What is the latest theory of why humans lost their body hair?

 
This is the question asked in this month's issue of Scientific American. Mark Pagel, head of the evolutionary biology group at the University of Reading in England and editor of The Encyclopedia of Evolution gives three adaptationist explanations.

Now, here's the question of the day for all you adaptationists. Why didn't he mention neoteny? Do you think it's because he has carefully reviewed all the evidence and reaches the conclusion that there's more data to support running on the savannah?

Nobel Laureate: Richard Kuhn

 

The Nobel Prize in Chemistry 1938.

"for his work on carotenoids and vitamins"



In 1938, Richard Kuhn (1900-1967) won the Nobel Prize in Chemistry for his work on the structure of several different vitamins, including the carotenoids [Vitamin A (retinol)] and the B₆ family [Pyridoxal Phosphate and the Vitamin B6 Family].

The award overlaps considerably with the prize for the previous year [Nobel Laureate: Paul Karrer], which suggests that the prize committee may have been pressured to recognize Kuhn after slighting him in favor of Karrer. The two men were friendly competitors for many years and much of their work is similar.

Kuhn was not able to accept the prize in 1938 because at the time he was working at Heidelberg University and the political situation did not allow him to travel to Sweden. There was no formal presentation speech but the following account of his work is posted on the Nobel Prize website.

When Richard Kuhn in 1926 took over the Chair for General and Analytical Chemistry at the Federal Institute of Technology Zurich he set in motion a comprehensive series of investigations into the so-called conjugated double bonds which make up the essential arrangement of the atoms of the polyenes.

The group of the diphenylpolyenes had at this time aroused especial interest because the presence in the carotenoid Crocetin of a chain of double bonds had been successfully demonstrated. Kuhn's sixth report on conjugated double bonds already contains structure determinations of polyene dyes from vegetable materials. With his syntheses of over 300 new materials belonging to this group Kuhn has by no means sought merely to liberate new substances. In this work he was much more concerned to clarify the general relationships between the chemical structure of these unsaturated substances and their optical, dielectric, and magnetic properties. The results which he has obtained in this respect form the starting-point for new lines of development in organic chemistry.

Kuhn's work on polyenes led him straight into the chemistry of the carotenoids. In 1930 Karrer clarified the constitution of carotene. The elementary composition of carotene, C40H56, had previously been ascertained by Willstätter. In 1931, R. Kuhn (at that time already Professor at Heidelberg), Karrer in Zurich, and Rosenheim in London discovered simultaneously and independently of each other the fact that the carotene in carrots consists of two separate components: one of these, b-carotene, rotates the plane of polarized light to the right, while the other, a-carotene is optically inactive. In 1933 Kuhn discovered a third carotene isomer which was called g-carotene.

The great physiological and biological significance of carotene lies in the fact that it is hydrolysed in the liver of certain animals so that from one molecule of b-carotene or from two molecules of a-carotene two molecules of Vitamin A, Axerophtol, are formed. This substance is necessary for growth in higher animals and especially for maintaining the normal condition of the mucous membranes.

With several collaborators Kuhn carried out a large number of investigations into the occurrence of carotenoids in the animal and vegetable kingdoms. Among his most important results, his discoveries of the following carotenoids and their structure determination should be mentioned:

Physalien from berries of species of Physalis, Helenien, Flavoxanthin, isolated from species of Ranunculus, Violaxanthin from Viola tricolor, unstable Crocetin from saffron, Taraxanthin, Cryptoxanthin from Zea Mays Rubixanthin.

Kuhn also had an important share in establishing the composition of Rodoxanthin and Astaxanthin as well as in discovering the connection of this latter carotenoid with the chromoproteids of the Crustaceans.

Of great interest also are the many contributions Kuhn and his school have made to the perfection of the chromatographic method which is one of the most important aids to the isolation and synthesis of the different representatives of the carotenoid group.

Kuhn's second great field of activity concerns the clarification of the Vitamin B complex. Kuhn has the great merit, together with von Szent-Györgyi and Wagner-Jauregg, of having been the first to isolate the extraordinarily important substance Vitamin B2 (Lactoflavin or Riboflavin). He has made very important contributions to the elucidation of the chemistry of this substance.

From 5,300 litres skim milk Kuhn and his collaborators succeeded in liberating about 1g of a pure yellow substance, Lactoflavin, whose composition was found to be C17H20O6N4. A breakdown product of the Lactoflavin, which was called Lumiflavin, could be identified with a substance previously prepared from the yellow ferment occurring in yeast. By drawing up a structural formula for Lumiflavin later confirmed in various ways, Kuhn furnished a key to the chemical clarification of Lactoflavin. He himself demonstrated the Lumiflavin formula, which had been found by analytical methods, by a synthesis - namely through the condensation of an odiaminobenzene derivative with Alloxan.

At the beginning of 1939 Kuhn made his second significant discovery in relation to the Vitamin B complex. Together with Wendt, Andersag, and Westphal, he succeeded in isolating that component of the Vitamin B complex which is designated Vitamin B6, the antidermatitis vitamin, and in a remarkably short time he was able to establish its chemical composition and structure (Ber., 71 (1938) 1534; 72 (1939) 309). The substance which Kuhn thus elucidated, which he called Adermin, proved to be 2-methyl-3-hydroxy-4,5 -dihydroxymethylpyridine.

The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes

Ultraconserved elements are stretches of DNA that are 100% identical in mouse, rat, and human genomes. In order to qualify as an ultraconserved element, the length has to be greater than 200 bp. This eliminates most sequences that might be identical by chance.

The most interesting elements are those that fall outside of coding regions. These ultraconservative elements are most likely to be involved in regulating gene expression or some other essential feature of non-coding DNA. The fact that they are identical in species who last shared a common ancestor 100 million years ago is powerful evidence of adaptation.

Ahitiv et al. (2007) set out to test this hypothesis by selecting four examples of ultraconservative elements for further analysis. They discovered that the elements function as tissue specific enhancers in a test designed to look at how they control expression of a maker gene in mouse embryos. The results are shown in Figure 1 (left) of their paper, which was just published in the open access journal PLoS Biology.

The figure shows the genomic location of the four ultraconserved elements; uc248 (222 bp), uc329 (307 bp), uc467 (731 bp), and uc482 (295 bp).

Of these, uc467 is the most remarkable because it is 731 bp in length and resides in the last intron of the DNA polymerase alpha 1 gene (POLA1) on the human X chromosome. The enhancer trap experiment shows that this segment of conserved DNA directs expression of the marker gene in embryonic brain cells (shown as the dark blue area in the embryo above the 467 site). This is usually taken as evidence of specific regulatory sequences that bind transcription factors.

Ahituv et al. then deleted the four ultraconserved sequences from the mouse genome using standard knockout technology. Mice that were homozygous for the knockouts showed no evidence of any defect compared to wild-type mice. In other words, the ultraconserved elements seemed to be completely dispensable—a result that is not consistent with their extreme conservation.

THEME:
Junk DNA
What are the possible explanations? It's possible that the authors missed a phenotype that can only be detected outside the laboratory. It's also possible that the sequences really aren't conserved because they perform an important function but for another reason. Here's how the authors explain their results,

Based on the compelling evidence that ultraconserved elements are conserved due to functional constraint, it has been proposed that their removal in vivo would lead to a significant phenotypic impact [7,8]. Accordingly, our results were unexpected. It is possible that our assays were not able to detect dramatic phenotypes that under a different setting, for instance, outside the controlled laboratory setting, would become evident. Moreover, possible phenotypes might become evident only on a longer timescale, such as longer generation time. It is also possible that subtler genetic manipulations of the ultraconserved elements might lead to an evident phenotype due to a gain-of-function-type mechanism. All four elements examined in this study demonstrated in vivo enhancer activity when tested in a transgenic mouse assay (Figure 1) [6], which would suggest regulatory element redundancy as another possible explanation for the lack of a significant impact following the removal of these specific elements. Just as gene redundancy has been shown to be responsible for the lack of phenotypes associated with many seemingly vital gene knockouts, regulatory sequence redundancy [22] can similarly provide a possible explanation for the lack of a marked phenotype in this study. While our studies have not defined a specific need for the extreme sequence constraints of noncoding ultraconserved elements, they have ruled out the hypothesis that these constraints reflect crucial functions required for viability.

[UPDATE: Ryan Gregory at Genomicron discusses the same paper with a more thorough coverage of the background information and the relevance to junk DNA (Ultraconserved non-coding regions must be functional... right?). R. Ford Denison at This Week in Evolution has some thoughts on the paper (If it's junk, can we get rid of it?")]

---

Ahituv, N,, Zhu, Y., Visel, A., Holt, A., Afzal, V., Pennacchio, L.A., and Rubin, E.M. (2007) Deletion of Ultraconserved Elements Yields Viable Mice. PLoS Biol 5(9): e234 doi:10.1371/journal.pbio.0050234.

Denyse O'Leary's New Book

 
We've been waiting with baited bated^* breath but the big day has finally arrived. Denyse O'Leary announces that we can now buy her new book The Spiritual Brain [ Just released - a neuroscientist's case for the existence of ... the soul!].

The first author is Mario Beauregard, a scientist at the Université de Montréal (Canada). According to Denyse, Beauregard is one of the "One Hundred Pioneers of the Twenty-First Century" selected by World Media Net. What the heck is "World Media Net"? Canadian Cynic also wants to know The hilarity just never ends].

Beauregard (and O'Leary) have solved the mind-body problem. It turns out that there's more going on inside the brain than just the firing of neurons. Apparently, your brain is capable of contacting a different reality during intense religious experiences.

Beauregard uses the most sophisticated technology to peer inside the brains of Carmelite nuns during a profound spiritual state. His results and a variety of other lines of evidence lead him to the surprising conclusion that spiritual experiences are not a figment of the mind or a delusion produced by a dysfunctional brain.

I'm not going the buy the book. If someone wants to read it I'd be happy to see a review from a real scientist.

^* I actually knew that "baited" was wrong but I typed it anyway. For an explanation of what "bated" means see World Wide Words.

Pyridoxal Phosphate and the Vitamin B6 Family

 
Vitamin B₆ is actually a family of related molecules consisting of a six-membered ring with a single nitrogen atom. The various members differ only in the group attached to position 4 of the ring. The ring is called a pyridine ring and the various derivatives are named after the pyridine ring (see below and Monday's Molecule #41). The most common vitamin B₆ molecules are pyridoxal or pyridoxamine. They are widely available from plant and animal sources and it's unusual for human diets to be deficient in vitamin B₆.


By definition, a vitamin is a compound that humans can no longer synthesize. Some vitamins act directly as cofactors or coenzymes but many them serve as precursors for the synthesis of the final product. This is true of the B₆ vitamins. They are rapidly converted to pyridoxal 5′-phosphate (PLP). Humans have retained the ability to catalyze this conversion.

PLP is a cofactor that's bound to many enzymes in the cell where it participates in a number of different reactions. The most important reactions are those involving transfer of amino groups from one molecule to another. There is a large class of transaminases that require PLP.

The transaminases are required for amino acid synthesis and for synthesis of many neurotransmitters such as serotonin and epinephrine. An example of a transamination reaction is shown below. Note that PLP is covalently bound to the enzyme through a lysine side chain. An amino acid donates its amino group to PLP in an exchange reaction giving rise to pyridoxamine phpsphate (PMP), which remains firmly bound to the enzyme. The entire sequence of reactions can then be reversed using any α-keto acid as a substrate to generate a new amino acid.

Many of the transaminases are evolutionarily related. Similarly, the transaminases are often related to enzymes that catalyze different PLP-reactions such as isomerizations and decarboxylations. The evidence indicates that a primitive PLP-enzyme gave rise to a number of different enzymes that make use of the basic mechanism shown below. The enzymes differ in a few amino acids that bind the substrates.

The Evolution Poll of Sandwalk Readers

 
The poles are closed and the results are in. Richard Dawkins is the clear winner (boo!).

The good news is that 87% (499/573) Sandwalk readers have legitimate scientific views of evolution (Dawkins + Gould + Futuyma). Only a small number of readers are creationists or proponents of theistic evolution.

The bad news is that most readers are split between three different views of evolution. Some people have asked me to explain these three views so here's a brief summary of how I distinguish between Dawkins, Gould, and Futuyma.

Richard Dawkins holds the Charles Simonyi Chair for the Public Understanding of Science at Oxford University (UK). In his first book, The Selfish Gene (1976), he promoted the idea that evolution can be viewed as a competition between genes. This concept was amplified in The Extended Phenotype (1982) where he also answered the main criticism of the selfish gene concept. Dawkins' most popular book was The Blind Watchmaker, first published in 1986. In that book he made the case for design by natural selection and attempted to dismiss, or minimize, all other mechanisms of evolution. The emphasis on the power of natural selection was expanded in Climbing Mt. Improbable (1996).

Dawkins is the leading exponent of adaptationism—or Ultra-Darwinism—the idea that everything interesting in evolution can be explained by adaptation. This is especially true of traits that give rise to visible phenotypes. Dawkins is not very interested in macroevolution and he dismisses punctuated equilibria and species sorting. He believes, along with most adaptationists, that macroevolution is just an extension of natural selection acting on populations. (See RichardDawkins,net for a complete list of books and articles.)

Stephen Jay Gould was Alexander Agassiz Professor of Zoology at Harvard University from 1967 until his death in 2002.

He published Ontogeny and Phylogeny in 1977 where he made the case for a relationship between development and evolution. In The Mismeasure of Man (1981) he criticized biological determinism. Wonderful Life (1989) described the Burgess Shale fossils and explained Gould's ideas about the role of chance and contingency in evolution. In 2002, Gould published The Structure of Evolutionary Theory where he attempts to explain macroevolution, punctuated equilibria, and species sorting. These are part of Gould's hierarchical approach to evolutionary theory. Gould identifies himself as a pluralist—one who recognizes many different mechanisms of evolution that can give rise to important and interesting features. He tends to place much more emphasis on chance and accident in evolution than Dawkins.

Gould, along with Niles Eldredge, is famous for the concept of punctuated equilibrium. This is the idea that much of the change in the characteristics of species is concentrated in brief speciation (by cladogenesis) events.

Gould wrote a regular column for Natural History magazine and many of his articles have been collected in a series of anthologies: Ever Since Darwin, The Panda's Thumb, Hen's Teeth and Horse's Toes, The Flamingo's Smile, Bully for Brontosaurus, Eight Little Piggies, Dinosaur in a Haystack, Leonardo's Mountain of Clams and the Diet of Worms, The Lying Stones of Marrakech, and I Have Landed. Some of his essays and some of his scientific articles are widely cited. (For a complete list see SJG Archive.)


Douglas J. Futuyma is a Professor of Ecology & Evolution at the State University of New York at Stoney Brook. He is best known for his textbooks on evolution; Evolutionary Biology (1998) and Evolution (2005). His major research interests are evolutionary theory [see Hypotheses, Facts, and the Nature of Science] and the interactions of plants and insects [see Insect Pests: Resistance and Management].

Futuyma's view of evolution is different from that of Richard Dawkins because Futuyma is interested in random genetic drift and speciation. Futyuma is much more aware of population genetics than Dawkins or Gould and he (Futuyma) frequently refers to it in his books and papers. Unlike Gould, Futuyma is skeptical of punctuated equilibria and particularly species selection/sorting, although, ironically, he is credited with proposing the best explanation of the connection between cladogenesis and evolution.

You can check out some of Futuyma's ideas in this interview. In response to the question, "Is natural selection the only mechanism of evolution?", Futuyma replies,

No, certainly not. There cannot be evolution without genetic variation in the first place. So there must be mutation and often recombination to generate the different genotypes or the different versions of the genes, known as alleles, which then may or may not make a difference in the ability of an organism to survive and reproduce. You can’t have any evolutionary change whatever without mutation, and perhaps recombination, giving rise to genetic variation. But once you have genetic variation, there are basically two major possibilities:

First, there is simply no difference between the different genotypes or different genes in their impact on survival or reproduction, and in that case, you can have random changes of one versus the other type in a population or a species until eventually one replaces the other. That is an evolutionary change. It happens entirely by chance, by random fluctuations. That is what we call the process of genetic drift.

Genetic drift is very different from possibility number two, natural selection, which is a much more consistent, predictable, dependable change in the proportion of one gene vs. another, one genotype vs. another. Why? Simply because there is some consistent superiority, shall we way, of one genotype vs. another in some feature that affects its survival or some feature affecting its reproductive capabilities.

Neither Gould or Dawkins would respond in this way. Dawkins would admit to random genetic drift but downplay its importance. Gould would focus on higher mechanisms of evolution like species sorting.

Futuyma also thinks about the role of mutation in a different way than either Dawkins or Gould, especially Dawkins. While Dawkins is very much opposed to crediting mutations per se with any substantial influence on evolution, Futuyma is more sympathetic to a limited mutationism point of view. For example, when asked what would happen if the tape of life were re-played he says.

Of course, it wouldn’t be the same, because first of all, random processes are involved in the evolutionary process. For example, the origin of new mutations: a lot of evolution is dependent on particular mutational changes in genes that were very, very rare or unlikely, but that just happened at the right time, in the right species, in the right environment, but it need not happen that way. So, there’s this unpredictability.

This is very unlike Dawkins who is more inclined to think of evolution as design and strongly resists any attempt to sneak randomness into the equation. For the most part, Dawkins believes that all possible mutations will be available for selection so mutations can never determine the direction of evolution. Gould prefers to focus on developmental constraints as possible limits to the effectiveness of natural selection.

Monday's Molecule #41

 
Today's molecule is actually three related molecules. You have to name all three by giving the common names and the complete IUPAC names. There's a direct connection between these molecules and Wednesday's Nobel Laureate(s). (Hint: The Nobel Prize winner was not allowed to receive the prize.)

The reward goes to the person who correctly identifies the molecules and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this Wednesday's reward. Both of them are waiting to collect their prize this week or next week. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecules and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The three molecules are:

1. pyridoxine: 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine


2. pyridoxal: 3-hydroxy-5-(hydroxymethyl)-2-methyl-pyridine-4-carbaldehyde


3. pyridoxamine:
   4-(aminomethyl)-5-(hydroxymethyl)-2-methyl-pyridin-3-ol

Nomenclature for Vitamins B-6 and Related Compounds

Modern women are excellent gatherers

 
Here's an article form this week's New Scientist [Modern women are excellent gatherers]. I'd be curious to know what our adaptationist friends think about it. Is this a good example of how to do research?

Men hunted, women gathered. That is how the division of labour between the sexes is supposed to have been in the distant past. According to a new study, an echo of these abilities can still be found today.

Max Krasnow and colleagues at the University of California, Santa Barbara, have discovered that modern women are better than men at remembering the location of food such as fruit and veg in a market.

The researchers led 86 adults to certain stalls in Santa Barbara's large Saturday farmer's market, then back to a location in the centre of the market from where the stalls could not be seen. They were then asked to point to each stall's location. This requires dead reckoning - a skill that men may once have used to return from hunting, and one that men today still usually perform better than women in experiments. Despite this, the ...

The news report refers to a paper that will soon be published in Proc. Roy. Soc. B [New et al. 2007]. Here's the abstract.

We present evidence for an evolved sexually dimorphic adaptation that activates spatial memory and navigation skills in response to fruits, vegetables and other traditionally gatherable sessile food resources. In spite of extensive evidence for a male advantage on a wide variety of navigational tasks, we demonstrate that a simple but ecologically important shift in content can reverse this sex difference. This effect is predicted by and consistent with the theory that a sexual division in ancestral foraging labour selected for gathering-specific spatial mechanisms, some of which are sexually differentiated. The hypothesis that gathering-specific spatial adaptations exist in the human mind is further supported by our finding that spatial memory is preferentially engaged for resources with higher nutritional quality (e.g. caloric density). This result strongly suggests that the underlying mechanisms evolved in part as adaptations for efficient foraging. Together, these results demonstrate that human spatial cognition is content sensitive, domain specific and designed by natural selection to mesh with important regularities of the ancestral world.

As indicated in the news report, 86 adults (41 women and 45 men) were tested for their ability to remember the location of food stalls in a farmers market. The women were 9% better at this than the men.

The result confirms the authors' hypothesis that women are genetically superior at this task because of adaptation during our hunter-gatherer past.

Silverman & Eals (1992) argue that the female advantage on pencil-and-paper and desktop measures of object location memory reflects a selective pressure on ancestral women for plant-foraging efficiency. But their measures did not involve foods, tested spatial memory on a very small scale, and included no measure of vectoring; as a result, a female advantage on their measures is open to many alternative interpretations. For this reason, we deemed it important to examine whether a female advantage could be demonstrated on a task that closely resembles foraging for plant foods. From this theory, we predicted that women should remember the locations where they have previously encountered immobile resources (e.g. plants, honey) more accurately than do men.

The authors don't explain exactly how this adaptation might have happened. Presumably it went something like this ...

At some time in the ancient past all humans had a single allele for the (unknown) gathering gene. A mutation in this gene arose producing an allele where the ability to gather food was improved. Since women were the principle food gatherers, this mutant allele conferred a selective advantage on women who carried it: presumably because they didn't share their food with their friends who carried the old allele. Over time, the new allele became fixed (or very frequent) in women but men did not benefit.

The first three authors are in Departments of Psychology and the senior author is in a Department of Anthropology.

---

New, J., Krasnow, M.M, Truxaw, D. and Gaulin, S.J.C. (2007) Spatial adaptations for plant foraging: women excel and calories count. Proc. Roy. Soc. B. DOI 10.1098/rspb.2007.0826.

[Photo Credit: The drawing is "An artist’s impression of early Hunter-Gatherers" from Manx National Heritage]

Adaptationomics

 
Jonathan A. Eisen is an evolutionary biologist with a blog called The Tree of Life. He's also one of the authors of a new textbook on evolution published by Cold Spring Harbor Laboratories [A New Textbook on Evolution]. I'm about to order a copy.

I mention this because Eisen is a pluralist. He's as annoyed by adaptationist just-so so stories as I am. Over on the Dennett on Adaptationism thread I'm encountering commenters who question whether there really are modern scientists who believe in the adaptationist program. I can assure you there are. Eisen has discovered some of them in the field of genomics—he didn't have to look very hard—and he decided to label their approach adaptationomics [Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes]. This is tongue-in-cheek so don't all you adaptationists get your knickers in a knot.

Here's how Jonathan sets up the issue.

For years I have been fighting against the tide on the tendency for people doing genomics work to resort to silly adaptationist arguments for observations. The argument goes something like this. We sequenced a genome (or did some type of genomics). We made an observation of something weird being present (take your pick - it could be a gene order or a gene expression pattern or whatever). We conclude that this observation MUST have an adaptive explanation. We have come up one such adaptive explanation. Therefore this explanation must be correct.

Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.

And this is so common in genomics I have decided to invent a new word - Adaptationomics. And I am giving out my first award in this to Jack Warren and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).

Does this sound familiar?

What did the authors say that makes them adaptationists? In order to understand their statement you have to be familiar with their findings. They discovered that the genome of a parasite (Wolbachia) has been integrated into the geonome of their insect host. There are several reasons why this might have happened. It could just be an accident, since these kind of recombinant events occur frequently and most insects don't carry a full complement of their parasite's genome. In other words, it could be junk.

On the other hand, the parasite genome could possibly confer some (unknown) selective advantage on the host. But here's the rub. When the author of the article, Julie Dunning Hotopp, was interviewed for the the Nature News article here's what she said.

You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."

That's a classic adaptationist statement. The result "must be" explained by natural selection. There are no other options. I agree with Jonathan Eisen, this is a fitting recipient of his new Adaptationomics Award.

Congratulations to Julie Dunning Hotopp.

Theories of Speciation

 
In order to understand real evolution you have to understand speciation. This fact usually comes as a great surprise to adaptationists who tend not to think of such things. (Or, if they do, they adopt a grossly simplified version of speciation based on adaptation.)

John Wilkins tries to explain theories of speciation in his latest posting on Evolving Thoughts [Theories of Speciation]. John is a philosopher but don't let that fool you. He's an expert of speciation. The problem is, he explains it like a philosopher. :-)

Here's a nifty chart that I stole from John's article (he published it in his latest paper). If, after looking at the chart, it all becomes crystal clear to you then you have my sympathy. This is a very difficult problem but it can't be swept under the rug if you want to debate hierarchical theory and punctuated equilibria.

A genetic trigger for the Cambrian explosion unraveled?

 
Here's an interesting press release [A genetic trigger for the Cambrian explosion unraveled?]. This is the abstract, there's much more but I can't make sense of any of it.

A team of scientists led by young Croatian evolutionary geneticist Tomislav Domazet-Lošo from Ruder Boškovic Institute (RBI) in Zagreb, Croatia, developed a novel methodological approach in evolutionary studies. Using the method they named 'genomic phylostratigraphy', its authors shed new and unexpected light on some of the long standing macroevolutionary issues, which have been puzzling evolutionary biologists since Darwin.

We won't be able to discuss this "revolutionary" paper because it won't be published until November. The journal is Trends in Genetics, which is billed as "the most established monthly journal in Genetics."

RPM at Evolgen didn't seem to be too impressed either [Genomic Phylostratigraphy]. Go there if you want to see a list of the really best journals in genetics.

I wish there were some way of enforcing standards on places that issue scientific press releases. This one from the Ruder Boškovic Institute (RBI) is worse than useless.

Blog Day 2007

 
The rules for today are that we recommend five blogs you may not be reading on a regular basis. Here are my choices. Four Canadians and one honourary Canadian. How's that for chauvinism?

One of these is the most northern blog on my blogroll. Can you guess which one? One of the bloggers is very horny. Which one? One of the bloggers was recently at Montebello protesting George Bush (and what's-his-name, the Canadian Prime Minister). Two of them are Professors. One of them has the longest hair of any blogger I've met.

Mike's Weekly Skeptic Rant

Primodial Blog

Runesmith's Canadian Content

Genomicron

Sex, genes & evolution

Defining Irreducible Complexity

So many IDiots, so little time ....

Granville Sewell has posted a message on Uncommon Descent asking What if we DID find irreducibly complex biological features?. He writes,

In any debate on Intelligent Design, there is a question I have long wished to see posed to ID opponents: “If we DID discover some biological feature that was irreducibly complex, to your satisfication and to the satisfaction of all reasonable observers, would that justify the design inference?” (Of course, I believe we have found thousands of such features, but never mind that.)

If the answer is yes, we just haven’t found any such thing yet, then all the constantly-repeated philosophical arguments that “ID is not science” immediately fall. If the answer is no, then at least the lay observer will be able to understand what is going on here, that Darwinism is not grounded on empirical evidence but a philosophy.

Here's how Michael Behe defines irreducible complexity in Darwin's Black Box (p. 39).

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

There are many irreducibly complex systems in biology. One of my favorites is the citric acid cycle or Krebs cycle. This is a circular pathway of enzymes that oxidize acetate groups to two molecules of CO₂.


If you remove any one of the enzymes then there is no cycle and it will be impossible to oxidize acetyl groups to CO₂ and regenerate oxaloacetate. You cannot evolve a cycle for the complete net oxidation of acetate by starting with a more simple circular pathway then adding additional enzymes to improve the initial function; namely, the cyclic pathway of oxidation. Thus, by Behe's definition this is an irreducibly complex system whose function is to oxidize acetyl groups and regenerate the original precursor.

We have a damn good idea how the citric acid cycle evolved so the answer to Granville Sewell's original question is: no, the discovery of an irreducibly complex system does not justify the design inference. There are many ways of evolving irreducibly complex systems. This is the same answer that we've been giving for over ten years. Please try and keep up.

Now I have a question for the IDiots. If we can prove to your satisfaction that a particular system is irreducibly complex and demonstrate how it could easily have evolved, will you stop claiming that irreducibly complex systems can't evolve?

Dichloroacetate (DCA) Website Shut Down by the FDA

 
Dichloroloacetate (DCA) is a potent inhibitor of pyruvate dehydrogenase kinase [Regulating Pyruvate Dehydrogenase]. There have been suggestions in the scientific literature that the inhibition of this enzyme may lead to the death of cancer cells.

Over the years a minor cottage industry has grown up around the synthesis, sale, and promotion of DCA as a magic bullet for the cure of cancer. The lure of the drug is enhanced by the fact that it is so simple and can't be patented. Thus, according to its proponents, the drug companies don't want you to know about this fabulous cure because they can't make a profit. Abel Pharmboy at Terra Sigillata has written a lot about this drug [Perversion of good science].

THEME:
Pyruvate
Dehydrogenase
The problem is that the clinical trials have not been done and there's some danger of toxic effects when you take too much of the drug. The websites that sell DCA claim that it's only for animals but nobody is fooled by that ruse.

Now, according to New Scientist the FDA has ordered the main DCA website to cease selling DCA ['Cancer drug' site shut down]. When you go to the site at buydca.com you read the following disclaimer, " It is against US government law to sell substances with the suggestion that they are cancer treatments unless they are approved by the FDA."

A Blue Moon Is the Second Full Moon to Occur in a Single Calendar Month

 
Friday's Urban Legend: DEFINITELY FALSE, MAYBE

The term "blue moon" dates back to the middle ages where it meant something quite impossible. Over time the term came to be used in the phrase "once in a blue moon" to mean "it ain't ever going to happen" [Wikipedia: Blue Moon].

Gradually the phrase took on the meaning of something that happens rarely, instead of never. Following World War II there was an attempt to relate the term "blue moon" to a real astronomical event. The most common explanation was that a "blue moon" was the second full moon in the same calender month. The average time between two successive full moons is about 29.5 days. This means that you can have two full moons in any month except February. This will occur, on average, every two-and-a-half years. This year for example, you might have seen a "blue moon" in May, June, or July depending on where you live [The Blue Moon of 2007]. This interpretation of "blue moon" was promoted by Sky & Telespcope in 1946 and it was due to a misinterpretation of the Maine Farmer's Almanac of the preceding decade.

The Sky & Telescope website has a detailed explanation of the error [What 's a Blue Moon?].

So, if you accept the new definition of "blue moon" then the title statement is correct and this is an example of an urban myth that has transformed the meaning of a phrase. However, if you stick to the original meaning of the term then the title statement is false because a "blue moon" is about as likely as one made out of green cheese.

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[Photo Credit: The photograph of the "blue" moon is from miramiramazing]