Are You as Smart as a Third Year University Student? Q3

Question 1
Question 2PDB's (Protein Data Bank) molecule of the month for September is citrate synthase, one of the enzymes of the citric acid cycle. Read the PDB website to find out more about this interesting enzyme. [Hat Tip: Philip J at Biocurious]

Citrate synthase catalyzes the following reaction,


One of the most interesting things about this reaction is that the standard Gibbs free energy change of the reaction (ΔG^°′) is −31.5 kJ mol^-1. Here's a question that I ask of my second year students.

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Like most reactions in vivo, the actual Gibbs free energy change for this reaction is zero. Normally you might expect that such a large negative standard Gibbs free energy change would indicate that the forward reaction is coupled to the synthesis of ATP. Indeed, the hydrolysis of the similar thioester bond in succinyl CoA (Step 5 of the citric acid cycle) is coupled to the synthesis of GTP (or ATP). However, in the case of the citrate synthase reaction, the available energy is used for a different purpose. What is this purpose?

Are You as Smart as a Third Year University Student? Q2

 
Question 1
I thought it might be fun to post some multiple choice questions from old exams to see if Sandwalk readers are as smart as my old third year molecular biology students. Here's a question from 1998.

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The sequence of the coding region of an E. coli ribosomal protein mRNA consists of 21% G's and 23% C's. What do you predict would be the composition of the part of the gene (double-stranded DNA) from which this mRNA coding region is derived?

            a) 56% T's
            b) 44% T's
            c) 28% T's
            d) 23% T's
            e) impossible to answer correctly

Framing a Press Release

 
There's been an ongoing debate about framing in the blogosphere. You can see the latest manifestation on Pharngula [When did ‘framing’ become a synonym for religiosity?]. The idea behind framing is to present your science in a way that appeals to and engages the public. The opposition to framing comes from those—I am one—who fear that framing is another word for spin and that in attempting to appeal to the public you often distort or misrepresent the science.

Let's look at how press release writers use framing. This press release is from Ohio State Medical Center. It reports on a paper by Calin et al. (2007) that has just been published in Cancer Cell. The paper looks at the expression of RNA's from highly conserved sequences that do not encode proteins. These are similar to the conserved noncoding elements that we discussed before [Adaptive Evolution of Conserved Noncoding Elements in Mammals] except that they are transcribed.

The first two lines of the press release say,

COLUMBUS, Ohio – Research here shows that an obscure form of RNA, part of the protein-making machinery in all cells, might play an important role in human cancer.

These ultraconserved non-coding RNAs (UCRs) have been considered “junk” by some researchers, but a new report in the September issue of the journal Cancer Cell indicates that this may not be the case.

This is quite ridiculous. I don't know of any researcher who would declare that ultraconserved sequences are junk. This just seems like a distortion of the paper in order to frame the work in a way that's more appealing to the public. The idea is to make it look like this paper overturns the current dogma about junk DNA.

But maybe that's unfair. Maybe the authors themselves make such a claim in their paper and the press release isn't engaging in spin.

Here's part of a paragraph from the introduction to the paper.

A large portion of transcription products of the noncoding functional genomic regions have significant RNA secondary structures and are components of clusters containing other sequences with functional noncoding significance (Bejerano et al., 2004a). The UCRs represent a small fraction of the human genome that are likely to be functional but not encoding proteins and have been called the “dark matter” of the human genome (Bejerano et al., 2004a). Because of the high degree of conservation, the UCRs may have fundamental functional importance for the ontogeny and phylogeny of mammals and other vertebrates.

Oops! The authors themselves admit that these sequences are thought to be functional. There's nothing in the paper about junk DNA and there's certainly nothing about researchers who think these sequences might be junk.

The more I see examples of framing the more I dislike it. It's bad enough that the practice exists but the attempts by Mooney and Nisbet [Framing Framing] to justify it are not going to help us clean up science writing. If Mooney and Nisbet would take on the worst abusers of framing then I would have a lot more respect for their position.

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Calin, G.A. et al. (2007) Ultraconserved Regions Encoding ncRNAs Are Altered in Human Leukemias and Carcinomas. Cancer Cell 12:215-229. [Summary][PDF]

Quick, Get the Popcorn

 
Yesterday Jeffrey Shallit dissected the arguments of one, Tom Bethell, who tried to argue that Intelligent Design Creationism and Creationism were different things. It was fun to read even though we've heard the same nonsense from the IDiots several dozen times. (Bethall even used the Colin Patterson quote, for God's sake!)

I thought that would be the end of it but, oh no, the IDiots have come back for more. Michael Egnor has posted a challenge to Jeffrey Shallit on the Discovery Institute blog Evolution News & Views [Jeff Shallit, Blueprints, and the Genetic Code]. After whining about how mean Jeffrey was to poor old Tom, Ednor gets to the heart of the issue. Apparently the IDiots are really taken with the fictional movie Contact. They think that because Jodie Foster can detect intelligent aliens by deciphering a signal from Vega, this means that Intelligent Design Creationism is real science.

Egnor demands that Jeffrey answer the following question ...

If the scientific discovery of a ‘blueprint’ would justify the design inference, then why is it unreasonable to infer that the genetic code was designed?

Pull up your chairs and get out the popcorn. This is going to be fun.

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[Photo Credit: The photograph is from the official website of the movie Contact]

Learning to Love Bacteria

 
We live now in the "Age of Bacteria." Our planet has always been in the "Age of Bacteria," ever since the first fossils—bacteria, of course—were entombed in rocks more than 3 billion years ago.

On any possible, reasonable or fair criterion, bacteria are—and always have been—the dominant forms of life on Earth.
Stephen J. Gould (1996)Bacteria don't get much respect in spite of the fact that many scientists have written about their importance [see Planet of the Bacteria by Stephen Jay Gould (1996)]. Over at Deep Sea News they're trying, once again, to rectify this unfortunate situation. This will be an entire week devoted to microbes [Intro to Microbial Week by Christina Kellogg].

Here are some important facts from the first posting to keep in mind whenever you're inclined to dismiss bacteria.

"The number of prokaryotes [i.e., bacteria + archaea] and the total amount of their cellular carbon on earth are estimated to be 4-6 ×: 10³⁰ cells and 350-550 Pg of C (1 Pg = 10¹⁵ g), respectively. Thus the total amount of prokaryotic carbon is 60-100% of the estimated total carbon in plants, and inclusion of prokaryotic carbon in global models will almost double estimates of the amount of carbon stored in living organisms." (Whitman et al. 1998)

and

Numerically dominant--there are approximately 1 million bacteria and 10 million viruses in a milliliter of seawater. There are approximately 0.00000000000000000002 sperm whales per milliliter of seawater.

The point about learning to love bacteria is that it's crucial to a full understanding of our place in the world of living things. This is going to come up discussions about complexity. We need to understand that our perspective is heavily biased. As Gould (1996) writes,

Our failure to grasp this most evident of biological facts arises in part from the blindness of our arrogance but also, in large measure, as an effect of scale. We are so accustomed to viewing phenomena of our scale—sizes measured in feet and ages in decades—as typical of nature.

Individual bacteria lie beneath our vision and may live no longer than the time I take to eat lunch or my grandfather spent with his evening cigar. But then, who knows? To a bacterium, human bodies might appear as widely dispersed, effectively eternal (or at least geological), massive mountains, fit for all forms of exploitation and fraught with little danger unless a bolus of imported penicillin strikes at some of the nasty brethren.

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[Hat Tip: Christopher Taylor at Catalogue of Organisms]

Gould, S.J. (1996) Planet of the Bacteria. Washington Post Horizon 119:(344). An essay adapted from Full House New York: Harmony Books, 1996, pp. 175-192.

Stupidist Blogging Tory of the week

 
Canadian Cynic has started a new award called the "Blogging Tory inanity of the week" [ Blogging Tory inanity of the week: Sep 2-8, 2007]. Now you may think that this would be a hard choice since there are so many examples to choose from. Not so. There's one hands-down winner this week and it's a Blogging Tory who tells us that "supernatural phenomena are tangible and observable." Normally I would quote the winning post but it's far better to read it on Canadian Cynic.

Mendel's Garden #18

 

The 18th version of Mendel's Garden has just been posted on Balancing Life [Mendel’s Garden at Balancing Life]. Can you guess which one of my recent postings is included?

Monday's Molecule #42

 
Today's molecule is a very big molecule. You have to describe what you are seeing in the photograph and then relate it to this Wednesday's Nobel Laureate(s). Extra points if you can relate it to a recent posting. [Hint: The Nobel Prize is the most innovative, creative, and daring prize that the Nobel Committee has ever awarded.]

There will be no free lunch this week because the contest is too easy. You can win bragging rights by sending your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the photo and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

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

Parole Officer Can't Make You Attend Alcoholics Anonymous (because It's Religious)

 
A few months ago I posted a message about Alcoholics Anonymous. It was news to me that the program was very religious and required belief in God.

Friendly Atheist reports on a recent court decision in the United States [Forced Attendance at Alcoholics Anonymous is Unconstitutional, Says Court]. You should read the entire story as he reports it. A Buddhist was released on parole on condition that he attend a Salvation Army treatment program that included Narcotics Anonymous. The Buddhist went to some meetings but refused to participate and was sent back to jail.

The court ruled that,

… requiring a parolee to attend religion-based treatment programs violates the First Amendment… While we in no way denigrate the fine work of (Alcoholics Anonymous and Narcotics Anonymous), attendance in their programs may not be coerced by the state.

The Centre for Inquiry (Toronto) sponsors the Secular Organizations for Sobriety Group of Toronto (SOSGT), a non-religious organization for alcoholics [SOSGT].

SOSGT credits the individual for achieving and
maintaining his or her own sobriety and is ideal for those
uncomfortable with the spiritual content of 12-step programs.
The group is secular and religiously neutral.

Atheist Win Another One by Huge Majority

 
The results of a new Pew Research Center poll are just out. People were asked if they would be less likely to vote for someone with a variety of characteristics, including not believing in God. FriendlyAtheist has summarized the results as shown in the table on the left [I Would Be Less Likely to Vote for a(n) _____ as President].

Atheists win again! That makes it several hundred years in a row that Americans hate us more than anyone else—although those pesky Muslims are gaining.

You know, this is all because of Dawkins, Hitchens, and Harris. It's all their fault. Nisbet and Mooney warned us this would happen.

Neville Chamberlain Would Love this one!

 
Most of you probably don't realize that Richard Dawkins has a new book called The Fascism Delusion. Those people who criticized his earlier book (The God Delusion) have been quick to jump all over this one. Check out this devastating review at the Valve [More on Dawkins]

[Hat Tip: PZ Myers at Pharyngula (Dawkins demolished]

As It Turns Out, Not all Conservatives Are Smart ....

 
In an earlier posting I commented on how pleased I was that some of John Tory's supporters realized that teaching creationism is wrong [see John Tory Tries to Clarify]. I'm still pleased with the majority of conservative commentators but, naturally, there are some who still don't get it.

One of them is Matthew at ThePolitic.com, a widely read Canadian political blog. Mathew reveals that some Canadians are IDiots [Warren Kinsella’s Documentary Sequel]. Matthew really crams his foot in his mouth all the way up to his kneecap but I won't bore you with all the details. Instead, let me just mention one or two of the most obvious examples of stupidity.

5) Creation science is a real scientific theory — if you want to challenge it, please don’t insult us by just offering a fancy and long-winded “nuh-huh”. I find it funny that Wikipedia attempts this too, but I’ve seen this movie before; it’s called the Consensus on Climate Change (and we all know how that one will end!).

Where do these IDiots come up with stuff like this? Creation science is not a real scientific theory by any stretch of the imagination. If Matthew is talking about Biblical Creationism then that fairytale has been disproved by science. If he's talking about any other version of "Creation science" than it's either; (a) also disproved, or (b) vacuous.

The fact that Matthew is so confused about this means that it's extremely important that we teach evolution in school. It's pretty clear that Matthew skipped all the science classes when he was in school. Probably because they required more than 6th grade mathematics.

6) Someone still has to address for me how teaching an alternative view on the origin of species will forever ruin students’ lives and deny them jobs, houses and weekends up at the cottage. They’re not your kids so what do you care what they learn if it doesn’t affect you?

Look at it this way Matthew. We have basically two choices in the classroom. We can teach children things that are correct or we can teach them lies. Call me old-fashioned, but I think it's better to teach the truth. It makes for better citizens in the long run.

I actually think we should address Creationism in school. Traditionally we use astrology as the example of something that masquerades as science. It's a way of teaching what science really is and it provides a good lesson on how to think. Creationism would be another good example. We should make sure that all children learn why Creationism is not science.

9) Ala the Flintstones comment, blindly believing in evolution is like believing Star Trek is a documentary about the future. Reality is though that we’re not eliminating all wars, humanity isn’t evolving past its character flaws and evil tendencies and no matter how much some in our society might like it, we’re not going to grow beyond religious faith. Even the television series outlived this optimistic faith in the human will by DS9. Evolution might be wonderful science fiction with things spontaneously mutating everywhere, but we shouldn’t be confusing it with a scientific principle. Maybe we should also be keeping it in it’s proper place too — media class!

No comment, other than to point out there's a reason why we call them IDiots.

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[Photo Credit: The photograph shows a typical Boston Red Sox fan celebrating something that got them all excited (Red Sox Connection). (I think their team just lost another game against Toronto.)]

[Hat Tip: Canadian Cynic]

Gene Genie #15

 

The 15th edition of Gene Genie has just been published on Cancer Genetics [Gene Genie #15].

As you might expect, there's a lot of stuff about Craig Venter's genome. You won't read anything about it here so if you're really interested in Craig then your kicks from the carnival postings.

Play Creationist Bingo!

 
The rules are on Skeptico [ID Creationist Bingo].


[Hat Tip: FriendlyAtheist]

Theories Don't Become Laws

 
I'm pleased by the almost universal condemnation of John Tory's remarks about creationism in schools [John Tory Promotes Creationism]. Letters to the newspapers are running overwhelmingly against the leader of the Ontario Progressive Conservatives. However, there's still lots of misunderstanding out there even though their hearts are in the right place.

In today's Toronto Star there's a letter from a reader in Barrie, Ont. The title is Misunderstanding of the word `theory'. I'll quote most of the letter ...

John Tory's statement appearing to equate Darwin's theory of evolution with "other theories that people have out there" comes from a common misunderstanding the general public has about the scientific meaning of the word "theory."

When a scientist has an idea he or she wishes to test through observation or experimentation, this is termed a hypothesis.

Once a body of scientific data has been accumulated in support of the hypothesis, it is elevated to the status of theory.

After a time, certain theories receive considerable support from various scientists and no contradictory evidence turns up. Then, the theory may be elevated to the status of law.

There is now so much evidence from many branches of science supporting Darwin's theory of evolution by natural selection, that it may be time to give it the status of a law.

This is not right. Theories are explanations of natural phenomena and laws are simple descriptions of phenomena. Boyle's Law, for example, simply states that "For a fixed amount of gas kept at a fixed temperature, P and V are inversely proportional." It does not explain why this is so. That's what the theory of the behavior of gases would do.

Evolutionary Theory is a complex subject that attempts to explain how species evolved. It incorporates Darwin's Theory of Natural Selection and other things like random genetic drift and mechanisms of speciation. Evolutionary Theory will never become a law. Theory is as good as it gets in science.