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Messages - RAFH

1
 :911:
And another 4 pages of David being obtusely and militantly wrong.

How do you suppose the sequences which are transfered via hgt arose?

Leprechauns?

Menehuna
2
... 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
Hey! No hurry.
It's been 12 years.
What's another decade or three?
Yeah, after all, Bluffy does have a perfect record of revisting issues he's been shown to be wrong on.

Hey, it's even a Law, Second Law to be exact.
3
I've shown you the evidence for that over the years many times. Don't play dumb. Not gonna dig it up again.
Third Law.
4
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.
It could also mean he's never bothered to crack an introductory text on genetics.
And certainly didn't and doesn't want to. Ever.
5
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"
Where else, oh Great and Grand Bluffoon of Bluffoonylvania, is that definition stated other than by yourself?
Citations and references and copy-pasta including context.
6
"Errors" as I have defined them above ...

ARE NOT NEEDED

To ensure long lineages.

Pingu is wrong if she thinks they are needed.
Sez the guy living in a pile of straw bales with a tarp for a roof and shitting in a bucket and with no education, training and/or experience in any related field who sells shit to gullible rubes who don't need it and thinks the world is less than 10,000 years old.
7
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.

No, no, let's agree on this definition: Bluffy is an error. A mistake. A monstrous blooper. A colossal fuck-up. A complete and utter boo-boo. A gigantic clusterfuck. An unimaginably screwed up bogosity.
8
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.
One of your fundamental
This is your basic misunderstanding.
Your basic misunderstanding is thinking that you understand this stuff.

See: Dunning-Kruger effect.
No.

Your misunderstanding is that because I don't know everything, I must not know anything.

I obviously know more about this one narrow topic than Pingu.
By the way, Bluffy, you got that backwards. We understand that because you don't know anything, you must, therefore not know everything.
9
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.
One of your fundamental
This is your basic misunderstanding.
Your basic misunderstanding is thinking that you understand this stuff.

See: Dunning-Kruger effect.
No.

Your misunderstanding is that because I don't know everything, I must not know anything.

I obviously know more about this one narrow topic than Pingu.
That's exactly what a militantly ignorant narcissistic DK posterboy WOULD say. In other words, you APPEAR to be a militantly ignorant narcissistic DK posterboy, which means, of course, by your own reasoning, that you ARE a militantly ignorant narcissistic DK posterboy.
10
You do NOT need a "non-zero error rate" to ensure long lineages in bacteria because of HGT.
Wait, what? You were referring to Eukaryotes and recombination, not bacteria. Why are you now switching to bacteria and HGT?
By the way, HGT is a form of error rate. Being as the genome following successful HGT is not the same as the genome prior to HGT.

What a total bluffoon.
11
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. 
Bluffy, Pingu was not referring to an actual organism, but using a hypothetical organism, one that could not actually exist because perfect reproduction does not actually exist nor does your "perfect recombination". She was saying that if an organism did reproduce perfectly, it would be unable to adapt to any changes.

Because if it adapted (in other words, changed) to anything it would no longer be a perfect reproduction. Sort of a truism. Sort of like without a brain, one can not think. Which nearly perfectly describes yourself.
12
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?
WTF do YOU mean?
What is "perfect recombination" supposed to mean?
What "living cells" approach it, whatever it is?
By what criteria do you judge how closely these "living cells" (whatever they are) approach it (whatever it is)?

You have no idea what you're talking about.
Perfect recombination simply means that half of each parents genes are combined with no random errors like insertions or deletions or substitutions.

What else could it possibly mean?
Bluffy, that would still end up with a genome that is different from it's parent genomes. Unless, of course, those parents were identical clones.

Are you really so stupid you can't see that?
13
So make that Pingu ... AND Martin ... AND uncool ... that don't understand basic genetics.
Aaaaand ...
Here's Hawkins's signature totally inappropriate condescending  insulting bluster/bravado when trying to bluff his way through a subject in which he lacks the first clue.

No, Hawkins. It's YOU who doesn't understand basic genetics.

Remember how you went on for days (weeks? months?) condescendingly, insultingly, insisting that your biblical Adam and Eve must have had hundreds or thousands of alleles at every locus? 

:rofl:
:rofl::rofl:
:rofl::rofl::rofl:
:rofl::rofl::rofl::rofl:
:rofl::rofl::rofl::rofl::rofl:


Good times!  I suppose you would have us believe you've actually studied the subject since then, and now you've not only moved beyond such hilarious boners, your brilliant mind now runs circles around people who have studied molecular genetics all their lives.

Dave Hawkins:  poster child for narcissistic militant ignorance
FYP
14
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?
Bluffy, this is really lame. How could recombination be "perfect"? The only scenario in which it might occur would be if two identical clones mated.

So, once again, you made an assumption that was not based upon anything other than either your biases, your ignorance or both.
15
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.
Yes, that's what Pingu has said, and it's correct. There are mutations that are not related to recombination. Happens in Prokaryotes all the time. But it happens in Eukaryotes as well.

BTW, cells do not work "very hard" at anything. Cells don't know the difference between hard and easy. Cells don't know anything. Cells are not conscious.  There are mechanisms in cells that have evolved to repair DNA mutations. It's what those mechanisms do. Those mechanisms don't know the difference between hard and easy. Those mechanisms don't know anything at all. Those mechanisms are not conscious.

Does a spark plug work very hard to ignite gases? Do tires work very hard to roll? Does a test tube work very hard to hold its contents? Does a light bulb work very hard to produce light?

What a bluffoon.

16
I think Dave's off his meds.
Has he ever been, while at TR or virtually any other online forum, on his meds?
17
I cannot see how anyone can explain away the fact that this IS what she thinks.

And it's incorrect.

Hugely.
According to you. A nobody guy with no education, training or experience in related fields who lives in a pile of straw bales with a tarp for a roof and shits in a bucket and drinks a gallon of milk a day and sells stuff to gullible rubes who don't need that stuff and is a militantly ignorant narcissistic DK posterboy.
18
How am I misreading this?
Quote
In an metaphorical sense, it may be that a certain rate of  copying "mistakes" is optimal for conferring robustness and evolvability.  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.  One that reproduces with a great deal of error may tend to go extinct rapidly because too few good viable variants are born.

Therefore populations in which the "error" rate is low but non-zero are likely to adapt best and thus leave long lineages.  This is the "evolution of evolvability" that is one of the core ideas of the Third Way people you love to reference, but apparently do not understand.
--Pingu

This indicates quite clearly that this "error rate" Pingu is talking about is referring to the same thing being discussed here ...  See especially the bolded ...
Quote
DNA replication is a truly amazing biological phenomenon. Consider the countless number of times that your cells divide to make you who you are--not just during development, but even now, as a fully mature adult. Then consider that every time a human cell divides and its DNA replicates, it has to copy and transmit the exact same sequence of 3 billion nucleotides to its daughter cells. Finally, consider the fact that in life (literally), nothing is perfect. While most DNA replicates with fairly high fidelity, mistakes do happen, with polymerase enzymes sometimes inserting the wrong nucleotide or too many or too few nucleotides into a sequence. Fortunately, most of these mistakes are fixed through various DNA repair processes. Repair enzymes recognize structural imperfections between improperly paired nucleotides, cutting out the wrong ones and putting the right ones in their place. But some replication errors make it past these mechanisms, thus becoming permanent mutations. These altered nucleotide sequences can then be passed down from one cellular generation to the next, and if they occur in cells that give rise to gametes, they can even be transmitted to subsequent organismal generations. Moreover, when the genes for the DNA repair enzymes themselves become mutated, mistakes begin accumulating at a much higher rate. In eukaryotes, such mutations can lead to cancer. https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409
Except when that mutation of the genes for DNA repair enzymes is beneficial, ie - is more effective at repairing mutations that are not beneficial and not repairing those that are.
19
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.

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.
1) Ayala is not the final authority on this issue. Nobody is. These are his opinions.
2) Ayala is, has to be, talking about eukaryotes, not prokaryotes, because prokaryotes do not reproduce by sexual recombination.
3) You denigrate any statements he makes that clarifies his opinions which conflict with your desired meanings of his word (using the parathesied phrase  - believes on faith) but totally accept whatever statements he makes you agree with. That's unethical, asymmetrical cherry picking. Something you don't suck at.
Ayala doesn't KNOW that these are "previously accumulated mutations" ... he BELIEVES IT ... on faith
Another statement of faith here
20
There's no such thing as an error ... or a mistake.  So I'm told.

I cannot believe you are stupid enough not to get this but on the offchance that this really is stupidity, not dishonesty, here goes:

A mistake is something you did instead of something you intended to do.

So it only literally applies to an agent capable of forming an intention.  That would include you.

But it sometimes used as a metaphor when applied to a molecule or a biological process.

You are literally making something out of a nothing burger.  Which is apparently what you do a lot because you don't have anything substantive to say.  No rational person would misunderstand what is being said about DNA copying errors in this article. https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409  ... which I suppose means that you are an irrational person.  Also, according to your view, there's nothing fundamentally different between a human being and a cell from the perspective of forming "intentions."   The difference - according to you - is merely in degree ... that is, the degree of complexity.

But according to MY view of humanity, there IS something fundamentally different between a complete human and a single cell, namely, the human has a "soul" or a "spirit" which is "attached" to the brain and interacts with it.  My view is that no other organism whether single cell or multi cell has this feature.

Bluffy, got evidence for this "soul" or "spirit"? Physical evidence?
Not anecdotes, not myths, not religious doctrine, not rumor, not feelings, not suspicions, not views, not beliefs.
Physical evidence. Mass and/or energy. Effects based in physics and/or chemistry. Reproducible evidence.

BTW, you're still using your own davinitions of the terms "error" and "mistake", meaning deleterious and a failure. You refuse to use the scientific meaning of the terms. Because you have a bias.
21
Pingu: "mutations aren't mistakes."

Ayala:

Quote
Ayala, Francisco J., "The Mechanisms of Evolution," Scientific American, vol. 239 (September 1978), pp. 56-69.
p. 58
"A mutation can be considered an error in the replication of DNA prior to its translation into protein."

Lol

Important Words: "can be considered"

Subtle distinctions in the definition and interpretation of words: consider: "error" vs "mistake"
Don't be silly. It's not like:
In the real world (as opposed to your fantasy world) there are many shades of meaning that people attach to various words.  We only get the detailed view of what they mean when we hear them describe what they mean.
...That would be preposterous! Walks like a duck, it's a fucking duck I tells ya!
Or maybe a fish.
22
I refuse to entertain this perennial bullshit nonsense about copying errors in DNA not being mistakes. Utterly ridiculous and I refuse to waste my time.
Which is one reason nobody around here gives anything you post any credibility whatsoever.
Just like they don't give much credibility to the opinions of the clowns at the circus on evolution or quantum physics.
23
Politics and Current Events / Re: Trumpocalypse
The best people


Was he being interviewed by a Senate Committee? If so, was he under oath? If so, it would appear he's committed perjury and lying to federal officials. Maybe Mueller can indict him as well. Should be an easy conviction.
24
No one ever said "ORGANISMS are like code."

It's DNA that's "like code" ... somewhat ... but it's far more sophisticated. 

Quote
World J Biol Chem. 2014 Aug 26; 5(3): 275-278.
Published online 2014 Aug 26. doi:  10.4331/wjbc.v5.i3.275
PMCID: PMC4160521
Life is more than a computer running DNA software

Therefore, DNA organized in chromatin is far more complex than the human-made "software system", except that we are confusing the algorithm-based simulation of real-life storage with the real life, the computer machines with the living cells and organisms, and the self-reproducing automatons with the real-life organisms that can replicate since the origins of life[5,9,14].

You didn't even read the last part of that sentence, did you. The part about "except that we are confusing the algorithm-based simulation of real-life storage with the real life, the computer machines with the living cells and organisms, and the self-reproducing automatons with the real-life organisms that can replicate since the origins of life". In other words, don't buy into the confusion, Bluffy. There are only minimal analogies to be derived from computer science with regard to biology.
25
Does this have to be an Either God Or Evolution question?
Isn't it possible that evolution itself is God's design?
Why would God do things the same way we humans would? I think it is arrogant of any human to claim to understand the mind of God.
Well, if God made evolution, there's not a lot else left for him to do. He could just sit back and watch. Or just leave.
Also, does evolution need creating? If evolution doesn't need God to exist, what is he even for?
It appears to me that some extremely intelligent "made evolution" - which, rightly defined, could be called "pre-programmed adaptability" ... In other words, however organisms came to be (believe what you will) it does indeed appear that they are pre-programmed to adapt to various niches. 
What appears to be to you is of no consequence. You are a bluffoon.