Is there any real evidence of the effect of natural selection on the genome?

Question

Despite ingenious ways of trying to pull the wool over

the eyes of other scientists, there is a growing consensus

in the academic community that natural selection may be

a hoax after all:

http://mbe.oxfordjournals.org/cgi/content/abstract/msi240v1

By examining instances of polymorphism and linkage

disequilbria throughout the genome, the evidence for

selection is far from convincing.

Looking for the evidence of natural selection in bacteria has proved problematic:The "directed mutation" controversy sparked by Harvard molecular biologist John Cairns has undermined the claims of Lenksi etc.

http://en.wikipedia.org/wiki/Adaptive_mutation

And experiments with fruit flies have shown just how

ineffective natural selection is

http://www.genetics.org/cgi/content/abstract/140/2/821

So what is the hard evidence of natural selection at the

level of the gene?

Note that I am differentiating between selection and

common descent.

Answer 1

If One Wants to See Natural Selection, Driven By Mutation, Occurring In the Lab, See the Ames Test.

EDIT: Since you Disregard All Evidence to the Contrary. Disregard the Following Link:

http://en.wikipedia.org/wiki/Ames_test

Answer 2

Evolution is a biological fact.  End of story.  The theory explains the fact and it has stood the test of time and improvements have been made.  Other theories have been proposed to explain evolution but it never, ever, changes the fact itself.

It is no hoax.  Are you trying to say natural selection is all there is to biological evolution?  Try studying evolution properly and thoroughly.  You question and statements are ridiculous.

Your sources and interpretations are pitiful and there is no growing consensus, you are either lying or are misguided.

Answer 3

Ahh...ummm...I suppose I might ask you about...I don't know...say...

....dinosaurs.  I would be fascinated to see how you could explain a fossil record that dates back hundreds of millions of years, with ever-changing species.

Answer 4

Of course there is.  Natural selection is one of the two key elements of the theory of evolution (genetic variation is the other), and since both of these phenomena are demonstrated in practice, the theory of evolution is proved to be correct.  In the case of human evolution, a particularly convincing case has to do with the origin of human chromosme 2 -- which turns out to be a fusion of two chromosomes that existed in an ancestor species.  See:

Answer 5

Natural selection is not detected by statistical analysis of whole genome data.  Natural selection operates on alleles of individual genes, and it is detected by analysis of these variants.

The human genome has about 3 billion base pairs.  It is estimated that humans vary from each other at 15,000,000 sites in the genome, and at least 3,000,000 of these loci have been identified.  To prove that humans are not evolving, one would need to show that in all human populations, all the alleles at these 15,000,000 sites are in fixed equilibria.  And if you want to invalidate natural selection entirely, you would need to do this for all populations of all species.

Conversely, to show that natural selection is occurring in humans, or any other species, one would only need to demonstrate disequilibrium of the alleles of a single gene.  Here are two papers that statistically demonstrate ongoing positive selection in human populations.

And, BTW, you have it backwards:  the vast majority of researchers recognize natural selection as valid.  The few lunatics who do not have voluntarily pulled the wool over their own eyes.

1.  Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans

Patrick D. Evans, et al.

Science 309, 1717 (2005)

"We show that one genetic variant of Microcephalin in modern humans, which arose [about] 37,000 years ago, increased in frequency too rapidly to be compatible with neutral drift. This indicates that it has spread under strong positive selection, although the exact nature of the selection is unknown."

2.  Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens

Nitzan Mekel-Bobrov, et al.

Science 309, 1720 (2005)

"Here, we show that one genetic variant of ASPM in humans arose merely about 5800 years ago and has since swept to high frequency under strong  positive selection."

Answer 6

cheetas! since the population has depleted, the gene pool is so limited, that APPARENTLY all the fittest survive, but because of this, dieseases that affect one cheetah, affect them all, in the same way...coz of no gene variation. hope this answer helps in SOME way! :)

Answer 7

<<Despite ingenious ways of trying to pull the wool over

the eyes of other scientists, there is a growing consensus

in the academic community that natural selection may be

a hoax after all:>>

I know a number of scientists, and none of them are part of that bogus "growing consensus", and you know damned well there's no such "growing consensus".  Telling lies in public is bad manners.  In your case it appears to be a habit.  Please seek professional assistance to deal with your problems.

Answer 8

Ah, Pastor Winthrop ... this post makes you look just a *tad* dishonest.

Nowhere in those two abstracts, or on that wikipedia page, is there even a trace of a whiff of a hint that any of these scientists are doubting natural selection ... much less that it may be (in your words) a "hoax" ... much less that this is a "growing consensus" (it's not even close to a majority, much less a consensus) ... or that there is "overwhelming evidence against it."

You have cherry-picked the literature to find just two abstracts and a wikipedia article, and then badly misrepresented all three of them.

The first paper is about lack of evidence of "frequent positive selection" in humans ... that "positive selection in the human genome might not be as frequent as previously thought."   To read that as "natural selection may be a hoax" is just a tad bit of a leap, don't you think?

The wikipedia page is about adaptive mutation, which is at best a controversial idea (the controversial nature of which is discussed on that very page).   But nowhere does adaptive mutation, even if true, contradict natural selection ... in fact it *depends* on it!   So to imply that John Cairns, or any biologist is concluding from adaptive mutation that natural selection is a "hoax" is again, just a bit dishonest, would you agree?

The second paper is about linkage and hitchiking genes and how this results in a *limit* to natural selection ... not that it *invalidates* it!   So again, you read "limit to natural selection" and hear "natural selection may be a hoax."  Again, just overstating things a bit, eh?

So even if any of the scientists you are citing showed any trace of doubt about natural selection (which they don't) ... to state this as a "growing consensus" or the "overwhelming evidence against it" is quite dishonest.

>"So what is the hard evidence of natural selection at the level of the gene?"

Hydrochoerus provided an outstanding list.

Here's more:

"Evidence of positive selection acting at the human dopamine receptor D4 gene locus"

http://www.pnas.org/content/99/1/309.abs...

"Evidence for positive selection and population structure at the human MAO-A gene"

http://www.pnas.org/content/99/2/862.abs...

"Strong balancing selection at HLA loci: Evidence from segregation in South Amerindian families"

http://www.pnas.org/content/94/23/12452....

"Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene"

http://www.pnas.org/content/100/23/13413...

"Widespread purifying selection at polymorphic sites in human protein-coding loci"

http://www.pnas.org/content/100/26/15754...

"A large family of ancient repeat elements in the human genome is under strong selection"

http://www.pnas.org/content/103/8/2740.a...

"Positive selection on protein-length in the evolution of a primate sperm ion channel"

http://www.pnas.org/content/100/21/12241...

"More genes underwent positive selection in chimpanzee evolution than in human evolution"

http://www.pnas.org/content/104/18/7489....

(Side note:  That paper provides a nice contrast to your first paper.)

"Positive Darwinian selection after gene duplication in primate ribonuclease genes"

http://www.pnas.org/content/95/7/3708.ab...

"Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences"

http://www.pnas.org/content/102/38/13526...

"Prion protein gene ( PRNP ) variants and evidence for strong purifying selection in functionally important regions of bovine exon 3"

http://www.pnas.org/content/101/42/15142...

"Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals"

http://www.pnas.org/content/98/5/2509.ab...

"Ancient and continuing Darwinian selection on insulin-like growth factor II in placental fishes"

http://www.pnas.org/content/104/30/12404...

"The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations"

http://www.pnas.org/content/104/43/16992...

So much for your "growing consensus" that "natural selection may be a hoax after all".

You need to stop cherry picking.  You just end up with cherries.

{edit}

>" 'Detecting natural selection' requires statistical analysis on the whole genome that the researcher in the first paper I referred to HAS done"

No.  Read your own link.  Dr. Zhang (who is a she, not a he, BTW) and Dr. Li looked at a few hundred genes with SNPs ... not "the whole genome" (30,000 genes).   If by statistical analysis you mean a representative sampling, then this is precisely the same kind of statistical analysis used all the genetics papers cited above by me and by Hydrochoerus.

>"he has found NO evidence for positive selection"

... *at the SNP level*! (See andymanec's reply).  Again, you are taking a very narrow result (no evidence of positive selection at the SNP level in a subsampling of the human genome) ... and blowing it up to a *MASSIVE* overgeneralization (there's no evidence of natural selection at all), and then applying yet another *MASSIVE* illogical leap ("overwhelming evidence" against natural selection itself!) and then even more with a truly *MASSIVE* contempt for all scientists (that the world's scientific community, has been populated by two groups: one group criminally fraudulent enough to perpetrate a huge "hoax", and the rest stupid enough to fall for it for over 150 years).  Don't you see how this comes off as absurdly dishonest?

But just for the record, there *is* plenty of statistical genomic evidence of positive selection ... in humans and other primates ... found by other researchers.  See eight of the first nine links I post above (one of them is about negative selection).

Again, you are cherry picking, and then misrepresenting the few things you do find.

This isn't just a difference in "prejudice."  There isn't a *single* link listed on this page that supports the claim of a "a growing consensus in the academic community that natural selection may be a hoax after all."

Answer 9

I think you're drawing a little too much from these papers.  

The first one doesn't say anything about a lack of selection, since it's scope is limited to SNPs.  Of course there isn't much selection on the SNP level.  DNA is degenerate code.  One alteration in a codon won't necessarily alter the amino acid it codes for, and even if it did, it wouldn't necessarily cause a change in the protein's function, and would thereby slip past selection.  The paper isn't revolutionary, and certainly doesn't go against selection as a whole - it just supports what we knew before.

The second paper establishes an equation that predicts selective pressure in the presence of other, secondary selective pressures.  Of *course* there's a limit on selection, especially when it's being modeled mathematically, but just because it's limited doesn't mean that it's not there.  If there were no selection, the equation would read X=0, which I most certainly don't see in the paper.

In my book, you don't need a degree to be a scientist.  You just have to look at the world objectively and consider the evidence in front of you.  You, sir, are not a scientist.  Stop pretending you are.

Answer 10

I read the first paper.  I think you have misunderstood it.  for one thing, they confirm something that other people have found... housekeeping genes are less likely to have polymorphisms than tissue specific genes.  that, by definition, is natural selection.

the point of the paper, however, was regarding positive selection... and that is in the human genome which contains genes etc plus a lot of junk DNA.  positive selection is only one facet of natural selection.

they even state "Because deleterious mutations can rarely reach a high frequency ..."   why is that?  because of natural selection.

Answer 11

"Looking for the evidence of natural selection in bacteria has proved problematic"

i disregarded your entire case the moment i read this statement..

clearly you lack the understanding of evolution, even at it's most basic elements, to not be able to see evidence of this yourself.. without any formal scientific training..

have you never heard of the flu or drug-resistant bacteria?

that's natural selection at it's most fundemental.. this is the example that's taught to 4th graders.. and even THEY understand at that point...

good_guy... i'm not even going to go into cutting up your 'answer'

"Sometimes you will "see" what you want to find...I think this is true for many evolutionary scientists."

it's also the reason many creationist, or at the very least creationist "science", statements, arguments, and statements againt evolution are immediately disregarded as being in any way scinetific..

following the scientific method that last thing ro be drawn is a conclusion.. in all creation ''science'' the conclusion is drawn first and the facts are fitted around this conclusion, instead of looking at what is an deducing how it came about.. they simply state how it came about based on their pre-drawn conclusions.

any apparent facts that are un-answered by that conclusion are beyond the 'finite mind of man to understand the infinite God.'

such 'discoverys', 'revelations', and 'findings' discredit those claiming them, and in my personal and heartfelt opinion, creation science as a whole

edit-

from your wikipedia link

"The introduction to this article provides insufficient context for those unfamiliar with the subject.

Please help improve the article with a good introductory style.

This article or section is written like a personal reflection or essay and may require cleanup.

Please help improve it by rewriting it in an encyclopedic style.

This article does not cite any references or sources.

Please help improve this article by adding citations to reliable sources. Unverifiable material may be challenged and removed."

not to mention you are dealing with wikipedia.. a site where anybody.. litterally ANYBODY can change an article to say whatever they want untill it's deleted by their rather inactive moderators

and actually if you could paraphrase that last link for me, i have a feeling you didn't grasp much from it at all.. i honestly feel that entire article was a bunch of technically, jargonic, mumbo-jumbo to you.. and all you cared to take (out of context mind you) was the title of the article..

Answer 12

Wow.

All of theories trying to disprove Natural Selection are starting to get old -.-

Answer 13

Ignoring the fact that there is more to evolution than natural selection, genetic drift and sexual selection to name two.... ( http://www.newscientist.com/channel/life... )

Your first article shows a lack of evidence for positive mutations in humans.  On the site you gave, one of the articles siting your site shows research of evidence for negative selection in humans.  Both positive and negative selection is a part of natural selection.

Inference of Expression-Dependent Negative Selection Based on Polymorphism and Divergence in the Human Genome

http://mbe.oxfordjournals.org/cgi/conten...

Your second article from wiki (not a reliable source) states:

The introduction to this article provides insufficient context for those unfamiliar with the subject. (May 2008)

This article or section is written like a personal reflection or a personal reflection or essay and may require cleanup. (May 2008)

This article does not cite any references or sources. (May 2008)

Your third article was written in 1995, and there has been tons of new research in the past 13 years.  Again, there is a link on the page you provided of an article that helps explain:

Beneficial Mutation–Selection Balance and the Effect of Linkage on Positive Selection

http://www.genetics.org/cgi/content/abst...

Other research that helps shed some light:

Interrogating a High-Density SNP Map for Signatures of Natural Selection

http://www.genome.org/cgi/content/full/1...

Natural selection and the evolution of genome imprinting.

http://www.ncbi.nlm.nih.gov/pubmed/14616...

Human Culture Subject To Natural Selection, Study Shows

http://www.sciencedaily.com/releases/200...

Darwin's Natural Selection Still at Work in Humans

http://www.livescience.com/health/051102...

Detection of Natural Selection in the Human Genome by Hidden Markov Model

http://bio.informatics.indiana.edu/capst...

Natural selection in the human genome: new paths to understanding our predisposition to illnesses

http://www.france-science.org/Natural-se...

Natural selection shapes genome wide patterns of copy number polymorphism in D. melanogaster

http://www.cees.uio.no/events/seminars/n...

Evidence for natural selection in the mitochondrial genome of Mycosphaerella graminicola

http://cat.inist.fr/?aModele=afficheN&cp...

Structural and Evolutionary Genomics - Natural Selection in Genome Evolution

http://www.cplbookshop.com/contents/C253...

Gene Flow and Natural Selection in Oceanic Human Populations Inferred from Genome-Wide SNP Typing

http://mbe.oxfordjournals.org/cgi/conten...

Natural selection on protein-coding genes in the human genome

http://www.nature.com/nature/journal/v43...

Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster

http://www.sciencemag.org/cgi/content/ab...

Natural Selection and the Evolution of Genome Imprinting

http://arjournals.annualreviews.org/doi/...

The question seems to be: when you ask about evolution, are you really interested in learning about it, or are you just trying to prove a point without doing proper research?

EDIT:

<HYDRO: Well Darwin released his theory in 1859 - does that also invalidate it because it is so old?>

Suprisingly, yes. It actually does.  However, modern scientists don't base evolution on whether or not Darwin was right, we base it on the current evidence for such.  Although Darwin happened to be right in many areas, there were also many areas where he was wrong, and his original theory has been modified to reflect such.

Current evidence for evolutlion falls in at least these following fields of science: Theory of Chromosomal Inheritence, Gene Theory, Comparitive Anatomy, Comparitive Embryology, Thoery of Perpetual Change, Theory of Common Descent, Theory of Multiplication of Species, Theory of Gradualism, Theory of Natural Selection, and more...

Darwin lacked a correct theory of heredity and assumed the current theory of blending inheritance was correct.

Darwin’s theory as modified by incorporation of genetics is called “neo-Darwinism.”

There's a good story that one of my professors once told me about the "validity" of Darwin's ideas.  When the study of genetics became big in the 20th century, the Theory of Evolution was up in arms!  This could be it!  Genetics would completely disprove evolution, or it would validate it.  Turns out, genetics  validated evolution, it fit nearly perfectly into the current theory, and what was wrong with evolution was studied again until proven wrong and taken out.  But for the most part, the current idea of evolution at the time was right, and scientist kept on trucking, trying to disprove evolution even more, and unable to.

"The modern theory of the mechanism of evolution differs from Darwinism in three important respects:

1) It recognizes several mechanisms of evolution in addition to natural selection. One of these, random genetic drift, may be as important as natural selection.

2) It recognizes that characteristics are inherited as discrete entities called genes. Variation within a population is due to the presence of multiple alleles of a gene.

3) It postulates that speciation is (usually) due to the gradual accumulation of small genetic changes. This is equivalent to saying that macroevolution is simply a lot of microevolution."

The Modern Synthesis of Genetics and Evolution by Laurence Moran ( http://www.talkorigins.org/faqs/modern-s... )

The rest of your second edit has been covered by Secretsauce below.