Hundreds of Natural-Selection Studies Could be Wrong, Study Demonstrates

Mar 30, 2009
The image depicts the structure of the bovine rhodopsin protein. The blue circles represent amino acid sites that have undergone natural selection as determined through experiments, while the red circles represent amino acid sites that have undergone natural selection as determined through statistical analyses. Masafumi Nozawa, Penn State (Adapted from Yokoyama et al. 2008 PNAS)

(PhysOrg.com) -- 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. For example, in one published study the scientists used a statistical method to demonstrate pervasive during human evolution. "This group documented adaptive evolution in many genes expressed in the brain, thyroid, and , which are assumed to be important for human evolution," said Masafumi Nozawa, a postdoctoral fellow at Penn State and one of the paper's authors. "But if the statistical method that they used is not reliable, then their results also might not be reliable," added Nei. "Of course, we would never say that natural selection is not happening, but we are saying that these statistical methods can lead scientists to make erroneous inferences," he said.

The team examined the branch-site method and several types of site-prediction methods commonly used for statistical analyses of natural selection at the molecular level. The branch-site method enables scientists to determine whether or not natural selection has occurred within a particular gene, and the site-prediction method allows scientists to predict the exact location on a gene in which natural selection has occurred.

"Both of these methods are very popular among biologists because they appear to give valuable results about which genes have undergone natural selection," said Nei. "But neither of the methods seems to give an accurate picture of what's really going on."

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." Nei also believes that the methods are inaccurate when the number of nucleotide substitutions observed is small.

To demonstrate the faultiness of the statistical methods, Nei's team compiled data collected by their Emory University colleague, Shozo Yokoyama, on the genes that control the abilities of fish to see light at different water depths and on the genes that control color vision in a variety of animals. The team used these data to compare statistically predicted sites of natural selection with experimentally determined sites. They found that the statistical methods rarely predicted the actual sites of natural selection, which had been identified by Yokoyama through experiments. "In some cases, statistical method completely failed to identify the true sites where natural selection occurred," said Nei. "This particular exercise demonstrated the difficulty with which statistical methods are able to detect natural selection."

To demonstrate how small sample sizes can lead to incorrect results, the team used computer simulations to examine the evolution of genes in three primates: humans, chimpanzees, and macaques. The scientists mimicked the procedures used by the authors of a 2007 paper, which applied the branch-site method to 14,000 orthologous genes -- genes that are genealogically identical among different species -- and which found that the method predicted selection in 32 of the genes. Nei and his team also studied selection using Fisher's exact test, but this test did not detect any selection. "The results indicate that the number of nucleotide substitutions that occurred were too small to detect any selection; therefore, all of the 32 cases obtained by the branch-site method must be false positives," said Nozawa.

"These statistical methods have led many scientists to believe that natural selection acted on many more genes in humans than it did in chimpanzees, and they conclude that this is the reason why humans have developed large brains and other morphological differences," said Nei. "But I believe that these scientists are wrong. The number of genes that have undergone selection should be nearly the same in humans and chimps. The differences that make us human are more likely due to mutations that were favorable to us in the particular environment into which we moved, and these mutations then accumulated through time."

Nei said that to obtain a more realistic picture of natural selection, biologists should pair experimental data with their statistical data whenever possible. Scientists usually do not use experimental data because such experiments can be difficult to conduct and because they are very time-consuming.

Provided by Pennsylvania State University (news : web)

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User comments : 16

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Modernmystic
3.7 / 5 (6) Mar 30, 2009
The IMPORTANT thing to take from this article for some of you is simply this...

FTA:

"Of course, we would never say that natural selection is not happening, but we are saying that these statistical methods can lead scientists to make erroneous inferences,"...

nuff said.
el_gramador
5 / 5 (1) Mar 30, 2009
I can and will vicariously agree with that.
DonR
5 / 5 (1) Mar 30, 2009
@el gramador

I imagine you mean VIGOROUSLY agree. To agree vicariously would be a very odd thing to do, indeed.

And yes, I agree too.

Nature doesn't make errors. Humans make errors, nature makes mutations.
Doug_Huffman
1 / 5 (2) Mar 30, 2009
Vicariously!
latersville
4 / 5 (1) Mar 30, 2009
And what exactly are those "statistical methods that can lead scientists to make erroneous inferences"?

...small sample sizes

In addition to that lesson, the other is: "Nei said that to obtain a more realistic picture of natural selection, biologists should pair experimental data with their statistical data whenever possible. Scientists usually do not use experimental data because such experiments can be difficult to conduct and because they are very time-consuming."

I imagine the "intelligent designers" will miss the point completely and erroneously use this research for years to come or at least until .... no, they'll keep using it forever.
freethinking
2.1 / 5 (14) Mar 31, 2009
Proof of natural selection? No lets just have faith that natural selection happens like we say it happens, then lets laugh at those that dont believe in natural selection. Oh, we should also say we have statistical analysis to prove that natural selection occurs, at least until the proof turns out to be in error.
latersville
not rated yet Mar 31, 2009
"...then lets laugh at those that dont believe in natural selection."

okay
ealex
3.7 / 5 (3) Mar 31, 2009
Proof of natural selection? No lets just have faith that natural selection happens like we say it happens, then lets laugh at those that dont believe in natural selection. Oh, we should also say we have statistical analysis to prove that natural selection occurs, at least until the proof turns out to be in error.


I was wondering when you'd show up. Never late, are you.

Read it again. Then read the comments. Then go away.
Modernmystic
2.2 / 5 (6) Mar 31, 2009
Proof of natural selection? No lets just have faith that natural selection happens like we say it happens, then lets laugh at those that dont believe in natural selection. Oh, we should also say we have statistical analysis to prove that natural selection occurs, at least until the proof turns out to be in error.


Natural selection is a fact, not a theory. You might as well debate about whether or not the Earth is round.

Biogenesis via natural selection is a theory and a very specious one at that. The article has no bearing whatsoever on that theory or on intelligent design in so far as it relates to the origins of life. NO ONE knows how that happened yet. What the "other side" seems to forget is that observations of a self propagating process in action is not the same as an explanation as to how said process began...far from it.

To use an analogy this article is stating that we know the Earth is round, but our methods about determining just how large the circumference is may be flawed.
Ethelred
3.7 / 5 (6) Mar 31, 2009
Proof of natural selection? No lets just have faith that natural selection happens like we say it happens, then lets laugh at those that dont believe in natural selection.


Or we could actually go on the evidence. Like the megatons of fossils showing evolution over time.

Natural selection simply cannot not happen.

Mutations occur. There is no doubt about it. The study in this article SHOWS mutations. Not all mutations are going to be detrimental. The detrimental mutations are going to be selected out. Those the are not detrimental will continue in the gene pool.

That is the heart of Natural Selection and there is no way for it to not occur. Except to stop mutation. Selection inherently follows from mutation.

Ethelred
rab96
3.4 / 5 (5) Mar 31, 2009
This article is only the tip of the ice berg. There is no way to produre hard experimental evidence for the evolution theory except by twisting the statistics and make them fit to our speculations.
SDMike2
2.3 / 5 (3) Mar 31, 2009
Lies, damned lies, and statistics!



Statistics, sufficiently advanced, is indistinguishable from Truth. Although it is often not true...
Ethelred
5 / 5 (3) Apr 01, 2009
There is no way to produre hard experimental evidence for the evolution theory except by twisting the statistics and make them fit to our speculations.


Nonsense. Experimental evidence is available and the fossils are more than adequate. Heck this article has evidence of evolution.

No matter how you slice it, if there are mutations evolution is inevitable.

Of course long term evolution would take long term experiments. That is impractical. Despite that there is some actual lab evidence.

http://www.talkor...ion.html

http://www.talkor...ion.html

Nothing stunning of course. No one is going to turn a squirrel into a bat in the lab. The time constraints are rather severe.

There is the obvious case of human evolution in the historical era. Europeans have evolved a strong resistance to smallpox. When the highly resistant Europeans came to Mexico the Conquistadors did not get smallpox but the Mexicans were not so fortunate. They had not spent thousands of years dying to select out the vulnerable. There were many smallpox plagues in European history. Yet by the time of the American Revolution few Europeans were contracting smallpox anymore and most were surviving(George Washington being the most obvious), unlike the historical plagues. Smallpox is suspected in several Roman plagues that killed a significant fraction of the population in parts of the Empire.

Ethelred
Ethelred
5 / 5 (3) Apr 01, 2009
SDMike2

Tit for tat.

If you go around giving a one to well reasoned posts just because you don't like the facts you deserve a one.

Please note the rab96 has not descended to this odious behavior and thus is not getting a one a from me.

He deserves a two since he is quite wrong about the possibility of experimental evidence but I will refrain.

Ethelred
SDDuude
1 / 5 (1) May 02, 2009






Or we could actually go on the evidence. Like the megatons of fossils showing evolution over time.





Accept for the small detail that in the megaton of fossils, they still don't have the needed transitional fossils to support the hypothesis of evolution. But lets not dirty up the evolutionary argument with an actual call for factual evidence to support.
Ethelred
5 / 5 (2) May 02, 2009
Accept for the small detail that in the megaton of fossils, they still don't have the needed transitional fossils to support the hypothesis of evolution


The voice of ignorance arises. Well at least you didn't settle for a single post on your fist day.

Here have a clue.

http://www.talkor...mediates

Sample from link:
In the case just mentioned, we have found a quite complete set of dinosaur-to-bird transitional fossils with no morphological "gaps" (Sereno 1999), represented by Eoraptor, Herrerasaurus, Ceratosaurus, Allosaurus, Compsognathus, Sinosauropteryx, Protarchaeopteryx, Caudipteryx, Velociraptor, Sinovenator, Beipiaosaurus, Sinornithosaurus, Microraptor, Archaeopteryx, Rahonavis, Confuciusornis, Sinornis, Patagopteryx, Hesperornis, Apsaravis, Ichthyornis, and Columba, among many others (Carroll 1997, pp. 306-323; Norell and Clarke 2001; Sereno 1999; Xu et al. 1999; Xu et al. 2000; Xu et al. 2002). All have the expected possible morphologies (see Figure 3.1.1 from Prediction 3.1 for a few examples), including organisms such as Protarchaeopteryx, Caudipteryx, and the famous "BPM 1 3-13" (a dromaeosaur from China now named Cryptovolans pauli; Czerkas et al. 2002 ) which are flightless bipedal dinosaurs with modern-style feathers (Chen et al. 1998 ; Qiang et al. 1998; Norell et al. 2002). Additionally, several similar flightless dinosaurs have been found covered with nascent evolutionary precursors to modern feathers (branched feather-like integument indistinguishable from the contour feathers of true birds), including Sinornithosaurus ("Bambiraptor"), Sinosauropteryx, Beipiaosaurus, Microraptor, and an unnamed dromaeosaur specimen, NGMC 91, informally called "Dave" (Ji et al. 2001). The All About Archaeopteryx FAQ gives a detailed listing of the various characters of Archaeopteryx which are intermediate between reptiles and modern birds.


But lets not dirty up the evolutionary argument with an actual call for factual evidence to support.


No lets not bother having evidence for Creationism either as that seems to be against Creationist rules. Don't try running a bluff either. Especially one based on knowing nothing about biology.

Evolution cannot not happen. It is inherent in biology. ALL fossils are transitional. Or none depending on your definition of transition. If you are typical your definition will change as you learn that you have been fed a load of crap. You will either accept the reality of evolution or you will change your definition in each reply.

Do try to be atypical.

Ethelred

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