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).
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 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. 
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 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.
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.
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 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 heart of democratic politics is public debate of public concerns.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?
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.
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.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.
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.
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.
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.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?
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.
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.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.
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.
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.
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. 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.
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. .
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."1. Origin of protein foldsThere 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.
There seem to exist ~1,000 or, by other estimates, a few thousand distinct structural folds the relationships between which (if existent) are unclear.
2. Origins of VirusesThe reason why there's no evidence of a common ancestor for all viruses may be because there is no common ancestor for all 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.
3. Origin of CellsThe 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.
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.
4. Origin of the major branches (phyla) of bacteria and archaeaIn 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.
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.
5. Origin of the major branches (supergroups) of eukaryotesSubstantial 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.
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.
6. Origin of the animal phylaActually, 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 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.
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.]
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: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.
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: ....
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 earlieste-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. (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.
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]. 
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 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.
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. 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.]
[Hat Tip: Monado at Science Notes ( "Intelligent Design on Trial" - Nova, PBS TV)]
There are a lot of studies suggesting that a substantial percentage of the genome is transcribed even though less than 5% is known to be functional. This leads to the idea that it encodes some unknown function. The argument is that these regions would not be transcribed unless they were doing something useful.Wyers, F., Rougemaille, M., Badis, G., Rousselle, J.C., Dufour, M.E., Boulay, J., Régnault, B., Devaux, F., Namane, A., Séraphin, B., Libri, D. and Jacquier A. (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725-37.
The 2007 Nobel Prize in Chemistry goes to Gerhard Ertl "for his studies of chemical processes on solid surfaces." The prize is really for working out the mechanisms of catalysis on metal surfaces [Press Release].Gerhard Ertl has founded an experimental school of thought by showing how reliable results can be attained in this difficult area of research. His insights have provided the scientific basis of modern surface chemistry: his method-ology is used in both academic research and the indust-rial development of chemical processes. The approach developed by Ertl is based not least on his studies of the Haber-Bosch process, in which nitrogen is extracted from the air for inclusion in artificial fertilizers. This reaction, which functions using an iron surface as its catalyst, has enormous economic significance because the availability of nitrogen for growing plants is often restricted. Ertl has also studied the oxidation of carbon monoxide on platinum, a reaction that takes place in the catalyst of cars to clean exhaust emissions.It's interesting that this award comes almost 100 years after Wilhelm Oswald got the Prize for his work on catalysis in solution. See yesterday's Nobel Laureate [Nobel Laureate: Wilhelm Ostwald].
The Biotechnology and Biological Sciences Research Council is one of seven Research Councils sponsored through the UK Government’s Office of Science and Innovation and invests around £336 million per annum in the biosciences.Pretty impressive, eh? With a mission like that you'd expect a world-class press release, right? Let's see how they do ...
BBSRC sustains a world-class bioscience research community for the UK. Its mission is to fund internationally competitive research, provide training in the biosciences, foster opportunities for knowledge transfer and innovation and promote interaction with the public and other stakeholders on issues of scientific interest.
Embryologists at UCL (University College London) have helped solve an evolutionary riddle that has been puzzling scientists for over a century. They have identified a key mechanism in the initial stages of an embryo’s development that helps differentiate more highly evolved species, including humans, from less evolved species, such as fish. The findings of the research, funded by the Biotechnology and Biological Research Council (BBSRC), were published online today by the journal Nature.Undergraduate students in my university are taught that humans and fish share a common ancestor. They have both evolved for the same length of time from that common ancestor, therefore you cannot say that one is more evolved and one is less evolved. People who say that are demonstrating a fundamental misunderstanding of evolution.
Early on in development, the mass of undifferentiated cells that make up the embryo must take the first steps in deciding how to arrange themselves into component parts to eventually go on to form a fully developed body. This is a process known as ‘gastrulation’. During this stage, the cells group into three layers, the first is the ‘ectoderm’ which then in turn generates the ‘mesoderm’ and ‘endoderm’ layers. In higher vertebrates, such as mammals and birds, the mesoderm and endoderm are generated from an axis running through the centre of the embryo. However, in lower vertebrates, such as amphibians and fish, the two layers are generated around the edge of the embryo.Using the terms "higher vertebrates" and "lower vertebrates" is just as bad as using "more evolved" and "less evolved."
Scientists have been speculating for over a century on the difference between the embryonic development of higher vertebrates and lower vertebrates, to help answer how the simple cell structure of an embryo goes on to form the various highly complex bodies of different species. Research leader Prof Claudio Stern explains: “This is a significant find as it is a clear difference between the embryonic development of more advanced species and less advanced species. It suggests that higher vertebrates must have developed this mechanism later on in the history of animal evolution.Scientists who use terms like "more advanced" and "less advanced" to distinguish modern species are demonstrating their ignorance. They should not be publishing papers about evolution.
We propose that local intercalation in the epiblast is responsible for positioning and shaping the primitive streak and can also explain the polonaise movements without the need for long-range gradients. Convergent extension of the axial mesoderm and neural plate in anamniotes is almost certainly conserved in amniotes, but our study reveals an additional, much earlier (pre-gastrula) cell intercalation, required for morphogenesis of the primitive streak independently of mesendoderm specification. This is apparently unique to amniotes and provides a possible answer to the classical question of how evolution converted the equatorial blastopore or shield of Anamnia into the radially oriented primitive streak of amniotes.There's nothing wrong with this. It does not claim that amniotes are "higher" than fish or amphibians and it does not claim that fish have stopped evolving.
Voiculescu, O., Bertocchini, F., Wolpert, L., Keller, R.E. and Stern, C.D. (2007) The amniote primitive streak is defined by epithelial cell intercalation before gastrulation. Nature (advance online pubication: doi:10.1038/nature06211).
Zimmer, Carl (2005) How and Where Did Life on Earth Arise? Science 309:89. [Text] [PDF]Carl Zimmer is one of the best science writers on the planet. He has just won the National Academies 2007 Communication Award. It goes with his many other prizes and awards. Carl has a blog [The Loom].
Just where on Earth these building blocks came together as primitive life forms is a subject of debate. Starting in the 1980s, many scientists argued that life got its start in the scalding, mineral-rich waters streaming out of deep-sea hydrothermal vents. Evidence for a hot start included studies on the tree of life, which suggested that the most primitive species of microbes alive today thrive in hot water. But the hot-start hypothesis has cooled off a bit. Recent studies suggest that heat-loving microbes are not living fossils. Instead, they may have descended from less hardy species and evolved new defenses against heat. Some skeptics also wonder how delicate RNA molecules could have survived in boiling water. No single strong hypothesis has taken the hot start's place, however, although suggestions include tidal pools or oceans covered by glaciers.
Research projects now under way may shed more light on how life began.
