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Author Topic:   Does Neo-Darwinian evolution require change ?
Percy
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Posts: 22394
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 91 of 114 (601392)
01-20-2011 8:56 AM
Reply to: Message 83 by slevesque
01-20-2011 1:24 AM


Re: Mutation rates
slevesque writes:
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
As rebuttal to what the evidence currently indicates to be true you're offering someone's opinion about what might someday be discovered to be true. What do you think about maybe basing your arguments upon what the evidence currently in hand indicates?
--Percy

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sfs
Member (Idle past 2534 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 92 of 114 (601403)
01-20-2011 10:17 AM
Reply to: Message 90 by RAZD
01-20-2011 8:34 AM


Re: circling around the peak with oscillating lineages
RAZD writes:
If you haven't followed the argument, then how do you know the analogy is not a good one?
Because the point of the analogy was clear, regardless of what argument it was deployed in, and that point was based on an error. You make the error explicit below.
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.
Yes, I gathered that.
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.
No, you can't. That's why your analogy is a bad one. My point was that there are many, many orthogonal directions to take away from fitness. In biological terms, there are an enormous variety of ways that you can screw up an organism which are nearly independent of one another; even if you already have mutations that cause some of those defects, the next set of mutations is still overwhelmingly likely to cause new defects, not to fix the old ones. Just think about how many sites there are for potential deleterious mutations in the genome. If you flip 50 of them to become sites for potential beneficial mutations (which is what your first round of mutations does), how much have you changed the overall number of deleterious sites?
And we definitely are not neglecting selection.
I know. But your analogy was about the selective landscape, not about how populations respond to selective pressures.
Enjoy.
I try.

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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 93 of 114 (601430)
01-20-2011 12:26 PM
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. 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.
Which can still be neutral.
And all that I have said would still hold.
As would all I've said on the subject, especially the things I said about purifying selection.

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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 94 of 114 (601431)
01-20-2011 12:29 PM
Reply to: Message 84 by slevesque
01-20-2011 1:27 AM


Re: The Dance of the Population Curves
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.
Where were these figures pulled from?
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.
It is far from obvious, and indeed there will always be a population size above which it is false.
And this, perhaps, explains why what you think should happen in principle is the opposite of what we observe happening in practice.

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RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 95 of 114 (601463)
01-20-2011 5:34 PM
Reply to: Message 92 by sfs
01-20-2011 10:17 AM


Re: circling around the peak with oscillating lineages
Hi sfs, becoming pedantic to maintain your original position?
No, you can't. That's why your analogy is a bad one. My point was that there are many, many orthogonal directions to take away from fitness.
Or towards fitness. Seeing as it is virtually impossible to be 100% fit, there is always room to become more fit, the more so for second generation offspring when the first generation is moved away from their parents locus to a lower fitness topology.
In biological terms, there are an enormous variety of ways that you can screw up an organism which are nearly independent of one another; even if you already have mutations that cause some of those defects, the next set of mutations is still overwhelmingly likely to cause new defects, not to fix the old ones.
But it isn't necessary to fix old ones, it is just a matter of becoming more fit than the first generation.
I know. But your analogy was about the selective landscape, not about how populations respond to selective pressures.
Curiously, I thought it was about visualizing the fitness landscape, and whether third generation offspring can move towards, or away, from fitness, according to their survival and reproductive success relative to their parent/s.
Enjoy.

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by our ability to understand
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molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 96 of 114 (601464)
01-20-2011 5:55 PM
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. 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.
Are you under the impression that a mutation in a gene "breaks" it? Renders it useless? Is deleterious 100% of the time?
That is simply not true.
From an interview with Misha Angrist, otherwise known as member four of the Personal Genome Project:
And similarly, we know that common diseases tend to be caused by a combination of many genes and the environment, probably interacting in subtle and complicated ways that make a deterministic scenario extremely unlikely.
When I look at my own genome I see dozens and dozens of broken genes. I see hundreds of mutations that, by all rights, should have put a stop to me when I was a microscopic ball of cells inside my Mom. But here I am, reading Harry Potter to my healthy and amazing kids, both of whom have half of my broken genes and half of their otherwise perfect mother
A Conversation with Misha Angrist, Publisher of His Genome - The Awl

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sfs
Member (Idle past 2534 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 97 of 114 (601470)
01-20-2011 6:47 PM
Reply to: Message 95 by RAZD
01-20-2011 5:34 PM


Re: circling around the peak with oscillating lineages
RAZD writes:
Hi sfs, becoming pedantic to maintain your original position?
No, I've always been this pedantic.
No, you can't. That's why your analogy is a bad one. My point was that there are many, many orthogonal directions to take away from fitness.
Or towards fitness. Seeing as it is virtually impossible to be 100% fit, there is always room to become more fit, the more so for second generation offspring when the first generation is moved away from their parents locus to a lower fitness topology.
Of course there are many directions that can take you toward higher fitness. But if the offspring are anywhere in the vicinity of the fitness peak (as real organisms almost always are), there are far more directions taking you away. This is the point your 2-d analogy gets wrong. In two dimensions, a random step in any direction is almost as likely to take you toward a specified point as it is to take you away (something you noted in your original use of the analogy). As the dimensionality increases, the probability decreases -- and fitness landscapes have very many dimensions indeed.

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slevesque
Member (Idle past 4641 days)
Posts: 1456
Joined: 05-14-2009


Message 98 of 114 (602186)
01-26-2011 4:55 PM


Not forgotten
I just want to say I haven't forgotten this thread. I just ordered Dr.Sanford's book to have the references to discuss three critical things in order for this discussion to continue:
- The human mutation rate per individual per generation
- the beneficial-to-deletirious ratio of mutations
- The functional % of the human genome

  
shadow71
Member (Idle past 2934 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 100 of 114 (608333)
03-09-2011 7:45 PM
Reply to: Message 91 by Percy
01-20-2011 8:56 AM


Re: Mutation rates
Percy posted
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
--------------------------------------------------------------------------------
Percy then wrote;
As rebuttal to what the evidence currently indicates to be true you're offering someone's opinion about what might someday be discovered to be true. What do you think about maybe basing your arguments upon what the evidence currently in hand indicates?
--Percy
Just to clarify, Mattick wrote the above quote in 2004. He has since written in 2010 the following;
The central role of RNA regulation in human development and cognition - John Mattick
Professor John Mattick
It appears that the genetic programming of humans and other complex organisms has been fundamentally misunderstood for the past 50 years, because of the assumption that most genetic information is transacted by proteins. The human genome contains about 20,000 conventional protein-coding genes, surprisingly about the same number and with largely similar functions as those in tiny worms that have only 1000 cells. On the other hand, the extent of non-protein-coding DNA, traditionally thought to be junk, increases with increasing complexity, reaching over 98.8 percent in humans. Moreover, it is now evident that these non-coding sequences are transcribed in a dynamic manner, to produce tens, if not hundreds of thousands of noncoding RNAs, and that most complex genetic phenomena are RNA-directed, which suggests that there exists a vast hidden layer of regulatory RNAs that control human development and brain function.
Is it agreed in the scientific biological community that Mattick is correct about "junk DNA" and their effect on the conrol of human development and brain function?

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 Message 102 by Theodoric, posted 03-09-2011 10:16 PM shadow71 has replied
 Message 103 by Wounded King, posted 03-10-2011 4:16 AM shadow71 has replied
 Message 109 by Taq, posted 03-10-2011 3:22 PM shadow71 has replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 101 of 114 (608357)
03-09-2011 9:41 PM
Reply to: Message 100 by shadow71
03-09-2011 7:45 PM


Re: Mutation rates
Is it agreed in the scientific biological community that Mattick is correct about "junk DNA" and their effect on the conrol of human development and brain function?
No.
Some of what you quote isn't even English. Look at it. "Most genetic information is transacted by proteins". Does that have a meaning? OK, what about: "The extent of non-protein-coding DNA, traditionally thought to be junk, increases with increasing complexity"? These are all English words, and yet if you put them together in that order they do not convey anything, true or false.
If this is a fair sample of Mattick's ideas, then he doesn't have any ideas --- good or bad. His writing is, in the words of Wolfgang Pauli, "not even wrong".

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Theodoric
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Posts: 9076
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 3.7


Message 102 of 114 (608366)
03-09-2011 10:16 PM
Reply to: Message 100 by shadow71
03-09-2011 7:45 PM


Re: Mutation rates
Maybe you could show us the source material for the latest MAttick writings.

Facts don't lie or have an agenda. Facts are just facts

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 103 of 114 (608395)
03-10-2011 4:16 AM
Reply to: Message 100 by shadow71
03-09-2011 7:45 PM


Re: Mutation rates
Mattick is right in terms of the potential role of non-coding RNAs in development and evolution. He is wrong to try and characterise there having been a 'failure to recognise the implications of the non-coding DNA'. For a start that 50 years should only be about 20 since people were putting forward functions for non-coding DNA by the late 70's and by the early 90's there were several well established cases of regulatory non-coding RNAs in yeast and C. elegans.
The real thing holding back the realisation of the extent of the role of non-coding RNAs was not any sort of preconceived dogma but technology. Without reliable highly sensitive sequencing technologies and whole genomes to work with I'm not sure how Mattick thinks these things could have been readily identified.
So seriously? A gap of ~20 years from the discovery of the structure of DNA to the beginning of appreciation for the role of non-coding RNAs? If that is the biggest mistake in the history of molecular biology then molecular biology is doing pretty damn well.
Mattick also extrapolates well beyond the evidence in his claims for the extent of RNA based mechanisms, and his suggestion that virtually the whole of the non-coding genome is functional is simply unsupported.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 104 of 114 (608400)
03-10-2011 5:01 AM
Reply to: Message 102 by Theodoric
03-09-2011 10:16 PM


Re: Mutation rates
Maybe you could show us the source material for the latest MAttick writings.
I think Shadow71's exact quotes came from Mattick's home page at The University of Queensland, but a pubmed search for Mattick JS will bring up several relevant papers.
I think people are throwing a lot of unwarranted ad hom attacks at Mattick. He has a perfectly creditable research record and I think Dr. A's criticisms are pretty weak. What he mean's by "The extent of non-protein-coding DNA, traditionally thought to be junk, increases with increasing complexity" is that the proportion of the genome that is non-coding tends to increase with apparent morphological complexity (Amaral and Mattick, 2008).
I agree that "Most genetic information is transacted by proteins" is not as clear however, although I would suggest that if we subsitituted 'regulation' for 'information' we would be pretty close to his meaning. I think he uses information to broaden the scope to all functional activity encoded in the genome and to interactions between the genome and the environment (Mattick, 2009)
I feel that like Lynn Margulis he just tends to over-emphasise the importance of his particular hobby horse, although to be fair he has a better case than Margulis as the full extent of the regulatory role of non-coding regions has yet to be established but probably will be in the foreseeable future. It just seems to me that Mattick is taking the very highest extents of those estimates to be the true level.
TTFN,
WK
Edited by Wounded King, : No reason given.

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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 105 of 114 (608407)
03-10-2011 5:39 AM
Reply to: Message 104 by Wounded King
03-10-2011 5:01 AM


Re: Mutation rates
What he mean's by "The extent of non-protein-coding DNA, traditionally thought to be junk, increases with increasing complexity" is that the proportion of the genome that is non-coding tends to increase with apparent morphological complexity.
Now that is meaningful.

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shadow71
Member (Idle past 2934 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 106 of 114 (608438)
03-10-2011 11:14 AM
Reply to: Message 102 by Theodoric
03-09-2011 10:16 PM


Theodoric, here is the paper by Mattick. The quote is also on his web site page.
Anais da Academia Brasileira de Cincias
version ISSN 0001-3765
An. Acad. Bras. Cinc. vol.82 no.4 Rio de Janeiro Dec. 2010
doi: 10.1590/S0001-37652010000400016
BIOLOGICAL SCIENCES
The central role of RNA in the genetic programming of complex organisms
John S. Mattick
Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia

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