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]

Where Did Sea Anemones Get Human Genes?

 
A recent paper by Putman et al. (2007) discusses the newly completed genome of the starlet sea anemone Nematostella vectensis. Kevin Z, a marine biology researcher, blogged about this paper last month [Cnidarian Double Whammy: Anemone Genome Completed and a Worm Thats a Jelly!].

The IDiots were also interested in the paper because it reveals that humans and sea anemones share some genes. Someone named "dacock" posted a message on Uncommon Descent revealing that Darwinism had been overturned (again) [Where Did Sea Anemones Get Human Genes?].

I was going to blog about the stupidity of the IDiots but I just don't have time. Anyway, Kevin Z beat me to it [Anemone's Raise a Tentacle in Support of Evolution]. I don't agree with everything he says about the sea anemone genome and why the Intelligent Design Creationists get it wrong but it will have to do for now. Kevin's responses to some of the IDiots who posted comments over on Uncommon Descent are well worth the visit to his blog.

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[Photo Credit: The photograph of the starlet sea anemone and its description is from Summary of Professional Exchanges on Coral Genomics]

Putnam, H.M. et al. (2007) Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization. Science 317: 86 - 94.

Tangled Bank #87

 

The latest version of the Tangled Bank has been posted on Balancing Life [Tangled Bank #87].

I really like the article on "Standing on the shoulders of giants." It explains what Newton really meant when he wrote that to Hooke. Look it up.

THEME: Pyruvate Dehydrogenase

Pyruvate dehydrogenase is one of the most important enzymes in the cell. It catalyzes the reaction that converts pyruvate to acetyl-CoA with the release of CO₂.

Acetyl-CoA is the molecule that enters the citric acid cycle (Krebs Cycle) to be broken down to two additional molecules of CO₂.

April 16, 2007
Monday's Molecule #22 (pruvate). The series began with an unknown molecule that turned out to be pyruvate.

April 17, 2007
Pyruvate. A more complete description of the properties of pyruvate.

(April 18, 2007)
Pyruvate Dehydrogenase Reaction. This posting described the reaction catalyzed by pyruvate dehydrogenase.

April 18, 2007
The Structure of the Pyruvate Dehydrogenase Complex was described in some detail, including the techniques used to elucidate it.

April 18, 2007
Nobel Laureate: Aaron Klug. Aaron Klug worked out the technique used to describe the structure of the pyruvate dehydrogenase complex.

April 20, 2007
Some Bacteria Don't Need Pyruvate Dehydrogenase. There are other ways to catalyze the formation of acetyl-CoA.

April 20, 2007
Pyruvate Dehydrogenase Evolution. The evolution of the genes encoding the pyruvate dehydrogenase subunits is explained.

April 20, 2007
Human Genes for the Pyruvate Dehydrogenase Complex. Identifying the genes for the subunits of the complex.


April 23, 2007
Regulating Pyruvate Dehydrogenase. How pyruvate dehydrogenase is regulated, including the effect of the inhibitor dichloroacetate (DCA).

August 31, 2007
Dichloroacetate (DCA) Website Shut Down by the FDA

August 3, 2012
On the Evolution of New Enzymes: Completely Different Enzymes Can Catalyze Similar Reactions

Dennett on Adaptationism

I've been trying to avoid the discussion of Dawkins vs Gould until the results of the poll are in (see left-hand margin). Those of you who voted for Dawkins will need some major reorientation to bring you into the 21st century. My task is enormous. (I know who you are!)

But since I brought up Daniel Dennett in reference to the aquatic ape just-so story [Aquatic Ape Speculation], I couldn't resist quoting him from Darwin's Dangerous Idea. After outlining the main points in favor of the speculation Dennett says,

The details—and there are many, many more—are so ingenious, and the whole aquatic-ape theory is so shockingly antiestablishment, that I for one would love to see it vindicated. That does not make it true, of course.

The fact that its principal exponent these days is not only a woman, Elaine Morgan, but an amateur, a science writer without proper official credentials in spite of her substantial researches, makes the prospect of vindication all the more enticing. The establishment has responded quite ferociously to her challenges, mostly treating them as beneath notice, but occasionally subjecting them to withering rebuttal. ... I have often asked them just to tell me, please, exactly why Elaine Morgan must be wrong about the aquatic-ape theory. I haven't yet had a reply worth mentioning, aside from those who admit, with a twinkle in their eyes, that they have often wondered the same thing.

We all love an underdog but this is going too far. The fact that Dennett can't see what's wrong with the aquatic ape speculation suggests that his understanding of evolution and how it works is vastly overrated. He then goes on to prove it.

My point in bringing up the aquatic-ape theory is not to defend it against the establishment view, but to use it as an illustration of a deeper worry. Many biologists would like to say, "A pox on both your houses!" Morgan deftly exposes the hand-waving and wishful thinking that have gone into the establishment tale about how—and why—Homeo sapiens developed bipedalism, sweating, and hairlessness on the savanna, not the seashore. Their stories may not be literally as fishy as hers, but some of them are every bit as speculative, and (I venture to say) no better confirmed. What they have going for them, so far as I can see, is that they occupied the high ground in the textbooks before Hardy and Morgan tried to dislodge them. Both sides are indulging in adaptationist Just So Stories and since some story or other must be true, we must not conclude that we have found the story just because we have come up with a story that seems to fit the facts. To the extent that adaptationists have been less than energetic in seeking further confirmation (or the dreaded disconfirmation) of their stories, this is certainly an excess that deserves criticism. [my emphasis in red—LAM]

This is classic adaptationist thinking. It assumes, without evidence, that there must be an adaptationist explanation for every feature. Hairlessness, for example, must be explained by some sort of just-so story involving running on the savanna or wading by the seashore. All the stories seem silly—including the aquatic ape speculation—but since one of the stories must be true we shouldn't reject it just because it makes no sense. There's no room for a non-adaptationist explanation in such a worldview.

Let's see how a pluralist might approach this problem.

For many reasons, ranging from the probable neutrality of much genetic variation to the nonadaptive nature of many evolutionary trends, this strict construction [adaptationism] is breaking down, and themes of unity are receiving renewed attention. ... One old and promising theme emphasizes the correlated effects of changes n the timing of events in embryonic development. A small change in timing, perhaps the result of a minor genetic modification, may have profound effects on a suite of adult characters if the change occurs early in embryology and its effects accumulate thereafter.

The theory of human neoteny, often discussed in my essays (see my disquisition on Mickey Mouse in The Panda's Thumb), is an expression of this theme. It holds that a slowdown in maturation and rates of development has led to the expression in adult humans of many features generally found in embryos or juvenile stages of other primates. Not all these features need be viewed as direct adaptations built by natural selection. Many, like the "embryonic" distribution of body hair on heads, armpits, and pubic regions, or the preservation of an embryonic membrane, the hymen, through puberty, may be nonadaptive consequences of a basic neoteny that is adaptive for other reasons—the value of slow maturation in a learning animal, for example.

                        Stephen Jay Gould in How the Zebra Gets Its Stripes

If you are a Dawkins/Dennett adaptationist then your explanations are confined to the sorts of adaptationist just-so stories promoted by the likes of Elaine Morgan. If you are a pluralist like Gould, you have more choices. Some of the pluralist nonadaptationist explanations might be right. In this case I think Gould is more likely to be right about the evolution of hairlessness. Unfortunately, Dennet and his ilk can't imagine such explanations because it doesn't fit with their idea of how evolution works.

Cleopatra VII (69 BC - 30 BC)

 
According to some sources, Cleopatra committed suicide on this day in 30 BC [On this day: August 30]. Other sources say it was August 12th and still others claim that it was on the last day in August.

The situation was serious. The armies of Mark Antony and Cleopatra has just deserted to Octavian and Antony had committed suicide. Cleopatra was a prisoner in Alexandria. She had no hope of escaping Octavian.

Legend has it that she died after being bitten by an asp but it wasn't the modern asp, Vipera aspis, since that snake is only found in Europe. It's likely that the Romans used the word "asp" to describe all poisonous snakes. If it's true that Cleopatra used a snake to commit suicide then it was most likely the Egyptian cobra Naja haje that did the deed [Cleopatra’s Asp].

Corba venom contains a number of toxins and enzymes. For the biochemist, it's most famous for the presence of phospholipase A₂, an enzyme that cleaves glycerophospholipids, the main components of cell membranes. This leads to disruption and death of cells, especially red blood cells and lymphocytes in the blood stream. A picture of cobra venom phospholipase A₂ bound to a lipid molecule (left) can be found in most biochemistry textbooks.

Hyaluronidase is an enzyme found in many snake venoms. It degrades hyaluronic acid, a complex carbohydrate of the sort found in many glycoproteins. Hyaluronic acid is an important component of cartilage where it forms a central strand for attachment of proteoglycan molecules. The breakdown of cartilage lining the blood vessels leads to massive hemorhaging. The combination of phospholipase A₂ and hyaluronidase could eventually lead to death but it probably wasn't the immediate cause of death for Cleopatra. As it turns out, there are other things in the cobra venom that are even more lethal.

These other components of cobra venom include various cobra venom factors that interfere with the complement pathway leading to an extreme over-stimulation similar to that seen in septic shock. The venom also includes a number of neurotoxins that gain access to the central nervous system when blood vessels break down. The combination of all these proteins can cause death within minutes of receiving a cobra bite. However, many people survive cobra bites suggesting that the Cleopatra story may not be true.

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[The painting is The Death of Cleopatra by Reginald Arthur (d. 1896), 1892 [The Death of Cleopatra.]]

Genetic Discrimination in Denying Health Benefits

 
Hsien-Hsien Lei of Eye on DNA links to an article in the Los Angeles Times [U.S. military practices genetic discrimination in denying benefits].

The issue concerns a Marine who was discharged without medical benefits because he was found to have a genetic disease—in this case it was Von Hippel-Lindau syndrome.

Apparently the US military doesn't take responsibility for soldiers who develop medical problems as a result of a genetic pre-disposition.

The regulation appears to have stemmed from an effort to protect the armed services from becoming a magnet for people who knew they would come down with costly genetic illnesses, according to Dr. Mark Nunes, who headed the Air Force Genetics Center's DNA diagnostic laboratory at Keesler Air Force Base in Mississippi.

As you might expect, the lawyers got involved and some of these men and women have won some compensation from the US government. But some lost their case and they face bankruptcy.

Only in America.

There's a simple solution to all these disputes about health coverage and your genes. It's called universal health care. Try it. You'll like it. (Unless you're a lawyer.)

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[Photo Credit: The photograph shows Dr. Mark Nunes (center) with Jay Platt, a former US Marine Corps drill instructor (left) and Susannah Baruch, senior policy analyst at the Genetics and Public Policy Center (right). The panelists are discussing Genes in Uniform: Don't Test, Don't Tell.]

Ohmygod! These photographs are faked!

Jonathan Wells, the author of one of the stupidest books on Intelligent Design Creationism (Icons of Evolution) has just posted a message on the Discovery Institute website [Exhuming the Peppered Mummy]. Wells says,

The peppered myth died several years ago when scientists discovered that photos of peppered moths on tree trunks - used in most biology textbooks to convince students of Darwinian evolution - had been faked.

In his book he reveals the extraordinary deception that has confused thousands of biology students. The photographs of peppered moths on tree trunks were staged. In some cases dead moths were pinned to the tree trunks and in other cases the moths are alive but they were carefully positioned by scientists.

Can you believe it? Look at the pictures above. I bet you thought that some photographer had set up a camera and waited for years to photograph two moths—one black and one white—to land next to each other in the camera's field. Silly you. You've been fooled. Those moths have been deliberately staged. So much for the Theory of Evolution.

Now, as it turns out there's more to the peppered moth story than this "deception." The real issue is whether the moths spend significant amounts of time on tree trunks. But that's not the point that Wells choose to make in his posting. Instead, he emphasizes the "faked" photographs as though that's the most significant aspect of the peppered moth story. Maybe it is. Maybe Wells and his friends were totally taken in by the photographs in the biology textbooks. I wouldn't be surprised. After all, that's we we call them IDiots.

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[Photo Credit: The photographs are from bill.srnr.arizona. The original source is unknown.]

Aquatic Ape Speculation

 
Read all about the speculation concerning our aquatic ancestry in an impressively researched article by laelaps [Scuttling the Aquatic Ape Hypothesis]. This is a typical adaptationist just-so story. Even people who should know better, like Daniel Dennett, have fallen for it.

Animals and Research

 
There are lots of people who object to the use of animals in medical research. They're usually referring to warm fuzzy animals and not to fruit flies and nematodes, or even fish.

Some of these people write for prominent newspapers like The Guardian in the UK [Ivory tower mentality blamed for 50% rise in animal tests].

Nick Anthis at The Scientific Activist has exposed the myth expressed in the Guardian article [Animal Rights Activists Hijack the Brains of Three Respectable Scientists!]. So has PZ Myers over on Pharyngula [You can't replace animals with petri dishes and computers]. Now Abel Pharmboy at Terra Sigillata has jumped into the fray with a plug for the Foundation for Biomedical Research [Great Animal Research Poster]. I'm copying the poster from their website.

Normally I don't like the kind of rhetoric that's on the poster. I doubt very much that the statement is correct. However, it's an attention grabber and somebody needs to counter the animal activists with a different (gasp!) frame. My life and the lives of everyone in my building are much less comfortable because we have to worry about security on a daily basis. It's not Islamic terrorists that we fear, it's animal rights terrorists. There have been several incidents where property has been destroyed and one bomb has been exploded.