Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 78 (8896 total)
Current session began: 
Page Loaded: 03-23-2019 8:43 PM
35 online now:
Tanypteryx (1 member, 34 visitors)
Chatting now:  Chat room empty
Newest Member: WookieeB
Post Volume:
Total: 848,599 Year: 3,636/19,786 Month: 631/1,087 Week: 221/212 Day: 36/27 Hour: 0/1


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Prev12345
6
78Next
Author Topic:   Does Neo-Darwinian evolution require change ?
PaulK
Member
Posts: 14751
Joined: 01-10-2003
Member Rating: 1.7


Message 76 of 114 (601289)
01-19-2011 5:00 PM
Reply to: Message 70 by slevesque
01-19-2011 3:42 PM


Re: Mutation rates
quote:

Ok I think I got misunderstood there. What I was saying was: The % of functioning genome has been ever increasing in the past few years, as I'm sure you know. Right now, anyone can safely say that at least 30% of the genome is functional.

Is that really true ? I'd have thought that the discovery of fewer genes than expected by the Human Genome Project would have cut the amount of functional DNA, and I very much doubt that the relatively small number of regulatory sequences etc. discovered makes up the difference.

So is the figure really 30% ? Do you have any evidence ?


This message is a reply to:
 Message 70 by slevesque, posted 01-19-2011 3:42 PM slevesque has responded

Replies to this message:
 Message 83 by slevesque, posted 01-20-2011 1:24 AM PaulK has responded

    
RAZD
Member
Posts: 19758
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.7


(2)
Message 77 of 114 (601292)
01-19-2011 5:35 PM
Reply to: Message 75 by slevesque
01-19-2011 4:04 PM


circling around the peak with oscillating lineages
Hi slevesque.

But this is statistically very unrealistic. If a generation moved away from the peak by 50 mutations, in a genome of 3 billion, it is extrememly improbable that the next generation will move back towards the peak on not simply farther away.

Why?

Draw a circle around the original individual and then draw the same size circles around a point on the circumference of that circle. The first circle represents the range of possible mutations away from the position of the parent individual, the second is the possible range of mutations away from one of the outermost the offspring -- how much of that outer offspring circle is inside the parent circle? I get 39.1%, which I do not count as extremely improbable, and that is the worst case. You could have second generation individuals slightly away from center such that >90% of their offspring would be within the parent circle.

With neutral drift there could be a slight tendency to move subsequent offspring gradually away from the parent center, but when selection is included, the portions inside are differentially selected from the portions outside, thus weighting the proportion within the parent circle higher than the proportion outside the circle.

If sexual selection is involved there would be a strong selection for individuals at the center to reproduce more, to the disadvantage of outer individuals, where some may be left entirely out of the picture for the next generation.

If we disregard sexual selection, there can still be significant selection pressure. Just because the population appears to be in stasis, this does not mean that there is no selection pressure in the population: if the population has expanded to consume the limits of the ecology (which is normal in a stable ecology), and reproduction produces many more offspring than needed to replace the losses, then competition for limited resources can produce high survival selection, such that any second generation individuals within the circle could reproduce significantly more than those outside, thus moving the offspring back towards the center.

You can also envisage fitness topologies around the peak, and the further away an individual is, the more of their offspring circle is inside the topology line, and the stronger would be the selection pressure to benefit those inside versus those outside the topological boundary.

It becomes very easy, imho, to see that most of the population would always be near the peak, that the trend for the offspring of the outer individuals would be towards the center, overcoming any slow trend of the offspring of central individuals away from the center, thus generating oscillations in the lineages where movement away in one generation is balanced by movement back towards the center in other generations.

Enjoy.

(2/3-(3)0.5/2π) = 0.391

Edited by RAZD, : clrty


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

This message is a reply to:
 Message 75 by slevesque, posted 01-19-2011 4:04 PM slevesque has not yet responded

Replies to this message:
 Message 78 by dwise1, posted 01-19-2011 6:20 PM RAZD has acknowledged this reply
 Message 82 by sfs, posted 01-19-2011 10:47 PM RAZD has responded

  
dwise1
Member
Posts: 3310
Joined: 05-02-2006
Member Rating: 4.6


Message 78 of 114 (601299)
01-19-2011 6:20 PM
Reply to: Message 77 by RAZD
01-19-2011 5:35 PM


Re: circling around the peak with oscillating lineages
Two rather influential graphics early in my studies were both from the circa-1980 article in either Science or Nature which covered the introduction of Punc Eq -- I have a xerox copy of that article stored away in a box somewhere. One graphic illustrated that highly specialized species that are finely tuned to their environments tend to be very short-lived, going extinct when that environment changes to rapidly for them to adapt, whereas less-specialized species tend to be much longer-lived, being better able to weather changes in their environments as well as a wider range of environmental conditions, such that they would appear in the fossil record as being in stasis.

The other graphic is the one that's more apropos here. It illustrated a period of "rapid" change by a slanted line between two conditions of stasis. Over that line was a long parade of bell curves representing individual generations. Each generation's bell curve overlapped the bell curves of the neighboring generations.

Over the years, I have arrived at the opinion that there really isn't any such thing as actual "evolutionary processes." Rather, evolution is mainly just the end result of life doing what life does, of populations of plants, animals, and protista surviving-or-not and reproducing-or-not. What we describe as evolution and evolutionary processes is our observation of and analysis of the cumulative and aggregate effects of life. Nothing magical about it. And the only way for evolution to violate the laws of thermodynamics would be if life itself were to violate those laws, which it does not. And the only way for evolution to be impossible would if life itself were impossible. Just throwing that out there, in part to see how much fire it will draw.

But I do have one question about these graphing models of the individuals of a population clustering and oscillating about local adaptive peaks. Instead of graphing their genomes about those adaptive peaks, shouldn't we be graphing their phenotypes? Because selection does not directly select for or against the genotypes, but rather for or against the phenotypes that those genotypes would express.

Edited by dwise1, : just throwing that out there, ...


This message is a reply to:
 Message 77 by RAZD, posted 01-19-2011 5:35 PM RAZD has acknowledged this reply

    
AZPaul3
Member
Posts: 3814
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.0


Message 79 of 114 (601318)
01-19-2011 8:02 PM
Reply to: Message 68 by slevesque
01-19-2011 3:34 PM


Re: The Dance of the Population Curves
Yes, but even taking those in the population closer, their babies will be farther then there parents because of the high mutation rates.

The mutations will always force a population to drift away from the optimal peak ...

Really? Based on what?

First, why do you assume mutation moves the individual away from the optimum? Why do you assume mutation moves the offspring further away than is the parent?

Is it possible for the offspring to have a mix of beneficial mutations for some attributes, mildly dilitarious for others, neutral for most and have the kid wind up at the same point or better then the parent.

Second, those with dilitarious mutations have the least effect on the population, especially larger populations. Do you understand why?

And those closer to the optimum have a better chance of having offspring with beneficial mutations. Do you understand why?


This message is a reply to:
 Message 68 by slevesque, posted 01-19-2011 3:34 PM slevesque has responded

Replies to this message:
 Message 84 by slevesque, posted 01-20-2011 1:27 AM AZPaul3 has responded

  
Dr Adequate
Member
Posts: 16085
Joined: 07-20-2006
Member Rating: 10.0


Message 80 of 114 (601340)
01-19-2011 10:13 PM
Reply to: Message 74 by slevesque
01-19-2011 3:57 PM


Of course, and the most deletirious mutations will be wiped out of each generation without any problem.

But some individuals most survive and reproduce, and what I'm sayign is that the high mutation rates imply that those individuals will have inherited lots of mutations, and although they may have the least deleterious set of mutations to have appeared in that generation, doesn't mean they still don't have those mutations.

So we'll get neutral drift, which is technically evolution but not in the interesting sense of the word, and which needn't show up in the fossil record.


This message is a reply to:
 Message 74 by slevesque, posted 01-19-2011 3:57 PM slevesque has responded

Replies to this message:
 Message 85 by slevesque, posted 01-20-2011 1:32 AM Dr Adequate has responded

  
sfs
Member (Idle past 611 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


(1)
Message 81 of 114 (601345)
01-19-2011 10:39 PM
Reply to: Message 70 by slevesque
01-19-2011 3:42 PM


Re: Mutation rates
slevesque writes:

Ok I think I got misunderstood there. What I was saying was: The % of functioning genome has been ever increasing in the past few years, as I'm sure you know.


I assume you're talking about the human genome. The estimates for the functional fraction of the human genome that I'm familiar with started around 100%, dropped to 20%, dropped to "at least 5%", and are now hovering in the range of 6 - 10%. I'm not aware of any secular trend in this estimate.

quote:

Right now, anyone can safely say that at least 30% of the genome is functional.


Well, you can safely say it in the sense that no one will throw a brick through your window for doing so, but I don't know of any geneticists who think that.

quote:

What I said concerning ENCODE was simply that it ''opened up the possibility'' that the entire genome had a function. I'm not saying it proved anything, and I certainly know the difference between functional and transcribed.


Yeah, but the entire genome almost certainly isn't functional, and even their estimates for the transcribed fraction were probably much too high (at least if what the people who do that sort of thing have told me is correct).

quote:

Therefore, all I'm saying is that when seeing how genetics has been unravelling the secrets of previously thought ''junk DNA'', and how more evidence comes to open the possibility that maybe the whole genome is functional, I think it is the idea that any part of the genome is junk that should be regarder with great skepticism, not the other way around.

Geneticists keep finding functional bits of noncoding DNA, and the bits they keep finding constitute only tiny fractions of the genome. Meanwhile, vast swathes of the genome look and act exactly like junk: transposons, pseudogenes, and the like, almost all showing no sign of selective constraint. The fact that a single experiment, using rather dubious methodology, concluded that much of the genome is transcribed shouldn't weight very heavy in your thinking.
This message is a reply to:
 Message 70 by slevesque, posted 01-19-2011 3:42 PM slevesque has not yet responded

    
sfs
Member (Idle past 611 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 82 of 114 (601349)
01-19-2011 10:47 PM
Reply to: Message 77 by RAZD
01-19-2011 5:35 PM


Re: circling around the peak with oscillating lineages
quote:

Draw a circle around the original individual and then draw the same size circles around a point on the circumference of that circle. The first circle represents the range of possible mutations away from the position of the parent individual, the second is the possible range of mutations away from one of the outermost the offspring -- how much of that outer offspring circle is inside the parent circle? I get 39.1%, which I do not count as extremely improbable, and that is the worst case.


I haven't been following the argument here, but this analogy is not a good one. Mutations are, to a first approximation, orthogonal to one another, so you should be working in a much higher dimensional space. Imagine the 50 mutations to be fifty unit steps in 50 of perhaps a million dimensions. The next 50 mutations will be in another 50 random dimensions. The probability of heading back toward the peak (neglecting selection) is tiny.
This message is a reply to:
 Message 77 by RAZD, posted 01-19-2011 5:35 PM RAZD has responded

Replies to this message:
 Message 86 by slevesque, posted 01-20-2011 1:32 AM sfs has not yet responded
 Message 90 by RAZD, posted 01-20-2011 8:34 AM sfs has responded

    
slevesque
Member (Idle past 2718 days)
Posts: 1456
Joined: 05-14-2009


Message 83 of 114 (601363)
01-20-2011 1:24 AM
Reply to: Message 76 by PaulK
01-19-2011 5:00 PM


Re: Mutation rates
For example:

quote:
Therefore, more than one third of the mouse and human genomes, previously thought to be non-functional, may play some role in the regulation of gene expression and promotion of genetic diversity.

http://www.sciscoop.com/2004-10-13-33731-304.html

I think that we are starting to see a paradigm shift in this field. The paradigm was that, DNa was mostly junk, and so it was a waste of time to try searching for it's use. Once more and more parts are being unravelled and found to have a use, I think an avalanche of discoveries in that field will come. But, as prof. John Mattick said:

quote:
the failure to recognise the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology

This message is a reply to:
 Message 76 by PaulK, posted 01-19-2011 5:00 PM PaulK has responded

Replies to this message:
 Message 87 by PaulK, posted 01-20-2011 1:44 AM slevesque has not yet responded
 Message 91 by Percy, posted 01-20-2011 8:56 AM slevesque has not yet responded

  
slevesque
Member (Idle past 2718 days)
Posts: 1456
Joined: 05-14-2009


Message 84 of 114 (601364)
01-20-2011 1:27 AM
Reply to: Message 79 by AZPaul3
01-19-2011 8:02 PM


Re: The Dance of the Population Curves
Really? Based on what?

First, why do you assume mutation moves the individual away from the optimum? Why do you assume mutation moves the offspring further away than is the parent?

Is it possible for the offspring to have a mix of beneficial mutations for some attributes, mildly dilitarious for others, neutral for most and have the kid wind up at the same point or better then the parent.

The most conservative estimate of the deleterious-to-beneficial ratio of mutations was 50 to 1. I've seen some suggest perhaps as high as a million to 1.

But even with the 50-1 ratio, it's still pretty obvious that the high mutations rates will push the next generation farther away from the peak then their parents from the optimal peak.


This message is a reply to:
 Message 79 by AZPaul3, posted 01-19-2011 8:02 PM AZPaul3 has responded

Replies to this message:
 Message 88 by AZPaul3, posted 01-20-2011 3:19 AM slevesque has not yet responded
 Message 94 by Dr Adequate, posted 01-20-2011 12:29 PM slevesque has not yet responded

  
slevesque
Member (Idle past 2718 days)
Posts: 1456
Joined: 05-14-2009


Message 85 of 114 (601365)
01-20-2011 1:32 AM
Reply to: Message 80 by Dr Adequate
01-19-2011 10:13 PM


So we'll get neutral drift, which is technically evolution but not in the interesting sense of the word, and which needn't show up in the fossil record.

Kimura's ''neutral evolution'' only works if the vast majority of the genome has no function. Even if only 5% of it were functional, a mutation rate of 40mpipg would result in two mutations falling into the functional part of it. And all that I have said would still hold. Of course, this problem becomes increasingly more difficult the more functional the genome turns out to be.


This message is a reply to:
 Message 80 by Dr Adequate, posted 01-19-2011 10:13 PM Dr Adequate has responded

Replies to this message:
 Message 89 by Wounded King, posted 01-20-2011 5:31 AM slevesque has not yet responded
 Message 93 by Dr Adequate, posted 01-20-2011 12:26 PM slevesque has not yet responded
 Message 96 by molbiogirl, posted 01-20-2011 5:55 PM slevesque has not yet responded

  
slevesque
Member (Idle past 2718 days)
Posts: 1456
Joined: 05-14-2009


Message 86 of 114 (601366)
01-20-2011 1:32 AM
Reply to: Message 82 by sfs
01-19-2011 10:47 PM


Re: circling around the peak with oscillating lineages
This is about exactly what I was going to say.
This message is a reply to:
 Message 82 by sfs, posted 01-19-2011 10:47 PM sfs has not yet responded

  
PaulK
Member
Posts: 14751
Joined: 01-10-2003
Member Rating: 1.7


Message 87 of 114 (601368)
01-20-2011 1:44 AM
Reply to: Message 83 by slevesque
01-20-2011 1:24 AM


Re: Mutation rates
quote:

For example:
quote:
Therefore, more than one third of the mouse and human genomes, previously thought to be non-functional, may play some role in the regulation of gene expression and promotion of genetic diversity.

http://www.sciscoop.com/2004-10-13-33731-304.html


So all you've got is speculation ? I'd have thought that things would have moved on a bit since 2004. So much for your claim that practically all geneticists would agree with your 30% figure.

quote:

I think that we are starting to see a paradigm shift in this field. The paradigm was that, DNa was mostly junk, and so it was a waste of time to try searching for it's use. Once more and more parts are being unravelled and found to have a use, I think an avalanche of discoveries in that field will come. But, as prof. John Mattick said:

quote:
the failure to recognise the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology


Wake up. The truth is that the existence of regulatory sequences has been known for a long time. And the search for function in non-coding sequences has been going on for quite a time too - where do you think all the results you use to try to "prove" that so much of the genome has a function come from ?


This message is a reply to:
 Message 83 by slevesque, posted 01-20-2011 1:24 AM slevesque has not yet responded

    
AZPaul3
Member
Posts: 3814
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.0


Message 88 of 114 (601371)
01-20-2011 3:19 AM
Reply to: Message 84 by slevesque
01-20-2011 1:27 AM


Re: The Dance of the Population Curves
Look

Look

Look

The most conservative estimate of the deleterious-to-beneficial ratio of mutations was 50 to 1. I've seen some suggest perhaps as high as a million to 1.

But even with the 50-1 ratio, it's still pretty obvious that the high mutations rates will push the next generation farther away from the peak then their parents from the optimal peak.

BS. Your numbers are either very wrong or very purposefully skewed.

[ABE] No, I do not mean by you, but by your sources. Which are where, btw?

Edited by AZPaul3, : No reason given.


This message is a reply to:
 Message 84 by slevesque, posted 01-20-2011 1:27 AM slevesque has not yet responded

  
Wounded King
Member (Idle past 2173 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 89 of 114 (601375)
01-20-2011 5:31 AM
Reply to: Message 85 by slevesque
01-20-2011 1:32 AM


Kimura's ''neutral evolution'' only works if the vast majority of the genome has no function.

Oh really? Do you have any clue what you are talking about? Kimura was principally talking about protein evolution, i.e. that portion of the genome that is already accepted as having biologically relevant function. Once again you conflate transcriptional activity with biologically relevant function, exactly the same thing half a dozen people just called you out on and you made wounded noises about having been misunderstood over.

Have you never heard of synonymous mutations? Do you not understand third base wobble? Even going by just this one phenomenon you can mutate ~30% of a protein coding gene without changing a single amino acid in the resultant protein.

That is before you even touch upon the fact that many amino acids can functionally substitute for one another and that in many instances almost any amino acid will do as long as it has the correct level of hydrophobicity.

What you say just highlights, once again, that you don't understand what you are talking about.

TTFN,

WK


This message is a reply to:
 Message 85 by slevesque, posted 01-20-2011 1:32 AM slevesque has not yet responded

    
RAZD
Member
Posts: 19758
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.7


Message 90 of 114 (601388)
01-20-2011 8:34 AM
Reply to: Message 82 by sfs
01-19-2011 10:47 PM


Re: circling around the peak with oscillating lineages
Hi sfs, thanks,

I haven't been following the argument here, but this analogy is not a good one.

If you haven't followed the argument, then how do you know the analogy is not a good one?

Mutations are, to a first approximation, orthogonal to one another, so you should be working in a much higher dimensional space. Imagine the 50 mutations to be fifty unit steps in 50 of perhaps a million dimensions. The next 50 mutations will be in another 50 random dimensions. The probability of heading back toward the peak (neglecting selection) is tiny.

What was being discussed was the relation of the individual to a fitness map, with a peak of fitness for the population in a static ecology.

You can correlate all your 50 dimensional mutations into direction to or away or orthogonal to fitness and from that derive a radius for each individual relative to the parent.

(neglecting selection)

And we definitely are not neglecting selection.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

This message is a reply to:
 Message 82 by sfs, posted 01-19-2011 10:47 PM sfs has responded

Replies to this message:
 Message 92 by sfs, posted 01-20-2011 10:17 AM RAZD has responded

  
Prev12345
6
78Next
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2019