The Toronto Star Editorial Cartoon

 
Today's editorial cartoon in The Toronto Star is worth sharing. If Canadians were allowed to vote in the US Presidential elections, the McCain people would have waved the white flag months ago.

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The Toronto Star Opposes PR, Again

 
I don't get it. Why are the editors of The Toronto Star against proportional representation? Their reasoning doesn't make sense.

Last year the editorial board opposed the Ontario referendum on electoral reform. Their arguments were so stupid and factually incorrect that "Public Editor" Kathy English was obliged to defend the newspaper's editorial opinions [The Toronto Star Defends Its Editorial Policy on MMP].

She didn't do a very good job.

Today The Star has an editorial opposing any proportional electoral system. The paper notes that a nationwide proportional system of voting would have given a different distribution of seats than the result of last Tuesday's election. They note that the Green party would have probably gotten a number of seats.

The editorial states, correctly, that we can't just recalculate the results based on Tuesday's voting because if we had voted under a proportional system people wold have voted differently. They say ...

Furthermore, the analysis is backward looking – transposing last week's results onto a new system. In all likelihood, if Canada had a system of proportional representation, the outcome would be very different, given the demographical and geographical diversity of the country. The pro-life Christian Heritage Party, for example, might win enough votes to get seats. And new parties might emerge to win seats – say, an Alberta First party or even ethnic parties.

So Harper might be kept in power by entering a coalition with pro-life and Alberta First parties. Now that, indeed, is a scary prospect.

This is scary. It looks like the editors of The Star are afraid of proportional voting because (horrors!) some people might elect MP's who truly represent their points of view.

Now we certainly can't have that in a democracy, can we?

The scare tactics are not based on rational analysis of what happens in other countries. Most Western democracies have moved into the 21st century and they find it beneficial to let the people have their say. Sticking with an unfair first-past-the -post system only breeds disillusionment and bitterness with a system that disenfranchises a majority of voters. (Voter turnout on Tuesday dropped below 60%.)

It's time for The Toronto Star to find new editors—ones who are as progressive as the newspaper they work for. The current editors are clearly not up to the job.

But maybe we shouldn't expect too much from editors who put Madonna on the front page under a banner about a rape probe.

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Barack Obama Is my Cousin!

 
George Bush and I share a common ancestor. This isn't as surprising as it might seem. Just about anyone in North America who has relatives from the British Isles will be able to trace some of their ancestors back five or six hundred years if they dig hard enough.

There's an excellent chance that you can connect at some point to several well-known lineages, usually those involving kings and queens. In my case I eventually hook up with Mary Stewart (1380 - 1458) who is the daughter of Robert III, King of Scotland. She married George Douglas (1376 - 1402).

George Bush descends from Mary's sister Elizabeth Stewart who married James Douglas, brother of George Douglas [The Ancestry of George Bush].¹

Now, most of you might not be too excited about being related to George Bush but here's the good news ... I'm also related to Barack Obama according to Obama and Bush related.

That's pretty cool. It explains a lot.

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1. It's possible that Bush descends from Beatrice Sinclair and not Elizabeth Stewart—the website is confusing. Even if this is an error there are several other connections.

If you build it, will they follow?

I'm going to subject you to one of my pet peeves.

The University of Toronto is in the process of replacing all its pathways. I really like the new style of path even though it's probably very expensive. It will improve the look of the university.

That's not the peeve. Look at the photograph below. It shows the newly completed paths leading up from the subway stop on the corner of University and College (behind me). The ramp is the easiest access to my building. Several hundred people a day walk up the path from the subway stop and up the ramp into the building.

When the stone masons were building the path I mentioned that the old pathway didn't align with the much newer ramp and, consequently, people were cutting across the grass in order to save time. That's why the grass is worn away at the base of the ramp. The guys who were laying the stones agreed that the fancy new path should at least clip off the corner by the lamp post to encourage people to follow it.

They were overruled by their supervisor who claims he doesn't have the authority to move or change the paths. So they simply replaced the old paved pathway with the nice new stone blocks and moved on.

How ridiculous. My pet peeve is this. You should build pathways where people actually walk and not where you want them to walk.

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What Questions about Evolution Can Students Safely Ask?

 
Denyse O'Leary is upset about the fact that students who challenge evolution may be perceived as being unworthy [Intelligent design and popular culture: What questions about evolution can students safely ask?].

She was impressed with the suggestions made by some photographer so she reproduced them on her blog. Here's what Densye O'Leary thinks will stump the average Professor. This is just for amusement on a Friday afternoon.

Don't argue against him. Agree with him. Then ask a question like one of those below:

1. I’d like to shut up those stupid IDers once and for all. Please tell me where I can find a book that shows clearly all the transitional fossil forms between fish and amphibians or reptiles and birds or some such major transition. I’d like to see it spelled out in detail with pictures and measurements and explanations of each fossil so I can crush those idiots.

2. I know that evolution is the most solidly proven theory in all of science, so please show me the mathematical proof of how random changes create information. I’m sure there must be one because this is a fundamental truth of evolution.

3. I know that in any system like life on earth that is open and receives outside energy the system will steadily grow more and more complex but I don’t really understand the physics of this. Could you explain it to me?

Just in case you've forgotten, this is what passes as the best evidence for Intelligent Design Creationism. We should think up a name to describe these people.

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Jonathan Wells reviews the Christiane Nüsslein-Volhard and Wieschaus Experiment

In his book, Icons of evolution, Jonathan Wells has ten chapters devoted to refuting evolution. This is typical behavior for an Intelligent Design Creationist. There's no mention anywhere in the book of positive evidence for intelligent design.

One of the chapters is "Four-Winged Fruit Flies." The main point of the chapter is that most of the Drosophila developmental mutations are lethal or extremely deleterious so they can't be transitional states in evolution. Yet, according to Wells, the textbooks are full of misleading statements claiming that morphological mutations supply the raw material for evolution. Wells says that there's no evidence for any beneficial mutations in spite of the fact that they have been looked for.

Yet the evidence cited in these textbooks falls far short of supporting those sweeping claims. To be sure, biochemical mutations lead to antibiotic and insecticide resistance, and human beings carrying the sickle-cell trait are more likely to survive malaria as infants. But only beneficial morphological mutations can provide the raw materials for morphological evolution, and evidence for such mutations is surprisingly thin. As we have seen, four-winged fruit flies do not provide the missing evidence, despite their current popularity.

If textbook-writers have no good examples of beneficial morphological mutations, it's not because biologists haven't been looking for them About the time that Lewis was studying Ultrabithorax, German geneticists Christiane Nüsslein-Volhard and Eric Wieschaus were using a technique called "saturation mutagenesis" to search for every possible mutation involved in fruit fly development. They discovered dozens of mutations that affect development at various stages and produce a variety of malformations. Their Herculean efforts earned them a Nobel prize (which they shared with Lewis), but they did not turn up a single morphological mutations that would benefit a fly in the wild. [my emphasis]

The experiment that was performed by Christiane Nüsslein-Volhard and Eric Wieschaus was designed to detect recessive lethal mutations that affected development. These kind of mutations are likely to identify genes that are essential for development. I described the experiment in a separate posting [Balancer Chromosomes].

Note that the experiment was specifically designed to detect deleterious mutations—lethal being about as deleterious as you can get. It could not possibly have detected beneficial mutations, as Wells claims, since these would have been discarded early on when the mutant lines were established.

Was the true purpose of the experiment a well-kept secret known only to insiders? Hardly. Everyone who read the papers knew that the screen was for recessive lethals. In her Nobel lecture Christiane Nüsslein-Volhard says,

In 1979, Eric Wieschaus and I, at that time in the EMBL, Heidelberg, had developed the methods for the large scale screening for embryonic lethal mutations in Drosophila. The screening procedure focused on the segmented pattern of the larval epidermis (8). In this and subsequent screens, a number of new genes acting in the embryo and required for the formation of a morphologically normal larva were discovered (9-11).

Should Wells have known this? You be the judge.

Wells has a Ph.D. in biology, molecular and cell biology, from the University of California, Berkeley (USA). He worked on embryology and evolution as a graduate student and subsequently as a post-doctoral fellow in the laboratory of Carolyn Larabell at Berkeley. He published two papers on development in 1996 and 1997.

It's safe to assume that Wells understands the basic principles of genetics and developmental biology.

Could Wells have misunderstood the purpose of the Nüsslein-Volhard & Wieschaus experiment? No, Wells may be an IDiot but he's not that stupid. When Wells makes an issue of the fact that Nüsslein-Volhard & Wieschaus did not find any beneficial mutations there's only one rational conclusion: Wells was deliberately misrepresenting the truth.

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[Photo Credit: Jonathan Wells from Conservapedia]

Way to Heaven

 
This woman was greeting people at the subway stop outside of the Pharmacy Building on the university campus. You don't see this very much aroound here so I thought I take a picture.

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Parliament

 
I was cleaning up the photos on my cellphone and I found this. The buildings in the background are Canada's Parliament Buildings on "the hill." It's where all the MP's elected on Tuesday will be meeting in a few weeks. Does anyone recognize where I was when I took the picture?

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Tangled Bank #116

 
The latest issue of Tangled Bank has been published on Pro-Science [116th Tangled Bank].

Welcome to the 116th edition of the Tangled Bank. As usually, we have a lot of good stuff for you all. Unlike some former hosts, I am not a very creative writer, and I'll spare you all from any attempts of making some kind of theme for this Tangled Bank. So, without any further ado, let's get to the posts.

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Send an email message to host@tangledbank.net if you want to submit an article to Tangled Bank. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger.

Balancer Chromosomes

Monday's Molecule #92 was a depiction of an inversion in a Drosophila chromosome (right).

The chromosomes shown here are the large polytene chromosomes of the salivary glands. They are made up of 1000-2000 aligned stands of DNA that form when successive rounds of DNA replication are not followed by separation of cell division. Flies that are heterozygous for a wild type chromosome and one with a large deletion inversion, will form the loop structure shown in the diagram.

In normal cells, you won't see this structure as the chromosomes align during mitosis and meiosis, but it still exists. What the structure tells us is that the presence of an inversion, or any other type of chromosomal rearrangement for that matter, doesn't have much effect on chromosomal alignment and segregation during cell division.

Today we want to focus on another point. Imagine that a recombination event (crossover) occurs when the chromosomes are aligned like this. If the crossover takes place in the inverted region then each of the recombined chromosomes will be missing some genes and the cells that are produced from such an event will die.

Imagine that the crossover occurs between point C and D. If we trace the new chromosome staring from A on the black chromosome (the AR chromosome) then you get A B G F E D on the black chromosome followed by C B A on the normal white chromosome. The other product of the crossover will begin with A B C from the normal white chromosome and end with D E F G B A from the black homologue.

There won't be any viable crossovers in the region covered by the mutation. We will see what this has to do with balancer chromosomes in a minute.

Imagine that you are working with an important mutation (x) that affects embryonic development in Drosophila. Flies that are homozygous for the mutation (x/x) are blocked at a particular stage of development and the visible phenotype of the mutations tells you a great deal about the genes that control development. These mutations are recessive lethals. The heterozygous flies with one mutant chrmosomes and one normal chromosome (x/+) are viable.

You want to maintain a stock of these flies so you can have mutant flies whenever you need to do an experiment. If you put a heterozygous male and female together in a fly bottle and leave them for a few weeks, you won't be surprised to find that there are no flies that are homozygous for the lethal mutation. However, repeated crossings of heterozygotes will result in 25% wild-type flies (+/+) and these flies will continue to mate with each other and with the heterozygous flies. You won't be able to tell which flies carry your valuable mutation.

One way around this is to mark your mutant chromosomes with a visible marker. Let's say that your mutation is on chromosome 2. (There are three autosomes and one pair of sex chromosomes in Drosophila.) You will need a dominant marker for reasons that will soon become apparent so let's choose detached (Dt), a mutation that effects the vein pattern on the wings. The chromosome carrying your valuable developmental mutation (x) will also carry the Dt allele.

Now all you have to do is look in your stock bottle for flies with the detached phenotype and you know that those flies should be heterozygous for x (Dt x/+ +). Flies that have normal wings can be recognized and killed. (Drosophila genetics is the ultimate blood sport.)

Problem solved, right?

No. It won't be long before a recombination event separates Dt and x, especially if they are far apart on chromosome 2. After a while you still won't know which flies carry your valuable mutation.

This is where balancers come in handy.

Let's look at the experiment done by Christiane Nüsslein-Volhard and Eric Wieschaus in the late 1970's. This is the experiment that won them the Nobel Prize.

In one of their experiments they were looking for mutations on chromosome 2 that affected embryo development.

They started with a line of flies that had eye color markers on chromosome 2; cinnabar (cn) and (bw). This is the red chromosome in the diagram. They treated males from this line with the potent mutagen ethyl methanesulfonate (EMS) and crossed them to a strain carrying a balancer chromosome (black) and a non-balancer homologous chromosome (blue).

The balancer chromosome is called CyO and it has several interesting features. First, it has a large inversion called In(2LR)O that covers most of the chromosome leaving only the ends intact. Second, it carries a dominant mutation called Curly (Cu) that produces flies with curly wings. This is a homozygous lethal mutation. Third, it carries another homozygous lethal mutation called dumpy-lethal (dp^1vI). Finally it carries cn. (Also purple (pr).)

The blue chromosome carries an allele called DTS-91. DTS stands for dominant temperature sensitive. Flies that carry even a single copy of this alleles will die at high temperature. DTS also stand for David T. Suzuki, the man who created these alleles but that's just a coincidence.

The first cross is done at high temperature. The flies produced from the first cross are the F1 generation. None of them will carry the blue chromosome because those flies will be killed at high temperature. All of them will carry one mutagenized chromosome 2 and the CyO balancer chromosome. These flies are crossed again with DTS-91/CyO flies at high temperature to get the second generation (F2) of flies that all contain one mutagenized chromosome 2 and CyO. The second cross helps eliminate other mutagenized chromsomes so that the workers will only be looking at mutations that affect chromosome 2.

Now the cn x bw/CyO flies are allowed to mate with each other until it's time to look at the effect of the mutations. The stock will never produce homozygous cn bw flies as long as the mutated chromosome carries a recessive lethal. Stocks that have flies with cinnibar eyes and not curly wings are discarded.

The stock will never produce flies that are homozygous for the balancer chromosome since it carries two recessive lethal mutations. All flies will have curly wings because they carry the balancer chromosome with Cu. There will never be a recombination event that transfers the developmental mutation to the balancer because the balancer contains a large deletion inversion.

This is why balancer chromosomes are so important n Drosophila genetics. They are essential for maintaining fly stocks carrying homozygous lethal mutations. Such mutations have been extremely important in sorting out fly development.

Christiane Nüsslein-Volhard and Eric Wieschaus created thousands of lines carrying recessive lethal mutations on chromosome 2, and thousands on the X chromosome and chromosome 3, each of which have their own balancers. Then they examined each line to look for embryos that were blocked during early development. (25% of the eggs will be homozygous for the mutant chromosome.)

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[Lower Figure credit: St Johnston (2002)]

St. Johnston, D. (2002) THE ART AND DESIGN OF
GENETIC SCREENS: DROSOPHILA MELANOGASTERNature Reviews: Genetics 3:178-188. [PDF]

Nobel Laureates: Christiane Nüsslein-Volhard and Eric Wieschaus

 

The Nobel Prize in Physiology or Medicine 1995.

"for their discoveries concerning the genetic control of early embryonic development"

Christiane Nüsslein-Volhard (1942 - ) and Eric F. Wieschaus (1947 - ) received the Nobel Prize in Physiology or Medicine for their contribution to understanding the genetics of development in the fruit fly, Drosophila melanogaster.

Their main contribution was to identify a number of genes that controlled the development of the embryo. The approach was to create mutations at random then screen large numbers of flies for recessive lethals affecting various stages of early embryogenesis. The initial large scale experiment was carried out at the EMBL Labs in Heidleberg, Germany. They established 27,000 lines containing mutated chromosomes and characterized 139 mutations affecting embryogenesis. Of these, 15 were described in the classic 1980 Nature paper. (See Silver Screen, a tribute to the paper on it's 25th anniversary.)

The original 15 genes were: cubitus interruptus, wingless, gooseberry, hedgehog, fused, patch, paired, even-skipped, odd-skipped, barrel, runt, engrailed, Kruppel, knirps, and hunchback. To anyone familiar with the field this reads like a who's who of Drosophila development. Dozens (hundreds?) of papers have been published on each of these genes.

The experimental approach is described in the Press Release below. I am only including the part that refers to Nüsslein-Volhard and Wieschaus. They shared the prize with Edward Lewis.

THEME:
Nobel Laureates

Brave decision by two young scientists

Christiane Nüsslein-Volhard and Eric Wieschaus both finished their basic scientific training at the end of the seventies. They were offered their first independent research positions at the European Molecular Biology Laboratory (EMBL) in Heidelberg. They knew each other before they arrived in Heidelberg because of their common interest: they both wanted to find out how the newly fertilized Drosophila egg developed into a segmented embryo. The reason they chose the fruit fly is that embryonic development is very fast. Within 9 days from fertilization the egg develops into an embryo, then a larvae and then into a complete fly.

Fig. 1 Regions of activity in the embryo for the genes belonging to the gap, pair-rule, and segment-polarity groups. The gap genes start to act in the very early embryo (A) to specify an initial segmentation (B). The pair-rule genes specify the 14 final segments (C) of the embryo under the influence of the gap genes. These segments later acquire a head-to-tail polarity due to the segment polarity genes.

They decided to join forces to identify the genes which control the early phase of this process. It was a brave decision by two young scientists at the beginning of their scientific careers. Nobody before had done anything similar and the chances of success were very uncertain. For one, the number of genes involved might be very great. But they got started. Their experimental strategy was unique and well planned. They treated flies with mutagenic substances so as to damage (mutate) approximately half of the Drosophila genes at random (saturation mutagenesis). They then studied genes which, if mutated would cause disturbances in the formation of a body axis or in the segmentation pattern. Using a microscope where two persons could simultaneously examine the same embryo they analyzed and classified a large number of malformations caused by mutations in genes controlling early embryonic development. For more than a year the two scientists sat opposite each other examining Drosophila embryos resulting from genetic crosses of mutant Drosophila strains. They were able to identify 15 different genes which, if mutated, would cause defects in segmentation. The genes could be classified with respect to the order in which they were important during development and how mutations affected segmentation. Gap genes (Fig 1) control the body plan along the head-tail axis. Loss of gap gene function results in a reduced number of body segments. Pair rule genes affect every second body segment: loss of a gene known as "even-skipped" results in an embryo consisting only of odd numbered segments. A third class of genes called segment polarity genes affect the head-to-tail polarity of individual segments.

The results of Nüsslein-Volhard and Wieschaus were first published in the English scientific journal Nature during the fall of 1980. They received a lot of attention among developmental biologists and for several reasons. The strategy used by the two young scientists was novel. It established that genes controlling development could be systematically identified. The number of genes involved was limited and they could be classified into specific functional groups. This encouraged a number of other scientists to look for developmental genes in other species. In a fairly short time it was possible to show that similar or identical genes existed also in higher organisms and in man. It has also been demonstrated that they perform similar functions during development.

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[Photo Credits: Nüsslein-Volhard - Encylopaedia Britanica, © Patrick Piel/Gamma Liaison, Wieschaus -News at Princeton]

Fair Vote Canada Election Results

 
Here's what the result would have been with a nation-wide proportional system from Fair Vote Canada.

Conservatives - 38% of the popular vote: 117 seats (not 143)
Liberals - 26% of the popular vote: 81 seats (not 76)
NDP - 18% of the popular vote: 57 seats (not 37)
Bloc - 10% of the popular vote: 28 seats (not 50)
Greens - 7% of the popular vote: 23 seats (not 0)

I don't favor such a system. I like the Mixed Member Proportional MMP) system based on provinces.

The British Columbia referendum on the Single Transferable Vote (STV) system for provincial elections is set for May 12, 2009. 58% of voters supported the new voting system in the last referendum (2005). This was just short of the required 60%. It is very likely that the new proportional system will be adopted this time around, making British Columbia the first of many provinces to enter the 21st century.

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Nigeria Has Competition

 
I just got this email message and I thought I'd share it with the rest of you. All my money is tied up in deals with Nigerians and investments in Viagra so I can't take advantage of this fabulous offer.

I expect to be flush with cash by next week because I just won the European lottery but I'll be spending most of it to enlarge one of my vital organs.

Hello Pal,

I hope my email fine you well. I am in need of your assistance. My name is Sgt. Jarvis Reeves. I am an American soldier serving in the 1st Armored Division in Iraq, we have just been posted out of Iraq and to return in a short while. My colleague and I need your help to transfer out the sum of Twenty Five Mllion U.S Dollars ($25 MUSD). If you are interested I will furnish you with more details

As awair your response.
Email:sgt.jr@hotmail.com

Yours,
Sgt. Jarvis Reeves

God Bless America!!

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Move to Canada

 

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[Hat Tip: The Unexamined Life]

Bacteria Phylogeny: Facing Up to the Problems

There are millions of species of bacteria. Sorting out their evolutionary history has been a major challenge for decades. Unlike the much bigger, multicellular, eukaryotes, there are few morphological markers to assist scientists in classifying bacteria. The fossil record is mostly silent.

Molecular evolution came to the rescue thirty years ago when cloning and sequencing became common. Soon there were elaborate and detailed phylogenetic trees based on comparing sequences of conserved genes from many species.

The gene of choice was the one for the small subunit ribosomal RNA (SSU rRNA). This gene was well conserved in bacteria and it was easy to get sequences simply by PCR. (The ends of the SSU rRNA gene are conserved and this means that you can develop universe primers for PCR.)

Over the years, the SSU rRNA gene has become what is called the "gold standard" in bacterial phylogeny and taxonomy. Many species have been assigned to taxa based entirely on the sequence of their SSU rRNA gene. Unfortunately, the "gold standard" has become somewhat tarnished lately.

Our fellow blogger, Jonathan Eisen of The Tree of Life, has recently published a paper that looks at the problems with bacterial phylogeny (Wu and Eisen, 2008). He posted a brief summary of the paper and commented on why he likes the journal Genome Biology [Happy Open Access Day: Back to Genome Biology for Me].

There is much to like about this paper. The authors face up to the problems with the current bacterial phylogeny, which is based almost entirely on a single gene (SSU rRNA). They point out that this is risky given what we know about molecular phylogenies. Furthermore, in the case of the SSU ribosomal RNA gene we know for a fact that this has led to problems and inconsistencies. In addition to the practical difficulties there are good theoretical reasons for being suspicious of phylogenies constructed from nucleotide sequences.

What to do? One possible solution is to abandon SSU rRNA as a "gold standard" and replace it with a highly conserved protein coding gene. Unfortunately, this doesn't get around the problem of relying on a single gene. The way around this is to use an artificial concatenated sequence made up of several different conserved genes laid out end-to-end in one large string of amino acids.

So why isn't this done? Because, as Wu and Eisen point out, it ain't that easy. The main difficulty in any phylogenetic study is getting a proper alignment. This is a problem that many workers simply ignore when they use automated alignment software like CLUSTALW. These workers assume that the alignments are valid.

They aren't, and this is another example of facing up to the problem. Many scientists agonize over what program to use when constructing their trees—should they use maximum likelihood, parsimony, etc. etc.? In most cases these decisions are a complete waste of time because their alignments aren't good enough to make a difference.

Here's how Wu and Eisen explain it ...

It has been shown that alignment quality can have greater impact on the final tree than does the tree-building method employed [20]. Therefore, preparing high quality sequence alignments is a most critical part of any molecular phylogenetic analysis. This preparation typically involves careful but tedious manual editing and trimming of the generated alignments, and thus remains the biggest challenge to automation. When scaling up this process, the trimming step is often simply ignored. Automated trimming based on the number of gaps in each column or each column's conservation score can be used to select conserved blocks, but still is not satisfactory when a high quality tree is required.

Keep in mind that what is being proposed is a large tree based on concatenated sequences from many genes. You don't want to do multiple sequence alignments for every gene by hand, and yet up until now, that was the only way to get accurate results.

Wu and Eisen have written a program called AMPHORA that hopefully solves this problem. They begin by manually creating "seed alignments" that are manually curated. Then they use AMPHORA to align all the other sequences to the seed alignments. In this way they hope to overcome the limitations of automated multisequence alignment without having to align everything by hand.

None of this would be possible, of course, unless there were large numbers of species where every one of the target genes have been cloned and sequenced. In the 20th century this would have been impossible but now there are hundreds of completely sequenced bacterial genomes. This means that each one of them has a sequenced copy of the genes required for this kind of analysis.

All that's left is to identify the completely sequenced genomes and pick the set of genes. There are 578 genomes in the database but many of these are close relatives that will not be useful in constructing a large tree of all bacterial sequences. The final set contains 310 genomes with representatives of all the major groups.

The authors selected 31 genes for their initial proof of principle paper (dnaG, frr, infC, nusA, pgk, pyrG, rplA, rplB, rplC, rplD, rplE, rplF, rplK, rplL, rplM, rplN, rplP, rplS, rplT, rpmA, rpoB, rpsB, rpsC, rpsE, rpsI, rpsJ, rpsK, rpsM, rpsS, smpB, tsf). Those of you who recognize these genes will see that 21 of them are small ribosomal proteins. This was not the best choice, in my opinion, but the authors of the paper note that they are continuing the study by incorporating better genes such as HSP70 (dnaL) and EF-Tu (tufA). You can't just choose any conserved gene because it has to be present in most species and there are surprisingly few genes that meet that criterion.

After all that, what's the bottom line? The grand phylogeny is shown at the top of this posting. It resolves many groups that are unresolvable using the SSU rRNA tree. In some cases this tree reveals species that have been incorrectly assigned to higher taxa. These species will have to be reclassified if this result holds up.

The most important finding is that the method works and it yields trees with excellent resolution of the major bacterial taxa.

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Wu, Martin, Eisen, Jonathan (2008). A simple, fast, and accurate method of phylogenomic inference Genome Biology, 9:R151 [Genome Biology] [doi:10.1186/gb-2008-9-10-r151]