Science Daily: Hundreds Of Natural-selection Studies Could Be Wrong, Study Demonstrates.
ScienceDaily (Mar. 31, 2009) — Scientists at Penn State and the National Institute of Genetics in Japan have demonstrated that several statistical methods commonly used by biologists to detect natural selection at the molecular level tend to produce incorrect results.
"Our finding means that hundreds of published studies on natural selection may have drawn incorrect conclusions," said Masatoshi Nei, Penn State Evan Pugh Professor of Biology and the team's leader. The team's results will be published in the Online Early Edition of the journal Proceedings of the National Academy of Sciences during the week ending Friday 3 April 2009 and also in the journal's print edition at a later date.
Nei said that many scientists who examine human evolution have used faulty statistical methods in their studies and, as a result, their conclusions could be wrong.
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13 comments:
Funny you use a pic of Charles Darwin. He didn't know about genetics at all. In fact, he was of the opinion that inheritance collected in the cells of animals and that little trait particles were passed on.
The rediscovery of Mendel, and the work of Watson and Crick corrected him big-time.
The article is about Natural Selection so I chose a picture of Darwin.
I didn't even know that they were basing their conclusions on statistics, one thinks it would be something more solid...
"Nei said that for many years he has suspected that the statistical methods were faulty. "The methods assume that when natural selection occurs the number of nucleotide substitutions that lead to changes in amino acids is significantly higher than the number of nucleotide substitutions that do not result in amino acid changes," he said. "But this assumption may be wrong. Actually, the majority of amino acid substitutions do not lead to functional changes, and the adaptive change of a protein often occurs by a rare amino acid substitution. For this reason, statistical methods may give erroneous conclusions."
Actually, I wrote some software to model this process. As I recall 70 percent of DNA point mutations cause a change in the amino acid, thus affecting the protein and its function. Here is some data for one computer run I did:
Program to compute statistics for DNA point mutations
Total number of point mutations to run = 10000
Initial number of amino acids = 100
Initial number of nucleotides = 303
Mutations with no change in amino acid sequence: 24.4%
Mutations with one change in amino acid sequence: 70.5%
Mutations with truncated amino acid sequence: 4.1%
Mutations with extended amino acid sequence: 0.9%
Average number of amino acids truncated = 49.2
Average number of amino acids extended = 19.3
Consecutive mutations in the same gene
Total number of consecutive mutation runs = 1000
Avg # of consec. mutations for length to change = 20.4
Random DNA sequence containing 303 nucleotides:
CTA,TAC,CCT,AAC,CCG,CGT,CAT,CCT,ATT,TAC,
AAG,GTG,TTG,CAA,GCA,AAC,TTT,TCA,ATT,CCG,
ACA,AAT,CAG,CTC,TTC,TCT,CCT,ATC,AAG,CCC,
GAT,GAG,ATG,GCC,ATA,GCC,CCC,TAT,GCT,GCC,
GTT,CAT,ACC,TAC,AAA,ATA,CTT,CTG,GCT,CTT,
TTA,ATG,CTT,TAC,GTA,GAC,TCA,AAC,GAG,GGA,
ACT,CTA,AGT,CTT,GAT,ATA,GTA,GAT,AAA,AGC,
TCC,GCG,GTG,AAT,CGT,ACA,CAC,AAC,CAA,ACG,
GGG,GGT,GTT,CGG,TCC,GTC,GTG,AAG,GTA,CAT,
TAC,GAA,CCT,TTT,CCC,AAT,TCC,ATA,ATT,ACT,
TGA
Total molecular weight of DNA sequence = 187086
Total number of atoms in DNA sequence = 19863
Length of the DNA sequence = 103.02 nanometers
Sequence of amino acids containing 100 amino acids:
Leu,Tyr,Pro,Asn,Pro,Arg,His,Pro,Ile,Tyr,
Lys,Val,Leu,Gln,Ala,Asn,Phe,Ser,Ile,Pro,
Thr,Asn,Gln,Leu,Phe,Ser,Pro,Ile,Lys,Pro,
Asp,Glu,Met,Ala,Ile,Ala,Pro,Tyr,Ala,Ala,
Val,His,Thr,Tyr,Lys,Ile,Leu,Leu,Ala,Leu,
Leu,Met,Leu,Tyr,Val,Asp,Ser,Asn,Glu,Gly,
Thr,Leu,Ser,Leu,Asp,Ile,Val,Asp,Lys,Ser,
Ser,Ala,Val,Asn,Arg,Thr,His,Asn,Gln,Thr,
Gly,Gly,Val,Arg,Ser,Val,Val,Lys,Val,His,
Tyr,Glu,Pro,Phe,Pro,Asn,Ser,Ile,Ile,Thr
Total molecular weight of amino acid sequence = 11152
Total number of atoms in amino acid sequence = 1589
It may surprise some folks on this blog but I am NOT a strong believer in natural selection as the dominant mechanism in evolution.
Rather, I subscribe to the theories of Stuart Kauffman on self-organizing complexity:
http://en.wikipedia.org/wiki/Stuart_Kauffman
http://www.edge.org/3rd_culture/kauffman06/kauffman06_index.html
""While it may sound as if 'order for free' is a serious challenge to Darwinian evolution, it's not so much that I want to challenge Darwinism and say that Darwin was wrong. I don't think he was wrong at all. I have no doubt that natural selection is an overriding, brilliant idea and a major force in evolution, but there are parts of it that Darwin couldn't have gotten right. One is that if there is order for free — if you have complex systems with powerfully ordered properties — you have to ask a question that evolutionary theories have never asked: Granting that selection is operating all the time, how do we build a theory that combines self-organization of complex systems — that is, this order for free — and natural selection? There's no body of theory in science that does this. There's nothing in physics that does this, because there's no natural selection in physics — there's self organization. Biology hasn't done it, because although we have a theory of selection, we've never married it to ideas of self-organization. One thing we have to do is broaden evolutionary theory to describe what happens when selection acts on systems that already have robust self-organizing properties. This body of theory simply does not exist." (Chapter 20, "Order for Free", The Third Culture, 1995)"
Hey Tom!
Welcome back and thanks for your analysis..=)
This Kauffman guy may be on to something. Chemistry is self-organizing, behaving in ways restricted by the laws of physics.
@Jeffery "This Kauffman guy may be on to something. Chemistry is self-organizing, behaving in ways restricted by the laws of physics."
Not only that, but natural selection makes a lot of overreaches IMHO. For example, half of your chromosomes are different from your mother's chromosomes.
Q: What percentage of this difference is attributable to natural selection?
A: If you guessed Zero give yourself a big cigar.
That's right. Zero of the genetic differences are due to natural selection. Why do we need natural selection in this case when we have an efficient mechanism (e.g., meiosis) which explains all of the genetic differences?
Now, replace this scenario with animals of different species. Now ask your typical evolutionary biologist how much of the genetic difference is caused by natural selection. You are likely to get an answer close to 100 percent. But they can't provide any evidence to show this - they just know it in their bones.
So that's where I part company with most of the Darwinists (e.g., P.Z. Meyers, Richard Dawkins, etc.).
sadunkal,
Welcome to the website...=)
@Tom
"Zero of the genetic differences are due to natural selection. Why do we need natural selection in this case when we have an efficient mechanism (e.g., meiosis) which explains all of the genetic differences?"
I've never heard anyone claim natural selection causes genetic differences. Other causes, meiosis among them, account for genetic differences. Natural selection is just a term that refers to the idea that what exists is what has been able to reproduce.
Natural Selection is not responsible for genetic change in individuals. That's the job of Random Mutation. Without errors, gene duplication and other additive processes, Natural Selection has nothing to work with.
@Pleroma "I've never heard anyone claim natural selection causes genetic differences. Other causes, meiosis among them, account for genetic differences. Natural selection is just a term that refers to the idea that what exists is what has been able to reproduce."
Of course natural selection is supposed by its supporters to cause the genetic differences one sees between different species or different populations. If it couldn't the whole theory would collapse immediately. Mutation produces the immediate genetic differences (that's what a mutation is) but then natural selection is supposed to determine which ones become widespread in the population.
@Jeffery Keown "Natural Selection is not responsible for genetic change in individuals. That's the job of Random Mutation. Without errors, gene duplication and other additive processes, Natural Selection has nothing to work with."
It does not cause the mutations, which are supposedly random (another unproven assumption), but natural selection does claim to explain which mutations survive in nature.
"but natural selection does claim to explain which mutations survive in nature."
It claims that some mutations survive--the ones that continue to reproduce--and that detrimental mutations don't. It's actually a kind of tautological concept, which is why it is so persuasive. The name is unfortunate because it leads people who haven't read detailed accounts of the modern understanding of the process of evolution to set up a straw man of a blind force that actually selects the direction of a species' evolution. But there is no such force. Individually mutated genes either survive via reproduction or don't--that's the entirety of natural selection.
I think the process is likely more complicated than anyone understands today. I've read good arguments for directed self organization, as well as for intelligent design, though none of these explain precisely what the mechanisms at work are, as mainstream evolutionary theory does.
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