The Panda's Thumb

Einstein on God and the Bible

2008-05-17T04:13:56Z

In the creationist literature of various kinds an assertion is often made that Einstein was a believer in God, and this assertion is often suggested as allegedly an argument favoring religious faith. However such statements are contrary to what can be found in various documents, for example in Einstein’s letters to various people. The fate of one more such letter is revealed by Associated Press in the following message:

Einstein letter dismissing ‘childish’ religion sells for 200,000 pounds.

By The Associated Press

The letter was written to philosopher Eric Gutkind in January 1954, a year before Einstein’s death. In it, the Einstein said that

“the word God is for me nothing more than the expression and product of human weaknesses, the Bible a collection of honorable but still primitive legends which are nevertheless pretty childish.”

Einstein also said he saw nothing “chosen” about the Jews, and that they were no better than other peoples “although they are protected from the worst cancers by a lack of power.”

Unfortunately for creationists, using the authority of Einstein as a supposed argument in favor of their beliefs is based on a distortion of the views of the great scientist. Of course, argument from authority is anyway of little value.

The subtly different squid eye

2008-05-15T19:50:38Z

By now, everyone must be familiar with the inside out organization of the cephalopod eye relative to ours: they have photoreceptors that face towards the light, while we have photoreceptors that are facing away from the light. There are other important differences, though, some of which came out in a recent Nature podcast with Adam Rutherford (which you can listen to here), which was prompted by a recent publication on the structure of squid rhodopsin.

Continue reading “The subtly different squid eye” (on Pharyngula)

Inordinately Fond of Viruses: ORFans and Intelligent Design

2008-05-15T13:52:36Z

J.B.S. Haldane, when asked “What has the study of biology taught you about the Creator, Dr. Haldane?”, replied
“I’m not sure, but He seems to be inordinately fond of beetles.”

Discovery Institute Fellow Dr. Paul Nelson is inordinately fond of ORFans, genes unique to one species that appear to have no relatives in other species. He feels that these unique genes represent a significant challenge to evolutionary biology. However, he has not noticed that the distribution of ORFans implies that the designer is more enamoured of viruses than humans.

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A very tiny mystery:
What are ORFans, and why should we care about them? ORFans take their names from Open Reading Frames (ORF’s ). ORF’s are stretches of DNA that apparently code for proteins. ORFans are ORF’s that appear to occur only in one species. Note that I say “appear to”. The computer programs that are used to identify genes during whole genome assembly can falsely identify segments of DNA as ORF’s, this can be a significant issue in some genomes. Also, our computer programs for identifying related genes can miss genes that have undergone rapid evolution.

An example is the rotating image below left. This is a 3D model of the protein Xc5848 from Xanthomonas Campestris (it is also the static molecule above), originally designated as an ORFan, it was identified to be part a of large class of proteins by sophisticated structure analysis. The model is coloured by amino acid conservation, with red being the highest conservation, and blue being poorly conserved. The model is mostly red (ie it’s part of a highly conserved protein family, not an ORFan at all).

ORFans come in two classes, short (often less than 100 amino acids long), which are unlikely to represent real genes as they are usually much shorter than most real genes, and long (usually over 150 amino acids long), which are likely to be real genes. There are far more short ORFans than long ORFans.

Paul Nelson thinks that ORFans represent a major blow to evolutionary theory. To him they break attempts to determine phylogenies and throw doubt on the idea that all organisms descended from a common ancestor. I’ve dealt with that aspect before (see also here), and I won’t go into detail here, but I would like to simply re-iterate a few points. We have a number of explanations, based on evidence, for the existence of ORFans.

1) Some represent artifacts
2) Some represent rapidly evolving genes whose origin is obscured by the pace of evolution
3) Some represent genes horizontally transferred genes from organisms that have not been sequenced yet.
4) Some represent genuine, de novo genes.

Now, as I said, we have evidence for all of these explanations, and ORFans will represent a combination of all factors. For example, it has been estimated that about half of all short ORFans represent artifacts, but some do represent genuine protein coding genes. In the Firmicutes (the family of bacteria that include the well known gut bacteria Escherichia coli, a large percentage of the genuine short ORFans represent bacteriophage genes (although the confirmed proportion of viral genes in prokaryotes generally is somewhat smaller), and as we add more genomes we discover relatives for things we previously thought were unique.

A tiny mystery gets tinier:
In 2003, a fair percentage of the ORF’s found in fully sequenced prokaryotic genomes were ORFans. However, even back in 2003, it was apparent that as we sequenced more genomes we found more relatives for ORFans and fewer new ORFans.

Figure 1c of Seiw & Fischer 2003, Proteins, 53:241-251, showing that the percent of the genome that is ORFans is decreasing, while the number of ORFans is flattening out.

A relentless fall of ORFans:
We have a lot more data now, and the extent of the fall in ORFans can be found by looking at the ORFan mine, a database of ORFans. As we add more genomes, we identify more relatives of things we thought were unique, and identify and purge more artifacts.

Consider the Escherichia coli genome. In 2003 the total ORFans (things likely to be artifacts) in the E. coli genome constituted 5.5% of the genome, and long ORFans (things likely to be genes) represented 2.4% of the genome. By 2008, total ORFans and long ORFans represented 0.4% and 0.1% of the genome respectively. Consider also the Heliobacter pylori genome, going from 17% and 9% total and long ORFans in 2003 to 2.3% and 0.6% total and long ORFans in 2008.

If you look at all 60 of the genomes reported by Seiw and Fischer in 2003, the total ORFans averaged 14%, by 2008 this was down to 6%. If you look at the genomes added after those 60 (ie all the late comers, not those that are already characterised), their ORFan precent is 7%. In 2003, the last 10 organisms to be added to the databased had an average of 12% ORFans when first sequenced, in 2008, the last 10 organisms had 6% ORFans when first sequenced.

Even those figures may overestimate the number of ORFans, of the 19 ORFans in the E. coli data base, 10 are annotated to viral or conserved proteins. Of the ones I’ve investigated, there is significant sequence similarity to other proteins (eg the alleged ORFan NC_000913orf2361 is annotated to be a CPZ-55 prophage, and forms a high significance phylogeny with other proteins and even has a PFAM domain in it!)

Some ORFans are not. The supposed ORFan NC_000913orf2361 is related to a whole range of conserved proteins.

So as we sequence new genomes, we are finding fewer and fewer ORFans. This entirely consistent with the position that ORFans represent rapidly evolving proteins, horizontally transferred proteins and annotation artifacts rather than unique proteins inserted by an unknown designer by unknown mechanisms. Paul Nelson like to emphasize the number of ORFans, as this is increasing. However, the pattern of increase is very instructive. Below I’ve plotted the total number of ORF’s and ORFan’s with increasing number of full genomes sequenced, and the fold increase of ORF’s and ORFans with respect to the numbers of ORF’s and ORFans when only 15 Genomes were sequenced (why do ID advoctes never do this type of thing?).

You can clearly see that the rate of increase in ORFan number is dramatically slowing. When we reached 60 sequenced genomes, this resulted in 4.5 fold increase of ORF’s over the numbers present at 15 genomes, but just over a doubling of ORFans, by the time we got to 330 genomes, ORF’s had increased 25 fold from the numbers at 15 genomes, but ORFans had increased less than eight fold. This is entirely consistent with the fact that as we add genomes, we find more relatives of these genes.

ORFan numbers increase as we sequence more genomes, but ORF’s (real genes with known relatives) increase much, much faster. This is consistent with the majority of ORFans representing under sampling of phylogenies. Data taken from Seiw and Fischer, 2003 and the ORFan mine).

enter the virus:
Paul Nelson is now particularly taken with a paper from Fischer’s group, that showed that around 38% of complete virus genomes are ORFans. This figure seems to impress Paul. However, the same issues that applied to prokaryotic genomes apply to viral genomes.

As shown in figure 4 of Yin and Fischer (above), as the number of viral genomes sequenced increases, the percentage of ORFans drops as relatives are found (just like prokaryotic ORFans). The phage groups with the most “ORFans” are those that have the fewest sequences (just like prokaryotes, which suggest that sampling of genomes is the main issue).

Furthermore, 18% of alleged “ORFans” turn out to be horizontally transferred prokaryotic genes (just as a fair proportion of prokaryotic “ORFans” turn out to be horizontally transferred bacteriophage genes). Looking at the authors conclusions we find them saying:

Because the current sampling of phages (and of bacterial genomes in general), is limited and biased towards particular groups, the percentage of ORFans in different phage groups varies significantly. This low sampling may be a factor contributing to the abundance of phage ORFans, but is not likely to be the only one. That is, even after many more genomes are sequenced, we expect to find a significant number of ORFans and near-ORFans, awaiting interpretation. There are also other possibilities to account for the ORFans’ origin, like rapid divergence after horizontal transfer (from hosts or from other viruses, from existent genomes or yet extinct genomes) or duplication.

Rapid divergence obscuring ancestry in rapidly evolving viruses is by no means unusual, and more careful sequence comparison will undoubtedly turn up more relatives (just as happened with procaryotes).

Summary: So, the solutions to the ORFan “puzzle”, as outlined by Yin and Fischer (poor sampling, horizontal transfer, rapid evolution) follow the same lines as my previous Pandas Thumb posts (I also included annotation errors, known to produce a proportion of alleged prokaryotic “ORFans”. These annotation errors are likely to be substantial in small genomes as well).

It is instructive to compare the number of ORFans in various genomes (as they currently stand). The Human genome has 0% ORFans [see note], Prokaryotes an average of around 7% and viruses around 30%. Now, if it may be that ORFans represent artifacts, poor sampling and rapidly evolving genes (which would explain why rapidly evolving, under sampled and exceedingly diverse groups like viruses have more ORFans than prokaryotes or Humans).

Or the Designer really has an inordinate fondness for viruses.

Note: Paul Nelson objects to the paper that eliminated the last of the ORFans from the human genome (Clamp et al., 2007), as he claims that they did this on purely evolutionary reasoning. He is wrong; they also looked at whether these sequences were significantly different to random sequences, and whether they were expressed as protein. They weren’t and they aren’t. This is good evidence that they are artifacts.

Larry Moran has a good discussion of ORFans at the Sandwalk.

References

Siew N, Fischer D. Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins. 2003 Nov 1;53(2):241-51.
Yin Y and Fischer D. (2006) On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer, BMC Evolutionary Biology, 6:63doi:10.1186/1471-2148-6-63
Daubin V, Ochman H: (2004) Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res, 14(6):1036-1042.
Wilson GA, Feil EJ, Lilley AK, Field D (2007) Large-Scale Comparative Genomic Ranking of Taxonomically Restricted Genes (TRGs) in Bacterial and Archaeal Genomes. PLoS ONE 2(3): e324. doi:10.1371/journal.pone.0000324
Yin Y and Fischer D. (2008) Identification and investigation of ORFans in the viral world. BMC Genomics. 9: 24. Published online 2008 January 19. doi: 10.1186/1471-2164-9-24.
Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19428-33. Epub 2007 Nov 26.

Tangled Bank #105

2008-05-15T02:11:57Z

It’s up! The latest Tangled Bank is at The Beagle Project Blog.

In the Light of Evolution I: Adaptation and Complex Design

2008-05-13T23:35:54Z

There are many excellent resources available online and I recently ran across a conference organized by John C. Avise and Francisco J. Ayala called In the Light of Evolution I: Adaptation and Complex Design

In the presentation that caught my initial interest, Robert Hazen explains the various steps necessary for the origin of life and defines complexity and shows how complexity can increase. I have combined notes on his lecture with additional papers and presentations by Robert Hazen, in order to outline that which many creationists insist, does not exist: a scientific explanation of the origins of life.

I predict that ID creationists will be quick to argue that these are just so stories, and yet, these are stories which present testable hypotheses. And thus I invited ID creationists to present the best explanation as to how ID explains these data?

Seems fair enough.

Read more at ID Exposes where comments may be left.

The Wedgewood files

2008-05-13T05:35:27Z

Sneer Review reports on an in-depth investigation into “The Wedgwood Document” which outlines how the teapot from the famous atheist Bertrand Russell was acquired to undermine the recent successes from atheists.

Remember that Bertrand Russell had stated

“If I were to suggest that between the Earth and Mars there is a china teapot revolving about the sun in an elliptical orbit, nobody would be able to disprove my assertion .….….….. But if I were to go on to say that, since my assertion cannot be disproved, it is an intolerable presumption on the part of human reason to doubt it, I should rightly be thought to be talking nonsense. If, however, the existence of such a teapot were affirmed in ancient books, taught as the sacred truth every Sunday, and instilled into the minds of children at school, hesitation to believe in its existence would become a mark of eccentricity and entitle the doubter to the attentions of the psychiatrist in an enlightened age or of the Inquisitor in an earlier time.”

This simple statement set in motion a series of events which will reverberate in history.

Flagella - Real and Fictional

2008-05-12T14:44:08Z

Intelligent Design advocates are fond of using the bacterial flagellum as, in Dembski’s words, a “mascot” of the Intelligent Design movement. In particular, during the recent TV debate between Behe and myself, Behe showed pictures of flagella and triumphantly asserted that they looked exactly like man-made machines, and therefore they must be designed. What ID advocates, including Behe, fail to mention is that the images of flagella they endlessly demonstrate are heavily doctored, and that the real observed flagella do not look like “machines” at all. In fact the structure of flagella is more typical of a bacteriophage virus. Seeing the actual cryogenic electron micrographs of flagella, as well as the images derived from X-rays analysis immediately reveals that showing artificial machine-like images of flagella, without explaining the degree of idealization applied, is sometimes perilously close to committing a fraud.

Read Flagella – Real and Fictional, at Talk Reason.

A thorny issue

2008-05-11T22:36:31Z

It seems that the evolution of thorns and plants is seen by some creationists as evidence against evolution and in favour of an Intelligent Designer. While I hate to spend time on debunking creationist foolishness on demand, I found the issue quite fascinating and relatively straightforward to rebut.

Read further at Plants that defy evolution: Datura stramonium (Jimson Weed) where also comments can be left.

PS: Joseph Alden and Gary McGuire are the same person. So any future postings by Joseph should continue under one of the two names as the use of multiple names is in violation of the board’s rules and can be grounds for moderation or removal. Jospeh Alden is Gary McGuire’s uncle and the two were sharing a similar email address and IP connection.

The platypus genome

2008-05-10T16:40:30Z

Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is "weird" or "odd" or worse, they imply that the animal is a chimera — "the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal". No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as birds are an independent and (directly) unrelated lineage; you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals. We can say with equal justification that we are part reptile, too. What's interesting about the platypus is that it belongs to a lineage that separated from ours approximately 166 million years ago, deep in the Mesozoic, and it has independently lost different elements of our last common ancestor, and by comparing bits, we can get a clearer picture of what the Jurassic mammals were like, and what we contemporary mammals have gained and lost genetically over the course of evolution.

We can see that the journalistic convention of emphasizing the platypus as an odd duck of a composite creature is missing the whole point if we just look at the title of the paper: "Genome analysis of the platypus reveals unique signatures of evolution." This is work that is describing the evidence for evolution in a comparative analysis of the genomes of multiple organisms, with emphasis on the newly revealed data from the platypus.

Continue reading "The platypus genome" (on Pharyngula)

Behe vs Lampreys: A modest proposal.

2008-05-10T16:09:50Z

Intelligent Design advocates regularly claim that Intelligent Design is science. However, a recent paper on the lamprey genome demonstrates the sharp gulf between science and ID. One of the key icons of ID is Michael Behe’s “irreducibly complex” clotting system. In 1996 he claimed that the clotting system was unevolvable, and no simpler clotting system could exist. In contrast, in 1987 evolutionary biologist Russell Doolittle hypothesised that the clotting system had been built up by co-option of duplicated genes. Doolittle specifically predicted that fish would lack key elements of the Mammalian clotting system (elements of the intrinsic or contact clotting system). Let’s see how those predictions fared.

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Since he first made his prediction, Russell Doolittle has been extensively examining the clotting systems of different organisms. By 2003, after over a decade of hard work, it was apparent that bony fish did lack the intrinsic clotting system, ironically the system that Behe describes in some detail in “Darwins Black Box”. By 2003 it also seemed that jawless fish also lacked key elements of the intrinsic clotting system, in line with Doolittle’s prediction and the opposite of Behe’s claim.

Now, it would have been easy for Doolittle to rest there, with favourable evidence for his prediction. But no, he and his colleagues put it to a more stringent test, searching for clotting factor genes in the trace archive of the lamprey genome (a representative jawless fish). This is a massive bit of work, the trace archive is all the gene fragments generated before assembly of the genome, so they had to laboriously assemble and test each putative gene. What did they find?

That jawless fish lack factors IX and V. Now, this is a pretty important chunk of the clotting system to be without. When it was revealed that whales and bony fish lacked the intrinsic clotting system, Behe effectively replied “So much the worse for them”. But in humans, lack of factor IX produces a bleeding disorder called haemophilia B, lack of factor V also produces haemophilia, and lack of both should result in a very severe bleeding disorder.

The reducible clotting system: Bony fish and jawless fish have a reduced complement of clotting factors compared to mammals. Jawless fish lack factors IX and V. Tissue factor and factor VII directly activate thrombin, but the explosive coagulation cascade is initiated by factors IX and V acting together. The older name for Factor V was proaccelerin, the activated from of factor V was known as accelerin, indicating its role in the explosive acceleration of clotting.

Factors IX and V are not peripheral pieces of the clotting system, but are the key section that produces the massive amount of thrombin needed for clotting in vertebrates. According to Behe, the severe bleeding disorder from loss of factors IX and V shows that the clotting system could not be built up from simpler systems, as the system can only function with all its parts.

To put it in Behe’s imagery, the clotting system of the Lamprey is a mousetrap without a spring.

Yet jawless fish are doing quite well without factor IX and V. The implications of this for “irreducible complexity” are profound. An ID advocate might concede that “yes, the clotting system isn’t really irreducibly complex, what about other systems?”. But this example not only falsifies the claim that the clotting system is “irreducibly complex”, but the logic of entire argument Behe uses. Behe has claimed that it is not possible to directly evolve a system such as the clotting system directly, because a smaller system will not work. Yet the jawless fish system shows just that, a system that lacks key component(s) of the mammalian system is completely viable and functioning. Behe’s central argument is broken, knocking out parts of a system and showing that the system breaks does not mean it cannot evolve directly from a simpler system. The work on lampreys provides strong evidence for Doolittle’s model of generating complex systems by rounds of duplication and divergence.

Note that in all this it has been the evolutionary biologists doing the heavy lifting. Generating predictions and models, testing clotting systems in various animals, cloning clotting factors, searching databases and finally, assembling genes from fragments. What have the ID apologists been doing in the 12 years since “Darwins Black Box” was published? Not a lot. Given the central role of the clotting system to their claims, one would have expected the ID folks would have been hard at work showing that the clotting system was irreducible.

Now, to be fair a lot of this is specialized work, that needs a serious biochemistry lab. But when the Fugu genome came out in 2003, nothing was stopping anyone from searching the Fugu genome for clotting factors. The databases were public, and you could do it at home in your spare time. No need to worry about discrimination from co-workers.

Did any ID person do that? No, it was the evolutionary biologists who came up with a testable hypothesis, and combed the Fugu database to test it.

Now the Amphioxus genome has come out. The Amphioxus is a simple, pre-vertebrate chordate, simpler than the Lamprey. We know that it clots its haemolymph (the Amphioxus equivalent of blood), and that it has a thrombin like molecule in its haemolymph, so we know it has a clotting system. Evolutionary biologists would predict that it has a reduced clotting system (see figure). ID advocates would predict that it would not.

So I have a modest proposal. I would like to invite Dr. Behe, or any other ID advocate, to predict which coagulation factors are present in Amphioxus, search the Amphioxus genome database and report on whether the genes found match their predictions. The database is free, you can do it at home, and the only cost is your time.

Time for ID advocates to do some science. How about it?

http://genome.jgi-psf.org/Brafl1/Brafl1.home.html

References

Doolittle RF, Jiang Y, Nand J. Genomic evidence for a simpler clotting scheme in jawless vertebrates. J Mol Evol. 2008 Feb;66(2):185-96.
Jiang Y, Doolittle RF. The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes. Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7527-32 (full article free access)
Doolittle RF.The evolution of vertebrate blood coagulation: a case of Yin and Yang. Thromb Haemost. 1993 Jul 1;70(1):24-8
Doolittle RF, Feng DF.Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins.Cold Spring Harb Symp Quant Biol. 1987;52:869-74.
Davidson CJ, Hirt RP, Lal K, Snell P, Elgar G, Tuddenham EG, McVey JH. (2003). Molecular evolution of the vertebrate blood coagulation network. Thromb Haemost. 89(3):420-8.
Davidson CJ, Tuddenham EG, McVey JH. 450 million years of hemostasis. J Thromb Haemost. 2003 Jul;1(7):1487-94.

More "Expelled" News

2008-05-09T18:25:28Z

It’s been a good week for science, and evolutionary science in particular so let me mention a few newsworthy events.

And in late breaking news:

Turkish Islamic author Oktar aka Harun Yahya given 3-year jail sentence

Oktar’s teachings echo those of Christian fundamentalists in the United States. He has publicly denounced Darwinism and Freemasonry in high-profile attacks.

Expelled Theatre count

Week	Theatres	Change
May 09	402	-254
May 02	656	-385
April 25	1041	-11
Launch	1052	0

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Alabama Kills Evolution Bill

The bill is in ‘good’ company

Hundreds of bills have died in the 2008 session of the Alabama Legislature because they did not pass in the house where they were introduced. Some of them would have:
- Repealed the state’s ban on sex toys.
…
- Protected teachers from being fired for giving personal opinion while teaching controversial subjects like evolution. - Allowed Alabama voters to decide if they want to legalize electronic bingo games at greyhound dog tracks in Mobile and Birmingham.

Ono gains temporary injunction against “Expelled”

A federal judge in Manhattan has told the makers of Expelled: No Intelligence Allowed that they cannot distribute the film any further, until a copyright infringement complaint is heard in court later this month.

Kenneth Miller reviews “Expelled”

Kenneth Miller Wrote:
Despite these falsehoods, by far the film’s most outlandish misrepresentation is its linkage of Darwin with the Holocaust.

and

Kenneth Miller Wrote:
“Expelled” is a shoddy piece of propaganda that props up the failures of Intelligent Design by playing the victim card. It deceives its audiences, slanders the scientific community, and contributes mightily to a climate of hostility to science itself. Stein is doing nothing less than helping turn a generation of American youth away from science. If we actually come to believe that science leads to murder, then we deserve to lose world leadership in science. In that sense, the word “expelled” may have a different and more tragic connotation for our country than Stein intended.

Jeffrey Schloss reviews “Expelled at ASA

A 33(!) page review by Jeffrey P. Schloss from the Center for Faith, Ethics, and Life Sciences at Westmont College that looks in depth at a variety of aspects and issues. Well worth reading.

Percival Reviews “Expelled”

The science and science education communities experience much the same exasperation from the on-going conflict first with the creation science community and then with intelligent design proponents. I agree with Expelled that a healthy academic community depends on the free exchange of ideas, but if the film has any impact at all, I can only see it leading to a reinforcement of the wall it seeks to criticize and to further cultural polarization.

NCSE: Eyeing ID

2008-05-07T03:52:52Z

While legislatures focus on antievolution bills, a new video at Expelled Exposed helps students see how evolution works.

Oakland, California, May 6, 2008 As attacks on evolution education remain in the news, with proposed antievolution legislation in Alabama, Florida, Louisiana, Michigan, and Missouri in the headlines, a new video rebutting the basic premise of intelligent design creationism is now available on www.ExpelledExposed.com.

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“Creationism Disproved?” is the third in a series of short videos commissioned by the National Center for Science Education, a non-profit organization that defends the teaching of evolution in the public schools. The video focuses on the evolution of the eye a favorite target of creationists.

“It’s common for creationists, especially ‘intelligent design’ creationists, to claim that complex structures like the eye or parts of the cell couldn’t have evolved step by step,” explains NCSE’s executive director, Eugenie C. Scott. “It’s a tired objection indeed, Darwin himself anticipated, and refuted, the argument. But opponents of evolution continue to insist that such structures had to be assembled all at once.”

Ken Dill, a researcher at the University of California, San Francisco featured in the video, adds: “In fact, complexity can evolve through small steps. We can infer the evolution of a very complex organ, like the eye, by looking at intermediate stages preserved in animals alive today. And just as a baby’s eye is built up step by step over nine months in the womb, the eye evolved in small steps over millions of years.”

Noting that the latest advances in science have only confirmed Darwin’s insights, Josh Rosenau, a biologist at NCSE, observed, “Scientists recently traced the evolution of a protein crucial to vision by comparing the genomes of many species, showing that the molecule, opsin, existed in the common ancestor of hydras, jellyfish, flies, fish, and people. Other researchers have traced the evolution of genes critical to the growth and development of eyes in different branches of the tree of life. All those lines of evidence match the predictions of evolution.”

Louise S. Mead, a biologist and teacher who heads NCSE’s outreach to educators, hopes that students and teachers will use the video to dispel a common misconception about evolution. “Evolution can be tough to learn and tough to explain, even independently of the prevalence of creationist misconceptions,” she explains. “Videos like this can help students see things in a new light.”

The National Center for Science Education is a non-profit organization dedicated to defending the teaching of evolution in the public schools. The NCSE maintains its archive of source material on the history of creationism at its Oakland, California, headquarters.

On the web at www.ncseweb.org.

NCSEs other website, www.ExpelledExposed.com, is a resource for journalists, teachers, and curious moviegoers who want the full story behind the creationist movie Expelled: No Intelligence Allowed.

Contacts: Eugenie C. Scott, [Enable javascript to see this email address.], 800-290-6006 Josh Rosenau, [Enable javascript to see this email address.], 800-290-6006 Louise S. Mead, [Enable javascript to see this email address.], 800-290-6006

Gambler's Ruin is Darwin's Gain

2008-05-05T18:21:42Z

by Joe Felsenstein
http://www.gs.washington.edu/faculty/felsenstein.htm

Over at Uncommon Descent Sal Cordova has opened a dramatic new thread “Gambler’s Ruin is Darwin’s Ruin”. Apparently improvement of a population by natural selection is now shown to be essentially impossible. He invokes the example of Edward Thorp, who developed the winning system for blackjack fictionalized in the movie 21.

Cordova uses the stochastic theory of gene frequency change of citing Motoo Kimura and Tomoko Ohta’s well-known 1971 monograph “Theoretical Aspects of Population Genetics”, and argues that

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Without going into details, I’ll quote the experts who investigated the issues. Consider the probability a selectively advantaged trait will survive in a population a mere 7 generations after it emerges:
if a mutant gene is selectively neutral the probability is 0.79 that it will be lost from the population … if the mutant gene has a selective advantage of 1%, the probability of loss during the fist seven generations is 0.78. As compared with the neutral mutant, this probability of extinction [with natural selection] is less by only .01 [compared to extinction by purely random events]. (bracketing is by Cordova)
This means is that natural selection is only slightly better than random chance. Darwin was absolutely wrong to suggest that the emergence of a novel trait will be preserved in most cases. It will not! Except for extreme selection pressures (like antibiotic resistance, pesticide resistance, anti-malaria drug resistance), selection fails to make much of an impact.

The Kimura/Ohta quote in question is on page 1 of their book, and describes a mutant with a selective advantage of 1%.

This would be a shocking disproof of decades of work in population genetics—if it accurately reflected the ultimate fate of those mutants. Fortunately, we can turn to an equation seven pages later in Kimura and Ohta’s book, equation (10), which is Kimura’s famous 1962 formula for fixation probabilities. Using it we can compare three mutants, one advantageous (s = 0.01), one neutral (s = 0), and one disadvantageous (s = -0.01). Suppose that the population has size N = 1,000,000. Using equation (10) we find that

The advantageous mutation has probability of fixation 0.0198013.
The neutral mutation has probability of fixation 0.0000005.
The disadvantageous mutation has probability of fixation 3.35818 x 10^-17374

In other words, yes, in this case there is a lot of loss of advantageous mutations, about 49 being lost of every one that makes it to fixation. But they are each nearly 40,000 times as likely to fix as are individual neutral mutations, and deleterious mutations are essentially never going to fix in such a case.

Why does this give such a different result than the comparison of 0.78 to 0.79? It is because after 7 generations the surviving mutants in the case of selective advantage are at a higher frequency than are those in the neutral case, and the result is a much greater chance of fixation.

In fact, the Gambler’s Ruin shows a similar behavior—its mathematics is similar to (but not identical to) the population-genetic case. If you toss coins with a stake of $1 against a house which has $1,999,999 to wager, and you both keep playing until one holds the whole $2,000,000, if the game is fair you will be the ultimate victor one time out of 2,000,000, and the rest of the times the house will win. But if you have a 1% advantage, so that on each toss you have a 50.5% chance of winning, you will be the ultimate victor nearly 1% of the time. Mostly you will be ruined, but you will bankrupt the house 20,000 times as often as you would if the toss were fair.

So yes, the mathematics of Gambler’s Ruin speaks to the issue of natural selection—but it confirms its effectiveness.

(The other issue raised by Cordova, that of interference between mutations at different loci, is the well-known Hill-Robertson effect. If the loci have more than a tiny amount of genetic recombination between them, the interference largely vanishes. Cordova and the other commenters there have forgotten this.)

Some Comments on McCreary v. Irons

2008-05-05T16:22:24Z

Chris Bell at Prometheus Retold has some interesting comments on Jana McCreary’s article in the Southwestern University Law Review as well as Peter Irons’ reply to it, both of which you can read here.

Tangled Bank #104

2008-05-04T15:59:18Z

Uh-oh, I almost missed it — the latest Tangled Bank is available. Get over there and read it belatedly!

I'm also looking for new hosts — if you're interested, volunteer.