Two Examples of "Alternative Splicing"

THEME:
Transcription
Last week I bumped into a colleague who teaches in our third year molecular biology course. I was lamenting about the sad state of science these days and we got to talking about alternative splicing. I repeated my complaint that much of the predicted alternative splice variants are artifacts. It makes no sense that conserved genes would be producing alternative protein variants that are species specific. I am convinced that the EST databases are full of artifacts and that most predicted splice variants do not exist.

My colleague was shocked. He is firmly convinced that most human genes express a number of different protein products that are produced as the result of alternatively spliced mRNA precursors. I asked him if he had ever looked at his favorite genes to see if the predicted variants make any sense. The ones that I've looked at certainly don't. (Join in the fun: see the challenge below.)

My colleague is very knowledgeable about the genes for the major subunits of eukaryotic RNA polymerase since it was his lab that cloned the first one. I suggested that he look at the predicted alternative splice variants of the two human genes and let me know if he is still convinced that these variants make biological sense. I'm not sure he will do it so let's take a look ourselves.

Eukaryotic RNA polymerase is a complex protein machine consisting of ten different subunits. Two of the subunits, Rpb1 and Rbp2, are more commonly known as A and B. In the human genome they are encoded by the genes POLR2A and POLR2B respectively [RNA Polymerase Genes in the Human Genome].

If you click on the Entrez Gene URLs you will end up at a page that summarizes what is known about the gene. Down the right-hand side of the page there are links to several other webpages, including a link to AceView, a database of alternative splice variants. Before following this link to the POLR1A variants, let's note that on the annotated Entrez Gene website there are no alternative splice variants listed. Apparently someone has decided that the predicted variants are probably artifacts.

Go to the AceView page for AceView POLR2A. The first thing you see is a short explanation.

RefSeq annotates one representative transcript (NM included in AceView variant.a), but Homo sapiens cDNA sequences in GenBank, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 11 spliced variants.

AceView summary
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at very high level, 4.8 times the average gene in this release. The sequence of this gene is defined by 537 GenBank accessions from 518 cDNA clones, some from breast (seen 40 times), marrow (29), head neck (19), brain (18), eye (18), leukopheresis (18), lung tumor (18) and 132 other tissues. We annotate structural defects or features in 13 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 29 different introns (28 gt-ag, 1 gc-ag). Transcription produces 13 different mRNAs, 11 alternatively spliced variants and 2 unspliced forms. There are 7 probable alternative promotors and 5 non overlapping alternative last exons (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, alternative splicing or retention of 4 introns. 337 bp of this gene are antisense to spliced gene pluvu, raising the possibility of regulated alternate expression.
Protein coding potential: 10 spliced and the unspliced mRNAs putatively encode good proteins, altogether 11 different isoforms (3 complete, 4 COOH complete, 4 partial), some containing domains RNA polymerase Rpb1, domain 1, RNA polymerase, alpha subunit, RNA polymerase Rpb1, domain 3, RNA polymerase Rpb1, domain 4, RNA polymerase Rpb1, domain 5, RNA polymerase Rpb1, domain 6, RNA polymerase Rpb1, domain 7, Eukaryotic RNA polymerase II heptapeptide repeat [Pfam]. The remaining 2 mRNA variants (1 spliced, 1 unspliced) appear not to encode good proteins.

Here's the figure showing the various predicted alternatively spliced transcripts and the various different proteins.


It's really difficult to imagine that any of these are biologically relevant. How could a small bit of the large RNA polymerase subunit ever be part of the RNA polymerase protein complex? It's not a surprise that the Entrez Gene annotators have ignored these predictions.

If, as I believe, most of the small ESTs on which these predictions are based are artifacts, then the overall pattern makes sense. What you see are examples of splicing errors where an intron has not been correctly removed. These extremely rare splicing errors are copied into cDNA during construction of EST libraries and specifically selected by screening out all the correctly spliced mRNAs. (That's how you make most EST libraries.)

Here's what AceView says about the gene for the other large subbunit [AceView: POLR2B].

RefSeq annotates one representative transcript (NM included in AceView variant.a), but Homo sapiens cDNA sequences in GenBank, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 9 spliced variants.

One again, AceView notes that the annotated human genome has ignored the predicted alternative plice variants but maintains that there are at least nine of them.

Here's the figure, decide for yourself whether this is credible.


There are several well-known examples of human genes producing different protein variants due to alternative splicing. The ones I can think of off the top of my head are the genes for class I antigens, α-tropomyosin, and calcitonin. I'm sure there are half a dozen others.

Here's the challenge. See if you can find a human gene for a well-studied protein where the structure of the protein is known and there are multiple protein variants derived by alternative splicing. I bet that readers of Sandwalk can't find very many where the predicted variants many any sense and are likely to be biologically significant.

What does this mean? Whenever you look at your favorite well-studied gene you see that the predictions of alternative splicing are silly. So why should we believe the genome wide analyses? Is it just a coincidence that the more we learn about a given gene the most we become willing to reject the ESTs as artifacts? Or is it possible that alternative splicing is mostly confined to those genes that have not been well studied?

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Genes and Straw Men

Just in case there's someone who doesn't understand the concept of "straw man," here's a good description from Wikipedia: Straw Man.

A straw man argument is an informal fallacy based on misrepresentation of an opponent's position.[1] To "set up a straw man," one describes a position that superficially resembles an opponent's actual view, yet is easier to refute. Then, one attributes that position to the opponent. For example, someone might deliberately overstate the opponent's position.[1] While a straw man argument may work as a rhetorical technique—and succeed in persuading people—it carries little or no real evidential weight, since the opponent's actual argument has not been refuted.[2]

The term is derived from the practice in ages past of using human-shaped straw dummies in combat training. In such training, a scarecrow is made in the image of the enemy, sometimes dressed in an enemy uniform or decorated in some way to vaguely resemble them. A trainee then attacks the dummy with a weapon such as a sword, club, bow or musket. Such a target is, naturally, immobile and does not fight back, and is therefore not a realistic test of skill compared to a live and armed opponent. It is occasionally called a straw dog fallacy, scarecrow argument, or wooden dummy argument.[citation needed] In the UK, it is sometimes called Aunt Sally, with reference to a traditional fairground game.

You'd be surprised how often this fallacy comes up—and it's not just IDiots who use it.

The other day I attended a seminar by Jacek Majewski of McGill University (Montreal, Quebec, Canada). The subject was alternative splicing.

As most of you already know, this is a controversial field. Many people believe that alternative splicing is very common and that 50-70% of all human genes produce multiple versions of proteins due to alternative splicing. Majewski is one of those people.

Others, I am one, believe that much of the data is based on artifacts—especially expressed sequence tag (EST) artifacts. We believe that there are some very well established, and well-studied examples of alternative splicing but these represent only a small percentage of the total genes in the human genome.¹ We'll call these two groups the "splicing is common" advocates and the "splicing is rare" advocates.

The "common" group likes to think of themselves as the leading edge of a paradigm shift. They believe that alternative splicing is so common that it requires a new way of looking at biology. Unfortunately, in their haste to promote the new paradigm, they often misrepresent the other side. As a matter of fact, the very existence of a legitimate scientific controversy is often deliberately overlooked because they set up a straw man that is easily refuted.

Here's an example. In Majewski's seminar he started by describing the current "dogma" of one gene-one enzyme. According to him, most biologists are wedded to the idea that each gene makes a single protein. They believe, according to Majewski, that the intermediate step of mRNA synthesis is unimportant. He even showed a slide illustrating the dogma. It represents the old paradigm.

At the end of the seminar I pointed out that we have been teaching a different version of information flow for over thirty years. I mentioned that all the leading textbooks talk about splicing and alternative splicing and, furthermore, this material has been in the textbooks for 25 years (e.g. Genes II by Benjamin Lewin published in 1983). I asked him if he actually knew any scientists who believed in the dogma that he described. His response was confusing but he didn't back down.

Why is this important? Because most of the "common" advocates focus on convincing us that alternative splicing is real rather than focusing on whether it is common. By refuting the straw man they hope to bolster their case for the prevalence of alternative splicing. But they do no such thing. Most scientists are well aware of alternative splicing and have been for decades. The dispute is not over whether it occurs but whether it is common. The straw man version of the opposition does not exist.

I was prompted to write about this form of rhetorical device by reading an article in Monday's New York Times. The article (Now: The Rest of the Genome) was written by Carl Zimmer. Most of you know what I think of Carl Zimmer. He is one of the best science writers on the planet [Carl Zimmer at Chautauqua] but this time he slipped up.

Zimmer writes about Sonja Prohaska, a bioinformatician at the University of Leipzig in Germany.

... new large-scale studies of DNA are causing her and many of her colleagues to rethink the very nature of genes. They no longer conceive of a typical gene as a single chunk of DNA encoding a single protein. “It cannot work that way,” Dr. Prohaska said. There are simply too many exceptions to the conventional rules for genes.

It turns out, for example, that several different proteins may be produced from a single stretch of DNA. Most of the molecules produced from DNA may not even be proteins, but another chemical known as RNA. The familiar double helix of DNA no longer has a monopoly on heredity. Other molecules clinging to DNA can produce striking differences between two organisms with the same genes. And those molecules can be inherited along with DNA.

The gene, in other words, is in an identity crisis.

I don't think there are any significant number of biochemists or molecular biologists who literally believe that every gene encodes a single protein. Everyone I know understands that there are ribosomal RNA genes, tRNA genes, and genes for all kinds of small RNAs. Everyone I know understands alternative splicing. (On the other hand, nobody I know thinks that epigenetics is any threat to our definition of a gene.)

If the gene has an identity crisis, which it does, it's not because of ignorance of these phenomena, it's because we can't all agree on a good definition. My own preference is to define as a gene as, "A gene is a DNA sequence that is transcribed to produce a functional product" [What Is a Gene?] and I've been using that definition in my own textbooks since 1989.

It's sad to hear that up until recently Sonja Prohaska and her colleagues believed in a long-discredited definition of a gene. It suggests that throughout her undergraduate and graduate education she never heard of ribosomal RNA genes or alternative spicing. (She got her Ph.D. in 2005.) Either that or she's deliberately setting up a straw man.

Carl Zimmer goes on to describe recent work on the analysis of the human genome, especially the work done by the ENCODE project.

Encode’s results reveal the genome to be full of genes that are deeply weird, at least by the traditional standard of what a gene is supposed to be. “These are not oddities — these are the rule,” said Thomas R. Gingeras of Cold Spring Harbor Laboratory and one of the leaders of Encode.

A single so-called gene, for example, can make more than one protein. In a process known as alternative splicing, a cell can select different combinations of exons to make different transcripts. Scientists identified the first cases of alternative splicing almost 30 years ago, but they were not sure how common it was. Several studies now show that almost all genes are being spliced. The Encode team estimates that the average protein-coding region produces 5.7 different transcripts. Different kinds of cells appear to produce different transcripts from the same gene.

With all due respect to Carl, these sentences contradict what he implied earlier on. Yes, it's true that scientists have known about alternative splicing for 30 years. In other words, they have known for at least that long that the old idea about one gene-one protein is incorrect. So what was the point of letting readers think that Sonja Prohaska's personal misunderstanding of a gene has any relevance?

As I mentioned above, the scientific controversy over alternative splicing is about how common it is and not about whether modern scientists recognize its existence. And it has nothing to do with the modern understanding of a gene since for the past 20 years everyone has incorporated alternative splicing into their understanding of a gene.

Thomas Gingras is clearly on the "common" side of the issue and not on the "rare" side. Unfortunately Zimmer doesn't do a good job of balance here. A better way to describe the results would be ...

Taken a face value, some of the published results from the ENCODE project suggest that, far from being a rare event, alternative splicing may be very common. In fact, some scientist think that most of our genes produce several different proteins due to alternative splicing. They even suggest that an average gene may produce five or six different alternatively spliced transcripts.

Other scientists dispute these results, pointing out that the predicted alternatively spliced transcripts make no sense for those genes that have been well-studied. These predictions are being quietly removed from the annotated human genome database. As more and more genes are being looked at, the number of proven protein variants gets smaller and smaller.

The original predictions rely heavily on the sequences of small bits of RNA called "ESTs" and it is becoming increasingly clear that many, perhaps most, ESTs are artifacts. It is quite possible that talk of changing paradigms is premature and the number of genes exhibiting alternative splicing may be closer to what scientists thought twenty years ago.

These are interesting times in genome research and, like all new fields, the preliminary results are exciting and provocative. Who knows whether the preliminary results will lead to new ways of looking at biology? Time will tell.

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1. I'm using the human genome as an example. The same arguments apply to other genomes.

[Image Credit The Information Paradox: A Favorite Theist Logical Fallacy: The Straw Man]

November 11, 2008

 
This is what the front campus of the University of Toronto looks like today, Remembrance Day 2008. This is the 90th anniversary of the end of World War I.

Each cross bears the name of one of 628 alumni, students, or faculty members who died in World War I. It reminds us of what happens when we fail to resolve our differences peacefully. War is the failure of peace.

The crosses remind us that war is evil and horrible. All of these lives were wasted in a war that never should have happened. War is not glorious. War is not something we should be proud of even though we may honor those individuals who answered the call, and sacrificed their lives, when the politicians and diplomats failed to do their duty.

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Enzyme Efficiency: The Best Enzyme

One of the first things you learn about enzymes is that they catalyze, or speed up, reactions that would normally take place at a much slower rate. This is a difficult concept for students to understand because they're used to thinking of biochemical reactions in terms of reactions that would never happen without an enzyme.

The trick in understanding the role of enzymes is to appreciate the difference in rates between the enzyme-catalyzed reaction and the spontaneous reaction. While it's true that all enzyme-catalyzed reactions would eventually proceed even in the absence of enzyme, the rate of the spontaneous reaction might be way too slow. We often emphasize that the spontaneity of a reaction can be determined from the thermodynamics (i.e. if ΔG <0 the reaction is spontaneous) but we sometimes forget to show real data on how fast such a reaction can occur under physiological conditions. Typical rates for enzyme-catalyzed reactions are described by a constant called k_cat.¹ These values are usually in the range of 100-1000 reactions per second but there are some enzymes than have rates of over 1,000,000 reactions per second.

Spontaneous reactions can often approach these rates but, as you might imagine, the ones that require enzymes are very much slower. Proteins, for example, will eventually break down into amino acids but the rate of the reaction is so slow that spontaneous protein degradation is not a problem in living cells. In order to degrade proteins for food, we need to make enzymes such as chymotrypsin, trypsin, pepsin, and elastin to do the job at a faster rate.

Most of the important metabolic reactions take years in the absence of enzyme. The spontaneous degradation of a protein, for example, takes about 100 years (rate constant ~ 4 × 10^-9). Since chymotrypsin catalzyes this reaction at a rate of about 1000 molecules per second, this means that the enzyme speeds up the reaction by a factor of more than 10¹¹ (100 billion times)!

This value (10¹¹) is sometimes called the catalytic proficiency of an enzyme although for technical reasons we won't go into here, the real measure of catalytic proficiency is higher by several orders of magnitude.¹ The catalytic proficiency of chymotrypsin is 2 × 10¹⁶.

Naturally, this invites a comparison with those enzymes showing the greatest rate enhancements. But there's a problem. You can measure spontaneous rates that are on the order of a few years because you don't have to wait until the reaction goes to completion. But if the spontaneous reaction takes hundreds of years it can be difficult to measure—even the most dedicated graduate student won't wait that long!

Fortunately there are a few tricks that will make the job easier. You can observe the spontaneous reaction at high temperatures, for example, and calculate what the rate would be at physiological temperatures. That's what Radzicka and Wolfenden did in 1995 when they reported that the spontaneous decarboxylation of ornithine 5′-phosphate (OMP) had a rate constant of 3 × 10^-16 s^-1. This is a half-life of 78 million years.

The enzyme that catalyzes this reaction is ornithine 5′-phosphate decaboxlyase and up until last week it was the record holder with a catalytic proficiency of 2 × 10²³. (OMP decarboxylase catalyzes an essential step in the synthesis of pyrimidine nucleotides that are required to make RNA and DNA.)

That record has now been broken. Lewis and Wolfenden (2008) studied a reaction catalyzed by uroporphyrinogen decarboxylase, an enzyme involved in the synthesis of porphyrins such as heme, the cofactor in hemoglobin, and the chlorophylls. There were able to model the reaction and determine that the rate of spontaneous decarboxylation is 9.5 × 10^-18 s^-1, which corresponds to a half-life of 2.3 billion years! Lewis and Wolfenden published a chart showing typical half-lives of spontaneous reactions.

The catalytic proficiency of uroporphyrinogen decarboxylase is 2.5 × 10²⁴, a new record.

Into the textbook it goes.

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1. A better description of an enzyme's real rate constant is k_cat/K_m.

Radzicka, A. and Wolfenden, R. (1995) A proficient enzyme. Science 267:90-93.

Lewis,C.A. Jr. and Wolfenden, R. (2008) Uroporphyrinogen decarboxylation as a benchmark for the catalytic proficiency of enzymes. Proc. Natl. Acad. Sci. (USA) published online November 6, 2008 [Abstract] [doi:10.1073/pnas.0809838105]

Saturday Night Live: Joan Baez

 
On Saturday night we went to see Joan Baez. She older than she used to be but still wonderful. I remember her from the 60s in spite of what they say.¹

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If you remember the 60s, you weren't there.

Molecular and Cell Biology Carnival #4

 

The 4th issue of the Molecular and Cell Biology Carnival has been posted by steppen wolf at the skeptical alchemist [Molecular and Cell Biology Carnival #4].

Welcome to the fourth edition of the Molecular and Cell Biology Carnival! Let's get down to business right away...

Submit your articles here.

The previous editions are ...

1. the skeptical alchemist
2. Cotch.net
3. ScienceRoll
4. the skeptical alchemist

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Monday's Molecule #96

 
You haven't been very successful lately at guessing Monday's "Molecule" so this week is going to be an easy one. All you have to do is identify the molecules (plural) that are responsible for this strange looking fly. Just naming the genes will be sufficient.

This week's Nobel Laureate won the prize for his work on these genes (and several others).

The first one to correctly identify the molecules/genes and name the Nobel Laureate(s), 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 only two ineligible candidates for this week's reward: Bill Chaney of the University of Nebraska and Dima Klenchin of the University of Wisconsin. Since they are two of the three most frequent winners, the competition is a bit easier this week.

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 mutant Drosohila melanogaster is called "bithorax" because it has two pairs of wings instead of just one pair. It actually doesn't have two thoraces, instead the 3rd thoracic segment is transformed into a duplicate of the second thoracic segment. The complete transformation requires two different mutations called bx, and pbx. Both mutations are in the regulatory region of the gene UBX and they affect expression of that gene. The Nobel Laureate is Edward Lewis.

The winner is Dale Hoyt from Athens, Georgia (USA).

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How 'molecular machines' kick start gene activation revealed

 
That's the title of a press release published on Biology News Net, and several other science news sites. Here's the opening sentence ...

How 'molecular machines' inside cells swing into action to activate genes at different times in a cell's life is revealed today (6 November) in new research published in Molecular Cell.

How could you not want to find out more? This sounds like a real breakthrough.

Try and guess what the new discovery is all about before reading on ...

From the website Biology News Net and Imperial College London ...

Genes are made of double stranded DNA molecules containing the coded information an organism's cells need to produce proteins. The DNA double strands need to be 'melted out' and separated in order for the code to be accessed. Once accessed, the genetic codes are converted to messenger RNAs (mRNA) which are used to make proteins. Cells need to produce particular proteins at different times in their lives, to help them respond and adapt to changes in their environment.

The new study outlines exactly how a molecular machine called RNA polymerase, which reads the DNA code and synthesizes mRNA, is kickstarted by specialised activator proteins. The scientists have discovered that RNA polymerase uses a tightly regulated internal blocking system that prevents genes from being activated when they are not needed.

I'm underwhelmed. How is science journalism ever going to be taken seriously if this is the sort of thing that university press offices publish?

We've known and understood the basics of transcription initiation by RNA polymerase and its activators for thirty years. This study concerns a minor variation of that process involving σ⁵⁴ in bacteria.

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Never Let Your Gas Tank Get Below Half Full

 
Friday's Urban Legend: True

How many of you have heard the story that you should always drive your car with the gas tank as full as possible? According to many, you should never let the gas in your tank fall below the half full mark on your gas gauge.

You probably thought this was a tale told by elderly wives—with apologies to old men who also tell tales.

Well, it turns out that there is actual, scientific, evidence to support this warning. Cliff Allen did the experiment according to the Sept. 13, 2008 issue of New Scientist [Petrol Gauge Challenge].

SLIGHTLY more practical routes to fuel economy occurred to Cliff Allen when he noticed that, according to his petrol gauge, the fuel in the top half of his tank lasted considerably longer than the bottom half. As any Feedback reader (and possibly only a Feedback reader) would, he investigated. Systematically.

Over several months he recorded the distances travelled using the fuel from the top and bottom halves. The average for the top was 400 kilometres (250 miles) and for the bottom a mere 300 kilometres (185 miles). Since then, he writes, "of course I have only used the top of my tank and have consistently achieved around 250 miles - I'm not stupid!"

Cliff was obviously keen to discuss this, at length, with his learned friends, "some of whom gained General Certificate of Secondary Education qualifications" at age 14. He was "mostly appalled at their incredulity and lack of interest".

However, his friend Alan suggested that the fact that petrol always comes out of the bottom of the tank causes it to use more petrol so we might benefit from turning the tank upside-down. John suggested the increased efficiency might be due to the height of the fuel, so the tank should be put on the roof. Mostyn proposed putting a brick in the tank, as this apparently works very well for saving water in toilet cisterns. Tony wants to make the top of the tank larger than the bottom, to increase the proportion of its volume at the top, and thinks a carrot shape would be optimal.

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P.S. for the irony impaired.

The Awesome Power of Prayer

 
James C. Dobson, Ph.D. is Founder and Chairman of Focus on the Family. He is not a fan of Barrack Obama and came to the realization that John McCain and Sarah Palin would be much better for the country.

Dobson urged his followers to pray [Dr. Dobson’s October Newsletter].

Regardless of your political views, I want to urge Christians everywhere to be in prayer about this election. There are many scriptural references wherein King David “inquired of God” when he was faced by troubling circumstances (1 Samuel 23:2,4; 30:8; 2 Samuel 2:1; 5:19,23). It is time for Christians everywhere to turn to Him for guidance and wisdom. Find some time to be still and listen to what He wants to tell you. The National Day of Prayer Task Force, led by my wonderful wife, Shirley, has embarked on a national campaign entitled “Pray for Election Day.” All around the country, individuals and groups are being encouraged to gather every Thursday leading up to Nov. 4 between 12 noon and 12:30 p.m. Spend time with the Lord, asking Him to guide and direct those privileged to cast a ballot. If you are able, I would also encourage you to fast and pray immed”ately before the election. After all, it was the Reverend Billy Graham who once said that “To get nations back on their feet, we must first get down on our knees.”20 Amen, Dr. Graham.

This election is about the future of the nation, but it will also go a long way toward determining the culture your children and grandchildren will come to know. I know you will vote with your children and your children’s children in mind. That certainly puts the election in a different light, doesn’t it?

Apparently God was listening. He answered their prayers on Tuesday. Here's how Tom Hess describes the result [‘We Need to Continue to be in Prayer for America’].

With an Obama administration forthcoming, Focus Action’s Tom Minnery says, “We’ve got a big challenge ahead of us.”

He and FRC Action President Tony Perkins encouraged CitizenLink viewers to remain hopeful of what God might do in the next four years — and to be in prayer.

“For those who have been praying for weeks, our responsibility does not end today,” Perkins said. “In Luke 18, Jesus said men should not lose heart, but they should pray. We need to continue to be in prayer for America.”

Minnery pointed out that in the Bible, God worked through pagan rulers such as Nebuchadnezzar, Darius and Cyrus to accomplish his purposes, and that values voters ought to begin praying for President-elect Obama.

“God can use any president for his own purposes,” Minnery said.

You can't make this stuff up.

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[Hat Tip: Primordial Blog]

It's Her Last Saturday in the Lab

 
Eva Amsen blogs at Expression Patterns on the Nature Network [Last Saturday]. My department will miss her when she leaves.

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Small Science Is Good Science?

 
I've been thinking a lot lately about what's wrong with science in the 21st century. Part of the problem is sloppy thinking that becomes apparent when you realize how many widely believed models are inconsistent with what we know about biology. I assume that similar problems occur in other disciplines.

One wonders if the proliferation of papers with huge numbers of authors is part of the problem. Maybe this fad of "multidisciplinary" science is part of the problem and not part of the solution? Is it possible to be an expert in two or more different disciplines?

I've seen plenty of example of biochemists and molecular biologists who publish papers about evolution without knowing much about evolution. Is this an isolated example?

Speaking of "big science," I was reminded of a paper published by Bruce Alberts back in 1985 in Cell. The title was "Limits to growth: In biology, small science is good science" (Alberts 1985).

These days, many people grow up believing that bigger is better. Giant factories that produce Wonder Bread have replaced thousands of corner bakeries, driven by the increased efficiency of scale. There is an unfortunate tendency to extend this view to the biological research community, and I have on occasion heard a major symposium speaker introduced in glowing terms as the coauthor of more than fifty papers per year. While I can admire the energy and management skills required to maintain a very large laboratory, the best biology is rarely done in this way. With a few notable exceptions, the biochemists and molecular biologists I most respect run relatively small laboratories and publish when they have something important to report. As I shall argue here, doing good science is very different from producing bread, and there are compelling reasons why large laboratories are in general less efficient and less interesting than smaller ones. To reflect this fact, I believe that changes in funding patterns and expectations would be useful in the biological sciences.

Some "big science" is good. The sequencing of the human genome, and other genomes, for example, was a big science project that benefited the entire biological community. But I'm not sure that significant advances in our understanding of how life works come from big labs. Does anyone have examples? What are the most significant conceptual advances to come out of big labs?

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Alberts, B.M. (1985) Limits to growth: In biology, small science is good science. Cell 41:337-338. [PubMed] [doi:10.1016/S0092-8674(85)80001-5]

Ignore, Reject, Answer? What to Do about Student Email Messages

 
Some of my colleagues are running courses where they ask students to write essays on science subjects. Part of the assignment is to contact a Professor in the discipline and get them to help with the scientific content of the essay. The idea is for the students to make sure they have their facts correct. A side benefit is that it gets the students in touch with active researchers.

Some of us object to this procedure on the grounds that if it became widespread there would be hundreds of students looking for Professors to help them on their assignment. Most Professors have other priorities, like teaching their own classes. To some extent, our colleagues who engage in this practice are downloading their teaching responsibilities onto others.

From 1992-2000 I ran a molecular biology course where the students had to write a major essay. They were told to do the research themselves but the instructors would be available if they need help with the interpretation of some papers. If necessary, we would put them in touch with an expert but only after the student had done enough work to ask intelligent questions on difficult material.

Here's an email message that was sent to my Sandwalk address last night. How should I respond? I don't feel comfortable ignoring the message. I will feel awkward if I refuse to help. I don't had time to answer the question—it's complicated and, besides, it's not my area of expertise.

Dear Professor Moran,

As part of a University assignment, I have been asked to email a group of experts to request their professional opinion on a particular question.

I have come to understand that a child with Dyspraxia should supplement their diet with a high dose of essential fatty acids. However, as non-Dyspraxic people age it is advised that they also should supplement their diet with these oils to combat age-related memory loss. Does this mean that people with Dyspraxia should augment their intake yet again when they age? If so, could this have an adverse effect on their health?

As your organisation came up in an internet search as being reputable, your answer to this question would be much appreciated.

I would like to thank you for taking the time to read this email and I hope to hear from you soon.

Yours sincerely,

This makes me angry. No matter what I do, I'm going to be disappointing a student who might really benefit from a reply. In my opinion the student's Professor is at fault for assigning such a task to the students.

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Barack Obama Will Save Religion in America

 
Frank Scaheffer writes in The Huffington Post [President Obama: Bad News For the New Atheists and Other Fundamentalists].

The Obama presidency is great news for almost everyone. It's bad news for some odd ideological bedfellows: the Religious Right and the so-called New Atheists.

Into the all or nothing culture wars, and the all or nothing wars between the so-called New Atheists and religion the election of President elect Obama reintroduces nuance. President elect Obama's ability to believe in Jesus, yet question, is going to rescue American religion in general and Christianity in particular, from the extremes.

There is no way to understand President elect Obama's victory as anything less than the start of not just a monumental political change but a spiritual revolution as well.

Who knew? I bet all atheists and agnostics are feeling pretty stupid right now knowing that they've been tricked by the slick-talking Obama.

And what is the "nuanced" spiritual revolution going to look like?

To the New Atheists who think that with the resounding defeat of the Religious Right, we are entering a secular age, think again. Obama will block your path. He'll do it for the same reason he'll make the Religious Right's paranoid fantasies about him soon seem shamefully ridiculous. That's because President elect Obama is that rarest of all rare people: a thoughtful, compassionate and likable statesman who also is a thoughtful, compassionate and likable religious believer.

Sounds like trouble. President Obama is going to block the path to a secular society. Gosh. I knew that American Presidents were leaders of the free world and the most powerful men (no women so far) on the planet but even I had no idea they were that powerful.

President-elect Obama brings another perspective to faith . It goes something like this:

How do cultures define themselves if not through ritual? In the "big moments" of life; birth, marriage, sickness, death "who" -- in the inimitable words of Ghost Busters -- "you gonna call?" As President elect Obama has said, and I paraphrase: Strip the human race of our spiritual language and what do we tell each other about hope?

As President elect Obama has pointed out, a world of all math but no poetry is not fit for human habitation. If everything feels flat and dull, stripped of mystery and meaning who will bother to do the science? Why bother, if all we're doing is serving those selfish genes for another round of meaningless propagation?

So does this faith always make "sense?" No. Because our perspective is from the inside, something like paint contemplating the painting of which it's a part. We're all in the same boat, all stuck on the same "canvas."

Ohmygod. Frank Shaeffer and Barack Obama have discovered the atheist dirty little secret. All of us atheists are flat and dull—we can't be born, get married, or die without calling upon God to help us.

Does anyone actually believe this stuff?

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[Hat Tip: RichardDawkins.net]

Evolution by Gene Duplication

Chymotrypsin (Monday's Molecule #95), trypsin, and elastase are enzymes that digest proteins in the stomach and intestine. All three enzymes have a similar mechanism of hydrolysis characterized by the presence of a catalytic triad of amino acid side chains consisting of aspartate, histidine, and serine residues. The serine side chain is directly involved in catalyzing the cleavage of proteins and that's why these enzymes are called serine proteases.

The three enzymes differ in specificity. Chymotrypsin cleaves foreign proteins primarily at tyrosine (Tyr) resides, trypsin is specific for cleavage at arginine (Arg) or lysine (Lys) resideus, and elastin cleaves at alanine (Ala) residues.

The genes for the three enzymes are homologous and the structures of the three enzymes are very similar as shown below (left: chymotrypsin [PDB 5CHA], middle: trypsin [PDB 1TLD], right: elastase [PDB 3EST]).


The active sites of the enzymes are slightly different so that specificity depends on which amino acid side chains of the substrate protein fit into the binding pocket.


It's reasonable to suppose that the primitive enzyme could bind weakly to many different substrates and cleave many different kinds of proteins inefficiently. An ancient gene duplication allowed one copy of the gene to evolve toward a much more active enzyme that cleaved only at certain residues. A second gene duplication gave rise to a third enzyme that cleaved at another residue. Finally the remaining gene evolved into a very active enzyme that cut at a third position.

The end result was a set of three enzymes that could cut up any protein into small peptides that can be taken up by the cells lining the intestine. The original non-specific enzyme was slower and less efficient.

This is an example of evolution by gene duplication and the important point is that the ancestral gene probably encoded a non-specific enzyme that could carry out several different reactions with different substrates. It's not a question of the duplicated copy evolving an entirely new specificity. Instead, the duplicated gene usually "perfects" an already existing minor activity by becoming more specific. Meanwhile, the other copy can also be selected for enhanced specificity for another substrate.

This model also explains the evolution of lactate dehydrogenase and malate dehydrogenase (Evolution and Variation in Folded Proteins) and the pyruvate dehydrogenase family (Pyruvate Dehydrogenase Evolution).

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