or recombination or other mechanism.

You were able to cite papers that didn't support your case.  Try citing one that does.
9
So[1], Dave:

You think that HGT, recombination, and presumably transposable elements are all mechanisms that can produce useful genetic variation in a population.  And you would not call any of these "errors".

However, you think that genetic variation that occurs because during reproduction a "wrong" nucleotide is incorporated into the sequence and escapes correction cannot produce useful genetic variation in a population.  You would call these "errors".

Am I right?

If so, can you provide evidence to support the claim?[2]


First paragraph, Yes.

Second paragraph, I would not say that an error cannot produce useful variation. It's just that it almost never does

Please provide evidence to support this assertion.

and in fact people have been looking for a long time and I'm pretty sure they haven't found any.

Please provide the evidence that makes you so sure.

Or maybe one or two or three examples that could sort of be construed as useful if you squint and hold your nose and the lighting is just right and it's the third Tuesday of the month of the moon is full.

So for all practical purposes, yes, the second paragraph is correct too.

So please provide the evidence that the second paragraph is correct.

Or are you simply making shit up?
sorry VoxRat
ETA: font enlarged to help Dave not miss it next time
10
So[1], Dave:

You think that HGT, recombination, and presumably transposable elements are all mechanisms that can produce useful genetic variation in a population.  And you would not call any of these "errors".

However, you think that genetic variation that occurs because during reproduction a "wrong" nucleotide is incorporated into the sequence and escapes correction cannot produce useful genetic variation in a population.  You would call these "errors".

Am I right?

If so, can you provide evidence to support the claim?



First paragraph, Yes.

Second paragraph, I would not say that an error cannot produce useful variation. It's just that it almost never does

Please provide evidence to support this assertion.

and in fact people have been looking for a long time and I'm pretty sure they haven't found any.

Please provide the evidence that makes you so sure.

Or maybe one or two or three examples that could sort of be construed as useful if you squint and hold your nose and the lighting is just right and it's the third Tuesday of the month of the moon is full.

So for all practical purposes, yes, the second paragraph is correct too.

So please provide the evidence that the second paragraph is correct.

Or are you simply making shit up?
sorry VoxRat
11
So[1], Dave:

You think that HGT, recombination, and presumably transposable elements are all mechanisms that can produce useful genetic variation in a population.  And you would not call any of these "errors".

However, you think that genetic variation that occurs because during reproduction a "wrong" nucleotide is incorporated into the sequence and escapes correction cannot produce useful genetic variation in a population.  You would call these "errors".

Am I right?

If so, can you provide evidence to support the claim?


sorry VoxRat
12
Quote
I told you how I personally was defining error in the context of my post.
Yeah and it's a goofy, useless definition.

It was entirely useful for my point, which is for a population to survive, at least some offspring HAVE to differ from their parents, i.e. "reproduction" needs to be done "with variance".  You can call a ginger-haired child from two black haired parents a "copying error" if you like, or not, if you don't like.  But the point is that without some imperfection in the reproduction process, i.e. without most, or at least some, offspring being unique, populations are doomed not to adapt. Which is why small populations tend to be vulnerable to extinction. Which is also why the Ark story is so bloody silly, but I do realise that the subtext here is that somehow you've got to get a lot of extra genetic variance into those animal pairs but you can't bring yourself to call them "errors".  But you won't get them from recombination either.  You need new alleles, which means that at least some of the gene sequences need to split and recombine mid-gene in a manner that will produce a gene different from both parents.  Some would call this an "error" in the recombination process.

You should adopt a mainstream definition of "error" ... you're always on me about that.  Practice what you preach.

I have never ever insisted on a "mainstream" definition of anything, Dave.  I have said that explicitly.  I don't care how people use words as long as they make it clear what their definition is, in the context in which they are using it, and stick to that definition throughout the argument. It's why we talk about "operational definitions" in science.  If you want to define "holistic" as "cares about pasture quality as well as animal productivity", or whatever, feel free. But don't assume people will take you to mean that if you don't spell it out, and don't then turn round and talk about Darwinists not being "holistic" when by then you are using some quite different definition.

13
OK listen ...

Let's adopt a definition of "error" that we can both use ...

How about this ... "a difference from the parent sequence that escapes the error correction mechanism because of an error correction system malfunction" ... this would not include recombination or HGT.

Can we agree on this definition?

If so, then I'd like to know if you stand by your statement 
Quote
Therefore populations in which the "error" rate is low but non-zero are likely to adapt best and thus leave long lineages.

You can use that definition if you like, Dave, but it makes no sense in the context of my post.  I am NOT restricting sources of deviation from the parent lineage to those unconnected with the process of reproduction.  What I'm saying that the "error rate" (my definition, which INCLUDES those mechanisms you want to include but ALSO includes other variance-producing mechanisms) has to be non-zero for a lineage to survive, because without variation there can be no adaptation.

I assume you agree that without variation there can be no adaptation?

If so, all we disagree on is whether that variation can usefully include variation that you would call an "error" (your definition).  If you think it can't, please supply the evidence.

14
Fucking weasel Darwinists.

Dave, what you see as "weaselling" is simply what "Darwinists" always meant.  The fact that it turns out that you have always misunderstood it doesn't mean anyone has been trying to confuse you.  It means that you didn't pay enough attention or were too rigid to understand what they actually meant.
15
DAVE'S DEFINITION OF "ERROR"

(AND AYALA'S ... AND EVERYONE ELSE'S EXCEPT PINGU)

"a difference from the parent sequence that escapes the error correction mechanism because of an error correction system malfunction ... HGT and sexual recombination are excluded"

Well, that's another definition.  If you want to use the metaphor to define a specific mechanism for producing genetic variants, that's fine. But don't ascribe that definition to me in the context in which I made my post and in which I defined the word very clearly.  I do NOT mean ONLY variants that arise during copying.  I used it to refer to ANY mechanism, INCLUDING but not RESTRICTED TO variants that arise during copying.

Now, if you want to make the case that a sequence that is different from the parent sequence because it "escape[d] the error correction mechanism" is necessarily deleterious in all environments, be my guest.

I await support for this claim with interest.
16
"Errors" as I have defined them above ...

ARE NOT NEEDED

To ensure long lineages.

Well I realise this is your view.  Restating it without evidential support doesn't make it any more persuasive.
Quote
Pingu is wrong if she thinks they are needed.

Dave, for the gazillionth time I did NOT specify that some specific variance-producing mechanism is essential.  I mentioned several that produce variants.  I did NOT define "error" in the narrow way you did, and so I did NOT make the point that you are so anxious to rebut.  It is a STRAW MAN. 

However, if you want to make the case, and you clearly do, that somehow variants that arise during the copying process cannot result in viable and potential variants, whereas variants that arise because of HGT or some other mechanism can, then please provide support for this cases.

Simply typing it in ALL CAPS doesn't provide that support,  Nor does linking to papers that do NOT make the case you want to make, provide support.  duh.
17
HGT is not considered an "error" ... Show me any mainstream paper that says it is ...

If you wanna talk about what real scientists consider to be "errors" read this that I've linked half a dozen times now ... https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409
That paper does not help you.
It simply defines "error" as inserting the "wrong" nucleotide(s).
Without defining "wrong".

But anyone with a high-school understanding of genetics understands it to mean: "different from the parental template", as I explained above.  HGT also results in progeny DNA different from the parental template.

Q.E.f.D.


He just can't see it.  It's like a guy who can't get a stereogram to pop out.  He's focussing on the wrong bit of the picture.

Either he can't see that "different from the parental template" can be brought about by several mechanisms, including "failure" of the "error correcting" mechanisms during reproduction, or HGT, or transposing elements, or he can't accept that the first of these could possibly result in a viable mutation.

I think his thinking is so suffused with the idea that complex mechanisms must be designed, therefore they must have been designed with the INTENTION of working a particular way that his brain is simply incapable of grasping what is, ironically, the key theme of the Third Way guys, that these variance-producing mechanisms are themselves selectable and thus evolvable, at population level.
18
HGT is not considered an "error" ... Show me any mainstream paper that says it is ...

"is not considered" - way to use the weasel passive, Dave.

And for you to suddenly treat "mainstream paper" as some kind of authoritative source when you habitually reject octohattery mainstreamers as victims of conspiracy and self-delusion is a bit risk.  I told you how I personally was defining error in the context of my post.  I meant exactly what I said, and that definition includes ANY mechanism by which an offspring ends up with a different DNA sequence to the equivalent one possessed by its parents.

If you want to insist that somehow only certain mechanisms ever produce variants that turn out to be beneficial while others never do, go for it. 

If you wanna talk about what real scientists consider to be "errors" read this that I've linked half a dozen times now ... https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409

Yes, Dave.  As I've said, the error rate needs to be low (but not zero).  Lineages that reproduce with a high error rate i.e. high rates of offspring with large deviations from the parent sequence/sequences are likely to go extinct.  We call it "reproduction" because offspring are "reproductions" of their parents - are very similar to the "original".  For reproduction to be reliable the mechanism has to basically work, or the population will go extinct, as I said.  So it is not surprising to find that there are lots of mechanisms involved in maximising accurate reproduction. The fact that those mechanisms exist isn't any kind of "proof" that they are somehow "supposed" to work perfectly.  And in fact, they don't.  And in fact, some of the resulting copying "errors" often result in perfectly viable sequences.

And sometimes those sequences turn out out to be useful at some point in the lineage's history.
19
You do NOT need a "non-zero error rate" to ensure long lineages in bacteria because of HGT.
You do not need HGT to ensure long lineages in bacteria.
Possibly true, IDK.  But I'm quite sure, contrary to Pingu,  you do not need "errors" ... i.e. copying errors as described here https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409 ... to ensure long lineages.

You keep putting words into my virtual mouth.  I defined "error" very precisely.  I do not exclude variants brought about by HGT or by transposable elements, or indeed anything.  I am referring to sequences that are not identical to the parent sequence.  Whether they occur during the "birth" process or sometime after "birth" is immaterial.  The point is that novel genetic sequences need to be produced at a non-zero rate in new organism for the lineage to be robust to environmental change and not vulnerable to extinction in the face of a novel threat.

Your antipathy seems to be specifically to variants that arise during copying as opposed to at some other point.  I am making no such distinction.  I'm saying that :airquote:errors:airquote: can arise from all kinds of mechanisms, including those involved in reproduction, but also HGT.  There's a sense in which sexual reproduction is itself a form of HGT, and may well have evolved from more obviously HGT mechanism.

Your perception of confusion in what people are telling you arises from your own rigid definition of :airquote:error:airquote:  It's a widely used METAPHOR in biochemistry, but it is only a metaphor, not a technical term. 
20
You do NOT need a "non-zero error rate" to ensure long lineages in bacteria because of HGT.


HGT is one source of :airquote:error:airquote: i.e. source of genetic sequences that are different from those of the parent cell.  There are others, transposable elements being one.

You keep getting hung up on this word "error" which I defined extremely carefully as a genetic sequence which is not identical to the parent sequence.  Lots of mechanisms can result in such an "error" i.e. deviation from the parent sequence.  My point, for the gazillionth time, is that for a lineage to be adaptable there needs to be a continuous supply of novel sequences, which are sometimes called :airquote:errors:airquotes: as they are non-identical copies of an original (as an analogy, think of a recopied passage of text - e.g. the various versions of Shakespeare's plays.  The copy may be full of "errors" i.e. deviations from the original.  Some may be improvements; some may even be "planned"; some may be simple substitutions of a word with a more familiar one with the same meaning, or a variant spelling.
21
So what organisms did you have in view that would be "identical to their parents"?  The main ones I can think of would be single celled organisms such as bacteria.  And if you had those in view, then you are wrong about needing a "non-zero error rate" to ensure long lineages.

For bacteria, who have a single parent, it is important that not all offspring are not identical to their single parent i.e. that the :airquote:error:airquote: rate is non-zero.  If it is zero, and all bacteria are absolutely identical to their parents, then a change in environment is likely to be catastrophic. A single vulnerability will affect every individual bacterium. However, if there is a pool of bacterial cells with variant sequences, there is a decent chance that one of those sequences will be protective against the new threat.  And those are the ones that will survive to continue the lineage.
22
I continue to be amazed at your lack of the most elementary understanding of basic biology and genetics.  For example, you say

Quote
A population that reproduces totally without "error" i.e. in which every offspring is identical to its parent would be incapable of adaptive evolution by natural selection.

which is completely false.

No, it is not false.  It is self-evidently true.  If every offspring is identical to its parents, then the population will be forever identical.  Therefore whether or not an offspring has one parent or two, the offspring will be identical to those identical parents.  Every member of the population will be identical to every other member.  No selection will be possible because there is nothing to select.  Every member of the population, being identical, will have an equally good/equally bad chance of surviving in any environment.

Therefore, for adaptive evolution to happen, it is important that offspring are NOT 100% identical to their parents.  In other words that reproduction is "imperfect" (metaphor alert).  The offspring are slightly DIFFERENT from their parent/parents.

In the case of cloning organisms like bacteria, then there needs to be some mechanism for ensuring that the DNA of the offspring is different from the DNA of the single parent.  In other words, to have an :airquote:errors:airquote:  in it, where :airquote:error:airquote: means "not identical to the parent.  As I said, there are lots of biochemical processes that can and do result in :airquote:imperfect:airquote: replication. 

And populations of bacteria in which these :airquote:errors:airquote: happen at an optimal rate - not so many that the offspring are frequently non-viable variants but not so few that the population can't adapt - will be adaptable to changes in the environment e.g. exposure to a novel antibiotic.

For sexually reproducing organisms these :airquote:errors:airquote: are built into the processes associated with sexual reproduction. This means that every child has a unique DNA that is unlike that of any other organism, including its parents, and is made from a recombination of genetic sequences from each of its four grandparents.  This is a very neat way of ensuring that there is always new variance in the population, including a steady supply of brand new alleles.  But it isn't the only mechanism - other processes also ensure that there is plenty of variety, as with bacteria.

You seem to want to class some of these processes as "mistakes" and some as "not-mistakes".  I don't care what you call them.  What I am saying is that for a population to be capable of evolutionary adaptation, there needs to be a continuous source of novel genetic sequences feeding into the population.  It needs to be continuous, as variants go extinct all the time, and without new soures of novelty, the amount of variance drops over time and the population becomes vulnerable to extinction when faced with environmental change.  So it can't be "there from the beginning".

So to summarise: for adaptation to be possible, replication needs to be :airquote:imperfect:airquote:  And populations that are adaptable will tend to leave long lineages. Therefore mechanisms that ensure a steady supply of novel genetic sequences at a rate and of a type that makes most of them viable, will themselves tend to be naturally selected.

Evolvability, in other words, evolves.  This includes the evolution of mechanisms like transposable elements, and, in sexually reproducing species, recombination.


I return again to Ayala (Repetition Aids Learning) ...

Quote
Ayala, Francisco J., "The Mechanisms of Evolution," Scientific American, vol. 239 (September 1978).

p. 63
"It therefore seems clear that, contrary to Darwin's conception, most of the genetic variation in populations arises not from new mutations at each generation but from the reshuffling of previously accumulated mutations [1]by recombination. Although mutation is the ultimate source of all genetic variation,[2] it is a relatively rare event, providing a mere trickle of new alleles into the much larger reservoir of stored genetic variation. Indeed recombination alone is sufficient to enable a population to expose its hidden variation for many generations without the need for new genetic input by mutation."
p. 64
"In any case there can be no doubt that the staggering amount of genetic variation in natural populations provides ample opportunities for evolution to occur. Hence it is not surprising that whenever a new environmental challenge materializes--a change of climate, the introduction of a new predator or competitor, man-made pollution--populations are usually able to adapt to it.

So Pingu does not understand basic biology or basic genetics.

But I'm the shyster.

Go figure.

Well, I'm saying what Ayala is saying.  So presumably you think Ayala doesn't understand basic biology or basic genetics either.

What Ayala DOES get a bit wrong of course is this:

Quote
contrary to Darwin's conception, most of the genetic variation in populations arises not from new mutations at each generation

Darwin didn't even know about genes, let alone DNA or mutations.  But where Ayala is right, and Darwin underestimated the power of his own theory, is the same as the point I made explicitly: that most genetic variation that natural selection acts on is already there, in the population.  Novel beneficial variants don't tend to appear at the time they are beneficial.  Most hang around as neutral variations for many years.  This is because Darwin, not surprisingly, did not understand drift ("not surprising" because he had no idea what was causing the variants in the first place). Now we understand the genetic basis of inheritance, we have a really good understanding of how near-neutral novel variants simply propagate through a population purely by drift. This means that populations always have a decent pool of potentially advantageous variants to provide survival advantage should the environment change.

Ayala doesn't KNOW that these are "previously accumulated mutations" ... he BELIEVES IT ... on faith
Another statement of faith here
23
I did read your post (see above) and you are very  confused. 

As usual.

This is not new.

Dave, as usual you attribute to others what is true of yourself. Apparently you cannot understand my post.  You think I must *really* mean something other than what I wrote.  You think that what I wrote does not make sense.

But instead of reflecting on whether you might have misunderstood something, you jump to the conclusion that the confusion is on my side. 

I simply meant what I wrote.  I didn't *really* mean something else.  In a minute I'll go through it again, to see if I can clarify it for you. But it isn't difficult.  I meant what I wrote, and what I wrote is entirely consistent with Ayala.

24
By realizing that, by the definition she used, either recombination is an "error", or it doesn't even make sense to ask if it is an error.
YOU are the one not reading carefully. 

When she talks about an "error rate" that's low but non-zero being best for adaptability and long lineages, she is definitely not referring to regular old vanilla recombination.  She's talking about the same thing the Nature article describes which the cell works very hard to prevent, but it happens an little bit anyway.

You people are idiots.
She explicitly said "i.e. in which every offspring is identical to its parent"

That doesn't happen with recombination.
I assumed she meant "perfect recombination" ... which living cells approach closely, but don't quite ever achieve.

If she didn't mean that, then WTH did she mean?
The thing I said.
So I guess all you had in view was single celled organisms like bacteria?
why don't you actually read my post?
25
By realizing that, by the definition she used, either recombination is an "error", or it doesn't even make sense to ask if it is an error.
YOU are the one not reading carefully. 

When she talks about an "error rate" that's low but non-zero being best for adaptability and long lineages, she is definitely not referring to regular old vanilla recombination.  She's talking about the same thing the Nature article describes which the cell works very hard to prevent, but it happens an little bit anyway.

You people are idiots.
She explicitly said "i.e. in which every offspring is identical to its parent"

That doesn't happen with recombination.
I assumed she meant "perfect recombination" ... which living cells approach closely, but don't quite ever achieve.

If she didn't mean that, then WTH did she mean?
The thing I said.