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Messages - DaveGodfrey

26
Interesting paper.  There's too much detail in there for my taste so I mainly read the intro and conclusions.  Seems to me that this might be a case of NGE.  That is, the body senses things about it's environment and changes it's own DNA in response. 

It would have to do so in a way that would be heritable. What kind of mechanism do you suggest?
It's a puzzle, isn't it?
Since lactose doesn't get past the gut wall (unless it's broken down), there's no obvious way the germ cells could ever "know" whether there's lactose in the diet or not.
But hey! In the mind of someone who believes in talking snakes, there's always the Magic! option.
Oh please.
Please, what?
Quote
Anyway, didn't the papers say that lactase persistence co-evolved with local dairying practices? I'm sure I'm not saying it right but the idea I got was that wherever dairy animals were kept, lactase persistence evolved ... or something like that.
You're just now figuring this out?
Yes. The idea is that where dairy is a significant dietary component, there is natural selection for the trait that allows people to consume it without getting sick.  You know... just like Darwin discussed in that famous book you lied about having read.
Wait.

Are you saying that the people with lactase persistence in areas where dairying was significant could reproduce better? Why couldn't the people without lactase persistence simply opt for a non dairy diet and still reproduce just fine? What does consuming Dairy have to do with reproductive abilities?
What if dairy is a potentially very large source of food for you. Think of the advantage you would have if you could use it without feeling like shit if you eat it.  You're presumably already herding these animals for meat, skins etc. They produce enough milk for you to use a bit. And yet when you eat it you get terrible cramps and feel like crap. Your neighbour Geoff however feels fine. He wins those "milk drinking contests" against the other young men that you refuse to enter because it makes you feel so bad afterwards. It seems to impress some of the ladies. Yes your wife loves you, and you have two fine kids who made it past five, but Geoff has a string of exes, and five of his kids have all got past the toddler stage, and they all seem to be able to drink milk. You tried feeding your kids this fermented stuff that Geoff's sister, Vicky's been experimenting with, and feeding her kids on, but yours still don't like how it makes them feel.

....30 years later....

The tribe is doing well, Most of the toddlers running round today are the grandkids of either Geoff or Vicky.  This drinking milk thing has saved the lives of several people when the crops failed.  The last time, you lost one of your grandkids, but fortunately your son married one of Vicky's kids and two of the four grandchildren you had can drink this milk stuff. So at least some of your genes will get passed on, even if its not looking like any of your great-grandchildren will have your "issues" with this milk thing.
27
Meanwhile on the other side of the pond ...


Dave quoting Farage seems appropriate somehow.
Braying misogynists of a feather...
28
Trump was "joined by the UK". The UK did this a week ago. 
29
Dave, try think my about it this way. Do you remember those word games where you have to go from one word, like say "Foot", to another, say "Ball", changing one letter at a time, where each change had to give you a new word?

Each of those changes in a "error". There are many other "errors" that don't result in words, or lead you down blind alleys that don't take you to where you need to be (yes there are some obvious flaws in this analogy, but bear with me). Do you now get why we talk about changes as "errors"? We only say it's an error because it's different from the original. Not because it's wrong.
30
I thought they beep-booped the wage gap as the "earnings gap" as if it was a distinction with a difference? There's usually a side order of "they took time out to have a family" (which in principle is understandable, but I'd like to see how badly it affects men in the same field if they take a career break, my guess is "not that much") but there's usually a big old heap of "wimmin atent competitiv innit" bullshit, and I just want to.set everyone on fire.
31
YouTube is throwing me down the Thunderfo0t rabbit hole. Or at least it wants me too. 

Dude, there's a reason I unsubscribed. 
32
Dave, I ask you again, if NHEJ changes a T to an A in one organism at a particular locus, but a copying error from a failure in DNA replication and error checking does the same in another, how will the cell tell if one is a degradation and one is a new beneficial change?
33
https://www.biorxiv.org/content/biorxiv/early/2017/12/13/233502.full.pdf
Quote
These temporal windows for the exit
69 of modern humans out-of-Africa are at odds with fossil,
70 archaeological and ancient DNA data.

Skeletal remains unearthed in
71 the Skhul and Qafzeh caves demonstrated that early modern
72 humans were present in the Levant between 125 and 80 kya [10].
73 The discovery of modern human teeth in southern China dated to
74 120-80 kya [11], also supports the presence of anatomically modern
75 humans (AMHS) in eastern Asia during this period. Several
76 archaeological studies uncovered Middle Stone Age (MSA) lithic
77 assemblages, dated around 125-75 kya, in different regions of the
78 Arabian Peninsula, presenting affinities with northeastern African
79 assemblages of the same period [12-14]. These findings suggest
80 that African AMHS may have extended its geographic range to
81 eastern and northern Arabia long before the time frame proposed by
82 molecular data
Yes. African people left Africa. You know, they came "Out" of "Africa". All this does is suggest that this migration happened earlier than we supposed. It matches up very nicely with the new data suggesting that AMHS are a rather older than we thought. Which comes from remains found in Africa Sucky.
34
No. I thought that might be where you were getting confused. The 125kya migration was a population of an L haplogroup basal to L3. Their point is that L3 arose from this basal group in Asia and not in Africa, as previously thought. They do not dispute that other L haplogroups arose in Africa prior to their proposal of L3 arising in Asia.
Agreed, they do not dispute the claim that other haplogroups arose in Africa prior to their proposal of L3 arising in Asia. I have said a few times that they have not gotten all the way to the Out of the Middle East theory. 
I have said a few times that the study does not support all the aspects of the Out of Africa theory. But it does support some very important aspects of the Out of the Middle East theory. For example it supports the idea that L3 evolved in the Middle East [they say "Asia"], that some of them migrated to Africa later and that all humans evolved from the modern humans that were in the Middle East circa 125kya.
No it doesn't. It explicitly talks about Africans who aren't members of L3, and who are not descended from L3 carriers, who never left Africa. At all. The fact that those people exist, and no matter how much you babble on about "reversing the arrows" or making shit up about how you can somehow derive them from the L3 haplogroup (you can't dickhead), changes the fact that your idiotic "Out of the Middle East" "theory* is utterly falsified. And more than a little racist as we have seen from previous comments you have made.
35
Dave, you need to understand the details, because you need to understand the bits that failed and the bits that didn't. And making up your own definition for "Neo-Darwinism" just makes you look like a fucking idiot. it does not, and never has meant solely the idea that "copying errors", (and note that failure of a repair enzyme to correct an error is also a "copying error", even if the efficacy of said enzyme is under some kind of cellular control) are responsible for much of evolution (specifically speciation in Vox's example). If it has mean that then you'd be able to show that it did.

Making up definitions for well accepted terms is dishonest and confusing. When everyone else knows what the "Neo-Darwinian Synthesis" is, a bit about how it was developed, and how its been extended and modified since it was invented in the 1920s you coming along with a personal definition that nobody else uses and not telling anyone what it is, just makes it impossible to have a conversation with you.

You do it all the time Dave. Fucking stop. Learn what terms mean. You have a choice Dave, either use them correctly, o don't use them at all.
36
Well, he seems clear to me, but someone thought they'd read somewhere where Shapiro seemed to include double-strand break repair systems as part of NGE.  Obviously some recombination processes involve double strand breaks, so that would make some sense.

The point is that Shapiro isn't drawing a bright line where Dave thinks he is drawing it.  He's pointing out that quite a lot of mutations arise from quite complex cell processes that preferentially produce combinations of existing functions or which are triggered by environmental stressors.  He does not say, for instance, that a bacterial cell reorganises its genome to cope with a new stressor, which is what Dave sometimes appears to think.

Indeed, which is why a dozen plus pages back I said that relaxing the fidelity of repair enzymes and error checking processes would be a really good way of boosting your mutation rate, these are things that happen all the time, so will turn up lots of small mutations very quickly.

Dave was, shall we say, not impressed by this notion.
37
Quote
What we mean by "random" is that mutations occur regardless of whether they would be good for the organism. That is, the chances of an adaptive mutation occurring is not increased if the environment changes in a way that would favor that mutation.

--Jerry Coyne

https://whyevolutionistrue.wordpress.com/2013/08/25/famous-physiologist-embarrasses-himself-by-claiming-that-the-modern-theory-of-evolution-is-in-tatters/
Dave, did you read the article?

Quote
The word "random" does not, to evolutionists, mean that every gene has the same chance of mutating, nor that mutation rates can't be affected by other things. What it means is that mutation is not somehow adjusted so that good mutations crop up just when they would be advantageous. My friend Paul Sniegowski, a professor at Penn, uses the term "indifferent" instead of "random," and I think that's a better way to describe the neo-Darwinian view of mutations.

The mutation rate increases, fine. That means that the chance of a beneficial mutation increases, Burt so does the chance of a deleterious one. Or a neutral one. The chance of a beneficial mutation compared to any other mutation does not change. Its still random. Its just higher than it was because the chance of any mutation is higher. It would be very big news if Noble showed that that was the case.
38
Hey Dave,

Let's say you start with a population with its entire genome sequenced. You let it run for several years, and then you sequence its genome again. In doing so, you determine at least some of the mutations in the population.

Is there a way to tell which of the mutations are NGE, and which are "copying errors"?
I certainly wouldn't know how to do it and I don't think there are many researchers trying to determine the difference. Shapiro was encouraging people to do experiments along these lines 5 years ago.
So, no. And yet you are sure. Why is that?
What I'm sure of is that copying errors didn't create the biosphere. 

So am I. 

I am getting so sick of this straw zombie


Nope.

Not a straw man. 

Here's a recent article in the prestigious journal Nature that repeats this Blind Orthodoxy ...
Quote
If DNA repair were perfect and no mutations ever accumulated, there would be no genetic variation--and this variation serves as the raw material for evolution. Successful organisms have thus evolved the means to repair their DNA efficiently but not too efficiently, leaving just enough genetic variability for evolution to continue. https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409

You really really need to once and for all own this nonsense that your team has been mindlessly repeating for decades.

It's flat out dishonest if you don't.

Dave, if DNA repair was perfect NGE couldn't work, given that one of the mechanisms it uses is DNA repair and control over how good it is at fixing it so its back to what it was before.

When people talk about "copying errors" (especially in multicellular eukaryotes) they're talking about the simple fact that when you go from one diploid cell to four haploid cells you have to produce more DNA than you had before. So you have a mechanism that replicates the DNA which isn't perfect, and a mechanism that checks for errors, which also isn't perfect. How do you think NGE works other than by exercising control over these processes and other ones like them? How are they not "copying errors", when the old sequence is different from the new one? That's all an error is. It just means that the sequence in the daughter cell is different from the sequence in the parent one.

More importantly if NGE changes a T to a C in one sperm cell, but a "copying error" does it in another one at the same nucleotide in the sequence, how would they possibly have different phenotypic effects?

It's not clear whether Shapiro counts "error-prone repair processes"as "NGE".  At one stage Dave thought yes - then I think he changed his mind.  In the paper we've mostly been discussing, Shapiro clearly differentiates "NGE" processes, which are all recombination processes of various kindsfrom other cell-mediated processes that can lead to "genomic change" e.g. e.g NHEJ.  However, he DOES cite NHEJ as process that will tend to become more common just when the population needs additional diversity  simply because an environment that causes more double-strand breaks will result in more repairs therefore more potential mutations.

Shapiro seems to be making two separate cases, and I think Dave is conflating them.

One is that "NGE" can combine existing functional sequences whole sale, thus getting novel functions fairly rapidly

The other is that a whole host of mutagenic processes are triggered by the very environments that will require adaptation from the population if it is to survive, and thus additional diversity just when needed.  He includes NGE in this, but he also cites other processes, including, in sexually reproducing species, hybridisation and inbreeding.
That makes sense. If Shapiro isn't being clear about what counts as an NGE and what doesn't then it explains why I thought what I thought. What's clearly not in doubt though is that copying errors of the sort I talked about and whether their rate is under celluilar control are part of the "Third Way" that Dave seems so enamoured with.

My response is that its all part of the "evolution of evolvability". Organisms that are good at diversifying and have ways of throwing up new variations are going to be at a greater advantage, and far more likely to have descendants (and many and varied ones) than ones that plod along doing the same thing in the same stable environment. (That said, when the sun starts boiling the oceans, those same plodders will probably still be here and will be the ones turning the lights out on Earth).
39
What do you mean that's not your statement? I copied it exactly from your post.

I wish you'd use the quote function.  I don't recognise that sentence as mine.

I don't see why you would. Its mine. From this post. If I've said anything that's obviously wrong please point it out. I haven't read Shapiro.
40
No Dave, you copied it from MY post. Learn to read.
41
Dave, I was talking about one particular aspect of NGE. One that has been mentioned several times. Including by you. More importantly its one of the few that can work in multicellular eukaryotes.

Now would you care to show that its not how any version of NGE works? Or would you like to wipe the egg off your face? And y'know maybe address Pingu's points rather than whining that she hasn't addressed your silly criticism of a statement she didn't make?
42
Quote
"Adaptation tools are silenced" does not in ANY WAY mean the same thing as "diversity drops".
Sure it does because as I understand it the cell stops manufacturing different wrench sizes so to speak because the cell has now has the right sizes it needs to do the job.
It's not "the cell" Dave. It's the population. Everyone in the population has lost the ability to make wrenches the wrong size fir a particular job. And when they come to a situation where that sized wrench is the wrong size they need to learn how to make new sized wrenches. And in the process, yet again, they forget how to make the old wrenches.
43
Why is it "misleading" to say that if a bunch of alleles become extinct then "diversity drops"?

How can that not be a decrease in diversity? You do know what "decrease" means Dave?
44
Dave, re-read that last quit from Shapiro, after looking up what "Purifying Selection" is. It won't just eliminate the novel changes that aren't optimal. It will also eliminate existing alleles that are no longer optimal.
45
Hey Dave,

Let's say you start with a population with its entire genome sequenced. You let it run for several years, and then you sequence its genome again. In doing so, you determine at least some of the mutations in the population.

Is there a way to tell which of the mutations are NGE, and which are "copying errors"?
I certainly wouldn't know how to do it and I don't think there are many researchers trying to determine the difference. Shapiro was encouraging people to do experiments along these lines 5 years ago.
So, no. And yet you are sure. Why is that?
What I'm sure of is that copying errors didn't create the biosphere. 

So am I. 

I am getting so sick of this straw zombie


Nope.

Not a straw man. 

Here's a recent article in the prestigious journal Nature that repeats this Blind Orthodoxy ...
Quote
If DNA repair were perfect and no mutations ever accumulated, there would be no genetic variation--and this variation serves as the raw material for evolution. Successful organisms have thus evolved the means to repair their DNA efficiently but not too efficiently, leaving just enough genetic variability for evolution to continue. https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409

You really really need to once and for all own this nonsense that your team has been mindlessly repeating for decades.

It's flat out dishonest if you don't.

Dave, if DNA repair was perfect NGE couldn't work, given that one of the mechanisms it uses is DNA repair and control over how good it is at fixing it so its back to what it was before.

When people talk about "copying errors" (especially in multicellular eukaryotes) they're talking about the simple fact that when you go from one diploid cell to four haploid cells you have to produce more DNA than you had before. So you have a mechanism that replicates the DNA which isn't perfect, and a mechanism that checks for errors, which also isn't perfect. How do you think NGE works other than by exercising control over these processes and other ones like them? How are they not "copying errors", when the old sequence is different from the new one? That's all an error is. It just means that the sequence in the daughter cell is different from the sequence in the parent one.

More importantly if NGE changes a T to a C in one sperm cell, but a "copying error" does it in another one at the same nucleotide in the sequence, how would they possibly have different phenotypic effects?
46
47
Science / Re: Status of disease eradication programs
I had a fairly stark reminder of how far we've come in combating polio- I was working in the Iron Lung collection a couple of days ago. We have this, "Smith-Clarke 'Baby' cabinet respirator". That's an iron lung for infants. Hospitals used to have dozens of them. People nowadays have no clue about this sort of thing.
48
Politics and Current Events / Re: Austin bombings
Well yes, but I was thinking more of the fact that the Unabomber was one person who wasn't a member of any particular organisation.
49
Politics and Current Events / Re: Austin bombings
If they'd said "no confirmed links to known terrorist groups" then that might be accurate as these people tend to cultivate the whole "lone wolf" thing. But it also means you can describe it as a "terrorist act" because I can't really think of a more obvious act of terrorism than sending bombs through the mail, etc. Everyone calls the Unabomber a terrorist, and that's exactly what he did.

But of course being white he can't possibly be a terrorist, but instead hangs out with "very fine people".
50
Think about this:

Quote from: Sagan
But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown.
Read more at: https://www.brainyquote.com/quotes/carl_sagan_163043
They were right to laugh at Columbus based on what was known at the time. He thought the world was much smaller than everyone else and you could easily sail to Japan the other way. Most other people thought Eratosthenes' estimate of the size of the Earth was about right, even if there was some disagreement about exactly how big it was, how big Eurasia was, etc.

Columbus didn't prove anyone wrong. He went to his grave thinking he'd found a bunch of islands off Asia. Another thing they could have legitimately laughed at him for.
Well, yes. I wouldn't be surprised if the other examples turned out to be more nuanced too, or mostly wrong even.
Maybe Sagan could have picked examples that were more accurate, but if nobody has heard of these people, its not really going to work.
I don't know much about the Wright Brothers, but the fact that they were using smaller high powered motors (rather than the steam engines that Hiram Maxim tried, with a surprising amount of success), indicates that they knew something that the people who laughed at them didn't. Columbus at least, got very lucky.