The Compositon of Ribosomes

 
The ribosome is an important part of the translation machinery. (The others are mRNA, aminoacyl-tRNAs, and translation factors). The translation machine makes polypeptide chains according to the information encoded in the mRNA molecule

All ribosome are composed of two subunits that separate when translation terminates and reunite when an new initiation complex is formed. The eukaryotic ribosome has 40S and 60S subunits and the prokaryotic subunits are 30S and 50S. As a general rule bacterial macromolecules are smaller that eukaryotic ones and the ribosome is no exception.


Each of the subunits is made up of a combination of RNA and proteins. The ribosomal RNA molecules are named 28S, 18S etc. The "S" at the end of these names stands for a Svedberg unit. It's a measure of the size and shape of a molecule. You can tell that the 28S ribosomal RNA molecule is larger than the 18S ribosomal RNA. Similarly, the 60S subunit is the large subunit and the 40S subunit is smaller

The behavior of molecules in a liquid in a centrifuge depends on many variables including the partial specific volume of the molecule (V_r), its molecular weight (M) and the density of the solvent (ρ). The behavior is expressed as s, which is the rate of sedimentation where

                                             s = M(1-V_r)D/RT

The values for biological molecules fall into range of "s" values between 1 and 500 × 10^-13 seconds. One Svedberg unit (S) is defined as 10^-13 s units.

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Monday's Molecule #47

 

Today's molecule is the eukaryotic ribosome. That's not what you have to identify. What you have to name is the two subunits and each of the RNA components of these subunits. Trivial, common names are required.

There's an indirect direct connection between the names of these ribosome components and Wednesday's Nobel Laureate(s). In order to win you have to tell us how the components were named and supply the relevant equation. See if you can guess the Nobel Laureate. This one is not easy.

The reward goes to the person who correctly identifies the molecules and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There is only ineligible candidates for this Wednesday'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.

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

UPDATE: We have two winners!

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Evolution in the Ashkenazi Jewish Population

 
Over at Eye on DNA Hsien-Hsien Lei has given over her blog over to Jon Entine to promote his new book Abraham's Children [Books About DNA: Abraham’s Children by Jon Entine].

Entine points out that Ashkenazi Jews (he is one) have higher frequencies of certain diseases like breast cancer, Tay-Sachs disease, Bloom's Syndrome etc. He notes, correctly, that Ashkenazi Jews are a relatively homogeneous population in spite of the fact that they are spread out over all of Europe and have since emigrated to North America and back to Israel.

There's nothing special about this group in terms of susceptibility to disease. Other genetically isolated populations, such as French Canadians, also have elevated incidences of some genetic diseases, and lower incidences of others. We usually assume that this altered frequency of alleles is due to random genetic drift: in this case the founder effect. Since the populations were founded by small numbers of people, there were certain alleles that just by chance happened to be over- or under-represented in the ancestors.

All reports suggest that Ashkenazi Jews descend from a small number of people who left the Middle East less than 2000 years ago. Possibly only four females contributed to most of the mitochondrial DNA in today's descendants (Behar et al. 2006). Most of these early descendants settled eventually in the Rhine Valley and from there they spread eastward. The main population expansion probably occurred after 1000 AD. Today their descendants number about 8,000,000 worldwide.

There is evidence for distinct subpopulations, suggesting a number of bottlenecks in the Middle ages (Feder et al. 2007).

Jon Entine is intrigued by stories that the Ashkenazi Jews have higher IQ's than many other ethnic groups. He offers the following speculation,

The book includes a chapter explaining the possible link between so-called Jewish diseases — certain neurological and LSD disorders, as well as DNA repair problems — and the high measured IQ of Ashkenazi (Eastern European origin) Jewry. Although this theory (most recently advanced by Gregory Cochran and Henry Harpending—two non-Jews—is best classified as informed speculation (as I acknowledge in the book) at the moment, it argues persuasively, I believe, that Ashkenazi Jews are a rather distinct population group in which positive selection pressures, balanced against the killer consequences of neurological disease mutations, have led to higher IQs. The “it’s environment and culture” argument are far less persuasive. This is only one chapter in the book–most of AC is a look at our shared Israelite ancestry and history–but it is the most provocative chapter. Wonder where others come down on this issue? Interestingly, “liberal” Jews (of which I’m one) are the one’s most uncomfortable about discussing or (even if they believe it) acknowledging this point.

Leaving aside the truth of the premise, it seems very unlikely that there was selection for higher IQ. We're dealing with a polygenic trait (intelligence) in a population of about 100,000 (average) over a maximum of 70 generations and possibly less than 25 generations. It's very unlikely that the adaptive benefit of a 10% increase in IQ would have an effect in that time frame.

Assuming there really is a genetic difference in intelligence then it is far more likely that it's due to the same factors that are responsible for differences in the allele frequencies of other alleles. It looks like the people in group that left the Middle East were smarter than the ones who stayed!

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[Figure Credit: The image is Figure 2 in Behar et al. (2006)]

Behar, D.M. et al. (2006) The Matrilineal Ancestry of Ashkenazi Jewry: Portrait of a Recent Founder Event. Am. J. Hum. Genet. 78:487-497. [PubMed]

Feder, J., Ovadia, O., Glaser, B. and Mishmar, D. (2007) Ashkenazi Jewish mtDNA haplogroup distribution varies among distinct subpopulations: lessons of population substructure in a closed group. European Journal of Human Genetics 15:498–500. [PubMed]

Why Pigs Don't Have Wings

 
Jerry Fodor publishes a critique of adaptationism in London Review of Books. The title is Why Pigs Don’t Have Wings and it's an excellent read. I wish I could write like this ...

In fact, an appreciable number of perfectly reasonable biologists are coming to think that the theory of natural selection can no longer be taken for granted. This is, so far, mostly straws in the wind; but it’s not out of the question that a scientific revolution – no less than a major revision of evolutionary theory – is in the offing. Unlike the story about our minds being anachronistic adaptations, this new twist doesn’t seem to have been widely noticed outside professional circles. The ironic upshot is that at a time when the theory of natural selection has become an article of pop culture, it is faced with what may be the most serious challenge it has had so far. Darwinists have been known to say that adaptationism is the best idea that anybody has ever had. It would be a good joke if the best idea that anybody has ever had turned out not to be true. A lot of the history of science consists of the world playing that sort of joke on our most cherished theories.

UPDATE: Read Jason Rosenhouse's take on the Foder essay [Fodor on Natural Selection]. Jason makes some good points but I think he misses the main idea; namely that many scientists (and philosophers) have an inordinate confidence in natural selection as the explanation for almost everything in biology that's important (to them).

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[Hat Tip: Andrew Brown at Helmintholog: Adaptationism contested. Andrew is the author of "The Darwin Wars."]

[Photo Credit: Uncyclopedia.]

Mendel's Garden: Halloween Edition

 
The 19th version of Mendel's Garden has just been posted on Discovering Biology in a Digital World [Mendel’s Garden: Halloween Edition]. I don't think Sandra Porter likes October very much but fortunately that didn't prevent her from posting an enlightened selection of blogs from the past month.

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Goodbye John Howard?

 

According to The International Herald Tribune John Howard has called an election for November 24th [Howard announces Australian elections in November]. Chances are he's going to lose. This might be a good thing for Australia except for the fact that the probable winners might not be a great improvement.

I look forward to enlightenment from all my Australian readers. Is Australia going to move away from its close relationship with George Bush?

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Al Gore Wins the Nobel Peace Prize for Framing

 
I'm a fan of Al Gore and I would have voted for him if I'd have been an American citizen in 2000. I'd vote for him today if I could. I think he's done a fabulous job of bringing the issue of global warming to the attention of the public. (I also like his latest book The Assault on Reason).

Gore's advantage is that he is not a scientist. That means that he can spin the global warming debate in a way that advances his cause. There is much that is true in An Inconvenient Truth and that's why I support him, but in order to frame the presentation in a way that resonates with the general public he has to drop some of the nuances and present the science in a way that makes it sound far more solid than it actually is.

This is why Gore will not be receiving a Nobel Prize in Science. There are very few scientists who would be comfortable making the same presentation that Gore makes in his public talks. Most scientists know that some of the "facts" are only half-truths and some of them are still disputed within the scientific community. They believe that scientific integrity requires them to be less dogmatic and more circumspect when they talk about science.

Chris Mooney and Matt Nisbet would like all scientists to adopt the Al Gore method of presenting science in situations where they advocate changes in public policy. It ain't gonna fly for the reason that I just mentioned. What's so astonishing is that Nisbet and Mooney just don't seem to get it. They don't understand why scientists are leery about framing. It's because we can't do what Gore does without feeling a little guilty over being less than honest about the science.

This does not mean that we don't like Al Gore and other politicians who have learned to appreciate science and base their policy on good scientific foundations. It simply means that pushing science and pushing policy are two different things and the tactics used in the political arena do not belong in science. Some scientists may be able to jump back and forth from one arena to the other but its' going to be very difficult to maintain a scientific reputation under such circumstances. What Nisbet and Mooney are suggesting requires that scientists abandon true science in favor of political science.

I suspect they have a hard time seeing the problem because they're not scientists.

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The Most Beautiful Experiment in Biology

 

John Dennehy at Evilutionary Biologust has done it again. This week's citation classic is, indeed, a classic. It's the Meselson-Stahl paper from 1958 demonstrating that DNA is replicated semi-conservatively [The Most Beautiful Experiment in Biology].

The description of the experiment as the "most beautiful experiment in biology" comes from John Cairns as quoted in Horace Judson's book The Eight Day of Creation [see The Story of DNA (Part 1)]. It's a description that few of us could dispute. I grew up on the stories of famous experiments like this one and everyone around me at the time wanted to be like Matt Meselson or Franklin Stahl. If they couldn't be Meselson or Stahl then maybe Jacob, Monod, Hershey, Pardee or a host of other members of the phage group. Personally, I was envious of those who worked on bacteriophage lambda.

Over the years we kept reminding each new generation of the Meselson-Stahl experiment by describing it in the textbooks. The figure on the left is from my 1994 book. I'm sure that any student who took biochemistry or molecular biology in the 70's, 80's, and even part of the 90's, was taught this experiment.

Alas, it's no longer in the textbooks and the current generation of students probably has no idea who Meselson and Stahl are. They're probably befuddled by the reference to the most beautiful experiment in biology.

I vividly remember the debate when we decided to take it out of the textbook. Now that we can describe the molecular machinery of DNA replication it follows naturally that replication has to be semi-conservative. It no longer seems necessary to describe a separate experiment that demonstrates this obvious fact. In fact, it is often counter-productive to do so since it requires setting up the context—a time when this strong prediction of Watson and Crick had not been tested. That's not easy when even high school students know the facts.

So out it went, but not without some sadness for the passing of an era. I suppose it won't be long before some other experiment takes its place as the most beautiful. It will probably be something to do with microarrays or florescent dyes.

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Many of the classic experiments are no longer taught to undergraduates. It's the nature of the beast, I suppose. Those experiments became classics because they showed us something we didn't know previously. That "something" was so important that it now seems obvious. We don't need to teach it.

Evolution: The Triumph of an Idea

 
Evolution: The Triumph of an Idea is a wonderful book by Carl Zimmer. The cover shows a bunch of different eyes ans it's meant to convey the idea that all these eyes have evolved from a common ancestor with primitive eyes.

Bill Dembski doesn't like this idea. He doesn't like the idea of evolution either. Here's a video where Dembski displays his ignorance about evolution in general and molecular evolution in particular. The title of his talk is "Molecular Machines and the Death of Darwinism."

I sometimes wonder just how intelligent Dembski is. Does he really think that the eye is our best example of the evolution of molecular machines. Does he think that the bacterial flagellum is the only other molecular machine? Apparently he does because he doesn't mention replisomes, photosynthesis complexes, blood clotting cascades, the citric acid cycle, or any of the other molecular machines and complex systems where we have a good handle on how they evolved.

But Dembski goes even further than complex machines. He has the inside track on some research that will bring down the Darwinian idol. It's at the level of individual proteins where we're finally going to see proof of the existence of God. I can hardly wait.

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HSP90 Structure

 
Hsp90 is a molecular chaperone that plays a role in the folding and assembly of other proteins. Current ideas suggest that it binds to substrate proteins at a "client" site and this either encourages folding into the proper conformation or prevents aggregation. The binding and release of polypeptides is accompanied by hydrolysis of ATP to ADP + Pi.

The bacterial version of hsp90 is called HtpG. Eukaryotes have several different members of the Hsp90 family including one that resides in the endoplasmic reticulum. The cytosolic protein is called Hsp90 and the ER version is called GRP94. Hsp90 is a highly conserved protein showing significant sequence identity between prokaryotic and eukaryotic proteins. The HSP90 family shares many of the same characteristics of the more highly conserved HSP70s [Heat Shock and Molecular Chaperones, Gene HSPA5 Encodes BiP-a Molecular Chaperone, The Evolution of the HSP70 Gene Family].

Daniel Gewirth and his colleagues have just published the complete structure of GRP94 from dog (Canis familiaris). The article appears in Molecular Cell and their structure is on the cover of the journal (Dollins et al. 2007). This is the endoplasmic reticulum version of Hsp90 and its the only ER version of this protein whose structure is known. Gewirth has been working on the structure since 2001 and he deposited the first structural coordinates of a fragment of this protein back in February 2004. (See the Protein Data Base (PDB) for the structures. Search for "hsp90".)

The complete protein is a dimer of two identical subunits. Each monomer has three distinct domains; an N-terminal domain (N); a middle domain (M); and a C-terminal domain (C). The ATP hydrolysis site sits at the interface between the N and M domains. The C domains interact to form the dimer. The presumed site of binding for misfolded proteins ("client" site") is in the V-shaped pocket formed when the C domains come together.

The mechanism of action of Hsp90 proteins is not known although it presumably involves a conformational change induced by ATP hydrolysis. This paper provides an important clue to that mechanism because the dimer structure differs from that seen with the yeast protein (Hsp82) and the E. coli protein (HtpG) (below).
Each of the structures seems to identify a protein in one of the conformations adopted in vivo. The most likely explanation is that the wings of the protein open and close to capture and release the substrate protein. This conformational change is induced by binding and hydrolysis of ATP.

Now that we have a structure for GRP94 from dog we can compare the structures of proteins from different species to see how closely they resemble each other. Let's look at the N-terminal domain to get an idea of how protein structure is conserved over billions of years. The four structures below are, from left to right, yeast (1zwh), dog (2fyp), human (1us7) and E. coli (2ior).


Aren't they remarkably similar! This is exactly the sort of thing you expect with a highly conserved protein.

By the way, anyone can create these images by going to the PDB site [2ior] and viewing the structures with the MBT SimpleViewer. If you haven't already installed this viewer it will automatically install in your browser and it only takes a few minutes.

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Dollins, E.D., Warren, J.J., Immormino, R.M. and Gewirth, D.T. (2007) Structures of GRP94-Nucleotide Complexes Reveal Mechanistic Differences between the hsp90 Chaperones. Molec. Cell 28:41-56.

The Toronto Star Defends Its Editorial Policy on MMP

 
The editorial page of today's Toronto Star contains a column by Kathy English, who is identified as "Public Editor." The point of the article is to respond to people who criticized the paper's editorials against the Mixed Member Proportional voting system [Sparking needed debate on MMP].

The column begins with the usual motherhood statements that you would expect.

The heart of democratic politics is public debate of public concerns.

During election campaigns, it is the media's role and responsibility to encourage this debate and to provide accurate, unbiased information about politicians, parties, policies and the electoral process so that citizens can cast informed votes.

No disagreement there. It is, indeed, the responsibility of The Toronto Star to provide accurate, unbiased information. Did it succeed in the case of the referendum issue?

Not surprisingly, our election coverage was not without its critics. One group in particular was highly critical of the Star – the supporters of electoral reform, specifically, the system known as "mixed-member proportional" that was soundly rejected in this week's referendum.

Yes, there was criticism and I'm one of those who was highly critical [Toronto Star Trashes MMP, Again, The Toronto Star Endorses First-Pass-the-Post].

Dissatisfaction with our coverage of MMP began on the second day of the campaign when my office and our Letters page were blitzed by MMP supporters who took exception to the word "appointed" in a news story that explained how under MMP, 39 members of the Legislature would be selected from party lists.

I discussed this with National Editor Alan Christie, who directed our election news coverage and has worked on more than a dozen elections at every level of government in his 30 years at the Star. We realized that the word had become something of a political football in this highly polarized campaign. In the interests of our news coverage not being seen as biased for either side of this crucial debate, Christie then advised reporters that referendum articles should avoid stating that list members would be appointed. We told MMP supporters this, adding that columnists and editorials were entitled to their own interpretation of whether this word was apt.

It's not just that the work "appoint" is loaded; it's factually incorrect. The list members are elected by democratic vote. It may not be the same kind of election as we're used to but that's because Canada is one of the few Western industrialized nations that retain the old first-past-the-post system.

There may be debate over how the party list are made up but that's a far different topic than declaring that the MMPs elected from the list are "appointed." Here's what the Sept. 30 editorial said.

Although the new system promises to deliver a legislature that mirrors the voters' intent, Tory notes it would also create two classes of members of the Legislature. Some would have a direct mandate from the voters; others could simply be appointed by party bosses.

After only a few minutes of research it became clear that this statement was misleading to the point of being factually incorrect. The experience in other countries tells us that the list members will almost certainly be candidates who have been nominated in various ridings across the province. They will definitely not be appointed by party bosses and any statement to that effect reveals a profound ignorance of how the system works. The order of candidates on the list will be decided by the party but that's something different. Besides, all parties are committed to an open and democratic process for making up the list so even that part of the selection procedure will be open and transparent, and possibly democratic in the sense of requiring a vote by party members.

(Incidentally, under MMP John Tory would now have a seat in the Legislature because party leaders are almost always at the top of the party list. Nobody would argue that he would have been "appointed" to the Legislature under those circumstances, would they? Also, I note that under our current system the party boss sometimes does "appoint" candidates in certain ridings, bypassing the nomination process. If those candidates are subsequently elected to Parliament is it fair to say that they were "appointed" to the Legislature? Is this a major flaw in the first-past-the-post systesm? If so, why didn't the Toronto Star editorials mention it?)

Kathy English continues,

Meanwhile, the Star's editorial board, under the direction of Editorial Page Editor Bob Hepburn, was researching and debating electoral reform in order to decide and declare the Star's position on this important issue that could have radically changed the way we elect our politicians in Ontario.

On Sept. 30, the Star's lead editorial spoke out strongly against electoral reform. The board concluded that MMP could lead to constant electoral chaos and that our current system, though not perfect, is preferable.

Some research! Did the editors really do a lot of "research" to conclude that the countries with proportional voting systems were all constantly chaotic? I'm sure that conclusion would come as a major surprise to most Europeans. I lived in Switzerland for four years and I didn't notice that the state was in constant chaos. I also missed the fact that the surrounding states (France, Germany, Italy, Austria) were in constant chaos. Isn't that strange?

Furthermore, did the editors' research include distinguishing between the various proportional systems or did they decide to lump them all together in order to make the best case against the Mixed Member Proportional system that was before the Ontario voters? Of course they didn't make the distinction. Whether this was deliberate or as a result of ignorance is something that only Kathy English can answer. If her claim is correct—that the editors did their homework—then the only possible conclusion we can come to is that the editors deliberately took the worst examples from a fully proportional system in order to make it seem as though this would apply to the MMP system as well. That's called fearmongering. And that's one of the more polite terms that I could use if what Kathy English says is correct.

Incidentally, the use of language is important here. While it's true that the new system would have "radically changed the way we elect our politicians," it's also true that the new system would have "created a more fair way of electing politicians" and it would have "brought Canada into line with voting systems in other democracies." One of these phrases invokes alarm and fear and two of them don't. Which one did Kathy English choose in her article. Why?

That editorial also said that electoral reform would create two classes of MPPs – some with a direct mandate from voters and some who could be appointed. That raised the ire of the pro-MMP side. A press release issued by Vote For MMP accused the Star of "fear-mongering and inaccurate journalism." Some contacted my office demanding that the Star retract its editorial.

The charge is accurate. The newspaper was presented with an opportunity to clarify it's position in a second editorial. It did publish a second editorial but it was no better than the first one. The inaccuracies and the fearmongering continued. As I pointed out in my second posting, "When people spread misinformation and fear for the first time you can put it down to ignorance. When they do it a second time there's something more serious going on."

Many did not seem to understand the difference between news coverage and editorial opinion. Editorials, which do not influence news coverage, represent a newspaper's institutional position on matters that affect its community.

Effective editorials should provide leadership on divisive, important issues, as this one did. It was a studied, well-argued, sound assessment of much-debated – and disputed – facts. It was not inaccurate, nor do I believe it created fear about electoral reform.

Don't be condescending, Kathy. We're all adults here and we know the difference between an editorial and a news item. The problem is not that we object to the editors publishing their opinion, it's that we object to the "facts" that they published. "Facts" upon which they based their opinion.

It absolutely astonishing to me that you would make the claim you just made. The idea that the Star's editorials were based on "studied, well-argued, sound assessment of ... facts" boggles the mind. What in the world are you thinking?

Let me give you an example of your "facts." Both editorials brought up certain governments, some of which have systems that are full proportional systems or other types that ar not MMP. In the second editorial the authors said,

Countries that have gone this route, including Israel, Italy, Germany and Belgium, have become notorious for chaotic, horse-trading minority governments and legislative gridlock.

In what universe does this become a "fact"? And even if there was some truth to the statement why didn't they mention all the other states with PR where it wasn't true? Even better,why didn't they tell us about the states with MMP systems? Under no possible circumstances can you claim that this is a well-argued assessment of facts.

As for fearmongering, while you may think that the editorials did not create fear about electoral reform, an objective analysis says otherwise. The titles of the two editorials were "Electoral reform a backward step" and "Electoral reform fraught with risk." They made liberal use of words like "chaos" "divisive" and "special-interest parties." The first editorial warned that a minority government under MMP , "...may make alliances with the pro-life, anti-gay marriage Family Coalition party. Or with another fringe party that might be pro-gun or anti-medicare."

If that doesn't count as fearmongering then I don't know what does. I suggest that Kathy English take a more careful, objective look at those editorials and think harder about the reaction they provoked.

She closes the opinion piece by pointing out that the Star published lots of letters for and against MMP and that one of their columnists wrote a pro-MMP piece. That's nice but it's irrelevant. The problem was with the editorials and that problem doesn't go away just because the newspaper published pro-MMP letters to the editor.

I was prepared to let this issue die since the referendum vote was overwhelmingly against MMP. But when the Star editors drag it up again with an article like this one, it can't be ignored. Now, on two separate occasions, the newspaper has had a chance to seriously address it's critics: one before the second editorial, and now after the referendum. On both occasions The Toronto Star has failed to live up to the standards good journalism.

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Eugene Koonin and the Biological Big Bang Model of Major Transitions in Evolution

 
Eugene Koonin runs a large laboratory at the National Center for Biothechnology Information (NCBI) in Bethesda, MD. (USA) [Evolutionary Genomics ResearchGroup]. His group tends to focus on new ways of analyzing sequences databases and on interesting findings from database mining expeditions.

Koonin and his coworkers are strong supporters of the Three Domain Hypothesis and they usually interpret their data in terms of three domains of life (Bacteria, Archaea, Eukaryotes) with eukaryotes being derived from archaea. As for other evolutonary relationships, Koonin tends to be a "lumper" rather than a "splitter." He will sometimes conclude that two genes or proteins are homologous based on evidence that others find inconclusive.

Creationist Link

Darwin Doubting Heretic Reveals Himself at National Center for Biotechnology
Evolution News & Views
According to Koonin, proteins with similar architecture (folds) are related by common descent even if there's no significant sequence similarity. This is not an uncommon position but it's controversial. Some scientists are not willing to accept that structural similarity alone is sufficient to establish homology. There are too many cases where this assumption leads to awkward and unreasonable implications. Convergence is a possibility that must be entertained.

Koonin has recently published a paper in Biology Direct where he attempts to explain a number of real—or imagined— problems in evolution. In case you're not familiar with this journal, it's a new "open access" journal with an unusual policy. The reviewers must identify themselves and their comments are posted at the end of the paper along with responses from the author(s). Koonin is one of the editors of this journal and he explains the basic philosophy in an editorial [A community experiment with fully open and published peer review].

In Biology Direct, we seek to live by the realities of the 21st century while addressing the issue of information overflow in a constructive fashion and offering a remedy for the ills of anonymous peer review. The journal will publish "essentially anything", even papers that receive three unanimously negative reviews, the only conditions being that three Editorial Board members agree to review (or solicit a review for) the manuscript and that the work qualifies as scientific (not pseudoscientific as is the case for intelligent design or creationism) – and, of course, that the author wants his/her paper published alongside the reviews it receives. Everything in Biology Direct will be completely in the open: the author will invite the referees without any mediation by the Editors or Publisher, and the reviews will be signed and published together with the article. The idea is that any manuscript, even a seriously flawed one, that is interesting enough for three respected scientists to invest their time in reading and reviewing will do more good than harm if published – along with candid reviews written by those scientists. Under the Biology Direct rules, an author is free to solicit as many members of the Editorial Board as s/he has patience for. The philosophy behind this approach is that what really matters is not how many scientists are uninterested in a paper (or even assess it negatively, which could be the underlying reason for declining to review) but that there are some qualified members of the scientific community who do find it worthy of attention. A manuscript will be, effectively, rejected only after the author gives up on finding three reviewers or exhausts the entire Editorial Board. We believe this is fair under the rationale that work that fails, after a reasonable effort from the author, to attract three reviewers is probably of no substantial interest, even if technically solid.

The paper that concerns me here is Koonin (2007) The Biological Big Bang model for the major transitions in evolution. In all cases, the "problems" that Koonin addresses seem to be the rapid and unexplained appearance of novel characteristics, especially those that count as major transitions in evolution. Examples are the origin of cells and the Cambrian explosion.

These events can all be explained by the Biological Big Bang (BBB) model of evolution as Koonin describes in his paper. The concept of the Biological Big Bang is explained in the abstract ...

I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on.

The BBB model is clearly not gradualistic. Koonin attempts to ally himself with other advocates of episodic change such as Niles Eldredge and Stephen J. Gould. (Where necessary, I have converted Koonin's number references to ones in which the author and date is displayed.)

However, the evolution of life is, obviously, a non-uniform process as described, e.g., in Simpson's classic book [3,4], and captured, more formally, in the punctuated equilibrium concept of Gould and Eldredge [Eldredge and Gould, 1997; Gould and Eldredge, 1993]. Lengthy intervals of gradualist modification are punctuated by brief bursts of innovation that are often called transitions, to emphasize the fact that they culminate in the emergence of new levels of organizational and functional complexity [Maynard Smith and Szathmáry, 1997]

I take issue with Koonin's description of punctuated equilibria (PE). PE is a pattern of evolution that describes speciation events. The morphological changes that characterize a new species are locked in place rapidly during cladogenesis (speciation by splitting). For the most part, these morphological changes are subtle and it often takes an expert to recognize them in the best documented cases. Furthermore, these small changes occur repeatedly in a number of distinct cladogenesis events spread out over tens of millions of years. The result is a very distinctive and well-defined phylogenetic tree that defines the punctuated equilibrium pattern. .

Science Link

Examine macroevolutionary concepts carefully
Nick MatzkePE has nothing to do with the major transitions that Maynard Smith and Szathmáry discuss in their books (The Major Transitions in Evolution, The Origins of Life). Nor is PE related in any way to the big bang problems that Koonin is addressing in this paper. It's difficult to decide whether Koonin misunderstands punctuated equilibria or whether he is just stretching an analogy. I suspect the former.

It is no coincidence that the Biological Big Bang model borrows terminology from cosmology. Koonin is very explicit about the similarities between his evolutionary model and the cosmological model for the origin of the universe. As a matter of fact, he explicitly addresses this issue in response to one of the reviewers (William Martin) who challenges the comparison. To me, the comparison between biology and cosmology seems forced and I think he weakens his case considerably by comparing the origin of the universe to the Cambrian explosion. Comparisons like that—and the false analogy with punctuated equilibria—contribute to the sense of unease that I had on finishing the paper. One has the distinct impression that Koonin is grasping at straws in order to knock down a strawman.

What are the major problem with evoluton according to Koonin? Are they strawmen? He identifies six major problems and claims that they can all be explained by a model where "evolutionary transitions follow a general principle that is distinct from regular cladogenesis." The BBB is characterized by a phase of rapid evolution with extensive exchange of genetic information between organisms. This phase is followed by a slow phase of evolution of the sort that generates the typical tree pattern.

Before describing the six examples, we need to address the differences, if any, between Koonin's Biological Big Bang and the "net of life" model that is replacing the traditional tree of life at the deepest levels [The Three Domain Hypothesis (Part 5, Part 6)]. The similarities are obvious. In the net of life model the early stages of evolution involved massive exchanges of genetic information such that it is now impossible to construct a traditional tree relating the major groups of species such as prokaryotes and eukaryotes. What Koonin is doing is to generalize this event "by proposing that a phase of rapid, promiscuous evolution might underlie many, if not most of the major transitions in the history of life."

The six transitions are listed below. Each one is followed by a brief comment where I attempt to evaluate its significance.

1. Origin of protein folds
There seem to exist ~1,000 or, by other estimates, a few thousand distinct structural folds the relationships between which (if existent) are unclear.

There is no reason to postulate that all proteins sharing a common fold will share a common ancestor. Some of these proteins might well have arisen entirely independently and evolved to a common fold by convergence. In other words, the underlying assumption that the origin of protein folds represents evolution of some sort may be false. Furthermore, there is even less reason to think that groups with different folds have an evolutionary relationship. In order for this to be true there would have to have been a primordial protein with one kind of fold that gave rise to a protein with another kind of fold. Instead different polypeptides with little three-dimensional structure (random coils) may have independently evolved into proteins with particular folds.

2. Origins of Viruses
For several major classes of viruses, notably, positive-strand RNA viruses and nucleo-cytoplasmic large DNA viruses (NCLDV) of eukaryotes, substantial evidence of monophyletic origin has been obtained. However, there is no evidence of a common ancestry for all viruses.

The reason why there's no evidence of a common ancestor for all viruses may be because there is no common ancestor for all viruses.

3. Origin of Cells
The two principal cell types (the two prokaryotic domains of life), archaea and bacteria, have chemically distinct membranes, largely, non-homologous enzymes of membrane biogenesis, and also, non-homologous core DNA replication enzymes. This severely complicates the reconstruction of a cellular ancestor of archaea and bacteria and suggests alternative solutions.

The existence of distinct bacterial and archaeal domains is hotly disputed. Many groups of bacteria have distinctive features that distinguish them from other groups. There is no need to postulate a radically new mechanism of evolution that accounts for bacteria and archaea if they really aren't much different than the major branches described below.

4. Origin of the major branches (phyla) of bacteria and archaea
Although both bacteria and archaea show a much greater degree of molecular coherence within a domain than is seen between the domains (in particular, the membranes and the replication machineries are homologous throughout each domain), the topology of the deep branches in the archaeal and, especially, bacterial phylogenetic trees remains elusive. The trees conspicuously lack robustness with respect to the gene(s) analyzed and methods employed, and despite the considerable effort to delineate higher taxa of bacteria, a consensus is not even on the horizon. The division of the archaea into two branches, euryarchaeota and crenarchaeota is better established but even this split is not necessarily reproduced in trees, and further divisions in the archaeal domain remain murky.

In addition to eurarchaeote and crenarchaeota there are other groups of prokaryotes that are easily resolved by current techniques (e.g., cyanobacteria, proteobacteria). It may be difficult to resolve the base of the tree because of extensive horizontal gene transfer as postulated in the "net of life" scenarios. This is the one case, along with #3, where the concept of an unusual type of evolution may be correct. I still don't like the term Biological Big Bang to describe it.

5. Origin of the major branches (supergroups) of eukaryotes
Despite many ingenious attempts to decipher the branching order near the root of the phylogenetic tree of eukaryotes, there has been little progress, and an objective depiction of the state of affairs seems to be a "star" phylogeny, with the 5 or 6 supergroups established with reasonable confidence but the relationship between them remaining unresolved.

Substantial progress has been made but the problem is very difficult because of the lack of reliable phylogenetic markers. That, plus the fact that we are trying to sort out events that took place more than one billion years ago. It is too early to conclude that our inability to reach consensus means that something strange must have been going on. That's a cop-out at this time.

6. Origin of the animal phyla
The Cambrian explosion in animal evolution during which all the diverse body plans appear to have emerged almost in a geological instant is a highly publicized enigma [32-35]. Although molecular clock analysis has been invoked to propose that the Cambrian explosion is an artifact of the fossil record whereas the actual divergence occurred much earlier [36,37], the reliability of these estimates appears to be questionable [38]. In an already familiar pattern, the relationship between the animal phyla remains controversial and elusive.

Actually, the relationships between animal phyla are quite well understood at the molecular level. The lineages do not appear to be scrambled by excessive recombination between species as Koonin's hypothesis would require.

The Cambrian explosion is an interesting example of fairly rapid morphological evolution. It may be true that dozens of independent animal lineages simultaneously acquired a new mechanism of evolution during the Cambrian but this does not seem to be the most parsimonious explanation of the data.

To sum up, I don't think that Koonin's examples cry out for explanation in the way he thinks they do. Some of them may not even be examples of evolution. It seems reasonable to attribute the origins of the major groups of bacteria, and the first eukaryotic cells, to a rapid exchange of genes in the beginning phase of life on Earth, but there's no need to postulate that this promiscuous phase was ever repeated at other stages and certainly no reason to assume that there were repeated waves of promiscuity followed by quiescent phases of stabilizaton.

The Biological Big Bang is not so much wrong as it is unnecessary.

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Koonin, E. (2007) The Biological Big Bang model for the major transitions in evolution. Biology Direct 2:21doi:10.1186/1745-6150-2-21.

[Photo Credit: The Tree of life is from Ford Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American.]

Darwin Awards

 
Friday's Urban Legend: MOSTLY FALSE

Haver you ever received an email message like this one?

It's that time again! Yes, it's that magical time of the again when the Darwin Awards are bestowed, honoring the least evolved among us. Here then, is the glorious winner:

Darwin Award winners:

1. When his 38-caliber revolver failed to fire at his intended victim during a hold-up in Long Beach, California, would-be robber James Elliot did something that can only inspire wonder. He peered down the barrel and tried the trigger again. This time it worked..... And now, the honorable mentions: ....

Did you think it was a true story? Unfortunately, these stories are about as accurate as the ones that tell you about your lottery winnings or your long-lost relative who just died and left you $350,000.

Go to snopes.com to get the inside story on the 2005 Darwin Awards and all the others.

Contrary to common belief, there is no panel of distinguished judges weighing each potential Darwin Award entry then sagely reaching agreement as to which deserves an official accolade. Darwin Awards e-mails have been circulating on the Internet at least since May 1991, with the earliest e-mails and newsgroups posts of this nature setting before posterity inventive works of fiction that had been labeled by their authors as true accounts of actual deaths. Years after the term "Darwin Award" was being used in connection with text descriptions of deaths by misadventure, a number of web sites sprung up to archive the variety of Darwin Award tales then in circulation. Those sites not only collected the fictional offerings then making the online rounds but also on their own dug up numerous true accounts of death by stupidity, thus building a vast body of such tales, some true and some not. While other sites have since faded into obscurity, one has emerged as the clear winner: www.DarwinAwards.com, a site owned and maintained by Wendy Northcutt. Ms. Northcutt has since authored three highly successful books based on her site.

The various "Annual Darwin Awards" e-mails (such as the one which is the topic of this article) do not originate with DarwinAwards.com; they are put together by unknown persons.

The cover of one of Wendy Northcutt's book is shown above. (It's the first volume.) The book lists hundreds of Darwin awards, Honorable Mentions, Urban Legends, and Personal Accounts. Many, but not all, of the valid Darwin Awards are marked "Confirmed by Darwin" to indicate that Wendy Northcutt has checked them out and they actually happened. Unfortunately, confirmation often consists of just tracking down a newspaper account that repeats the story. We all know that newspaper reporters can often be taken in by made-up stories.

They may be fake but they're still amusing. Here's one of the latest from www.DarwinAwards.com.

(21 June 2007, Philippines) Three enterprising individuals tried to make a buck by selling metal to the scrap heap. They entered a former US military complex in Clark, Pampanga, Philippines. Before them stood the prize: an abandoned water tank! Bedazzled by the profit to be made, the three gleefully abandoned logic, and began to cut the metal legs out from under the water tank. Guess where the tank fell? Straight onto the thieves. They have not yet been identified, as their bodies were severely flattened.

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The Genome of Chlamydomonas reinhardtii

 
This week's issue of Science (Oct. 12, 2007) contains a summary of the draft genome sequence of the green alga, Chlamydomonas reinhardtii (Merchant et al. 2007) [The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions].

Chlamydomonas is a single-cell green alga with a prominent chloroplast and cilia. It normally lives in the soil or in lakes and streams. Green algae are members of the division Chlorophyta, which includes all green algae. The complete genome sequencs of two other green alga, Ostreococcus tauri and Ostreococcus lucimarinus, have been published. Chlamydomonas is distantly related to Ostreococcus.

Interest in Chlamydomonas stems from the fact that it has long been a model organism and has a well-established genetic background. Furthermore, the relationship between the green algae and plants (mosses, liverworts, ferns, angiosperms etc.) is well established. The green algae share a common ancestor with all plants and this relationship is more recent than the relationship between plants and any other protists. (Red algae are the next closest group.)

The nuclear genome is 121 Mb (121,000,000 base pairs) in size and it's divided into 17 linkage groups (chromosomes). This is a draft genome sequence representing about 95% of the complete sequence with 13x coverage of the sequenced regions. The remaining 5% consists mostly of repeat regions and it's unlikely that they will ever be sequenced.

The preliminary analysis predicts 15,143 protein-encoding genes; three ribosomal RNA clusters; and 259 transfer RNA genes (tRNA). This is about the same number of genes as Drosophila melanogaster (fruit fly) but fewer than the number in mammals (~22,000). In most cases, the original estimates of gene number are inflated so we can expect this number to drop to about 12,000 as annotation continues. So far, 8631 genes have been confirmed.

There are 61 classes of simple repeat sequences; about 100 families of transposable elements; and 64 families of short interspersed elements (SINEs) that appear to be derived from tRNA genes. Most of the protein-encoding genes have introns (avg. 8 introns/gene). There are more introns and longer introns than in most unicelllar species.

Assuming 2Kb of coding region per gene, it looks like genes and their associated regulatory sequences make up about 30% of the genome. The remaining DNA (mostly junk) is evenly distributed between introns and intergenic regions.

The authors identified about 350 genes that are associated with chloroplast function. Most of these are genes that originally resided in the chloroplast DNA. Over time they have been transferred to the nucleus. These genes are easily recognized because they are related to genes from cyanobacteria, from which chloroplasts are derived, and they are only found in species that have chloroplasts.

The known genes in this group encode the proteins of the photosynthetic apparatus [A Simple Version of Photosynthesis] and the metabolic pathways found in the chloroplast (e.g., Rubisco, The Calvin Cycle). Surprisingly, over 200 of these genes have unknown functions and only half of those genes (100) belong to larger gene families from which putative functions can be surmised. This suggests that there may be some unknown pathways or functions in chloroplasts.

There are about 125 genes involved in assembly and function of the cilia (flagella) and most of these have been previously identified. Note that many different species of eukaryote contain cilia but they have been lost in plants. The only other sequenced genome from green algae is that from Ostreococcus and it's interesting to note that although Ostrecoccus does not have cilia its genome still retains half of the genes required for cilia assembly and function.

There are several other interesting features of Chlamydomonas that can now be studied with the aid of the genome sequence. For example, Chlamydomonas has a small eyespot that can detect light and trigger a phototactic response. The eyespot is related to plastids (chloroplast) except that the thylakoid membrane is packed with red pigment molecules. The specific genes involved in eyespot assembly are similar to genes found in mammalian retina and they probably interact with heme groups. The availability of a genome sequence should help to decipher the molecular architecture of this eyespot.

(The authors are from 63 different departments and institutes in the following countries: USA, France, China, Belgium, United Kingdom, Spain, Japan, Mexico, Germany, Australia, Canada, Turkey, Czech Republic, and Italy.)

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Merchant, S.S. et al. (117 authors) (2007) The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions. Science 318:245-250.

[Photo Credits: The phylogenetic tree is part of Figure 2 in Merchant et al. 2007. The diagram of Chlamydomonas is from this website. It is probably taken from a textbook. The photograph of living Chlamydomonas is from this website.]

Judgment Day: Intelligent Design on Trial

 
This is a NOVA TV show about the Dover, PA trial of 2005. It sure looks interesting and I'm looking forward to seeing it on November 13th.

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[Hat Tip: Monado at Science Notes ( "Intelligent Design on Trial" - Nova, PBS TV)]