DNA Is Life T-Shirt

 

Edmund Scientific is selling a T-shirt with a picture of a replicating DNA molecule [DNA is Life T-Shirt].

The caption reads "DNA Is Life. THE REST IS JUST DETAILS." Clever, but sometimes those details are important.

Look closely at the T-shirt. How many of you recognize what's wrong with the molecule on the T-shirt? It may be "just a detail" but I wonder why they couldn't have designed a logo that was scientifically accurate?

How difficult can it be? Would they sell fewer T-shirts if the molecule was accurately depicted?

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[Hat Tip: Hsien-Hsien Lei]

How to Make Cholesterol

 
Monday's Molecule was squalene, a thirty carbon lipid with a characteristic set of double bonds [Monday's Molecule #51]. Most species can synthesize squalene. In some, it serves as the precursor for biosynthesis of cholesterol and other complex steroids.

Cholesterol is an essential component of cell membranes and the initial substrate in pathways leading to hormones such as testosterone and β-estradiol.

A brief outline of the pathway from squalene to cholesterol is shown on the right. The first thing to note is that squalene can fold into a form that already resembles cholesterol. The reactions in the pathway result in closing the rings to make the four ring structure that's characteristic of steroids.

Lanosterol is a key intermediate in this pathway. Note that in addition to the ring closing reactions, an oxygen—in the form of a hydroxyl group—has been added to the ring.

The conversion of lanosterol to cholesterol requires up to 20 enzyme-catalyzed steps. There's more than one way to make cholesterol from lanosterol but in the end all molecules of cholesterol are identical.

Most species, including humans, are capable of synthesizing all the cholesterol they will ever need. In animals, the biosynthesis pathway is regulated by the amount of cholesterol in the blood plasma. If a large amount of cholesterol is derived from food then the biosynthesis pathway is down-regulated to compensate.

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National Center for Science Education

 
The National Center for Science Education (NCSE) has a new log by graphic artist Andrew Conti. Do you know what it depicts? [NCSE Logo Contest Winner].

Check out the NCSE homepage for a ton of useful information about the evolution/creationism debate [NCSE]. You can even sign up for a Grand Canyon River Raft Expedition with NCSE geologist Alan Gishlick to explain the real scientific history and "creationist" Eugenie Scott to explain the other kind of history.

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[Hat Tip: John Pieret]

Monday's Molecule Copycat

 
One of my offspring—who shall remain nameless—has decided to make fun of my Monday's Molecule feature. Go to her blog and tell her to behave herself [The Monday Molecule - Belgium Version].

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Monday's Molecule #51

 
Today's molecule may seem very simple but your task is to give it a complete IUPAC name as well as the common name. You also have to identify the origin of the common name. Pay close attention to the structure before you venture a guess.

There's a direct connection between this molecule and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward. 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 molecule, the origin of the common name, and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: We have a winner! Satoris guessed that the molecule was squalene [2,6,10,15,19,23-Hexamethyl-2,6,10,14,18,22-tetracosahexaene] and the name squalene is derived from squalus meaning "shark." Squalene was first isolated from shark liver. The word squalus comes from the Latin word squalus. It originally meant any marine fish.

Several people got this part right but Sartoris was the only person to guess the correct Nobel Laureate. I was thinking of the person who worked out the detailed pathway for biosynthesis of squalene. You will find out tomorrow.

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Reading Level Comparison

 
BarryA has posted the following comment on Uncommon Descent [Reading Level Comparison].

Thanks to one of our commenters for pointing out this website that calculates the reading level of blogs. Just for fun I inserted UD and it came back “High School,” which means that the general discussion at this blog is at a high school level. I then inserted Pandas Thumb and it came back “Elementary School.”

Make of this what you will.

This seems curious so I tried it myself. Here's the result for "www.uncommondescent.com."

Uncommon Descent

and here's the result for "pandasthumb.org"

The Panda's Thumb

Make of this what you will. For me, it brings to mind the word "IDiot."

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The Salem Conjecture

The Salem Conjecture was proposed by Bruce Salem on the newsgroup talk.origins [The Salem Conjecture]. Here's how he described it on Sept. 5, 1996.

My position is not that most creationists are engineers or even that engineering predisposes one to Creationism. In fact, most engineers are not Creationists and more well-educated people are less predisposed to Creationism, the points the statistics in the study bear out. My position was that of those Creationists who presented themselves with professional credentials, or with training that they wished to represent as giving them competence to be critics of Evolution while offering Creationism as the alternative, a significant number turned out to be engineers.

This should not be confused with the "hard" version of the Salem Conjecture (Hypothesis), which says that engineers are more likely to be creationists. Both versions are described in the Wikipedia entry [Salem Hypothesis].

Joshua Rosenau discusses the possibility that the hard version of the Salem Conjecture might be correct and this explains the soft version [The Salem Hypothesis explained!]. Read the comments.

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[Photo Credit: I pretty sure this is a photograph of Bruce Salem.]

Beyond Belief II: Enlightenment 2.0

 
By all accounts this year's Beyond Belief symposium in San Diego was a lot less exciting than last year's [Beyond Belief II: Enlightenment 2.0]. Perhaps it's because Richard Dawkins wasn't there. On the other hand, PZ Myers was there [Speakers].

There's a short review of the highlights in this week's issue of New Scientist [Does God have a place in a rational world?]. From the sounds of it, the lack of clear-headed atheists led to some very sloppy thinking.

The first firebrand is lobbed into the audience by Edward Slingerland, an expert on ancient Chinese thought and human cognition at the University of British Columbia in Vancouver, Canada. "Religion is not going away," he announced. Even those of us who fancy ourselves rationalists and scientists, he said, rely on moral values - a set of distinctly unscientific beliefs.

Oops. I've got news for you, Prof. Slingerland, you can't count yourself as a rationalist if you think that morality requires religion. And you can't lay claim to being a scientist if you think that moral values are unscientific. That's two strikes.

Where, for instance, does our conviction that human rights are universal come from? "Humans' rights to me are as mysterious as the holy trinity," he told the audience at the Salk Institute for Biological Studies. "You can't do a CT scan to show where humans' rights are, you can't cut someone open and show us their human rights," he pointed out. "It's not an empirical thing, it's just something we strongly believe. It's a purely metaphysical entity."

Strike three. It's a good thing Dawkins wasn't there or this kind of sloppy thinking would have been exposed.

Who said we all have a conviction that human rights are universal? Not me, that's for sure. I can't think of a single "human right" that qualifies. Furthermore, those human rights that we generally agree upon in the 21st century are not mysterious to me. They're mostly common sense designed to maximize our ability to live in groups. It's an empirical thing—and we're still working on the best compromises between absolute rights and qualified ones.

The mood at this follow-up conference was different. Last year's event was something of an "atheist love fest" said some, who urged a more wide-ranging discourse this time round. While all present agreed that rational, evidence-based thinking should always be the basis of how we live our lives, it was also conceded that people are irrational by nature, and that faith, religion, culture and emotion must also be recognised as part of the human condition. Even the title of this year's meeting, "Beyond Belief II: Enlightenment 2.0", suggested the need for revision, reform and a little more tolerance.

Hmmm ... I guess I can go along with that. I've known for some years that people are attracted to irrationality and superstition—we call it religion. We tolerate those who ignore rationality and evidence-based thinking but that doesn't mean we shouldn't criticize those who think that way, right? Tolerance doesn't mean the same as acceptance, does it?

There's one comment in that paragraph that puzzles me. Is it true that people are irrational by nature and it's part of human nature? My observations suggest the opposite. It seems to me that most humans strive to be rational as opposed to irrational. They may get confused from time to time about what is rational and what isn't but over the centuries rationalism tends to win out over superstition. Why do we have to concede that superstition is here to stay because it's pat of the human condition. That doesn't make sense.

Such was the message from evolutionary biologist David Sloan Wilson of Binghamton University, New York. He suggested that humans' religious beliefs may have evolved over time, thanks to the advantages they conferred as a sort of social glue holding together groups that developed them.

Wilson was not saying religion is good or bad, simply that it has evolved to be hard-wired into our brains, and therefore cannot be ignored. "Adaptation is the gold standard against which reality must be judged," he said. "The unpredictability and unknown nature of our environment may mean that factual knowledge isn't as useful as the behaviours we have evolved to deal with this world."

Hmmm ... if irrationality and superstition are hard-wired into our brains then how come it's so easy for many of us to escape from this sort of thinking?

I often wonder whether people like Wilson have thought seriously about what they're saying. Does he imagine a time when primitive humans didn't have religion because it hadn't yet evolved? How did those groups manage to survive? I wonder what went on in their brains when they couldn't think about supernatural explanations?

Or did the religion allele(s) arise before the hominid lineage? Have chimps got religion and that's what what makes them stick together? (Instead of sex.) What about gorillas? Who do they worship? Howler monkeys? Meerkats?

Chemist Peter Atkins of the University of Oxford, one of the more hard-line atheists in the room, did not let this go unchallenged. He chided fellow participants for not being sufficiently proud about what science can accomplish. Given time and persistence, science will conquer all of nature's mysteries, he said.

I'm glad to see there was at least one rationalist present.

So can scientific and religious world views ever be reconciled? Harris, author of The End of Faith, declared that they could not, and provided an uncompromising exposition on the evils of religion.

Away from the meeting, philosopher Daniel Dennett of Tufts University in Medford, Massachusetts, told New Scientist that as irrational as human minds may be, calm, firm introduction of reason into the world's classrooms could over time purge them of religion.

Maybe there were more rationalists present than the author of the piece is willing to admit?

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[PhotoCredits: Beyond Belief II: Enlightenment 2.0, Meerkats]

With Friends Like This ....

 
Greta Christina has a blog called Greta Christina's Blog (naturally). She posts lots of interesting stuff about atheism and other things. Today she strayed into science and posted a video about macroevolution (see below) [Macro-evolution" Vs. "Micro-evolution": More Video Fun]. Greta introduced it with ...

First, just so everyone's clear: "Macro-evolution" and "micro-evolution" are made-up words concocted by creationists to make themselves sound scientific. Biologists don't use them. They're scientifically meaningless. They're just different stages in the evolutionary process; "macro" is just "micro" over a longer period of time.

I posted this comment on her blog.

I'm afraid you have been mislead. Microevolution and macroevolution are perfectly good scientific terms and they are used by evolutionary biologists all the time.

There is legitimate scientific debate about whether macroevolution is more than just lots of microevolution or whether macroevolution encompasses mechanisms not seen in microevolution. It's the sufficiency of microevolution argument.

I happen to be one of those scientists who agree with Stephen Jay Gould that there are many levels of evolution (hierarchical theory). Thus, macroevolution cannot be sufficiently explained by lots of microevolution. There are other things going on at the higher levels [Macroevolution].

The video is very misleading because it assumes a simplistic version of macroevolution. There aren't any evolutionary biologists who believe in that kind of macroevolution. Thus, I have to conclude that the makers of the video are as ignorant of evolution as the creationists they mock.¹

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¹The video was made by cdk007 who claims to have a Masters degree in Biology and a Ph.D. in Molecular Neuroscience.

[The science book covers pictured are:

Macroevolution: Diversity, Disparity, Contingency: Essays in Honor of Stephen Jay Gould

At the Water's Edge: Macroevolution and the Transformation of Life

Genetics, Paleontology, and Macroevolution]

The Photosynthesis Song and a Pet Peeve

Photosynthesis is a process where light energy is captured and converted to chemical energy in the form of ATP. The basic process is similar to that in membrane-associated electron transport. In both cases an energy source (light or reducing equivalents respectively) is used to create a proton gradient across a membrane. The dissipation of this gradient as protons move back into the cell drives the synthesis of ATP.

In addition to ATP, most types of photosynthesis can also be coupled to synthesis of NADPH. The chemical energy molecules derived from photosynthesis (ATP and NADPH) are used in many different biochemical pathways such as DNA synthesis, protein synthesis, fatty acid synthesis and carbohydrate synthesis.

Most photosynthetic organisms can fix carbon dioxide and make carbohydrates using ATP and NADPH [The Calvin Cycle] [Fixing Carbon: the Rubisco Reaction]. Many nonphotosynthetic organisms can do this too. In photosynthetic bacteria and photosynthetic protists this pathway uses only a small part of the chemical energy created by photosynthesis. In large plants the synthesis of carbohydrates can use up a significant portion of the ATP and NADPH generated by photosynthesis.

The fixation of CO₂ and the synthesis of carbohydrates used to be called the "dark reactions" of photosynthesis back in the days when all we knew about were big plants. We didn't know anything about the biochemistry of photosynthetic bacteria or other species. Because our attention was focused on big plants, it was thought that photosynthesis was always coupled to the carbohydrate synthesis pathways. Now we know that this isn't true, so the old-fashioned equation,


is just not a valid representation of photosynthesis. The real products of photosynthesis don't even appear in the equation and, furthermore, those products are used for many different purposes inside the cell (especially in bacteria). Not only that, in some photosynthetic bacteria the electron donor isn't water but some other inorganic molecule like H₂S and S₂ is produced instead of oxygen. The equation is very misleading on many levels and should be abandoned.

Greg Laden has posted the video shown below and commented on the fact that the word "miracle" is used [The Photosynthesis Song ... Bad Word Choice?]. I'm much more worried about the misleading science in the video than I am about one instance of the word "miracle."

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FOX News Anchor Want USA to Support Terrorism

 
This is really quite incredible. Brain Kilmeade is the co-host of of the Fox and Friends morning news program. He thinks the USA should support terrorists inside Iran who will set off car bombs in Tehran. The conservative right really doesn't get it, do they?

The war against Iran is coming soon to a theater near you.

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[Hat Tip: Jim Lippard]

Cafe Inquiry

 

The Centre for Inquiry (Toronto) and the University of Toronto Secular Alliance are pleased to announce the first Cafe Inquiry. These monthly meetings will focus on topics of interested to the secular community.

The first meeting is going to be held in conjunction with a series of lectures sponsored by CFI. The speaker happens to be me, talking about Evolution as a Theory and a Fact. If you haven't had enough of me on this blog, then come out to the Centre for Inquiry on Wednesday November 28 at 7 pm or McMaster University on the evening of November 27th. The McMaster event is sponsored by the McMaster Association of Secular Humanists.

For more information see [Evolution Is a Theory and a Fact with Prof. Laurence Moran].

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Supermouse

 
This CNN report tells us about a supermouse created by Hansen's group at Case Western Reserve University (Hakimi et al. 2007). They inserted an extra copy of the PEPCK gene into the mouse genome and drove expression of that gene in muscle cells. The mice with extra PEPCK in their muscle cells were seven times more active than normal mice. As you can see in the CNN report, they can run on a treadmill for much longer times than mice without the extra PEPCK.



I'm sure most of know about Phosphoenolpyruvate carboxykinase (PEPCK) because it's a really important enzyme. For the very few who don't know their biochemistry pathways, here's a brief lesson.

Here's a simplified overview of the main biosynthesis pathways. The important ones are gluconeogenesis (the biosynthesis of glucose) and the citric acid cycle. Various intermediates in the citric acid cycle are used for synthesis of amino acids. One of them, oxaloacetate, is the substrate for PEPCK in a reaction that converts oxaloacetate to phosphoenolpyruvate.

This is a way to use the carbon atoms of citric acid cycle intermediates in the synthesis of glucose. Under normal circumstances the intermediates in the citric acid cycle don't change very much but their concentration can increase when amino acids are degraded in the reverse of the amino acid synthesis pathways shown here.

The activity of the supermouse is explained by increases in the number of mitochondria in muscle cells and more efficient utilization of oxygen. It is not clear why an increase in PEPCK levels causes such a drastic effect. It could be due to the fact that the mammalian version of PEPCK uses GTP ...


and one of the reactions in the citric acid cycle requires GDP. This could increase flux in the citric acid cycle leading to greater synthesis of ATP in the mitochondrial membranes. (The greater the flux, the more NADH is produced, and every mole of NADH makes 2.5 moles of ATP.)

Alternatively, the increase in stamina could be due to the fact that oxaloacetate is removed from the pool of citric acid cycle intermediates and this results in increased flux since the pools don't become too large when amino acid are broken down to citric acid cycle intermediates.

Finally, increased PEPCK activity could produce more phosphoenolpyruvate which is readily converted to acetyl CoA that can be used in the synthesis of triglycerides (fatty acids) [THEME: Pyruvate Dehydrogenase]. The storage of fatty acids supplies an energy-rich source that can be used up during exercise. In normal mice, the energy is derived from glucose molecules stored as glycogen but fatty acids are better.

All these possibilities are discussed in the paper but no definite conclusions are reached. Richard Hansen has been working on this enzyme for thirty years and it's truly remarkable that we still don't have a good idea about its role in mammalian metabolism. PEPCK is found in all species and it seems clear in most species that it plays a role in the biosynthesis of glucose from fatty acids. In species other than mammals, the citric acid cycle is short-circuited by the glyoxylate pathway which provides a route for acetyl CoA to be converted to glucose. Acetyl CoA is produced when fatty acids are degraded. Mammals don't have the glyoxylate pathway enzymes.

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Hakimi, P., Yang, J., Casadesus, G., Massillon, D., Tolentino-Silva, F., Nye, C.K., Cabrera, M.E., Hagen, D.R., Utter, C.B., Baghdy, Y., Johnson, D.H., Wilson, D.L., Kirwan, J.P., Kalhan, S.C. and Hanson, R.W. (2007) Overexpression of the Cytosolic Form of Phosphoenolpyruvate Carboxykinase (GTP) in Skeletal Muscle Repatterns Energy Metabolism in the Mouse. J Biol Chem. 282:32844-32855. [PubMed]

Curing Leg Cramps with a Bar of Soap

 
Friday's Urban Legend: ALMOST CERTAINLY FALSE

Some people, who shall remain nameless, sleep with a bar of Ivory soap in their beds. Now why in the world would anyone do this? Well, it turns out that the bar of Ivory soap prevents you from having leg cramps at night.

I kid you not. People swear by it.

After a little investigation it turns out that there are just as many people who swear that it has to be Dove soap and not Ivory soap. Then there are those who say it can be any kind of soap as long as it's not Dove. Some people say the soap has to be in its original wrapper and others say it has to be unwrapped.

The snopes.com website hedges their bets on this one since there are so many people who claim that it works [Soap Dope]. On the other hand, they do list it under "Old Wives Tales."

I'm not so hesitant. There's no possible scientific explanation that could explain how a bar of soap would prevent leg cramps. It sounds like a placebo effect, at best, and an overactive imagination, at worst.

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[Photo Credit Wikkepedia]

Best Countires for Academic Research

 
From TheScientist [Best countries for Academic Research].


Judging by the results for the other categories (e.g. Top 40 US Academic Institutions, Top 10 International Academic Institutions) I don't think this is a serious poll. It follows that TheScientist isn't a credible magazine.

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Blog Readability Test

 
I guess spelling doesn't count or I'd be at kindergarten level.

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[Hat Tip: A Blog Around the Clock]

What Is Framing?

Matt Nisbet is still puzzled over opposition to framing. He doesn't understand why some of us don't like the idea very much. Personally, I don't think it's much different than "spin."

Nisbet's latest lament is posted today [UPDATED SECTION: What is framing? [video]].

If the blog debate that ensued after publication of our article at Science showed anything, it was just how widely misunderstood the concept of framing might be. Not surprisingly, many bloggers offer strong opinions about framing and its relationship to science communication but have very little actual knowledge or expertise in the area.

Yes, that must be the answer. We don't understand framing but as soon as we do we'll get right to it. Not.

Matt, you've explained the concept as well as you can—which isn't very well as it turns out. On your website you give us some fine examples of framing [What Is Framing?]. Here they are in case anyone doesn't get it.

Frame devices are used strategically in almost any policy debate. Consider just a few prominent and successful examples of such devices that have been used to alter the focus of policy:

1. Republicans have used the frame device "death tax" to recast estate tax policy in populist terms and to trigger wider public concern.

2. Democrats have used the phrase "gun safety" to shift the traditional debate over "gun control" away from a focus on civil liberties and instead toward an emphasis on public health.

3. Greenpeace has used the term "frankenfood" to redefine food biotechnology in terms of unknown risks and consequences rather than the industry-promoted focus on solving world hunger.

4. Religious conservatives have relabeled the medical procedure know as "dilation and extraction" as "partial birth abortion," pushing decision-making on whether to use the procedure away from doctors and into the hands of Congress and the courts.

5. Anti-smoking advocates have promoted the term "big tobacco," a headline-friendly phrase that immediately emphasizes considerations of corporate accountability and wrongdoing.

6. Anti-evolutionists have coined the slogan "teach the controversy," which instantaneously signals their preferred interpretation that there are holes in the theory of evolution and that teaching rival explanations for life's origins is really a matter of intellectual freedom.

I get it. I don't want any part of that kind of "framing."

Matt says that scientists should engage in framing. I say they shouldn't, and it's not because I don't understand what framing is all about. These are the "successful" examples, in Matt's opinion, and he's supposed to be the expert. Why is he surprised at the opposition to framing? Why should scientists attempt to mimic these examples of misleading and highly deceptive spin?

Is framing just false spin? What may have led to this misperception is that several examples of highly effective messaging have originated from groups or individuals with special interests. While the content of some of these messages such as Greenpeace's "Frankenfood" is debatable, these messages have been more effective in reaching key audiences than many efforts that originated from the scientific community.

In other words; yes, successful framing can be the same as false spin. Thanks for explaining that, Matt.

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Succcinate Dehydrogenase and Evolution by Accident

Succinate dehydrogenase is one of the enyzmyes of the citric acid cycle. It catalyzes the following reaction .....


Students in my biochemistry class will recognize this as a classic oxidation-reduction reaction where succinate is oxidized to fumarate and quinone (Q) is reduced to quinol (QH₂). (The green carbons are the ones originally derived from the acetyl group that starts the cycle.)

The succinate dehydrogenase complex is also complex II in membrane-associated electron transport. This is the electron transport process that's coupled to ATP formation—part of what used to be called oxidative phosphorylation or respiration. The complexes are found in the inner membranes of mitochondria in eukaryotes and the inner plasma membrane in bacteria.


Within the complex, electrons are passed from succinate to FAD and then to three different iron-sulfur ([Fe-S]) clusters and finally to a molecule of quinone (Q) bound to the active site in the membrane (Q and QH₂ are only soluble in the membranes.)

The reverse reaction, where electrons flow from QH₂ to fumarate is common in bacteria. It is usually catalyzed by a separate enzyme called fumarate reductase. The two complexes (succinate dehydrogenase and fumarate reductase) are very similar in structure and the various subunits of the complexes are homologous.

The structure of succinate dehydrogenase from Escherichia coli was solved at good resolution some years ago [PDB 1NEK]. It reveals the presence of a heme b group in the membrane-bound part of the complex. The binding site for QH₂ is located close to the third [Fe-S] cluster near the inner side of the membrane.

The role of this heme is highly controversial. It's not present in fumarate reductase, demonstrating that it plays no role in electron transport for the reverse reaction. It seems as though the heme group might not be involved in the transfer of electrons from succinate to QH₂ either but it has been difficult to rule this out.

Tran et al. (2007) have investigated the role of heme b in a paper that has just appeared in the online version of PNAS. They created mutant enzymes that could not bind the heme b molecule and examined the effect of these mutations. Mutant bacteria grew normally under conditions where the activity of succinate dehydrogenase was essential. The levels of enzyme activity of two different mutant enzymes were only 6% and 30% lower than the levels of the wild-type enzymes.

These results demonstrate that the heme b group is not required for the chemical reaction. This confirms a lot of previous work that pointed to the same conclusion. However, the mutant enzymes are less stable than the wild-type enzyme; they tend to lose activity during purification. This indicates that the heme group helps to stabilize the complex although whether this is significant in vivo remains an open question.

The result is further proof that not every feature has adaptive significance—or, at least not the significance you would normally assign. When the heme b molecule was first detected it was assumed to be involved in the chemical reaction since that's what heme groups do in most other complexes. Now we know it is not required for electron transfer but may play a small role in stabilizing the enzyme. Maybe there used to be a heme in the primitive ancestor of succinate dehydrogenase (SQR) and fumarate reductase (QFR) but it has been lost in QFR and rendered almost obsolete in SQR. Perhaps it used to be an essential component of the reaction in the ancestor enzyme or perhaps a primitive heme b enzyme that bound quinone just happened to evolve a binding site for another enzyme containing [Fe-S] clusters and succinate oxidation properties.

The more we study these molecular machines, the more we are coming to realize that the evolutionary pathway leading to their formation was somewhat haphazard and accidental. These are not cases where the final product is so well designed that a very precise series of improbable events had to happen in order for them to exist at all. Instead, proteins that may have originally served another purpose are co-opted and modified in newly evolving complexes.

Modern enzyme complexes may contain fossil evidence of their evolutionary history (e.g. heme b) that has very little to do with their current function. It's like biochemical junk.

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Tran, Q.M., Rothery, R.A., Maklashina, E., Cecchini, G. and Weiner, J.H. (2007) Escherichia coli succinate dehydrogenase variant lacking the heme b. Proc. Natl. Acad. Sci. (USA) published online November 7, 2007, 10.1073/pnas.0707732104 [PNAS]

Judgment Day Is Coming

 
NOVA has produced a documentary on the Kitzmiller v. Dover Area School District trial that took place two years ago [Judgement Day: Intelligent Design on Trial].

The complete show will be available on the website [Watch Online] after November 14th. In the Toronto area we can watch it on WTVS Detroit (channel 163) on Tuesday Nov. 13th at 8pm or on WCTS Seattle (channel 164) at 11pm our time. Most people probably don't get these channels because they're part of a special timeshifting package. I find that WNED Buffalo, the regular PBS channel in this area, often doesn't show the documentaries I want to watch on PBS. It doesn't broadcast NOVA documentaries, for example. I assume they're too expensive.

Here's the trailer. The show looks really cool even if ultimately the trial will have very little effect on the creationist movement and may even have strengthened it.

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Rachel Marsden Fired by the Toronto Sun

 
Rachel Marsden is officially a Canadian although most Canadians would prefer than this not be widely known. She's currently based in New York city. Here's how she describes her upbringing in Vancouver [About Rachel Marsden].

Born in suburban Vancouver, British Columbia, Rachel grew up listening to Jack Webster, who pioneered combative political talk-radio long before it ever spread to the USA.

Fully bilingual in both French and English, Rachel survived growing up in Canada during the socialist regime of Prime Minister Pierre Trudeau, best known for his close friendship with Fidel Castro, decimation of the Canadian military, a wife who partied at Studio 54 with the Rolling Stones, and doing pirouettes behind the Queen of England's back.

Always a capitalist at heart, Rachel spent her childhood on her parents' farm selling eggs from the family driveway. To ensure the operation looked legit and to score an advantage over the competition (the neighborhood Safeway), she would hold her pet chicken, Brenda (named after her Sunday school teacher), on her lap as proof that the eggs were truly "farm fresh".

Here's a clip of Rachel Marsden on CNN from just last week. She's defending the torture of so-called terrorists¹—one of her favorite topics—while getting skewered by Jack Cafferty. One of her most famous recent quotes comes from this broadcast, "One man's torture is another man's CIA-sponsored swim lesson."

Marsden used to write a weekly column for the Toronto Sun. one of Canada's most idiotic right-wing rags. This relationship is now over according to her website [RachelMarsden.com].

Attention terrorists and Islamofascists: You can now read the Toronto Sun without having your delicate sensibilities offended, as my weekly column is no longer with Sun Media. I am currently exploring US syndication and other venues for the column. In the meantime, you can continue to read it here at RachelMarsden.com, every Monday. And yes (to respond to some of your queries), after more than 2 years of writing weekly for the Sun, I've been under a new Editor-in-Chief, Lou Clancy, since October 5th, who comes from Canada's most liberal newspaper: The Toronto Star. My column about Islam was spiked on his first day at the job. Best of luck to any principled conservatives who remain.

Now, the remarkable thing about this is that even the Toronto Sun has had enough of Rachel Marsden. Who woulda thunk?

I guess she'll just have to sell her brand of "principled conservatism" south of the border from now on. No doubt she'll find plenty of buyers. I understand that the USA is about to appoint an Attorney General who approves of torture.

Here's an excerpt from her last column in the Toronto Sun [Torture? Sounds like a swimmingly good idea].

When asked about it during a recent CNN appearance, I suggested that "one man's torture is another's CIA-sponsored swim lesson." In case anyone thought I was being facetious -- I wasn't.

I suppose that those who object to terror suspects getting water up the nose would say that, as a young competitive swimmer, I was also tortured. It was called "hypoxic training" -- swimming underwater and holding our breath until we passed out. Our coaches didn't call it torture, just an exercise in "mental toughness." So think of it this way -- terror suspects are getting some free mental toughness training courtesy of the U.S. government.

Here's another idea to make the concept more palatable to objectors: Call the place where waterboarding is performed "The CIA Centre For Aquatic Excellence," give all participants an "I survived training camp" T-shirt with the centre's logo on it, and treat them to a couple of carbo-loading pancake breakfasts. It worked for us.

Judge for yourselves.

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1. All of the people who are being tortured are merely "accused" of doing something wrong. Many of them are innocent. Very few of them are real terrorists.

[Hat Tip: Canadian Cynic]

Nobel Laureate: Emil Theodor Kocher

 

The Nobel Prize in Physiology or Medicine 1909.

"for his work on the physiology, pathology and surgery of the thyroid gland"

Emil Theodor Kocher (1841-1917) received the Nobel Prize in Physiology or Medicine for discovering that the thyroid gland was an essential organ. It secreted a component that was required for proper development and daily metabolism. We now know that the secretion consists of two iodine-containing hormones; thyroxine and triiodothyronine [Monday's Molecule #50].

The Presentation Speech was given by Professor the Count K.A.H. Mörner, Rector of the Royal Caroline Institute, on December 10, 1909.

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

The Nobel Medical Prize has been awarded this year to the famous surgeon, Professor Theodor Kocher of Bern, in recognition of his work concerning the physiology, pathology and surgery of the thyroid gland.

The thyroid gland, thyroidea, is one of the structures in the organism whose significance has only been made clear during the last few decades. At the close of the 1870's it was still stated in the physiology text-books that the function of this gland was a complete mystery. It was even questioned that it had an actual physiological significance, for the adult organism at least. On the other hand it was a common experience that it could be the site of pathological changes; in the course of these, considerable trouble could result, as, for example, when the pathologically enlarged gland exerted pressure on neighbouring parts, especially on the trachea.

Yet it was hardly right that this gland should have been undervalued, not to say disdained, for so long. Astley Cooper, who was working about a hundred years ago, had already observed disturbances in animals after removal of the thyroid. These were specified with greater precision by J. M. Schiff in Bern. He found that animals in which the thyroid had been extirpated, often died in circumstances which suggested that this gland might be of great importance to the organism; however, he did not gain any deeper insight into the gland's function. Unfortunately, these observations did not receive the necessary attention and development. It was only after similar results had been obtained with human beings that the question of the thyroid's significance was analysed successfully. Observations made by surgeons were the cause of this.

The disturbances which occur with a pathological enlargement of the thyroid are often so grave that people had already for many years been extirpating the thyroid occasionally to relieve them, despite the difficulty and dangers which the operation then presented. Indeed, in the days before the introduction of antisepsis it often happened that the patients died of the immediate results of the operation. After the introduction of antisepsis a significant improvement took place in this respect. As a result, the number of operations of this kind, in which the whole gland was removed, increased considerably. In the meantime it was gradually noticed that the position was by no means satisfactory, even if the operation itself and the subsequent healing had gone well. Not infrequently, after a period of apparent health, significant disturbances in the general health made their appearance. The conscientious investigation of these cases of illness resulted in the establishment of a new syndrome called «cachexia strumipriva», which was characterized by muscular weakness, swelling of the extremities and of the face, anaemia, decline in intelligence, and finally death from exhaustion. Once attention had been drawn to this condition, enthusiastic and productive research into the significance of the thyroid followed in many different centres. In this, reliance was placed on clinical observations on humans as well as on animal experiments. From this research an understanding of the physiology of the thyroid has evolved which is comprehensive, even if not complete in all respects.

We now know that this gland is a vital organ, whose total removal in experimental animals infallibly causes death within the course of a few days or weeks. The gland is of great importance in the general nutrition of the adult, and especially in individuals still undergoing development. The loss of thyroid function results in serious disturbances in this nutrition. Metabolism is significantly diminished; growth ceases; the skin and the subcutaneous tissues are the site of mucous infiltration; degenerative processes occur in internal organs; serious disturbances make their appearance in the functions of the nervous system and muscles. It became clear that the gland acts by elaborating a secretion, which reaches the various parts of the body. It is, as the expression goes, an internal «secretion». Later it became evident that such processes of internal secretion are of exceptionally great importance. Not only the thyroid, but also various other glands such as the adrenals and the pancreas play a characteristic part in the processes within the organism by elaborating a secretion peculiar to each gland, which is not excreted, but is diffused throughout the organism and is of the greatest importance to it.

The knowledge of the physiology of the thyroid has brought a valuable increase in our understanding within the field of pathology. Through it new light has been thrown on hitherto mysterious morbid conditions. Pathological changes in the gland can lead to suppression or decrease of its function. Various morbid conditions are explained by this, among which are cretinism and myxoedema. On the other hand one looks for the explanation of various other disturbances such as those in morbus Basedowi in abnormally increased or possibly qualitatively abnormal activity of this gland.

This briefly outlined important and momentous development, which has benefited medicine during the past 25 years, was brought into being, as I mentioned before, as a result of observations which have been made by surgeons. In this respect, the first public utterance was made in September, 1882, by Professor J. L. Reverdin in Geneva. At this time his colleague in Bern, Professor Kocher, had also turned his attention to the same subject, and in April, 1883, the latter gave a comprehensive exposition, which has been of fundamental importance to the later development of thyroid surgery as well as to other important areas of our knowledge of this gland. Through Kocher's exposition it became quite clear that complete extirpation of the thyroid is reprehensible. A portion of the gland which is capable of functioning, must be left behind at operation. This very important principle of surgical intervention has always been observed from that time onwards. With regard to the surgery of the thyroid, Kocher has subsequently continued to occupy a leading position. It should be possible to omit on this occasion a report concerning the development of the methods of operation and the suitability of the various types of intervention in different cases. It should suffice to recall that there are now several thousand people who owe their regained, lasting health directly to him after a goitre operation which he has successfully performed. A far greater number, which cannot be estimated, owes him a debt of gratitude indirectly for similar results. Fatal cases or secondary illnesses have become more and more of a rarity in goitre operations.

However, it is not only the treatment of the goitre which has been the subject of Kocher's research on the goitre. He has also carried out extensive investigations into the causes of the endemic occurrence of goitre in certain regions and into the cretinism connected with disturbances in thyroid function.

In the thyroid, as already indicated, other diseases can occur in addition to those which arise with the ordinary goitre. To these as well Kocher has devoted successful work, as a result of which it has been possible to define with more and more certainty the method of treatment best suited to each case; in addition, on the basis of Kocher's work a broader, deeper knowledge of the pathology of the thyroid has been achieved.

Through his research, which we have briefly described here, Kocher has carried out pioneering work of an enduring nature which is of the greatest importance to medical science and of the greatest value in the service of suffering humanity. It is this work which the Staff of Professors of the Caroline Institute has wished to honour by awarding him this year the Nobel Prize in Physiology or Medicine.

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[Image Credit: University of Manchester]

Evolution: Education and Outreach

 
A new journal called Evolution: Education and Outreach has just been launched. We've been hearing about this for almost a year and it's good to see the first issue. The publisher is Springer [Evolution: Education and Outreach]. The mandate is ...

The journal will connect teachers with scientists by adapting cutting-edge, peer reviewed articles for classroom use on a variety of instructional levels. Teachers and scientists will collaborate on multi-authored papers and offer tools for teachers such as unit and lesson plans and classroom activities, as well as additional online content such as podcasts and powerpoint presentations.

Dr. Niles Eldredge, Curator Division of Paleontology at the American Museum of Natural History in New York (USA) and Gregory Eldredge, of John F. Kennedy High School in Bronx, New York (USA) are the editors-in-chief.

The editorial board contains a lot of recognizable names so this should be a good journal. I'm looking forward to seeing the first articles.

Editorial Board:

Brian Alters, McGill University
Sarah Brem, Arizona State University
Daniel R. Brooks, University of Toronto
Roy Caldwell, University of California Museum of Paleontology
Joel Cracraft, American Museum of Natural History
Douglas Eernisse, California State at Fullerton and National Evolutionary Synthesis Center
Douglas Eldredge, Lincoln High School
Joseph Fail, Johnson C. Smith University and National Evolutionary Synthesis Center
Linda Froschauer, National Science Teachers Association, President-Elect
Douglas Futuyma, SUNY Stony Brook
Michael Gaspar, JFK High School
Adam Goldstein, Iona College, New Rochelle, NY
Myles Gordon, New York, NY
Joseph L. Graves, Jr., North Carolina A & T State University
T. Ryan Gregory, University of Guelph
Kristin Jenkins, National Evolutionary Synthesis Center
David Kohn, Drew University
Sir Harold Kroto, Nobel Laureate, Florida State University
Bruce S. Lieberman, University of Kansas
Ronald L Numbers, University of Wisconsin, Madison
William Miller III, Humboldt State University
Eugenie Scott, National Center for Science Education, University of California, Berkeley
Ian Tattersall, American Museum of Natural History
Telmo Pievani, University of Milan II
Judy Scotchmoor, University of California Museum of Paleontology
Ilya Temkin, New York University
Anna Thanukos, University of California Museum of Paleontology
John Thompson, University of California, Santa Cruz
Jory P. Weintraub, National Evolutionary Synthesis Center
Matthew Williams, Manhattan Village Academy
David Wilson, SUNY Binghamton

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[Hat Tip: The Panda's Thumb]

Tangled Bank #92

 
The latest version of the Tangled Bank has been posted on _Paddy K_ [Tangled Bank #92].

Welcome welcome one and all, to the eighty-twelfth edition of the ancient and worthy Tangled Bank Blog Carnival. And let the games begin…

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Fixing a Bad Design

 
Mark Hoofnagle on denialism blog has posted an interesting article on how to fix badly designed humans [Ask A Scienceblogger - Which parts of the human body could you design better?]. I agree with most of his suggestions but he left out some.

Childbirth is definitely a serious problem as Mark points out. It's one of the important proofs of evolution 'cause no intelligent designer would ever come up with the mechanism we have now. Another problem is menopause. Very few people who have lived through it (wives and husbands) think it's a good thing. Let's get rid of it entirely. I doubt very much that we would see a massive increase in fifty-year-old mothers.

I'm not a big fan of our immune system. Sure, it has some good points but a real intelligent designer could do a much better job. It looks like it was designed by Rube Goldberg or some drunken sailer. The only thing it's really good at is generating Immunology Departments and thousands of scientific papers.

Let's fix it so that it doesn't get confused by peanut antigens and other ridiculous things that can kill you. We don't want no more asthma and auto-immune diseases. How hard can it be? There's got to be a more simple way of doing the same job.

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[Hat Tip: John Dennehy, who has other suggestions for improvement.]

[Photo Credit: A rough diagram of the Immune system]

A Global Moritorium on the Death Penalty

 
The United Nations Human Rights Commission has voted every year from 1998 to 2005 on a resolution calling for a moratorium on the death penalty. Canada has been a sponsor of this resolution every single time along with countries such as the United Kingdom, France, and Australia and 71 other countries. I'm proud of Canada's leadership on this important issue.

This leadership is about to end according to CTV [Feds won't sponsor UN anti-death-penalty resolution].

OTTAWA -- The Conservative government will not co-sponsor a United Nations resolution calling for a global moratorium on the death penalty, breaking with a nearly decade-old tradition.

An official with the Foreign Affairs Department says Canada will vote in favour of the resolution when it comes to the floor of the UN General Assembly in December, but will not sponsor it.

"There are a sufficient number of co-sponsors already, and we will focus our efforts on co-sponsoring other resolutions within the UN system which are more in need of our support,'' said Catherine Gagnaire.

Yeah, right. This represents a substantial shift in policy for the Canadian government. It's consistent with another change recently announced whereby Canada will no longer oppose the execution of Canadian citizens in foreign countries.

Last week, Public Safety Minister Stockwell Day surprised the House of Commons by announcing that Canada will not oppose the execution of a Canadian citizen on death row in Montana for two murders. Day said the new policy will apply to "murderers'' such as Ronald Allen Smith who have had a fair trial in a democratic country. (Doesn't the idea of Stockwell Day as "Public Safety Minister" just want to make you cry? )

The government has not specified which countries it considers democracies.

One of those countries is surely the United States of America. A country that executes Canadian citizens and has voted against the UN Human Rights resolution every single time.

The UN resolution has never passed thanks to the USA and other nations that still have a death penalty (e.g. Iran, Iraq, Saudi Arabia). Canada abolished the death penalty in 1976 and there haven't been any executions in this country since 1962. Let's hope Stephen Harper doesn't try and bring back the death penalty remove us from the list of enlightened liberal democracies.

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[Photo Credit: see Abolish the Death Penalty for the significance of the photo.]

[Hat Tip: Canadian Cynic, Harper, Porcine Copulater]

The Logic of the IDiots

 
Intelligent Design Creationists are really upset that their views aren't taken seriously by real scientists. They want to claim that Intelligent Design Creationism is science. So far they haven't succeeded but that doesn't stop them from trying again and again.

The latest attempt by DaveScot has just been posted on Uncommon Descent [P. falciparum - No Black Swan Observed]. Let's look at this stunning example of creationist logic.

DaveScot says that scientific statements have to be capable of falsification in order to qualify as science. That's one view of what science is all about (Popperian) but it's not the only one. Nevertheless, let's run with this definition and see where it takes us.

DaveScot gives us an example of a falsifiable statement, "All swans are white." The discovery of a single black swan would falsify that statement. That's correct. Now he goes on to make a statement about intelligent design, "All complex biological systems are generated by intelligent agents."

Hmmm .... that's an interesting statement isn't it? There are no known examples of complex biological systems that have been generated by intelligent agents. From a logical perspective, it's like saying that Pluto is made of green cheese. But, what the heck, let's see where he's going with this.

What we don’t know is whether any non-intelligent means can generate complex biological systems. A single observation of a complex biological system generated by a non-intelligent cause will falsify the biological ID hypothesis.

Now I see the logic. All the evidence for the natural evolution of complex biological systems doesn't count for a damned thing. You have to actually see something like that evolve with your own eyes before you can believe it. If you don't actually witness the thing then it's logical to assume that it doesn't exist. Right?

What's the data? Well, according to DaveScot, scientists have given it their best shot and no complex biological system sprang into being. The experiment was performed with Plasmodium falciparum the protozoan that causes malaria [Plasmodium falciparum Causes Malaria].

P.falciparum replicating billions of trillions of times in the past few decades represents the largest search to date for a “black swan”. This is orders of magnitude more replications than took place in the evolution of reptiles to mammals wherein there are many exceedingly complex biological systems that separate them. If P. falciparum had been seen generating any complex biological systems such as those that distinguish mammals from reptiles then it would have falsified the ID hypothesis. None were observed. This doesn’t prove ID but it certainly lends strong support to it. All perfectly scientific.

Don't you just love creationist logic? Just because we haven't seen any complex biological systems spring naturally into existence in Plasmodium falicparum it follows that it's impossible for such thing to happen. Therefore Intelligent Design Creationism is strongly supported. QED.^1.

WARNING!!!

This experiment could be harmful to your brain. Don't try this at home.
Let's try using this logic ourselves. P. falciparum has replicated trillions of times and not once did we see an Intelligent Designer making anything. This scientific observation lends strong support to the idea that Intelligent Designers don't make complex biological systems, right? It means that evolution is correct.

Furthermore, after hundreds of years of observation involving billions of people, we haven't got a single documented case of anyone actually seing God. This doesn't prove the non-existence of God but it certainly lends strong support to it. All perfectly scientific. At least that's what DaveScot would say, I assume.

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1. The argument would make some sense if evolution predicted that complex biological systems should evolve in protozoa every few hundred years. Since evolution predicts no such thing then nothing has been demonstrated except that Intelligent Design Creationists are IDiots. But we already knew that.

[Photo Credit: photo by Graham Stephinson at canberabirds]

Monday's Molecule #50

 
Today's molecule may seem very simple but be careful. Pay close attention to the structure before you venture a guess. You need to give as complete a name as possible.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). The Nobel Prize winner(s) didn't know about this particular structure but its effects were detected.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward. 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 molecule 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. This one is easy. Get your response in quickly.

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

UPDATE: The molecule is triiodothyronine (2-amino-3- [4- (4-hydroxy-3-iodophenoxy)-3,5-diiodophenyl] propanoic
acid). We have a winner.

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Mendel's Garden: November Edition

 
The 20th version of Mendel's Garden has just been posted on VWXYNOt? [November Kickabout in Mendel's Garden]. CAE started her blog to satisfy her frustrated inner scientist but now that she's back in academia she continues to post good science articles. She lives in Vancouver, British Columbia (Canada) but we try not to hold that against her.

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"Animal Rights" Is a Complicated Issue

 
Ryan Gregory has put up an interesting posting on Genomicron [On speciesism]. He points out that most of the so-called "debate" about animal rights is at the level of 8th graders. Personally, I think he's being generous.

Ryan asks the following questions,

And so I ask, on what basis do you draw the sharp moral line between "humans" and "animals", "human rights" and "animal rights", "us" versus "them"? What rational argument do you bring in defense of speciesism? Perhaps you argue that only humans are capable of suffering, or that our intellectual capabilities are of a different kind from those of other animals. As Dawkins has noted, neither is compatible with what we understand about evolutionary history.

I don't have an answer to these questions even though I've been thinking about them far longer than youngsters like Ryan Gregory.

Swatting mosquitoes does not pose an ethical dilemma for me. Nor does eating beef, chicken, fish and shrimp. On the other hand, I don't fish and I don't hunt. I don't lose sleep over gorillas in a zoo but I do when they are killed in Africa.

There doesn't seem to be an easy answer to why some animals don't matter while others do.

I'd like to go beyond Ryan's question and include plants. What is the justification for caring about some animals and not about the weeds in your garden or the wheat plants that feed you? I don't think there is a rational basis for doing so. This seems to be one of those issues where rationality doesn't work. That makes me very uneasy.

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[Photo Credit: Smithsonian National Zoological Park]

Gene Genie #19

 

The 19th edition of Gene Genie has just been published on ScienceRoll [Gene Genie #19: Geneticalization].

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Goodbye Daylight Saving Time

 
Today we stopped using Daylight Saving Time in Canada.

Last Spring I posted an article about time zones [Happy Daylight Saving Time!]. It included the photograph shown here of a strange thing right outside my building on the University of Toronto campus. If you don't know what it is, follow the link.

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Note to students at the University of Toronto: This could be on the The University Exit Exam].

Are You Liberal or Conservative?

 
Today we start a new poll of Sandwalk readers. See the sidebar on the left of this posting.

Try and answer according to where you see yourself on the political left-right spectrum without paying too much attention to the labels. The "left wing" category isn't meant to imply radical Marxism; it's meant to encompass the views of most socialists in Europe. "Liberal" doesn't mean that you have to be a member of a "Liberal" (upper-case L) party. It just means somewhat left-of-center.

Similarly, "right-wing' doesn't mean you share the point of view some evil dictator. It means you have more in common with very conservative points of view than with more moderate conservatives.

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