Judge Jones & the Dover Trial

 
When the Jones decision was first published I read every word. I was very impressed. Here was a man who seemed to have learned a lot of sophisticated science in a very short period of time. His grasp of complexities like the evolution of bacteria flagella and blood clotting was impressive. His understanding of the meaning of science rivaled that of many advisors on the ACLU side. Frankly, I was jealous, and humbled.

Everyone was praising the Jones decision. For example, Timothy Sandefur on Panda's Thumb wrote,

Kitzmiller v. Dover Area School District is a major victory for science and a major blow to those who have tried to sneak religion into the classroom by disguising in scientific garb. But it’s more than that. It is a brilliant, insightful, profound decision that reaches to the bottom of ID and finds it empty.

Judge John Jones, a George W. Bush appointee, deserves the praise and thanks of every defender of rigorous, meaningful scientific education. He has taken the time to really understand not just the legal issues, but the scientific ones as well. This decision proves he is a credit to the federal judiciary.

These comments, and others, seemed to confirm that Jones had written this decision all by himself and deserved full credit for his brilliant analysis.

As it turns out, this isn't true and I feel deceived.


The Discovery Institute is reporting that the "Masterful" Federal Ruling on Intelligent Design Was Copied from ACLU and Timothy Sandefur acknowledges that this is true [Weekend at Behe's].

Apparently Judge Jones copied the most "scientific" parts of his decision from the ACLU ‘Findings of Fact and Conclusions of Law’ that was submitted a month before the decision was published. I'm told that this is standard practice. Judges often rely heavily on written submissions from the side they support. I'm told that it's common for judges to copy from those submissions.

That may be true—I have no reason to doubt it—but it does make a difference to me. The legal significance of the decision doesn't change but my opinion of Judge Jones does. He is no longer the brilliant man who was able to grasp complex scientific concepts in the blink of an eye. He's able to discern who's right and who's wrong, but that's all.

Now, the question is, who really wrote the ACLU "Finding of Fact?" Did they know from the beginning that the Jones decision had incorporated a lot of their material? If so, why did they leave us with the impression that Judge Jones "has taken the time to really understand not just the legal issues, but the scientific ones as well?"

E. coli O157:H7 Outbreak in Taco Bell Restaurants

 
The Centers for Disease Control and Prevention reports that 64 people have been hospitalized as a result of bacterial infection arising from contamination at Taco Bell restaurants in New York, Pennsylvania, New Jersey, and Delaware. Of these patients, 38 have been confirmed as E. coli strain O157:H7 infections. All of these patients have been infected with the same substrain as determined by DNA fingerprinting.

What this means is that all infections arose from a single source. There must be something in common among the restaurants in all four states. A preliminary analysis detected E. coli O157:H7 contamination of green onions in one of the restaurants but DNA fingerprinting showed that it was a different substrain, proving that this was not the soure of infection.

DNA fingerprinting is a powerful tool in tracing outbreaks of toxic bacteria. It also proves evolution. How is it done?

The figure below is an example of DNA fingerprinting from the following paper.

Hahma, B-K., Maldonadob, Y., Schreiberc, E., Bhuniab, A.K. and Nakatsua, C.H. (2003) Subtyping of foodborne and environmental isolates of Escherichia coli by multiplex-PCR, rep-PCR, PFGE, ribotyping and AFLP. Journal of Microbiological Methods 53; 387-399.

There are several different ways of making DNA fingerprints. In the one shown here, DNA is extracted from each substrain of bacteria and digested with a restriction enzyme called Xba I. This enzyme chops the DNA at specific sites in the genome corresponding to the DNA sequence TCTAGA. The result is that the genomic DNA is cut into large pieces of different sizes, ranging from about 100,000 base pairs (bp) to 500,000 base pairs (or 500kb). Since the whole genome of E. coli is about 4,600,000 bp in size, this means the there will be something like 20 DNA fragments produced by cutting with the enzyme.

The DNA fragments from different strains will show differences in sizes whenever the genome has been altered by the insertion of new DNA or the deletion of some existing DNA. These insertion/deletion events occur quite frequently in evolving populations as we saw recently in work done on human populations.

A solution containing the collection of fragments from a single strain is put on the top of an agarose gel and a strong pulsed field electric current is applied. Since DNA is negatively charged, the fragments will move into the gel and separate according to size—smaller fragments will move faster. In the example shown, the top of the gel is on the right and the bottom is on the left.

The large open bracket at the top right of the image covers various O157:H7 strains. The evolutionary tree on the left shows how this strain is related to other E. coli strains at the bottom of the image. Within the O157:H7 strains there are many serotypes that have descended recently from a common ancestor. Each serotype has a unique combination of restriction fragments of different lengths. That's the DNA fingerprint.

Note the cluster that's fourth from the top. It's labelled "Odwalla Juice" after an outbreak that occurred several years ago. (You may not be able to read it in the figure.) There are five lanes with identical DNA fingerprints indicating that these five different isolates (from five different patients) all came from the same source. The same technique is being used to trace the current outbreak.

The Centers for Disease Control and Prevention have already eliminated a number of cases by DNA fingerprinting. These patients are not part of the current outbreak. It's important to concentrate only on those patients that are part of the cluster having a common source and not be confused by other infections. That way, the source can be identified and eliminated.

Not to belabor a point, but none of this would be possible if it weren't for evolution and our understanding of how evolution works.

Stanley Cup Playoffs Are Bad for You!

 
Medical News Today warns us that Stanley Cup Playoffs Can Harm Your Hearing. Well, duh! Smart Toronto residents have known this for decades. That's why we've skipped the Stanley Cup playoffs so often and why we have carefully avoided winning the cup every single year since 1967. According to the latest results (seven losses in a row), the Toronto Maple Leafs are on track to protect us from hearing loss once again.

Kofi Annan's Final Speech

 
Delivered today at the Truman Presidential Library in Independence Missouri. [Full Text from BBC News]

That is why this country has historically been in the vanguard of the global human rights movement. But that lead can only be maintained if America remains true to its principles, including in the struggle against terrorism.

When it appears to abandon its own ideals and objectives, its friends abroad are naturally troubled and confused.

And states need to play by the rules towards each other, as well as towards their own citizens. That can sometimes be inconvenient, but ultimately what matters is not convenience. It is doing the right thing.

No state can make its own actions legitimate in the eyes of others. When power, especially military force, is used, the world will consider it legitimate only when convinced that it is being used for the right purpose - for broadly shared aims - in accordance with broadly accepted norms.

No community anywhere suffers from too much rule of law; many do suffer from too little - and the international community is among them. This we must change.

The US has given the world an example of a democracy in which everyone, including the most powerful, is subject to legal restraint. Its current moment of world supremacy gives it a priceless opportunity to entrench the same principles at the global level.

As Harry Truman said, "We all have to recognise, no matter how great our strength, that we must deny ourselves the licence to do always as we please."

A Deluded Scientist

 
The Language of God: A Scientist Presents Evidence for Belief, by Francis S. Collins, Free Press, New York (2006)

Francis Collins is the co-discoverer of the cystic fibrosis gene and the head of the Human Genome Project. His scientific credentials are impeccable. Collins is also a deeply religious man and he writes this book to explain why "... there is no conflict in being a religious scientist and a person who believes in a God who takes a personal interest in each one of us." (p. 6)

Collins claims he was an atheist when he finished his Ph.D. After enrolling in Medical School he began to encounter patients in North Carolina who asked him about his beliefs. He realized that rationalism wasn't working for him; "... if I could no longer rely on the robustness of my atheism position, would I have to take responsibility for actions that I would prefer to leave unscrutinized? Was I responsible to someone other than myself? The question was now too pressing to avoid."

Like so many others, Collins found his answers in the writings of C.S. Lewis. The result was a conversion to belief in God. But which God? This struggle took another year. The tipping point was the sight of a frozen waterfall in the Cascade Mountains.

As I rounded the corner and saw a beautiful and unexpected frozen waterfall, hundreds of feet high, I knew the search was over. The next morning, I knelt in the dewy grass as the sun rose and surrendered to Jesus Christ. (p. 225)

The language is important. The struggle that faces all of us is a struggle between rationalism and superstition. It's tough to be an atheist and it's easy to lapse into superstition, where you give up the fight and let others do your thinking for you. That's why "surrendering" is such an appropriate description of the event. I admire Collins for being so honest.

However, in spite of the fact that he threw in the towel in the struggle to remain rational, he tries to defend his decision in a logical way. According to Collins, there are two powerful arguments in favor of God. Both of them come from a series of apologetic books by C.S.Lewis—better known as the writer of another fantasy series, The Chronicles of Narnia.

The Moral Law refers to the idea that every human being possesses the same concept of right and wrong. It's built into our psyche and there's no explanation for this other than it was put there by God. (I'm not making this up!) Most rational beings would ask questions like; what are those universal laws?; what's the evidence that everyone shares them?; could they be memes?; etc. But once you've abandoned rationality in favor of superstition, these questions are no longer raised. Collins finds the Moral Law extremely persuasive and he doesn't recognize that it's existence is a scientific question.

Is this Moral Law a rational argument for God? It is according to Collins.

Encountering this argument at age twenty-six, I was stunned by its logic. Here, hiding in my heart as familiar as anything in daily experience, but now emerging for the first time as a clarifying principle, this Moral Law shone its bright white light into the recesses of my childish atheism, and demanded a serious consideration of its origin. Was this God looking back at me?

The second persuasive argument is the presence in all of us of a God-shaped vacuum. What the heck is that, you might ask? C.S. Lewis supplies the answer. It's the sensation of longing for something greater than ourselves. It's the "joy" you feel when you read a good poem, listen to Beethoven, or view the beauty of nature. The emptiness we are all supposed to feel cries out for an explanation, "Why do we have a 'God-shaped' vacuum in our hearts and minds unless it is meant to be filled?" (p. 38)

Apparently, there is no conflict between being a scientist and believing in such silly nonsense. Apparently, scientists don't have to ask the hard questions like, does everyone really feel this longing? Do Buddhists in China feel it? Do atheists lead miserable lives because they can never fill the void in their hearts?

What about miracles? To his credit, Collins faces up to the problem in a section titled, "How Can a Rational Person Believe in Miracles." A miracle is an event that "appears to be inexplicable by the laws of nature and so is held to be supernatural in origin." (p. 48) In other words, miracles conflict with science. But do they conflict with rationalism? Let's see if we get an answer from someone who has surrendered to superstition.

According to Francis Collins, you can assess the probability of a miracle using Bayes Theorem. This is a way of calculating the probability of an event given some "prior" knowledge. How does that help? Here it is in his own words.

Assume that you witness a patient who recovers from a "fatal"cancer. Is it a miracle, or is it a rare spontaneous remission?

This is, or course, where reasonable people will disagree, sometimes noisily. For the committed materialist, no allowance can be permitted for the possibility of miracles in the first place (his "prior" will be zero), and therefore even an extremely unusual cure of cancer will be discounted as evidence of the miraculous, and will instead be chalked up to the fact that rare events will occasionally occur within the natural world. The believer in the existence of God, however, may after examining the evidence conclude that no such cure should have occurred by any natural process, and having once admitted that the prior probability of a miracle, while quite small, is not quite zero, will carry out his own (very informal) Bayesian calculation to conclude that a miracle is more likely than not.

All of this simply goes to say that a discussion about the miraculous quickly devolves to an argument about whether or not one is willing to consider any possibility whatsoever of the supernatural.

So, to answer the question, how does a rational person believe in miracles? By admitting that they are possible and evaluating the evidence based on this prior assumption. Cute, eh? It's called "begging the question"—at least it used to be called that before the phrase acquired a new, very literal, meaning. In the world of the theist, it is rational to assume the answer to the question you're trying to answer in the first place. What a funny world.

Chapter Three is a defense of the compatibility of the Big Bang with the Biblical story of creation and of the fine tuning argument as an argument for the existence of God. Time to move along, there's nothing new here. Other chapters are devoted to explaining evolution and human genomes. These are followed by the mandatory criticisms of Young Earth Creationism, and Intelligent Design Creationism.

The interesting part of the book comes in Chapter Ten. This is where Collins explains Theistic Evolution and why it's rational to accept evolution but still believe in a active personal God who can perform miracles, create the universe, and answer prayers. According to Collins, God choose evolution as a way of creating a species who would be intelligent, know right from wrong, and want to worship their Creator. Collins says, "This view is entirely compatible with everything that science teaches us about the natural world" (p. 201).

Not so. The science that I know says there's no obvious purpose or direction to evolution. There is nothing in science to suggest that we are special. and there's nothing to suggest that evolution was designed by a supernatural being. There's no scientific evidence to indicate that humans have a longing or desire to worship the Christian God. To argue that Theistic Evolution is "compatible" with science is a misuse of the word "compatible." You might just as well argue that astrology is compatible with science simply because we can't prove that everything about astrology is definitely false.

As it turns out, Collins doesn't like the term "Theistic Evolution." He proposes that we replace it with "BioLogos" from the Greek "bios" (life) and "logos" (word). The new word, BioLogos, "expresses the belief that God is the source of all life and that life expresses the will of God" (p. 203). I don't think it's going to catch on.

This is a disappointing book. I expected much better from Francis Collins. He has not presented any evidence for belief that we haven't heard before from C.S. Lewis. Moreover, this "evidence" (Moral Law, longing for God) has been refuted half a century ago. Neither a universal Moral Law nor a universal longing for God are compatible with what we currently know about human societies. The conflict between science and religion still exists.

In the end, the only argument that Collins has is the same old last refuge of the superstitious, "Science is not the only way of knowing. The spiritual worldview provides another way of finding truth" (p. 229). This is only satisfying to those who have already surrendered to superstition and made up their minds that the touchy-feely world of human emotions is a valid way of discovering the truth. Those people are seriously deluded.

Ancient Roman Unearthed In London

 
When PZ Myers and I visited London in October, I took him to the cafeteria in the crypt of Saint Martin-in-the-Fields. We ate our lunch on top of the tombs of medieval Londoners. There was a lot of construction going on behind the church.

According to CNN, workers have uncovered a Roman sarcophagus dating to 410 AD. It would be interesting to find out whether this Roman was related to modern Britons. It should be easy to extract DNA and do the test.

Traffic in London is chaotic, especially around Trafalger Square where St. Martin-in-the-Fields is located. If it turned out that modern Londoners were related to Italians it would explain a lot.

More seriously, we need to have better data on the genetics of populations and any DNA samples from ancestors would help. What percentage of genes in modern Britons comes from Romans, Saxon, Jutes, Celts, Normans, or the rest of France?

Canadian Black Squirrels Take Over Washington D.C.

 
Okay, so "taking over" may be a bit of an exaggeration. But according to the Washington Post black squirrels now make up 5-25% of the squirrel population. They are descended from a small number of Canadian black squirrels released about 100 years ago.

Black squirrels are much more common in Toronto than gray squirrels so there's always been speculation about why that is. So far there's no evidence of a selective advantage so it's probably due to random genetic drift. In fact that's what the result in Washington suggests to me. But that's not what the newspaper article says, ...

Scientists say it's a real-life example of natural selection at work, which has rolled on for a century here without much public notice.

The IDiots have jumped all over this one and for once they may be partly right.


Denyse O'Learly criticizes the article in The Washington Post Thinks It Has Discovered Natural Selection. I agree with Denyse that this is probably not natural selection. It's a clear and wonderful example of evolution—because allele frequencies in the squirrel population are changing—but the mechanism is probably random genetic drift.

I wish people would understand the difference between evolution and natural selection. If you are a pluralist, you recongize several different mechanisms of evolution and natural selection is only one of them. That's why pluralists (i.e. most evolutionary biologists) are not Ultra-Darwinians.

[The photo is borrowed from the definitive website on blackskwerls. Don't go there unless you're prepared to be really, really frightened. The truth about the black squirrel invasion is ....]

There's Way More than One Born Every Minute

 
"There's a sucker born every minute" according to the famous saying incorrectly attributed to P.T. Barnum. Now we have further proof with an announcement by Coca-Cola that the new version of Diet Coke will be fortified with vitamins and minerals begining next Spring. CNNMoney reports that shares of Coca-Cola are up 0.3%, demonstrating that some people know how to profit from suckers.

Skeptical About the "Obesity Epidemic"

 
John Sullum on reasononline reviews two new book on obesity [Lay Off the Fatties]. The books are "Fat Politics: The Real Story Behind America’s Obesity Epidemic" by J. Eric Oliver and "The Diet Myth: Why America’s Obsession With Weight Is Hazardous to Your Health" by Paul Campos. Here's the opening prargraph of an excellent review, ....

The government seems to have made tremendous strides in its War on Fat. In 2004 researchers at the U.S. Centers for Disease Control and Prevention (CDC) said “poor diet and physical inactivity” were killing 400,000 Americans a year, a number that was widely presented as an estimate of “obesity-related deaths.” Just one year later, the estimate had been reduced to about 100,000. To cut the death toll by 75 percent in the space of a year, the anti-fat crusaders must be doing something right.

I'm not a big fan of diet books or any of the lifestyple books that are so common in the bookstores. These two books are probably not much different, but at least they raise an important issue. How much can we trust the headlines? Is there a real problem with obesity in our society?

It turns out that the "reduction" in deaths was entirely due to rational thinking in the face of stupidity. The orignal report of 400,000 deaths per year was as much as the combined total of all deaths due to disease. A bit of common sense prevailed and the Journal of the American Medical Association published a revised estimate of 112,000 deaths per year due to obesity. (Is that a peer-reviewed journal? If so, where were the peer reviewers the first time?)

What about the obesity epidemic? Well, it turns out that part of it is completely artificial. Back in 1985 you were considered obese if your BMI was above 27.5. A couple of years later the threshold was lowered to 25 making millions of American obese overnight. Neat trick, eh?

There's much more,

“Nearly all the warnings about obesity are based on little more than loose statistical conjecture,” says Oliver, adding that there is no plausible biological explanation for most of the asserted causal links between fatness and disease. “The health risks associated with increasing weight are generally small,” says Campos, and “these risks tend to disappear altogether when factors other than weight are taken into account.” For example, “a moderately active larger person is likely to be far healthier than someone who is svelte but sedentary.” Campos cites research finding that obese people “who engage in at least moderate levels of physical activity have around one half the mortality rate of sedentary people who maintain supposedly ideal weight levels.” Lest you think these facts have been noticed only by political scientists and law professors, Campos and Oliver draw heavily on the work of biomedical researchers such as Case Western nutritionist Paul Ernsberger, University of Virginia physiologist Glenn Gaesser (author of the 1996 book Big Fat Lies: The Truth About Your Weight and Your Health), and Steven Blair, the physician/epidemiologist who heads the Dallas-based Cooper Institute.

I don't know if Campos and Oliver are correct but what they say makes sense to me. The whole obesity epidemic nonsense has a bad smell. It doesn't make sense to this skeptic. Here are some examples of distorted science.

Yet none of this contradicts the main scientific point of these two books, which is that the public health establishment, abetted by a credulous and alarmist press, has greatly exaggerated both the strength of the evidence linking fatness to sickness and the level of risk involved. Oliver cites a 2004 New York Times story headlined “Death Rate From Obesity Gains Fast on Smoking,” based on the highly implausible 400,000-death estimate that was later repudiated by the CDC. He also mentions a 2003 A.P. article that announced “Obesity at Age 20 Can Cut Life Span by 13 to 20 Years.” He notes that “the obesity in question was at a BMI of 45 [305 pounds for an average-height man], which affects less than 1 percent of the population.” In a passage that could have been lifted from a critique of U.S. drug policy, Campos says “the basic strategies employed by those who profit from this war are to treat the most extreme cases as typical, to ignore all contrary data, and to recommend ‘solutions’ that actually cause the problem they supposedly address.”

We need more debate on this issue. We need more skeptics.

Are left-handers quicker thinkers than righties?

 
howstuffworks asks Are left-handers quicker thinkers than righties?.

No.

Octopus Skin Invisibility Cloak

 
Looking for a Christmas present for PZ Myers? Look no further. Nature reports that invisibility cloaks made from octopus skin are just around the corner.

P.S. PZ loves Christmas presents. He's only an atheist from January to November.

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

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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.

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