Let's Make a Deal! We'll give you Alberta for Minnesota (but only if you throw in Massachusetts as a sweetener)

 
The latest opinion poll in Canada shows the Liberals (red) ahead of the Troglodytes (blue) in every part of Canada except Alberta. Almost 60% of the cowboys would vote for Stephen Harper and the Conservatives.

Alberta was the only major province to prohibit same-sex marriage before they were forced to accept it by the Federal Government. Alberta consistently elects the most right-wing MP's in the country. It's the province that seems least committed to universal health care. They're against gun control, tend to be in favor of capital punishment, and like giving tax breaks to rich people and corporations.

As if that weren't bad enough, they traded Wayne Gretzky to Los Angeles.

I'm pretty sure that Albertans would be happier if they belonged to a country with more cowboys (like in Texas). So here's the deal. We'll give you Alberta and you give us Minnesota. Because there's a lot more oil in Alberta, you'll need to sweeten the pot in order to get rid of Minnesota. Throw in Massachusetts and you've got a deal.

Listen up UK ! We've got an offer you can't refuse

We're willing to give you Alberta. They already have the same Queen as you so that part won't be a problem. Think of the advantages. You'll have your very own cowboys and Charlie can go skiing in Banff instead of Gstaad.

What does Canada want in return? Well, here's the best part ... we'll take Scotland off your hands! How's that for a deal? Scotland would be a perfect fit for Canada. We already have a province that thinks it's a country, and Robbie Burns Day is practically a national hollidy.

Paging Australia

The competition is heating up so this is our last offer. You can have Alberta but we need to get something in return. Not much, mind you, but we can't give it away for free.

It occurs to me that we could kill two birds with one stone. You get the enormous advantage of having a province where everyone loves Crocodile Dundee and you get rid of New Zealand. We'll make a one-for-one swap; New Zealand for Alberta.

Now, I realize the Kiwis have some quaint notions about being an independent country but I don't think that should prevent you from giving it away.

The Three Domain Hypothesis (part 5)

[Part 1][Part 2][Part 3][Part 4]
If the Tree of Life Fell, Would We Recognize the Sound?

I've been summarizing a series of papers that appeared in a recent book, Microbial Phylogeny and Evolution. The underlying theme is the validity of the Three Domain Hypothesis. The Three Domain Hypothesis is the idea that life can be divided into three distinct (monophyletic) domains: archaebacteria, bacteria, and eukaryotes. An important part of the hypothesis is that eukaryotes are descended from ancient archaebacteria.

I've been arguing that the Three Domain Hypothesis has been refuted. It is effectively dead even though most people don't realize it. It continues to be touted in the textbooks in spite of the fact that experts have rejected it as an accurate model of early evolution.

Ford Doolittle has been thinking about molecular evolution for over three decades. Some of you might recall that he was one of the originators of the term "selfish gene." He was a strong supporter of the Introns-Early Hypothesis back in the 1980's but he abandoned it when it was falsified by the accumulation of nasty facts. This is one of the reasons why Ford Doolittle is so highly respected in the community of molecular evolutionists.

As usual, Ford Doolittle offers an insightful analysis of the controversy in his paper "If the Tree of Life Fell, Would We Recognize the Sound?" He points out that different genes give different trees at the deepest level and this is a serious problem. One that can't be ignored. Are there some "hard core" genes that have not been transferred during the exchange phase of evolution, where gene swapping was common? If so, these could reveal the "true" deep phylogeny?

His answer is no. Surprisingly, there are only about 100 genes found in all prokaryotic species. There don't appear to be any standard subset that are more reliable than others. All genes are candidates for orthologous replacement by gene transfer from another species. Doolittle makes the obvious, but often ignored, point that you can only determine if a gene has been exchanged when you have a true phylogeny to compare it with. You can't just assume that your favorite genes reveal the true phylogeny and all others conflicting with it are artifacts of lateral gene transfer. This is what disciples of the Three Domain Hypothesis often do. It's called begging the question.

Doolittle thinks this is bad science ...

There may be a real catch-22 in assessing how much LGT as orthologoous replacement afflicts the core at depth, but given that we know that orthologous replacement can happen and that rampant LGT drives genome (gene content) evolution at the strain-in-a-species level, there is no justification in retaining vertical descent as the null hypothesis and requiring stronger proof for LGT. Rather (at least with greater fairness), we might recast the notion of the existence of a stable core as a hypothesis that needs to be tested, not a truth that needs further elaboration. If the hypothesis is that there is a cadre of genes that have never been exchanged (and that thus track organismal phylogeny), and the test of it requires that there indeed be such universally shared genes that show the same phylogeny, then this hypothesis has yet to be proven.

What about the "complexity hypothesis?" This hypothesis refers to a core of genes that have never been transferred from one species to another because they are all part of a large complex. Presumably, the pieces of this complex are not interchangeable so new genes cannot be accepted. Thus, this core represents the true phylogeny of the lineage and all other genes have been acquired later.

The "true" core, according to this argument, is the complex of genes that are involved in translation. This includes ribosomal RNA and ribosomal protein genes.

There are three arguments against the complexity hypothesis. First, genes for some key translational components do not agree with the ribosomal RNA tree, refuting the idea that all genes of the complex evolved together.

Second, Doolittle points out that the logic is flawed. For example, the parts of ribosomal RNA that interact with ribosomal proteins are highly conserved so there is very little difference between species. The parts that don't interact are quite variable and those are the very parts that determine the phylogeny. Lateral gene transfer of ribosomal RNA genes from one species to another wouldn't have much effect since the only parts that differ are the parts the aren't necessary.

Thirdly, "One might suggest, only half facetiously, that the (still to be determined) congruence of their phylogenies does not mean that they have never been transferred but, radically otherwise, that they have always been transferred together."

The idea here is that the logic of the arguments made by Three Domain supporters does not stand up to close scrutiny. It seems superficially reasonable but falls apart when you poke at it. This is the same phenomenon that we witnessed with the Introns-Early Hypothesis. Clearly, Doolittle has been sensitized by his experience in that controversy. (Alternative splicing is another example of bad logic. We'll poke at that one some other time.)

So what is the alternative to the Three Domain Hypothesis? Doolittle says, "We claim that there are no data to contracdict the possibility that every gene we find in any genome today has experienced at least one between-species LGT in the 3-4 billion years since life began." This means there is no single tree of life and eukaryotes and not closer to archaebacteria than to bacteria. The way to represent early evolution is as a complex Web of Life.

Perhaps there is a plurality (most favored) pattern, or one tracked by several genes that we consider important, but this has yet to be proven. In any case, there is no compelling reason why this plurality pattern needs to correspond, by any simple mapping, to the tree of speciations and cell divisions. We cannot infer a unique tree of organisms from the pattern of relationships among genomes without making further assumptions about evolutionary processes that are just that: still-unproven assumptions. We have, for several decades, thought that our job was to uncover the structure of a Tree of Life, whose reality we did not question. But really, what we have been doing is testing Darwin's hypothesis that a tree is the appropriate representation of life's history, back to the beginning. Like any hypothesis, it could be false.

The figure below is taken from Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American

---

Microbobial Phylogeny and Evolution: Concepts and Controversies Jan Sapp, ed., Oxford University Press, Oxford UK (2005)

Jan Sapp The Bacterium’s Place in Nature

Norman Pace The Large-Scale Structure of the Tree of Life.

Woflgang Ludwig and Karl-Heinz Schleifer The Molecular Phylogeny of Bacteria Based on Conserved Genes.

Carl Woese Evolving Biological Organization.

W. Ford Doolittle If the Tree of Life Fell, Would it Make a Sound?.

William Martin Woe Is the Tree of Life.

Radhey Gupta Molecular Sequences and the Early History of Life.

C. G. Kurland Paradigm Lost.

---

How to Tell the Difference Between Kooks and Mavericks

The latest (Dec. 9, 2006) issue of New Scientist has a remarkably stupid series of articles written by so-called "lone voices." Who are these "lone voices" and why do they get a soapbox in New Scientist? Here's what the editors say, ...

Science works by consensus, right? Well, not entirely. Throughout the history of scientific endeavour there has been a scattering of people who, for good or ill, have swum against the tide.

In this special series of premium articles, we look at these lone voices and what they have brought to our understanding of the world. Harry Collins (see How we know what we know) and Bob Park (see Watch out for the UFOs) start by offering their ideas on how to distinguish true genius from the ravings of a crank.

We then speak to five people who represent very different kinds of outsider: a star who led the pack (David Deutsch, free feature: At play in the multiverse); a non-scientist making bigger waves than the professionals (Jane Elliott, An unforgettable lesson); an experimentalist who put his own health on the line to get heard (Barry Marshall, Hard to swallow); a scientist doing respected work in the context of unlikely beliefs (John Baumgardner, God said, let the dry land appear…); and a genius who is causing a stir outside his original field (Brian Josephson, Take nobody's world for it).

Each offers a unique challenge to the scientific status quo. Can we afford to be without any of them?

The answer to that one is easy. Yes, we can afford to be without some of them; notably, the Young Earth Creationist (YEC) John Baumgardner.

There's a big difference between "lone voices," or mavericks, and kooks. Kooks are genuine out-to-lunch, delusional pseudoscientists who should be ignored. It's easy to recognize kooks because their ideas conflict with fundamental, well-established principles of science.

Take YEC's for example. They aren't working on the frontiers of science where several different explanations are possible. Instead, they are advocating the overthrow of physics, geology, chemistry, astronomy, and biology because all of these sciences refute the idea that the world is only 10,000 years old. Young Earth Creationism is not a clever idea that the scientific establishment is suppressing because they might lose their grants. It is a genuine idiotic idea that only the most delusional Christian would believe. It's about as rational as believing that the moon landings were faked.

John Baumgardner is a genuine scientist with a Ph.D. in geophysics but he's still a kook. If New Scientist can't tell the difference between someone who's lost all credibility in the scientific community and someone who takes an unorthodox, but rational, position, then we're in a lot more trouble than I thought.

There have been plenty of mavericks in science as the lead editorial in New Scientist points out ...

TIME was when all scientists were outsiders. Self-funded or backed by a rich benefactor, they pursued their often wild ideas in home-built labs with no one to answer to but themselves. From Nicolaus Copernicus to Charles Darwin, they were so successful that it's hard to imagine what modern science would be like without them.

Their isolated, largely unaccountable ways now seem the antithesis of modern science, with consensus and peer review at its very heart. Yet the "outsider" tradition persists. Think of Alfred Wegener, the father of plate tectonics and, more controversially, of Gaia theorist James Lovelock. Both pursued their theories in the face of strong opposition from their peers.

Such mavericks can be crucial to progress (see Lone Voices), but are they a dying breed?

The concept is valid. There have been genuine maverick scientists who swam against the tide and won over the scientific community after a hard-fought battle. Peter Mitchell, Lynn Margulis, Carl Woese, and Stephen Jay Gould are good examples. Unfortunately, the editors of New Scientist have destroyed what little credibility they had left by picking Charles Dawrin as an example. What were they thinking? Darwin was 100% establishment. Within a couple of years of publishing Origin of Species, the scientific/intellectual community had been converted. He had a good idea, he spoke, they listened.

In discussions like this it's worth keeping in mind that there have been many more mavericks than we can recall. Most of them are very forgettable because they were wrong.

With this issue, New Scientist has shown us that it should be moved from the science section of good bookstores to the supermarket check-out counter.

Swiffer WetJet Kills Dogs!

Friday's Urban Legend from snopes.com

The claim is that Swiffer WetJet contains antifreeze and traces are left when the floor has been cleaned. If dogs lick the floor they will ingest the poison and die.

The claim circulates in a standard email message from a women who says that her dog and two cats died of liver failure because of Swiffer WetJet. This particular urban legend seems to be widely believed.

It is completely false. Nobody seems to have noticed that the product continues to be sold in stores and the company (Proctor & Gamble) has not been bankrupted by massive lawsuits from pet owners.

Why Kyoto Is Important

The Kyoto Protocols set out goals for industrialized nations to lower carbon dioxide emissions and other pollutants. On average, greenhouse gas emissions should be reduced by about 5% relative to 1990 levels. The Kyoto Protocols came into effect in February 2005. 141 industrialized nations signed on, the only significant countries that didn't ratify the treaty were Australia and the United States.

We all share this planet and it is every one's responsibility to behave in a manner that will make our children proud. The real meaning of Kyoto is not in the goals or whether they will be met. The significance is in the effort and the agreement to cooperate for the common good. Kyoto is a big step forward in international relations and that's why we need to support the effort. Turning your back on Kyoto is like slapping your friend in the face after you have shaken hands on a deal.

Canada has just done that when Stephen Harper announced that we would not try to meet our objective. Will things be any different if the new leader of the Liberal party becomes Prime Minister?


You bet they will!

Stéphane Dion is serious about environmental issues and he will reinstate Canada's commitment to the Kyoto Protocols when he becomes Prime Minister next Spring. This will help restore our credibility in the world.

I'm hoping he will be able to convince the Americans that they should join with other nations in making an effort to improve the planet.

Thanks to James Bowie for getting the photo of Stéphane Dion and his dog "Kyoto."

Same-sex marriage in Canada

Same-sex marriage has been legal in Ontario since June 2003. It gradually spread to other provinces as provincial courts declared that laws prohibiting same-sex marriage were unconstitutional. By June 2005, same-sex marriage was legalized in eight provinces and one territory.

The House of Commons passed The Civil Marriage Act (Bill C-38) on June 28, 2005 by a vote of 158-133. This law made same-sex marriage legal in all of Canada. (Alberta had been the major holdout against same-sex marriage.)

Recently, the new Conservative government of Stephen Harper put a motion to re-open the debate on same-sex marriage. The motion was voted on today and the result is ....



defeat for Harper. MP's voted 175-123 to not re-open the debate. The law stands and same-sex marriage is still legal.

Canada remains on the same side of this issue as most other civilized countries.

Why hasn't America legalized same-sex marriage? Is it because of religion? Is it because the American constitution, and the concept of human rights, is different than all other constitutions?

Don't Mess with Professors!!!

This guy is my hero! One of these days I'm gonna do the same thing when a student talks on the phone in class.

Why Woodpeckers Almost Went Extinct!!!

 

Stephen Lewis on AIDS

Tonight on "The Nature of Things with David Suzuki" the entire show was devoted to Stephen Lewis and his tireless battle against AIDS in Africa. Visit the Stephen Lewis Foundation Website for more information on this extraordinary man.

You must watch his final address from the XVI International Conference on AIDS in Toronto, August 2006. Lewis will be leaving his position as UN Special Envoy at the end of December. Let us hope we haven't heard the last of him.

John Wilkins on the Sandwalk

 

John Wilkins of Evolving Thoughts resting in the shelter on the Sandwalk.

What is he reading?

Two Kooks in a Pod

Casey Luskin, the chief IDiot over at Discovery Institute has posted an addendum to his inept article on junk DNA [Follow-up on Junk-DNA]. Luskin has discovered the junkdna.com website of Andras Pellionisz. Those two deserve each other.

More Sandwalk

Photos by Richard Carter.

Nobel Laureates: Hans Fischer

 

The Nobel Prize in Chemistry 1930.

"for his researches into the constitution of haemin and chlorophyll and especially for his synthesis of haemin"

Hans Fischer (1881-1945) determined the structure of "haemin," the prosthetic group in hemoglobin. We now refer to this molecule as heme. (Hemoglobin consists of a protein, globin, and a bound cofactor, heme.) The technical name for heme is Fe(II)-protoporphyrin IX (see figure below). In hemoglobin, oxygen is bound to the central iron atom.

Fischer worked out the structure of the porphyrin rings, a considerable feat in those days. He also discovered that the structure of chlorophyll was similar to that of heme.