Falling into a pit

 
Falling into a pit may be a much better analogy for evolution than adaptive peaks and climbing Mt. Improbable. To find out why read Chris Nedin's blog Ediacaran [Climbing Pit Improbable].

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Atheist Buses in Genoa

 
"The bad news is that God does not exist. The good news is that you do not need him."

I wonder how long it will take until these signs show up on buses in the major cities of North America? Anyone want to takes bets on when we'll see an atheist bus sign in Vancouver, Toronto, Montreal, or Calgary?

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[Hat Tip: Friendly Atheist]

The taste of MSG

 
Discount Thoughts has posted a wonderful description of how we taste the glutamate in monosodium glutamate [How we taste umami]. The taste is called "umami" and it's distinct from the four standard tastes of sweet, sour, salty, and bitter.

The figure shows a glutamate molecule (yellow) bound to the umami receptor with inosine monophosphate (IMP) (green). You need both glutamate and IMP in order to get the umami taste.

Theme
A Sense of Smell
I know lots of people who can taste MSG but that's not the problem. There appear to be some other effects of this chemical that are much less pleasant.

The umami flavor is common in meats, cheese, seafood, and lots of other foods that are rich in protein. Vegetarians don't know what they're missing!

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Do you know what this is?

 
If you can't identify the organism in the photograph then read The Beautiful Angel of Death on Catalogue of Organisms.

Life is stranger than most of us realize.

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ScieneOnline '09: Things to do in Durham

 
ScienceOnline '09 is being held in the Research Triangle, North Carolina (USA) this weekend. For those of you who aren't familiar with the region, the "triangle" consist of Chapel Hill, Raleigh, and Durham. I've spent a lot of time there over the past 25 years but unfortunately I can't make it this weekend.

Chapel Hill is one of the best places in America for all kinds of reasons. Raleigh is a pretty decent city.

Abel Pharmboy has the unenviable task of promoting Durham. You can read his attempt at: General cool stuff to do in Durham, NC, during ScienceOnline'09.

He did about as good a job as someone from Durham could possibly do.

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2008 Weblog Awards

 
Voting for the best science blog will close tonight. Pharyngula is in the running and so is Bad Astronomy.

The current leader in the voting is a climate change denialist blog called Watt's Up with That?.

Do NOT, repeat DO NOT, rush over and vote for Pharyngula or Bad Astronomy, or any other real science blog. PZ is not asking you to do that. Many science bloggers (including me) want the anti-science blog to win in order to completely discredit the whole notion of online voting for best blog.

It's about time we put an end to this nonsense and letting an anti-science blog win for "Best Science Blog" is an excellent way to send a message.

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Paleobet and Cambrian Fossils

 
PZ has discovered palaeobet¹ so, naturally, I had to post my initials as well.


Some of you may not recognize "laggania." It's Laggania cambria, one of several species related to Anomalocaris. Collectively they are known as Anomalocarids.

Here's a fossil of Laggania cambria from the Burgess Shale (right). It just so happens that I was looking at this very fossil on Saturday during our visit the the Royal Ontario Museum. The Burgess Shale fossils are stuck in a corner of the museum where they can easily be missed by people entering the dinosaur rooms. That's a shame since these are unique fossils and very few museums have such a wonderful collection of Cambrian fossils.

Most of you are probably more familiar with Anomalocaris canadensis, a much more fierce-looking cousin of L. cambria (see below). A comparision of the two species can be found on The Anomalocaris Homepage.

Anomalocaris and Laggania were among the species made famous by Stephen Jay Gould in his excellent book Wonderful Life. Gould pointed out that these species so not fit neatly into any of the existing phyla, although they have some of the characteristics of arthropods and onychophora (velvet worms).

Lumpers will now include them in Arthropoda and splitters assign them to a separate, extinct, phylum called Dinocaridida. What's clear is that there are no modern species that can trace their ancestry directly to the anomalocarids. They represent a body plan that has not survived and this lends support to Gould's idea that there were more fundamentally different kinds of animals in the past that we see today. As he put it on page 208 ...

The Burgess Shale includes a range of disparity in anatomical design never again equaled, and not matched today by all the creatures in the world's oceans. The history of multicellular life has been dominated by decimation of a large initial stock, quickly generated by the Cambrian explosion. The story of the last 500 million years has featured restriction following by proliferation within a few stereotyped designs, not general expansion of range and increase in complexity as our favored iconography, the cone of increasing diversity, implies. Moreover, the new iconography of rapid establishment and later decimation dominates all scales, and seems to have the generality of a fractal pattern.

Scientists have been chipping away at Gould's thesis over the years since the publication of Wonderful Life in 1989. Several problematic species have been reliably assigned to existing phyla and others have been tentatively squeezed into the standard animal phyla. The goal is to discredit the idea that life was more diverse (disparate) during the Cambrian and the conclusion that the evolution of animals is characterized by the extinction of major lines.

I think Gould's main point is still valid and I don't understand why so many people find it troubling. It may have something to do with people's perception of evolution as progress.

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1. Fossil animals for each letter of the alphabet.

[Hat Tip: P (pteraspis) Z (zalambalestis) Myers]

Trouble with Blogger Is Over

 
Blogger has finally fixed the problems with RSS feeds. As I mentioned earlier [Trouble with Blogger] this is a problem that the blogger team seem to have created back on December 19th. It was fixed on January 9th—21 days later.

The most obvious change is in the recent comments in the left sidebar. You can now actually see recent comments instead of comments from June 2007.

I suppose we shouldn't complain, after all Blogger is free and it's pretty good most of the time.

I'm sorry if I missed any of your comments during the outage. I was able to keep up with all comments on recent postings but if you commented on an old posting chances are I missed it.

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Drift vs. Selection

 
Daniel MacArthur of Genetic Future weighs in on the ongoing debate over the important of random genetic drift vs natural selection during human evolution [Genetic differences between human populations: more drift than selection?].

Daniel MacArthur seems to be a smart guy. Here's a teaser ....

I should emphasise that there's little doubt that at least some recent population-specific selection has occurred in humans (the signal around the lactase gene in Europeans is about as unambiguous as it gets) - but perhaps it has not been anywhere near as pervasive as some researchers (e.g. John Hawks) have argued.

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Monday's Molecule #103

 
Name this molecule. We need a biochemically accurate name and the formal IUPAC name. The role of this molecule in biological systems was discovered by one or more Nobel Laureate(s) almost one hundred years ago.

Your task is to correctly identify the molecule and name the Nobel Laureate(s). The first one to do so wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize.

There are three ineligible candidates for this week's reward: Timothy Evans of the University of Pennsylvania, John Bothwell of the Marine Biological Association of the UK in Plymouth, UK and Dima Klenchin of the University of Wisconsin.

John, Dale (twice), and a previous winner (Ms. Sandwalk) have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing so poorly in this contest, I'm going to make a special award this week. In addition to the normal winner, the first undergraduate student who can accept a free lunch will win a second prize. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

Mmmmmm .... poutine. Good luck.

THEME:

Nobel Laureates
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 names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is acetylcholine (2-acetoxy-N,N,N-trimethylethanaminium). The Nobel Laureates are Sir Henry Hallett Dale and Otto Loewi.

The winner is Bill Chaney of the University of Nebraska who was the first one to correctly identify the molecule and the Nobel Laureates. The undergraduate winner is Maria Altshuler of the University of Toronto. She can bring a friend to lunch.

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Postdoc Salaries: Foreigners vs Americans

 
Check out Biocurious for a discussion stimulated by Lou Dobbs on CNN. Watch the YouTube video.

A typical graduate student in our department gets $25,000 per year. A typical post-doc gets $40,000 per year (range 36-45) and a typical Assistant Professor is hired at about $80,000 per year (range 70-100, depending on the university).

What should a post-doc earn? Would salaries be higher if you couldn't hire any foreigners as post-docs?

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Homeschooling and Creationism

 
Not all homeschoolers are Creationists but for strong Biblical literalists homeschooling does offer an easy way of "protecting" children from evil ideas in the real world. Such ideas may cause them to doubt their religion.

If you are a Young Earth Creationist there are some problems associated with the anti-science approach to education. If would be nice to have some helpful advice in case your children ever have to deal with the real world outside the home.

The current issue of Home School Enrichment magazine comes to the rescue. They have an article called Creation and You that's available for free download. (You have to give them an email address.)

The main part of the article extols the virtues of the Answers in Genesis Creation Museum; "600,000 visitors have gone through its doors into an amazing experience demonstrating the power, creativity, and love of the Creator God." I suppose this is a good thing if you're into brainwashing. We just spent yesterday with two young girls in the Royal Ontario Museum in Toronto and there was very little evidence of the "power, creativity, and love of a Creator God." On the other hand, there was quite a bit of good science. Our two friends might have got a bad impression of Biblical literalism. If their parents had been Young Earth Creationists we would have been in big trouble for leading them astray.

Anti-science homeschoolers are right to keep their children away from real museums.

But that's not the only problem they face. What to do if your kids want to have a career in Creation Science? Hmmm ... that's a tough one, isn't it? Here's the answer ....

Preparing for a Career in Creation Science

Answers in Genesis content developers Gary Vaterlaus and Roger Patterson agree that more researchers are needed in Creation Science, but warn that the path may not be easy. Several Christian colleges across the country offer science courses taught from a Young-Earth Creationist perspective, but few research positions are available to those with anything less than a Master’s degree in their field; more likely a Ph.D. And, Roger says, getting those degrees will likely require spending some time in a secular university.

Furthermore, Gary explains that the evolutionary teachings at these secular universities are only part of the problem—there is also a very real prejudice against Creationists who attempt to embark upon a career in any of the relevant branches of science. Aside from the strong possibility of a known-Creationist student receiving failing grades merely for believing God created the universe, Gary cited a case where evolutionists actually petitioned a university to revoke a graduate’s Ph.D. when it was discovered he was a Creationist.

There is a need for young, up-and-coming students to enter the realm of Creation Science, but Gary and Roger emphasize that a student must have an unshakable foundation on the reliability and truthfulness of the Bible, and then be ready, willing, and able to face unbelievably strong opposition while pursuing a degree that will qualify them for the research positions they wish to obtain.

While none of this should dissuade students from choosing such a career, it is important for students and their parents to recognize the potential difficulties and take steps early to ensure a successful and victorious outcome.

For students wishing to be involved in the area of Creation Evangelism, such as speaking at churches or writing about creation related topics, Roger believes a Bachelor’s degree in some branch of science is important for establishing credibility. Several Christian colleges offer science programs, taught from a Young-Earth Creationist perspective, in which students can earn their Bachelor’s degrees. However, many Christian colleges have compromised in the area of origins and evolution, so this is something that should be carefully investigated when researching options for collegebound Creationist students.

Life is tough if you are anti-science but want a career in science. Not only are the secular universities trying to persuade you that truth is important in science but even some of the Christian colleges are "compromised."

But you can succeed if you resist education and maintain "unshakable foundation on the reliability and truthfulness of the Bible." Incredible.

What about average students who venture out into the secular world? What happens if they happen to pick up a book written by a (gasp!) real scientist, or if they mistakenly enter a real museum?

Roger Patterson of Answers in Genesis has some advice.

Homeschool parents often wonder how to protect their children from evolutionary ideas. We brought this up to Roger Patterson, a former biology teacher in a public school who is now one of the main content-developers at Answers in Genesis, and were impressed by his answer:

“As a ministry in general,” Roger explains, “we don’t say, ‘keep your kids isolated from evolutionary ideas.’We think that’s kind of a bad philosophy because when they do go out on their own, they’re going to face those things every day. Case in point: [my wife and I recently] got this space-age ant colony gel material. Flip open the book, and you’re reading through the instructions and all these fun facts about ants, [then] ‘Fossil ants have been found a hundred million years old.’ What we would hope parents can do through homeschooling is teach their kids how to spot those things, and then what the biblical response is for those things. Not to isolate them from those things, but to insulate them to some degree and then help them understand what the problems are there.

“Okay, this is a fun ant gel colony, [but] they didn’t need to throw that little tidbit [about millions of years] in there; it adds nothing to the product or your ability to enjoy and watch the ants. And when you look at it from the perspective that God created these creatures to do what they do, and it’s an amazing thing, it even gives an opportunity to give praise to God when you run across the idea of evolution. [We can say] ‘We know that’s not true. Praise God He did create us, that He is the one who’s sustaining all this.’ Rather than running away and hiding from all those things, let’s face up to it. And then if you’re with your friend, you can tell them about it if they don’t understand those things.

“So my encouragement is not to be afraid of going and getting the dinosaur book from the library, but [be sure to] teach your children as they go through it to understand that some parts [evolutionary statements] are made up, based on the idea of rejecting God in science, and other parts are facts—such as when it tells us what shape the egg was, what size it was, what food they probably ate. Those types of things, we can trust those; those are solid scientific ideas. It’s when we start adding our own assumptions into those things, and telling stories, that we run into trouble.”

Roger explains that there are certain “code words” that parents can teach their children to watch out for. Among these would be “millions or billions of years,” statements about kinds of animals changing into other kinds of animals, and questionable statements of what scientists “know.” Above all, Roger says, it’s important to make sure our children have a solid biblical foundation for
their education, and to help them stand firm on the full authority of scripture.

I can't imagine what it must be like to be constantly on the lookout for sneaky remarks about evolution and other scientific facts that challenge your religion. I can't imagine what it must be like to brainwash your kids into responding with, "We know that’s not true. Praise God He did create us, that He is the one who’s sustaining all this."

I not a huge fan of the idea that teaching your children to be Young Earth Creationists is a form of child abuse but there are times, like today, when Dennet and Dawkins seem to have a strong case.

Home schooling isn't always a good thing for children.

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A Shocking Discovery

 
Almost all proteins in Escherichia coli begin with the amino acid N-formylmethionine (f-met), a modified version of methionine.

N-formylmethionine is inserted at AUG codons at the beginning of the open reading frame in mRNA. The initiation mechanism requires a specific initiator tRNA called f-Met-tRNA (right).

Internal AUG codons are recognized by another tRNA and normal methionine is inserted at these positions. The observation that a single codon (AUG) can serve as the codeword for two different amino acids depending on their position was made over thirty-five years ago and it has been incorporated into the textbooks for decades.

You can imagine how surprised I was to read this in a press release written by Haley Stephenson of ScienceNOW Daily News. You can read it yourself on the Science website: Genetic Code Sees Double.

Call it the genetic version of a double-entendre. Scientific dogma dictates that various three-letter combinations of our genetic sequence each "mean" exactly one thing--each codes for a particular amino acid, the building block of proteins. But a protozoan named Euplotes crassus appears to be more versatile: One of its three-letter combinations has two meanings, coding for two different amino acids. Although the find may seem trivial, it poses a major challenge to more than 4 decades of scientific thinking.

The idea that a protozoan might use UGA to encode both cysteine and a modified form of serine called selenocysteine is quite interesting. It has long been known that UGA is a normal stop codon that is also used to encode selenocysteine. It has also been known for a long time that some organisms can use UGA to encode cysteine.

But the idea that scientific dogma has been overturned by the discovery of a single codon that can encode two different amino acids is just plain silly. It doesn't pose a "major challenge to more than 4 decades of scientific thinking" unless your scientific thinking is flawed to begin with.

This must be an example of hyperbole. Such a claim would never make it into a scientific publication, especially in a prestigious journal like Science. Or so I thought.

Here's the opening sentence in the paper by Turanov et al. (2009).

Although codons can be recoded to specify other amino acids or to have ambiguous meanings (1, 2), and stop codons can be suppressed to insert amino acids (3), insertion of different amino acids into separate positions within nascent polypeptides by the same codeword is believed to be inconsistent with ribosome-based protein synthesis.

It's enough to make me give up writing biochemistry textbooks. Apparently nobody reads them.

We seem to be producing a generation of scientists who don't know about the fundamentals of biochemistry and molecular biology that were elucidated in bacteria and bacteriophage in the mid-20th century. Doesn't anyone teach this stuff any more?

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Turanov, A.A., Lobanov, A.V., Fomenko, D.E., Morrison, H.G., Sogin, M.L., Klobutcher, L.A., Hatfield, D.L., and Gladyshev. V.N. (2009) Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon. Science 323:259-261. [DOI: 10.1126/science.1164748]

John Pieret Issues a Challenge

 
John Pieret took the American Civil Liberties Literacy Quiz.

In his posting, Flunking At Being American, he reports that he scored 32/33 or 96.97%. Impressive.

He then asks, "I would be interested to know how non-US citizens score on the test."

Ask, and you shall receive. Here's my result.

You answered 30 out of 33 correctly — 90.91 %

Average score for this quiz during January: 74.2%
Average score: 74.2%

You can take the quiz as often as you like, however, your score will only count once toward the monthly average.

I didn't know which amendment was which, and what the Bill of Rights specifically prohibited. I'm too embarrassed to reveal the third question I got wrong.

Here's one I got right.

27) Free markets typically secure more economic prosperity than government’s centralized planning because:

A. the price system utilizes more local knowledge of means and ends
B. markets rely upon coercion, whereas government relies upon voluntary compliance with the law
C. more tax revenue can be generated from free enterprise
D. property rights and contracts are best enforced by the market system
E. government planners are too cautious in spending taxpayers’ money

I got it right by thinking like an American! (Ouch!)     ;-)

It's a very strange "civil liberties literacy" question. Is it un-American to advocate socialist policies?

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What Could Be More Scary than the Flying Spaghetti Monster?

 
From the BBC News: Church removes 'scary crucifix'.

A large sculpture of Christ on the cross has been removed from outside a church in West Sussex after its vicar said it was "scaring young children".

The Reverend Ewen Souter said the 10ft crucifix was "a horrifying depiction of pain and suffering" which was also "putting people off".

The sculpture, located at the side of St John's Church in Broadbridge Heath, has now been given to Horsham Museum.

It will be replaced with a new stainless steel cross.

Stainless steel crosses are also pretty scary.

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[Hat Tip: RichardDawkins.net]