Stephen L Talbott's ideas on biology

#1
This series of 4 articles is a must read for anyone interested in recent developments in biology, and the real meaning of the epigenetics revolution.

http://www.thenewatlantis.com/publications/getting-over-the-code-delusion

I got the original link from one of Rupert Sheldrake's webpages.

There is a lot here to read, but I think he is really worth the effort - and might make an interesting guest on SKEPTIKO!

David
 
#3
I am glad you liked it!

As I read further into it, I did feel in retrospect that it could have been written in a clearer style, however it did convey the incredible complexity of life. To me, it seemed to nail the traditional concept of evolution by selection acting on random mutations of DNA! It makes me wonder if the relation between genotype and overall phenotype is even one to one - I mean could two vastly different creatures have the same genetic code!

David
 

Paul C. Anagnostopoulos

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#4
I am glad you liked it!

As I read further into it, I did feel in retrospect that it could have been written in a clearer style, however it did convey the incredible complexity of life. To me, it seemed to nail the traditional concept of evolution by selection acting on random mutations of DNA! It makes me wonder if the relation between genotype and overall phenotype is even one to one - I mean could two vastly different creatures have the same genetic code!
Only to the degree that the epigenetic markers are inherited consistently down through generations. If they are not, but instead are "refreshed" every generation or two by mechanisms that are coded in the genome, then the ultimate source is still the genome.

http://learn.genetics.utah.edu/content/epigenetics/inheritance/

The coffin of "natural selection is all there is" was nailed shut long ago.

~~ Paul
 
#5
Only to the degree that the epigenetic markers are inherited consistently down through generations. If they are not, but instead are "refreshed" every generation or two by mechanisms that are coded in the genome, then the ultimate source is still the genome.

http://learn.genetics.utah.edu/content/epigenetics/inheritance/

The coffin of "natural selection is all there is" was nailed shut long ago.

~~ Paul
Well of course, there is evidence that epigenetic effects occur - and that the evidence was ignored in the past:

http://sciencesetfree.tumblr.com/

David
 

Paul C. Anagnostopoulos

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#6
Well of course, there is evidence that epigenetic effects occur - and that the evidence was ignored in the past:

http://sciencesetfree.tumblr.com/
http://sciencesetfree.tumblr.com/
Why does Sheldrake have to exaggerate so much? He talks about giraffes and ostriches, making it appear that those are the sort of epigenetic characteristics we're talking about. Then he says the epigenetic "taboo" was lifted at the turn of the millennium. Except that DNA methylation was known to have something to do with the X chromosome many years before that.

~~ Paul
 
#7
Why does Sheldrake have to exaggerate so much? He talks about giraffes and ostriches, making it appear that those are the sort of epigenetic characteristics we're talking about. Then he says the epigenetic "taboo" was lifted at the turn of the millennium. Except that DNA methylation was known to have something to do with the X chromosome many years before that.

~~ Paul
Sheldrake was quoting Lamarck:
Lamarck’s most famous example was the giraffe. He thought giraffes’ long necks were acquired through the habit of stretching up to eat the leaves of trees. In this respect too, Darwin agreed with Lamarck. For example ostriches, he suggested, may have lost the power of flight through disuse and gained stronger legs through increased use over successive generations.
The taboo on the idea that the DNA in an offspring could be affected by what happened to the parent (e.g. semi-starvation) was indeed taboo until the turn of the century - indeed many people don't realise that Lamarck's research was (at least partially) validated by that discovery. Methylation may have been discovered earlier, but it wasn't credited with tagging DNA going into the germ cells.

(This is a bit tangential to the subject of Stephen Talbott's ideas.)

David
 

Paul C. Anagnostopoulos

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#8
Sheldrake was quoting Lamarck:
Yes, why, when Lamarckian "big changes" have nothing to do with the subject?

The taboo on the idea that the DNA in an offspring could be affected by what happened to the parent (e.g. semi-starvation) was indeed taboo until the turn of the century - indeed many people don't realise that Lamarck's research was (at least partially) validated by that discovery. Methylation may have been discovered earlier, but it wasn't credited with tagging DNA going into the germ cells.
It wasn't taboo until the turn of the century. Biologists knew about the importance of methylation in 1975 and probably even before.

The problem is words like taboo. Sheldrake insists on using words like that. It makes him look like an axe grinder. He should distinguish taboo from the way in which interest ramps up over time.

~~ Paul
 
#9
Yes, why, when Lamarckian "big changes" have nothing to do with the subject?
Well of course they were, because the standard evolutionary story is based on small changes compounding into large ones. As it is understood at the moment, the methylation does not last indefinitely, but who knows - perhaps there is a mechanism to incorporate that information back into the DNA.
It wasn't taboo until the turn of the century. Biologists knew about the importance of methylation in 1975 and probably even before.
I thought I made myself clear. - what was taboo, was the idea that acquired characteristics could be inherited - such as resistance to extreme food shortages. The whole thing got caught up in the whole East-West confrontation.
The problem is words like taboo. Sheldrake insists on using words like that. It makes him look like an axe grinder. He should distinguish taboo from the way in which interest ramps up over time.

~~ Paul
Taboo is fine by me - because that was what it was - call a spade a spade. The point is that no data should be taboo, but unfortunately this has been forgotten in too many areas of science.

Any, back to the main theme - what do you think Talbott's ideas tell us about evolution?

David
 

Paul C. Anagnostopoulos

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#10
Well of course they were, because the standard evolutionary story is based on small changes compounding into large ones. As it is understood at the moment, the methylation does not last indefinitely, but who knows - perhaps there is a mechanism to incorporate that information back into the DNA.
Yes, perhaps, but meanwhile Sheldrake exaggerates what we know.

I thought I made myself clear. - what was taboo, was the idea that acquired characteristics could be inherited - such as resistance to extreme food shortages. The whole thing got caught up in the whole East-West confrontation.
The what?

Any, back to the main theme - what do you think Talbott's ideas tell us about evolution?
It tells us that epigenetics is important. We still don't know the percentage of DNA that is junk. Biology is more complicated than we thought 25 years ago, when it was more complicated than we thought 25 years before that.

What I'm hoping is that it's another nail in the coffin of "Darwinian evolution based only on natural selection" and that there might finally be enough nails that IDers and other people stop bringing it up.

Also, I gotta, say, I'm not sure about Talbott's credentials. Though perhaps I am being unfair.

http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness
http://www.evolutionnews.org/2012/03/its_life_all_th057251.html

~~ Paul
 
#11
What I'm hoping is that it's another nail in the coffin of "Darwinian evolution based only on natural selection" and that there might finally be enough nails that IDers and other people stop bringing it up.
I hope I can quote you on that in future discussions - that you do not think evolution based only on natural selection is a viable concept.

Dare I ask what you think could possibly replace evolution by pure natural selection ;)
I think the point is that those four articles are very extensively referenced.

David
 

Paul C. Anagnostopoulos

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#12
I hope I can quote you on that in future discussions - that you do not think evolution based only on natural selection is a viable concept.
You didn't have to wait until now to quote me. I've talked about various other aspects of evolution all along.

Dare I ask what you think could possibly replace evolution by pure natural selection ;)
Evolution by natural selection, random mutation, genetic drift, epigenetics, gene flow, sexual selection, and so forth. It's complicated, cuz chemistry has no interest in keeping it simple.

I think the point is that those four articles are very extensively referenced.
One of the people he references is Tom Bethell.

http://recursed.blogspot.com/2007/09/bethell-buffoon.html

~~ Paul
 
#13
You didn't have to wait until now to quote me. I've talked about various other aspects of evolution all along.
OK - we are talking at cross purposes, because the other mechanisms - say genetic drift - achieve nothing useful in the absence of some sort of selection. Natural selection underpins conventional ideas of evolution.

Re Bethel: Creationism and intelligent design are indeed completely different. The former insists that the Earth was made 6000-odd years ago to conform with the Bible. The latter suggests that some form of intelligence was required to make life and to cause it to evolve. This need not be Christian, still less Fundamentalist - indeed don't you think the idea of Yaweh the biochemist to be rather preposterous?

David
 

Paul C. Anagnostopoulos

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#14
OK - we are talking at cross purposes, because the other mechanisms - say genetic drift - achieve nothing useful in the absence of some sort of selection. Natural selection underpins conventional ideas of evolution.
Well, it could achieve small useful things just by chance. But, indeed, an organism can't get away with anything big that doesn't work in the current environment.

I just ordered this book. It may prove interesting.

http://www.amazon.com/Arrival-Fitte...742772&sr=8-1&keywords=arrival+of+the+fittest

Re Bethel: Creationism and intelligent design are indeed completely different. The former insists that the Earth was made 6000-odd years ago to conform with the Bible. The latter suggests that some form of intelligence was required to make life and to cause it to evolve. This need not be Christian, still less Fundamentalist - indeed don't you think the idea of Yaweh the biochemist to be rather preposterous?
I'm willing to make the distinction between Creationism and Intelligent Design. However, I quite often discover that an ID "theorist" turns out to be a YEC or a Biblical literalist or whatever. ID was invented to paper over creationism. That does not preclude there being IDers who are not Christians, of course. If I was one of those people, though, I would not call myself an IDer. Too much bad press.

~~ Paul
 
#15
Well, it could achieve small useful things just by chance. But, indeed, an organism can't get away with anything big that doesn't work in the current environment.
Right - evolution based on natural selection is a crock of s**t - it can't work! To me, I found that a fascinating conclusion that I would probably never have realised without SKEPTIKO!
Let me know what that book has to say - it is really rather expensive to order as an unknown!
I'm willing to make the distinction between Creationism and Intelligent Design. However, I quite often discover that an ID "theorist" turns out to be a YEC or a Biblical literalist or whatever. ID was invented to paper over creationism. That does not preclude there being IDers who are not Christians, of course. If I was one of those people, though, I would not call myself an IDer. Too much bad press.
Well I agree to a point, but I don't think biology should ever have excluded the design hypothesis. As I have pointed out before, it isn't even necessarily a non-materialist concept DNA life might have been designed by some other kind of life that really could evolve more easily. As it is, if you want to do ID research, you really need to be backed by a Christian group.

Really, I don't think ID is a particularly Christian concept, because it has clearly allowed al sorts of biological cruelties to emerge. Also I don't think Christians would like to think of their god as a super-nerd!

David
 

Paul C. Anagnostopoulos

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#16
Right - evolution based on natural selection is a crock of s**t - it can't work! To me, I found that a fascinating conclusion that I would probably never have realised without SKEPTIKO!
You have reached a different conclusion than I have. Probably something to do with all the stuff about phenotype spaces and such.

Well I agree to a point, but I don't think biology should ever have excluded the design hypothesis. As I have pointed out before, it isn't even necessarily a non-materialist concept DNA life might have been designed by some other kind of life that really could evolve more easily. As it is, if you want to do ID research, you really need to be backed by a Christian group.
That's too bad, because it clouds the minds of the researchers. As far as I can tell, they don't give a crap about the science. They've been told 100 times that their math is wrong, but they never stop spewing the same stuff. If there was any good math, more biologists would jump on it.

You seem to think that X is excluded from science solely because X violates some sort of science rules. Mostly, though, it's because X is empty, vapid, infertile, and useless.

Really, I don't think ID is a particularly Christian concept, because it has clearly allowed al sorts of biological cruelties to emerge. Also I don't think Christians would like to think of their god as a super-nerd!
They just want to teach Christianity in public schools. To do so, they have to sneak in somehow. Science seems like a good gambit. Everything else is too much like religious studies.

~~ Paul
 
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#17
That's too bad, because it clouds the minds of the researchers. As far as I can tell, they don't give a crap about the science. They've been told 100 times that their math is wrong, but they never stop spewing the same stuff. If there was any good math, more biologists would jump on it.
No - the essential point is that no part of the evolutionary process in which natural selection cannot act, is immune from catastrophic combinatorial explosion. Thus every one of the original minimal set of proteins can't get there by evolution - the combinatorics are extreme.

David
 

Paul C. Anagnostopoulos

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#18
No - the essential point is that no part of the evolutionary process in which natural selection cannot act, is immune from catastrophic combinatorial explosion. Thus every one of the original minimal set of proteins can't get there by evolution - the combinatorics are extreme.
Too many negatives in the first sentence?

But why should we assume that the search needs to visit every case? The book I mentioned above addresses this question. Things like enzyme superfamilies suggest that an exhaustive search is unnecessary. Also, since we don't yet know what came before proteins, it could be that there was already useful scaffolding that narrowed the search.

Consider a brute force search for a sequence of 30 amino acids. That is 4^30 = 2^60 = 1.1e18 combinations. If we start with a population of 1 billion organisms that replicate once per day, it would take about 60 days to search it. Even if only 1% of the offspring survive, it would take only 4180 days.

Now consider that longer proteins might be build by duplication and catenation. We might not have to search the space of 300 or 3000 amino acids. Perhaps we only have to search up to 50 or 60, which is tractable.

~~Paul
 
#19
OK - but first you have chosen a very small protein (a more typical value might be 300), then you have assumed that none of the intermediate proteins might be harmful, and that the final product might not be harmful without a control mechanism already in place.

Given that we are interested in new proteins with new functionality, it seems less than obvious that we can rely on linking proteins with existing functionality. Besides, when you link two proteins, you are quite likely to end up with a totally different fold - which will put you back to square one!

David
 

Paul C. Anagnostopoulos

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#20
OK - but first you have chosen a very small protein (a more typical value might be 300), then you have assumed that none of the intermediate proteins might be harmful, and that the final product might not be harmful without a control mechanism already in place.
Yes, I chose a small one. I'm not sure what you mean by intermediate proteins. I calculated the time required to try all 30-residue peptides, assuming 99% of the combinations are lethal.

Given that we are interested in new proteins with new functionality, it seems less than obvious that we can rely on linking proteins with existing functionality. Besides, when you link two proteins, you are quite likely to end up with a totally different fold - which will put you back to square one!
It's not obvious that linking will work, but it's not obvious that it won't. My point is simply that an exhaustive search may not be necessary, which completely changes the math. The ID argument is "oh my gosh, look at those big numbers!" I don't think I would draw any conclusions from such an argument.

http://www.genomebiology.com/2010/11/7/126

~~Paul
 
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