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Sunday, December 31, 2006

Old Professors

Jonah Lehrer is an editor for Seed magazine. On his blog, The Frontal Cortex, he has resuscitated an old argument that I though we had settled. The issue is whether Professors over 60 should be put out on an ice flow to make room for, presumably smarter, young scientists [Old Professors].

The article defines old Professors as those over 60. I'm going to assume that young Professors are under 40. Since I'm 60 years old, that makes me still middle-aged and in a good position to present a totally unbiased opinion concerning the stupidity and naivety of youth.

It might be helpful to have some examples of old dotty Professors who clearly lost all ability to contribute to science once they turned 61. In the field of evolutionary biology we have; Ernst Mayr (101 when he died last year), Jared Diamond (69), E.O. Wilson (77), Richard Dawkins (65), and Stephen Jay Gould (61 when he died in 2002).

My faculty union and the University of Toronto recently concluded an agreement to abolish mandatory retirement at age 65 and the Province of Ontario has recently passed legislation abolishing mandatory retirement in the public sector. Let's not argue about whether Professors should be forced to leave their jobs on their 65th birthday. This is a rights issue. It is ethically wrong to discriminate on the basis of age. There is no justification for such discrimination in this day and age and it's about time that we did away with it. (Most American schools abolished mandatory retirement many years ago.)

Are there any conceivable arguments for reinstating mandatory retirement that meet the test of rationality? No there aren't. So why is there still a debate?

Lehrer quotes from an article in the Boston Globe on the Graying of US Academia. The article points out that since the abolition of forced retirement, the average age of Professors is increasing (duh!) and this is a bad thing.

Why is it a bad thing? The perceived wisdom is that old Professors are taking up space that should be going to younger faculty. Well, it turns out that this isn't very significant. It will always be the case that a new faculty member will be hired every time a Professor retires. Assuming a steady state, the rate of new hires won't be much different if some of the Professors stay on past 65 or 70. (Less than 25% of Professors continue to work after they turn 65.) That argument doesn't really cut the mustard. The real problem is that the number of Professors is not expanding very much so that new opportunities for junior faculty aren't being created. In our department, for example, budget cuts are forcing us to cut back on the number of Professors.

But even if the argument were true there is no ethical way to improve the situation by getting rid of old Professors. You can't just knock on the door of Professor Dawkins and tell him to get the hell out of Oxford because there's some 32 year old post-doc who wants his job. Be reasonable, people.

There's an underlying assumption in these discussions that I find troubling. If you read John Lehrer's posting and the comments that follow, you'll see lots of discussion about whether old Professors can still do their job. Lots' of people think that young Professors are better teachers, for example. That's nonsense. I've not seen any evidence to support that assumption in my forty years of experience in universities. Some young Professors are excellent teachers and some aren't. Some old Professors are excellent teachers and some aren't.

I can tell you one thing that seems to be a general rule. Whenever we sit down as a group to discuss teaching, the older Professors bring a great deal more to the table than the younger ones. I was reminded of this last month when we discussed changes to our undergraduate and graduate programs. This is a time when wisdom counts. My older colleagues know how to effect real change and they know how to avoid fads that will get us into trouble later on. They know how to work the system for maximum benefit.

(I should point out that in science departments teaching is a minor part of the job so it doesn't play a big role in deciding whether old Professors are better than young ones.)

Administrative tasks are a major part of the average Professor's job. There's no question about the fact that the longer you've been at a university the more capable you are of handling administrative tasks. This applies to local jobs like departmental chair, associate chair, and managing undergraduate and graduate programs. It also applies to higher level jobs like chairing university committees and becoming a Dean or assistant Dean.

Research is the big bogeyman. There's this persistent myth out there that young people are ever so much better at it that the old fuddy-duddys who already have one foot in the grave. There is no evidence to support this myth, even in mathematics where it originated. If you want to maximize research productivity in a department you don't do it by forcing out highly productive scientists just because they turn 65.

Please don't misinterpret me. Of course there are old Professors who are not being productive. There are ways of encouraging them to retire and if they don't take the hint there are ways of firing them even if they have tenure. This won't be required nearly as often as people imagine, but it will happen and it should probably happen more often. On the other hand, let's not forget that there are lots of younger people who don't make the cut. It's not a direct function of age.

This is an issue that demands more sensitivity than it gets. I find it very unsettling to hear people calling for the firing of old Professors just because we need to make room for younger ones. What do you imagine those old Professors are going to do when they are fired? In many cases they have been working for much lower wages than they could have gotten in the private sector and they still have mortgages to pay and kids to put through college. They often have decent pensions but still not enough to maintain their lifestyle. (I'm not talking about Harvard, I'm talking about state schools.) Do we really want to move to a cut-throat corporate model where youth and lower wages trump wisdom and maturity? Is that the kind of university we want?

The Three Domain Hypothesis (part 6)

[Part 1][Part 2][Part 3][Part 4][Part 5]

Evolving Biological Organization

Carl Woese discovered archaebacteria and he made them fit into a separate super-kingdom, or “domain.” He is the man behind the claim that archaebacteria are so different from other bacteria that they deserve equal taxonomic status with eukaryotes. Woese is the father of the Three Domain Hypothesis, which not only claims domain-level recognition for archaebacteria, but also claims that eukaryotes descend from a primitive archaebacterium.

Back in 1995, when evidence against the Three Domain Hypothesis was mounting, I made a bet with Steven LaBonne that Woese would recant by January 1997.

I lost that bet, but eight years later Woese has finally come to his senses ... at least partly ....

I’m reviewing articles that appeared in Microbial Phylogeny and Evolution edited by Jan Sapp. Carl Woese’s contribution (“Evolving Biological Organization”) describes his current thoughts about the emergence of defined species from the pool of primitive gene-swapping cells that characterized the early history of life.

Woese’s idea, which has been evolving of a period of ten years, is that primitive life existed as a community of cells that freely exchanged genes. They shared a basic translation system for making proteins, but had little else in common. These cells evolved as a community and not as distinct lineages.

Woese refers to this time as the “progenote era” where the word “progenote” refers to a cell that has not yet established a definite link between a stable genotype and a heritable phenotype. At some point in time, certain cells make the transition from progenote to the founders of a stable lineage. The transition point is known as the “Darwinian threshold.”
The real mystery, however, is how this incredibly simple, unsophisticated, imprecise communal progenote—cells with only ephemeral genealogical traces—evolved to become the complex, precise, integrated, individualized modern cells, which have stable genealogical records. This shift from a primitive genetic free-for-all to modern organisms must by all acounts have been one of the most profound happenings in the whole of evolutionary history. Although we do not yet understand it, the transition needs to be appropriately marked and named. “Darwinian threshold” (or “Darwinian Transition”) seems appropriate: crossing that threshold means entering a new stage, where organismal lineages and genealogies have meaning. where evolutionary descent is largely vertical, and where the evolutionary course can begin to be described by tree representation. (p. 109)
According to Woese, bacteria were the first species to emerge from the pool. From that point onwards, the evolution of bacteria was “Darwinian” and could be represented by a bifurcating tree.

What about archaebacteria and eukaryotes? They emerged later ...
At that point, though, both the archaeal and eukaryotic designs remain in the pre-Darwin progenote, condition: still heavily immersed in the universal HGT field, still in the throes of shaping major features of their representative designs; and so, their evolutions cannot be represented in tree form. In other words, the node in the conventional phylogenetic tree that denotes a common ancestor of the archaea and eukaryotes does not actually exist. The two cell designs are not specifically related; it is just that the tree representation made them “sisters by default.” (p.111)
Woese suggests that the archaebacteria were the next to cross the Darwinian threshold followed by eukaryotes. This explains why archaebacteria have simpler cell components and eukaryotes are more complex. (The precursors of the eukaryote lineage spent more time in the progenote era and accumulated more innovative structures, such as nuclear membranes.)

The progenote community may have spawned other “domains” but these are now extinct, although Woese suggests there are some clues pointing to their previous existence. I assume that the progenote community itself petered out shortly after the emergence of eukaryotes.

This new theory of Woese is not very satisfying. I find the explanation somewhat confusing. Woese is trying to preserve the distinctiveness of the Three Domains while denying that their relationship can be discerned. In other words, he wants to have his cake and eat it too.

In order to defend the monophyletic domains, especially archaebacteria, he has to postulate that each one descends from a single cell, or lineage, that pops out of the progenote community. That’s why each domain has a defined root (i.e. monophyletic). But in order to account for the massive amounts of data that show eukaryotes closer to bacteria than to archaebacteria, he postulates an extended period of evolution where cells exchanged genes in a communal pool. This is not unlike the ideas of many other workers in the field except that for Woese it represents a denial of one of the basic tenets of the original Three Domain Hypothesis.

Woese is very clear about this. He makes the case that the branches at the base of the ribosomal RNA tree are not meaningful. It is wrong to assume that archaebacteria and eukaryotes share a common ancestor. I’ll close this part with an extended quote from Woese to show you just how far he’s willing to go to make the case. (Note how much he has come to agree with people like Ford Doolittle [Part 5] who have been challenging the Three Domain Hypothesis for over a decade.)
Classical biology has also saddled us with the phylogenetic tree, an image the biologist invests with a deep and totally unwarranted significance. The tree is no more than a representational device, but to the biologist it is some God-given truth. Thus, for example, we agonize over how the tree can accommodate horizontal gene transfer events, when it should simply be a matter of when (and to what extent) the evolution course can be usefully represented by a tree diagram. Evolution defines the tree, not the reverse. Tree imagery has locked the biologist into a restricted way of looking at ancestors. It is the tree image, almost certainly, that has caused us to turn Darwin’s conjecture that all organisms might have descended from a simple primordial form into doctrine: the doctrine of common descent. As we shall discuss below, it is also the tree image that has caused biologists (incorrectly) to take the archaea and the eukaryotes to be sister lineages. Much of the current “discussion/debate” about the evolutionary course is couched in the shallow but colorful and cathected rhetoric of “shaking,” “rerooting,” “uprooting,” or “chopping down” the universal phylogenetic tree. (p.102)

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.

Saturday, December 30, 2006

Creation Sunday

 Looking for some entertainment in February? Check out Creation Sunday in Orangeville, Ontario (north of Toronto). On Sunday Feb. 11th and Monday Feb. 12th you can hear three of the leading IDiots from Creation Ministries International speaking on "Authority Begins With Genesis," "Genesis and the Gospel Connection," "Codes and Creation," and "What the Bible and Science say about the Age of the Earth."

It ought to be a barrel of laughs. Bring lots of popcorn.

Capital Punishment Is Barbaric

 With the hanging of Saddam Hussein, Iraq affirms its membership in the group of nations that don't deserve to be called civilized.

Thursday, December 28, 2006

New But Not New

Another major breakthrough in molecular biology has just been reported [Jefferson researchers discover new way nature turns genes on and off]. (I've lost track of how many times traditional molecular biology has been overturned in 2006—has anyone kept a list?)

Here's the startling news,
Peering deep within the cells of fruit flies, developmental biologists at the Kimmel Cancer Center at Thomas Jefferson University in Philadelphia may have discovered a new way that genes are turned on and off during development.
Reading a bit further, we find,
According to Dr. Mazo, the researchers found that one of the likely mechanisms behind ncRNAs' ability to regulate essential coding genes is through a "transcription interference" mechanism. "Such mechanisms are known in bacteria and yeast, but not much is known in higher organisms," he explains.
In other words, it's not new at all. I've been teaching transcriptional interference during bacteriophage lambda development since 1979 and it's in many textbooks, including mine (1994).

Question: What the heck is a "higher organism?"
Answer: It's a term we look for in order to identify people who don't understand evolution.

Tuesday, December 26, 2006

Can You Be a Theist and Believe In Evolution?

John Wilkins wonders about this in God, evolution and variation. I think it all boils down to purpose. Science doesn't reveal purpose but most religions demand it. (We're talking about interventionist Gods here.) Real evolution incorporates a large degree of accident and randomness and that's just not consistent with a God who has a plan. (Yes, I'm aware of the confused rationalizations of some theistic evolutionists.)

A Challenge to Denyse O'Leary

Denyse O'Leary writes in Thoughts on recent books on the intelligent design controversy: Some ways to spend your holiday cash.
Case in point: North American mainstream media report that the vast majority of Americans do not believe Darwinism, with the clear implication that there must be something wrong with them. It is almost inconceivable that media boffins, for whom materialism is the normal way of thinking, would actually be interested in knowing why so many who are at liberty to doubt take up that option. And the media boffins are not likely to change. The media they govern are more likely to simply decline in importance as a source of information.
Denyse, you claim to be a journalist. I challenge you to come up with a reasonable explanation. Keep in mind that you also have to explain one additional fact; the majority of Canadians and Europeans believe in evolution and they have just as much freedom to doubt as Americans. Possibly, more.

So, give it your best shot. If you think the "media" aren't interested in knowing why so many Americans are fooled by the IDiots then here's your chance to get them interested. More importantly, here's your big chance to do what nobody else has been able to do—explain why so many people in the USA are anti-science. You could be famous.

P.S. Why are you still using the term "Darwinism" to describe acceptance of the scientific facts of evolution? You haven't been paying attention, have you?

Monday, December 25, 2006

Looking for the Ideal Christmas Present?


Check out dnaPortraits(TM). For only a few hundred dollars they create artwork based on your personal DNA fingerprint. An ideal gift for any biochemist (hint, hint).


From M-LAW via Jim Lippard with one minor alteration.

Please accept with no obligation, implied or implicit, our best wishes for an environmentally conscious, socially responsible, low stress, non-addictive, gender neutral celebration of the winter solstice holiday, practiced with the most enjoyable traditions of religious persuasion or secular practices of your choice with respect for the religious/secular persuasions and/or traditions of others, or their choice not to practice religious or secular traditions at all. We also wish you a fiscally successful, personally fulfilling and medically uncomplicated recognition of the onset of the generally accepted calendar year 2007, but not without due respect for the calendars of choice of other cultures whose contributions to society have helped make our country great (not to imply that Canada is necessarily greater than any other country) and without regard to the race, creed, color, age, physical ability, religious faith or sexual preference of the wishee.

By accepting this greeting, you are accepting these terms: This greeting is subject to clarification or withdrawal. It is freely transferable with no alteration to the original greeting. It implies no promise by the wisher to actually implement any of the wishes for her/himself or others and is void where prohibited by law, and is revocable at the sole discretion of the wisher. This wish is warranted to perform as expected within the usual application of good tidings for a period of one year or until the issuance of a subsequent holiday greeting, whichever comes first, and warranty is limited to replacement of this wish or issuance of a new wish at the sole discretion of the wisher.

Disclaimer: No trees were harmed in the sending of this message; however, a significant number of electrons were slightly inconvenienced.

10 Truths About Atheism

From yesterday's Los Angeles Times: 10 myths—and 10 truths—about atheism by Sam Harris.

I'd like to express my disagreement with #4 "Atheists think everything in the universe arose by chance." Harris says,
The notion that atheists believe that everything was created by chance is also regularly thrown up as a criticism of Darwinian evolution. As Richard Dawkins explains in his marvelous book, “The God Delusion,” this represents an utter misunderstanding of evolutionary theory. Although we don’t know precisely how the Earth’s early chemistry begat biology, we know that the diversity and complexity we see in the living world is not a product of mere chance. Evolution is a combination of chance mutation and natural selection. Darwin arrived at the phrase “natural selection” by analogy to the “artificial selection” performed by breeders of livestock. In both cases, selection exerts a highly non-random effect on the development of any species.
That's not quite right.

Nobody denies the power of natural selection and nobody claims that natural selection is random or accidental. However, the idea that everything is due to natural selection is the peculiar belief of a relatively small number of people, of whom Richard Dawkins is the most outspoken.

A great deal of evolution is the result of chance or accident, as is a great deal of the rest of the universe. It's perfectly okay to say, as a first approximation, that lots of evolution is random or accidental. This is a far closer approximation to the truth than saying it's the all the result of design by natural selection.

See Evolution by Accident. As far as I'm concerned, it's Harris and Dawkins who represent an "utter misunderstanding of evolutionary theory."

Closed on December 25th

Imagine, my Timmy's is closed on the one day you need it the most.

Merry Christmas Everyone!

Sunday, December 24, 2006

Will Santa be Affected by Solar Flares?

An article posted on the Natural Sciences and Engineering Research Council of Canada (NSERC) website has the answer [Santa Claus and Solar Flares]. Learn the size of Santa's sled and how he manages to deliver all the presents.

The Hypocrisy of Scientific American

The editors of Scientific American are worried about PLoS ONE, the new online journal of science [Peer Review Is Sooooo Old School. They claim this is a big step backwards since the PLoS ONE articles reportedly circumvent peer review. Scientific American set itself up as the protector of scientific integrity and they vow to uphold these high standards in spite of the fact that the scientific community is letting them down.

This is wrong on so many levels that I hardly know where to begin. The real problem with science education is Scientific American, not PLoS ONE.

Here's what the Scientific American editors say,
With the burden of proof off of the reviewers, we in the science press will have to be more vigilant than ever. We can't rush to put stories out until we've focus- grouped findings with a number of experts in a study's particular field. It will force us to become better reporters and to resist the urge to sensationalize and invoke hyperbole--which, while it may not move magazine units or generate hits, will make our service more noble. We'll put in contingencies in order to avoid situations like the false alarm that plagued Lehigh mathematician Penny Smith--the poor woman who posted a flawed proof of the Navier-Stokes equations this fall on arXiv.

SciAm has already started on this path, by the way, as evidenced by JR Minkel's write-up of this morsel from the journal's inaugural issue: Rest easy, creationists, turns out we're a little less like chimps than we previously thought.

PLoS ONE is opening a possible Pandora's box into a brave new world of publishing that's as terrifying as it is exciting. From this point forth, information going from the lab to the journalist's wire (and then onto the public) will be less and less scrutinized and fact-checked. It's the dissemination of scientific information sped up to the breakneck velocity of the 21st century. Here we go...
Bullshit! This is not the end of peer review. The review of PLoS ONE articles is no different than that of many other scientific journals. I will be very surprised if the quality of papers ends up being any different than those published in Cell, Journal of Biological Chemistry, or Nature. All of these journals publish unadulterated rubbish from time to time and brilliant papers as well. The quality of papers in the leading "peer-reviewed" journals ranges from embarrassing to excellent.

PLoS ONE won't be any different.

I'm very upset by the fact that Scientific American editors see themselves as the guardians of scientific integrity, and I'm flabbergasted that they think they can recognize good science from bad science. Their record over the past few years proves them wrong. They have published all kinds of trash in my field, and probably other fields as well. They have hyped stories that don't deserve to be featured in Scientific American proving that their editors are suckers for press releases and self-promotion [The Alternative Genome, Why Are Some Animals So Smart?, The Real Life of Pseudogenes].

In the recent past, the "vigilance" of Scientific American editors and staff writers has left a great deal to be desired. If this crazy false alarm over PLoS ONE makes them pull up their socks and consult more widely before publishing then that's going to be good for science education.

I'm not holding my breath.

(RPM at Evolgen is also upset with Scientific American: Science Reporters Lament the Advent of PLoS ONE.)

E-Z Answer Squirrel

The E-Z Answer Squirrel will answer your most profound questions about religion, like "Does God hate me because I'm gay?"

Brought to you by the United Church of Canada, a church that understands sarcasm.

You Can Call Me Pope Larry !

I'm Pope Stephen! Hurrah.
Which Historical Lunatic Are You?
From the fecund loins of Rum and Monkey.

In the UK, 63% Are Not Religious

According to a Guardian/ICM poll 63% of the people in Briton are non-religious compared to 33% who describe themselves as religious. The non-religious group includes many who call themselves Christian but presumably don't practice the religion. Most people think that Religion does more harm than good - poll.

It's important for North Americans to understand the differences between us and Europeans. While religion still seems to be a powerful force in America, it is on the wane in most other western industrialized nations. That's a reason for optimism. It's possible that North America will soon abandon religion as well.

Saturday, December 23, 2006

Breaking News: the IDiots Don't Understand Neutral Theory

DaveScot reveals his ignorance in: The Sound of The Neutral Theory Exploding.

Poor Dave, he doesn't know that there are many examples of synonymous mutations having an effect on protein expression. They've been known for decades. Look up "codon bias" for one such example.

As usual, the IDiots get confused about the difference between exceptions and generalities. They think that every little exception to a general rule invalidates the rule and overturns all of biology. This is why we call them IDiots.

Jason Rosenhouse Reviews Orr's Review of Dawkins

Read it at Orr on Dawkins. Good job, Jason. Orr looks like one of them appeaser scientists who have to bend over backwards to defend religion against atheism. I especially like the argument that it's okay to believe in magic and superstition as long as you couch it in sophisticated, intellectual language.

Don't Forget Somalia

As we ponder what to do in Iraq and Afghanistan we do well to remember our failed attempt to impose democray in Somalia. The fighting is still going on and the United Nations is still making noises about it [UN urges end to Somalia fighting].

Would it have been any better if 50,000 western troops have tried to establish law and order? Was cut-and-run a good strategy for Somalia? I think so, and I think it might be the best strategy for Afghanistan and Iraq as well. Let them sort out their own problems and stop complicating things by giving the people a reason to unite against a common enemy (foreign invaders).

Friday, December 22, 2006

They Closed My Timmy's!

It was three weeks ago today and it was only for one day, but it's taken me this long to get over it.

I got up one Saturday morning and went off to my local Tim Horton's to get coffee and a donut. The store was closed and there were strange looking trucks parked on the road. What was going on? Timmy's are supposed to be open 24/7—they're not allowed to close Tim Horton's, are they?

There were famous-looking people living in the white trailers. Cameras were everywhere. There was even a hearse parked in the drive-through. (Look closely in the photo on the left.

The manager (below right) needed a police escort because of the rioting customers. He gave us all gift certificates but that was small compensation for our tragic loss. They opened up the next day but the damage had been done. I'm told we can see what they were up to by going to the movie theatre next summer. As if I'm going to believe that!


My Peculiar Aristocratic Title is:
His Excellency Laurence the Incomplete of Midhoop St Giggleswich
Get your Peculiar Aristocratic Title

The White House

Friday's Urban Legend

The Canadians soundly trounced the Americans in the War of 1812. One of the goals of the campaign was to demonstrate the ability of the mighty British Empire to deliver shock and awe to the enemy capital. To this end, Washington was invaded and looted in 1814 and the White House was set on fire. The Americans were so intimidated that President Monroe soon surrendered.

This is all well-known historical fact. Something that Canadian and British schoolchildren learn in history classes when they are 10 years old.

The name "White House" is thought to be derived from the whitewash that Americans put on the house when the fire damage was repaired. It seemed to have been part of a larger campaign to whitewash everything that had to do with losing of the War of 1812.

That part is urban myth according to [White House Wash]. The President's house was known as the White House before the War of 1812 and the original house, built in 1798, was whitewashed.

Skeptical Climatologists

Kevin Vranes of No Se Nada writes about impressions he got from a recent meeting of geophysicists [So what happened at AGU last week?]. Apparently, some climatologists are worried that they may have oversold climate change and supressed legtimate skepticism over some of the details.

This is a very important issue in science. It does not mean that warnings about climate change are totally wrong or misguided. What it means is that contrary opinions within the scientific community aren't getting attention for fear of diluting the important message that the public needs to hear.

It's an issue in other disciplines as well, such as evolutionary biology. Skepticism, which is the essence of science, doesn't play very well in the public arena. Scientists who are skeptical about some aspects of evolutionary biology are sometimes considered to be traitors to the cause of defeating creationism. I imagine that the same sort of thing might be happening in the field of climate change.

Varsity Centre Bubble Now Inflated

The new Varsity Centre bubble has now been inflated over the University of Toronto football field on Bloor Street. Students have been looking forward to this event for some time: it means they can now play Ultimate Frisbee all winter.

The press release talks exclusively about athletics but we all know the real reason for creating such a large, heated enclosure. In Canada, the gyms and arenas are stuffed with desks and chairs at this time of year and used for exams.

Rumor has it that the bubble is energy efficient. It recycles a lot of the hot air generated on campus.

Thursday, December 21, 2006

Mammalian Gene Families: Humans and Chimps Differ by 6%


The first issue of PLoS ONE has just been published. PloS ONE publishes peer-reviewed, open-access, articles that are freely available on the internet. The journal is supported by the Public Library of Science (PloS), a non-profit organization.

The article that I've been waiting to see is,
Demuth, J.P., De Bie, T., Stajich, J.E., Cristianini, N., and Hahn, M.W. (2006) The Evolution of Mammalian Gene Families
Demuth et al. examined gene families in five species whose genomes have been sequenced (human, chimpanzee, mouse, rat, dog). Gene families are normally defined as groups of related genes having more than one copy in a genome. For example, the globin gene family consists of multiple copies of related globin genes such as myoglobin, α-globin, β-globin, and others. The authors appear to use a different definition, which counts orthologous genes in different species as a gene family. Thus, their paper discusses "gene families" that have single genes in different species.

By scanning the available genome sequences, Demuth et al. were able to cluster all genes into 15,389 groups called "gene families." Of these, 3,114 were single genes confined to a single species. These were presumed to be annotation artifacts and were discarded. Not all of the remaining groups were present in all five species. A total of 2,285 additional groups were confined to distinct lineages on the mammalian tree indicating that they had been "created" after divergence from the common ancestor. This leaves 9,990 groups that were probably present in the ancestor of dog, human, chimp, mouse, and rat.

The question is, how many of these gene families show gain or loss of numbers during mammalian evolution? The answer is 5,622 or 56.3% (5622/9,990). The data is shown in Figure 1 (below). The red section of the pie chart represents groups that have experienced a reduction in the number of members of a gene family (or loss of the entire group) in a particular lineage. The green section represents a gain in the number of genes in a family.

Figure 1. Distribution of gene gain and loss among
mammalian lineages.
Creative Commons Attribution License

If we focus on the human/chimp comparison, it turns out that the human genome contains 1,418 genes that do not have orthologs in the chimpanzee genome. What this means is that if we look at the identical sections of human and chimp chromosomes one of them will have a gene that the other one does not have at that position. It turns out that the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans. If there are 22,000 genes in the genome, then this total of 1,418 differences represents 6.4% of the genes.

It's important to note that this does not mean that entirely new genes are created or destroyed. What it means is that there have been duplication events such that a gene has been duplicated in one of the lineages. For example, let's say that the region of the chromosome containing the α-globin genes was duplicated in the chimpanzee lineage. This would count as a gain in chimps relative to humans.

There are several problems with the analysis. One of the most severe is the lack of complete coverage of the chimp genome and the relatively poor annotation compared to the human genome. Only 94% of the chimp genome is available while the human genome is about 99% complete and much more accurate. This means that there will be a number of genes in humans that won't appear in chimps. It's unlikely that these problems lead to errors of more than 2-fold.

The authors are clearly aware of the fact that most of these changes in gene number have no effect on the organism. They are accidental changes due to random genetic drift. They are also aware of the fact that some of the duplications and losses are variants that are segregating in the human and chimp populations. In other words, they are not fixed differences.

Nevertheless, Demuth et al. point out that some of the gains and losses of genes could be responsible for the phenotypic differences between chimpanzees and humans. They caution us that the traditional 1% difference in the sequences of orthologous genes may not be the whole story.

An Example of High School Biochemistry

I don't know exactly what to make of this. It is not exactly correct, but it's not exactly wrong, either. I wonder what grade produced it?

Wednesday, December 20, 2006

Grading Exams

I've written about the difficulties of grading exams and about the fact that it's almost impossible to get the perfect distribution. We have our tricks. Now, Daniel J. Solove of Concurring Opinions has let the cat out of the bag by revealing one of our most garded secrets—the staircase technique. He spills the beans in A Guide to Grading Exams.

You'd think there ought to be a movement to drum him out of the teacher's union, but no, instead his article is advertised in The 98th Carnival of Education. What is this world coming to?

The Carl Sagan memorial blog-a-thon

Carl Sagan died ten years ago today. My contribution to the Carl Sagan memorial blog-a-thon is a quotation from page 297 of The Demon-Haunted World.
Have I ever heard a skeptic wax superior and contemptuous? Certainly. I've even sometimes heard, to my retrospective dismay, that unpleasant tone in my own voice. There are human imperfections on both sides of this issue. Even when it's applied sensitively, scientific skepticism may come across as arrogant, dogmatic, heartless, and dismissive of the feeling and deeply held beliefs of others. And, it must be said, some scientists and dedicated skeptics apply this tool as a blunt instrument, with little finesse. Sometimes it looks as if the skeptical conclusion came first, that contentions were dismissed before, not after, the evidence was examined. All of us cherish our beliefs. They are, to a degree, self-defining. When someone comes along who challenges our beliefs as insufficiently well-based—or who, like Socrates, merely asks embarrassing questions that we haven't thought of, or demonstrates that we've swept key underlying assumptions under the rug—it becomes much more than a search for knowledge. It becomes a personal attack.
Sagan combined skepticism with finesse. That was part of his charm.

The Blasphemy Challenge

The IDiots are making a fuss about The Blasphemy Challenge. If you don't know why the IDiots have their knickers in a knot then watch this video from YouTube .

Dissent Isn't Welcome on Uncommon Descent!

DaveScot says,
Larry, why do Darwinists insist on calling ID creationism?
I don't know. Why don't you ask a Darwinist?

If you want to ask me why I call your creed Intelligent Design Creationism then feel free to come on over here and ask. I don't ban IDiots. In fact, most science bloggers don't ban IDiots because the IDiots supply much of the comic relief on science blogs.
You’ll need to answer on your own blog because you’re no longer welcome on this one.

Libya Reverts to the Stone Age

Several bloggers are all over the this story [Six innocent people sentenced to death.] It concerns five foreign nurses and a doctor who went to Libya in 1999 to help look after sick children. Many of the children became infected with HIV and developed AIDS. Genetic testing has shown that the virus was present before the team of nurses and doctors arrived at the hospital but, in spite of the scientific evidence, the Tripoli Six have been convicted of spreading the disease and sentenced to death.

There has been rejoicing in the street in Libya as citizens demonstrate their support for an ignorant court.

Denyse O'Leary Never Learns

Since first meeting Denyse O'Leary a few months ago, we've had several interactions where I attempted to explain why "Darwinism" is not an appropriate synonym for modern evolutionary biology. From time to time she actually seems to get it. She's even agreed to try and be more honest about referring to evolution instead of harping on "Darwinism" as the number one bogey man.

Alas, it didn't last long. Denyse has posted a long diatribe based on some unsubstantiated claim that a professional society is "hassling" a scientist who dares to question Darwin. She says,
Darwinism is their perpetually virgin theory that can never be impugned. Have you noticed how absolute are the claims they make for it? You’d have as much luck discussing science-related questions about Darwin’s theory with them as discussing Mary’s state of grace with Mickey and Ladislaw.
Once again, you're dead wrong Denyse. Lots of us question classic "Darwinism," as did Stephen Jay Gould, the former President of the American Association for the Advancement of Science (AAAS, a professional society). Modern evolutionary theory has moved well beyond what Darwin knew in the nineteenth century. Science is constantly changing—it does not rely on the literal reading of ancient texts. When will you ever learn?

Nobel Laureates: Hans Krebs

The Nobel Prize in Medicine 1953.

"for his discovery of the citric acid cycle"

Hans Krebs (1900-1981) received the Nobel Prize for working out the pathway for oxidation of the two carbon acetyl group on acetyl-CoA via a series of tricarboxylic intermediates. The cyclic pathway is now known as the Krebs cycle, the citric acid cycle, or the tricarboxylic acid cycle (TCA cycle).

Krebs had previously been known for his excellent work on the urea cycle in the 1920's and 30's. However, the citric acid cycle was controversial from the beginning. (See Monday's Molecule #6.) By the time he received the Nobel Prize, most biochemists were convinced but there were some hold-outs, making this one of the more controversial awards.

The modern citric acid cycle differs very little from the one published by Krebs over fifty years ago. The main difference is that today we recognize cis-aconitate as an intermediate in the reaction catalyzed by aconitase and not as a separate intermediate in the pathway.

Monday, December 18, 2006

Michael Denton and Molecular Clocks

It's easy to construct a phylogenetic tree using cytochrome c sequences (left). The tree shows us that bacteria and eukaryotes form two separate branches just as predicted by evolution. Within the eukaryote branch, we see that plants, fungi, and animals form distinct groups. Again, this is exactly what evolution predicted.

One of the remarkable things about these trees is that the branches have similar lengths. Beginning at the base of the tree, the distance to plants, animals, fungi, and bacteria is about the same. It differs by a factor of two, at most, for any species. This is evidence of a molecular clock—a roughly constant rate of evolutionary change for every lineage over a period of hundreds of millions of years. (Cytochrome c is not the ideal sequence for showing this since it's pretty small as far as proteins go. Substitutions of only a few amino acids can make a big difference to branch lengths. Larger proteins show more regular molecular clocks.)

We know why there's a molecular clock. It's because the vast majority of changes in the amino acid sequences of proteins are due to fixation of neutral, or nearly neutral, mutations by random genetic drift. As with any stochastic process, the law of large numbers produces a predictable pattern. In this case, a relatively constant rate of change over hundreds of millions of years.

As it turns out, the overall rate of fixation of neutral alleles should be close to the mutation rate. This is a conclusion derived from population genetics models and those models are well supported by evidence. Since mutation rates are similar, if not identical, between species this rate becomes roughly constant in each lineage. The branch lengths in the cytochrome c tree reflect this indirectly since they result from a combination of fixation times and mutation rates. Furthermore, they are amino acid sequences so a lot of the underlying mutations at the nucleotide level are hidden.

Michael Denton knows of this population genetics explanation since he mentions it on page 289 of Nature's Destiny: How the Laws of Biology Reveal Purpose in the Universe.
Comparisons of these two rates, the rate of mutation and the evolutionary substitution rate, have revealed the very surprising fact that the two rates are the same. This remarkable finding that the difference between the DNA sequences of different species have been generated by mutation and that other factors such as natural selection could only have played a relatively minor role.
Denton knows that the data supports such an idea because he brings up cytochrome c on the next page.
By comparing sequences a curious pattern was observed. For example, in the case of cytochromes, all the higher organism cytochromes (yeasts, plants, insects, mammals, birds, etc.) exhibit an almost equal degree of sequence divergence from the bacterial cytochrome in Rhodospirillum. This means that all their cytochrome genes have changed to about the same degree—in other words, have evolved at a uniform rate.
The uniform rate of change is what impresses Michael Denton. As I mentioned above, Denton knows that adaptation (selection) is ruled out as an explanation. Unlike many other IDiots, Denton knows that pan-adaptationism (often called Darwinism) is not the prevailing view in evolutionary biology.

Random genetic drift is a perfectly reasonable explanation of the molecular clock but Denton rejects that explanation. He says that,
Explanations of uniform rates of evolution in protein genes in terms of genetic drift of neutral mutations fare no better. The rate of genetic drift in a population is determined by the mutation rate. This is not controversial. Although mutation rates for many organisms are somewhat similar per generation time—10^-6/gene/generation—the problem is that generation times are vastly different, so that the rate of mutation per year in, say, yeast, may be 100,000 times greater than a tree or a mammal such as man or elephant, organisms that have long generation times. (p. 291)
The generation time argument is a bit bogus for several reasons. First, mutation rates are based on changes per cell division (replication) and not generation time. Thus, in mammals such a mouse, there are about 50 cell divisions between zygote and gamete and the organism reproduces in about 100 days. Thus, there is, on average, one mutation-causing replication event every two days. This is no more than the average "generation time" of single-celled organisms such as yeast or bacteria. (Bacteria divide once every few days, at most, contrary to what most people believe.)

The second reason for skepticism is that for most of the history of life the "generation time" of different organisms isn't that much different. Large terrestrial mammals, for example, have only been around for about 15% of the time since single-celled life began.

Molecular biologists and population geneticists have thought about these things. They conclude that the evidence favors the idea that phylogenetic trees are due to fixation of nearly neutral alleles by random genetic drift. This explains the molecular clock.

Denton doesn't buy it. He thinks the molecular clock proves Intelligent Design Creationism.
These twin discoveries—that the mutation rate equals the evolutionary substitution rate, and that the rate of change in many genes is regulated by a clock which seems to tick simultaneously in all branches of the tree of life—may represent the first evidence, albeit indirect, that the mutational processes that are changing the DNA sequences of living things over time are indeed directed by some as yet unknown mechanism, or more likely mechanisms. Of course, these discoveries do not prove directed evolution, but it is far easier to imagine them as the outcome of some sort of direction than the outcome of purely random processes. (p. 292)
In other words, Michael Denton can't imagine how stochastic evolutionary processes might work, so God did it. Another argument from ignorance, albeit an ignorance that's on a much higher level than the ignorance usually on display on creationist websites and blogs. (Michael Denton is by far, the most knowledgeable IDiot when it comes to understanding evolution and molecular biology. Perhaps it's why he's out of favor with the true IDiots.)

Junk DNA Disproves Intelligent Design Creationism

Micheal Denton explains it in Nature's Destiny on page 289.
If it is true that a vast amount of DNA in higher organisms is in fact junk, then this would indeed pose a very serous challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary events, when it would not in a strict sense be junk in any case, could the finding be reconciled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. On any teleological model of evolution, most, perhaps all, the DNA in the genomes of higher organisms should have some functions.
Sorry Michael, it is true. The genomes of many complex multicellular organisms have vast quantities of DNA that serves no purpose. It's junk. The whole argument of your book just collapsed, as did any argument for intelligent design.

The fact of junk DNA disproves intelligent design and discredits strict Darwinism as well. The IDiots lose twice. Their strawman version of evolutionary biology is wrong and so is design by God.

FLASH! Dembski Will be Paid for his Expert Advice in Dover

I'm not making this up. Denyse O'Leary announces that the Thomas More Law Center will pay Bill Dembski for over 100 hours of expert advice on the Kitzmiller case in Dover PA.

Discerning readers might recall that this is the case where the IDiots were blown out of the water. Not a single one of their points was accepted by the judge. I wonder what the going rate is for IDiotic experts?

Separating Religion and Medicine

Apparently, there's a movement under way to integrate religion and medicine. "Orac" over at Respectful Insolence rips this idea to shreds in Separating doctoring from doctrine.

Mark Twain and the Eiffel Tower


A couple of weeks ago, we were watching the final episode of "The Amazing Race" and one of the sites they visited was the Eiffel Tower. It's in Paris, and it made my wife think of going to Paris in the Springtime. That's a great idea but, being somewhat less romantic, I have to admit that my first thought on seeing the Eiffel Tower was "Mark Twain."

Huh? Is there a connection between Mark Twain and the Eiffel Tower. Of course there is. There's a connecton between Mark Twain (Samuel Clemens) and everything, if you look hard enough. I thought of him because of this quotation from "Was the World Made for Man?"
Man has been here 32,000 years. That it took a hundred million years to prepare the world for him is proof that that is what it was done for. I suppose it is. I dunno. If the Eiffel tower were now representing the world's age, the skin of paint on the pinnacle-knob at its summit would represent man's share of that age; & anybody would perceive that that skin was what the tower was built for. I reckon they would. I dunno.
Turns out, Mark Twain said many things that are relevant to the debate between rationality and superstution.

Here's a selection from Twainquotes.
Man is the only animal that blushes. Or needs to.
I am the only man living who understands human nature; God has put me in charge of this branch office; when I retire there will be no-one to take my place. I shall keep on doing my duty, for when I get over on the other side, I shall use my influence to have the human race drowned again, and this time drowned good, no omissions, no Ark.
Man is a Religious Animal. He is the only Religious Animal. He is the only animal that has the True Religion--several of them. He is the only animal that loves his neighbor as himself and cuts his throat if his theology isn't straight. He has made a graveyard of the globe in trying his honest best to smooth his brother's path to happiness and heaven....The higher animals have no religion. And we are told that they are going to be left out in the Hereafter. I wonder why? It seems questionable taste.
God's noblest work? Man. Who found it out? Man.
In religion and politics people's beliefs and convictions are in almost every case gotten at second-hand, and without examination, from authorities who have not themselves examined the questions at issue but have taken them at second-hand from other non-examiners, whose opinions about them were not worth a brass farthing.
In the laboratory there are no fustian ranks, no brummagem aristocracies; the domain of Science is a republic, and all its citizens are brothers and equals, its princes of Monaco and its stonemasons of Cromarty meeting, barren of man-made gauds and meretricious decoractions, upon the one majestic level!
Scientists have odious manners, except when you prop up their theory; then you can borrow money off them.
The gods offer no rewards for intellect. There was never one yet that showed any interest in it..
The motto stated a lie. If this nation has ever trusted in God, that time has gone by; for nearly half a century almost its entire trust has been in the Republican party and the dollar--mainly the dollar. I recognize that I am only making an assertion and furnishing no proof; I am sorry, but this is a habit of mine; sorry also that I am not alone in it; everybody seems to have this disease.
What God lacks is convictions- stability of character. He ought to be a Presbyterian or a Catholic or something- not try to be everything.

Molecular Models

I often use molecular models to illustrate concepts in my biochemistry class. There are several types of models and the different types can be used for different purposes. For example, I have a big space-filling model of DNA that's very useful for understanding how sequences are read on double-stranded DNA.

I like ball-and-stick models for showing students how flexible small organic molecules can be in solution and for teaching stereochemistry. My favorite model is the Molecular Visions kit sold by a company called Darling Models Inc.

I logged on to the website and charged it to my credit card. The package arrived the following week.

Last night my wife was looking over our credit card statement to see if one of her charges had gone through. She noticed that I had charged $41 to Darling Models Inc.

It took some explaining. I'm still not sure if she believes me. I hope she reads this and follows the link.

Monday's Molecule #6

Name this molecule. You must be specific. We need the exact name. Bonus points for explaining why this molecule caused such a controversy in biochemistry. (Hint: it has something to do with the green carbon atoms.) Comments will be blocked for 24 hours. Comments are now open.

See Dunbar's answer in the comments for the correct answer with a good explanation of why Krebbs got in trouble and why his Nobel Prize was questioned by some.