Macromutations and Punctuated Equilibria

Olivia Judson has published a piece in The New York Times where she discusses "Hopeful Monsters" [The Monster is Back, and It’s Hopeful]. The basic idea here is that there can be single mutations that have a large effect on the phenotype of an organism. Think of a four-winged fruit fly, for example, that loses one set of wings.

The first organism to exhibit this new phenotype is a "Hopeful Monster." If it has aselective advantage, then the mutation will be passed down to its progeny and in a short time the species will be transformed in a single jump.

The term "Hopeful Monster" is associated with the views of Richard Goldschmidt. These views were thoroughly discredited in the 1940's at the time when the Modern Synthesis was being forged. The sudden leap in evolution due to macromutations was called "saltation" and we now know that this is not a common mechanism of evolution.

That does not mean that saltations never happen. Stephen Jay Gould wrote an essay in 1980 called Return of the Hopeful Monster in which he gave some examples of sudden changes. One of them is the acquisition of fertility by the axolotl of Lake Xochimilco. This amphibian never transforms into a normal-looking salamander but reproduces as a tadpole with external gills. The idea that mutations affecting development can have such effects is entirely in line with Gould's interest in the subject. His first book was Ontogeny and Phylogeny (1977).

Another example is the lobster Scyllus in which the second pair of antennae have been transformed into uropods in a manner highly reminiscent of homeotic mutations in Drosophila melanogaster (Dawkins, 1996 p. 252). Dawkins (1996 p. 103) also mentions the evolution of snakes, which have hundreds of vertebrae.

The number of vertebrae in different species of snakes varies from about 200 to 350. Since all snakes are cousins of each other, and since vertebrae cannot come in halves or quarters, this must mean that from time to time, a snake is born with at least one more, or one fewer, vertebra than it its parents. These mutations deserve to be called macro-mutations, and they have evidently been incorporated in evolution because all these snakes exist.

I think it's safe to say that the concept of macromutations and saltations is not ruled out in evolution although it is certainly rare. Gould makes the point in his essay that this kind of evolution, while dramatic, is Darwinian.

Jerry Coyne does not like macromutations or hopeful monsters and he has written a strong rebuttal of Olivia Judson's article. Carl Zimmer published it on his blog [Hopeless Monsters--A Guest Post from Dr. Jerry Coyne].

I don't want to get into the details of the Judson article. I think Coyne makes some very valuable points about the specific examples used in the article and I agree that the general tone of the New York Times piece is wrong. Macromutations are not common.

I want to make another point. Coyne says,

The idea of macromutational hopeful monsters, or "saltations," had a prominent resurrection in 1980 when Stephen Jay Gould, as part of his and Niles Eldredge's theory of punctuated equilibrium, proposed that macromutations could explain the "jumps" in the fossil record. After getting a severe drubbing from geneticists, Eldredge and Gould retreated in 1993, claiming that they never suggested the idea of saltations.

The idea that Gould's example of hopeless monsters was connected to punctuated equilibria is not correct. This is the same mistake that Greg Laden makes in his discussion of the topic [Hopeful Monsters and Hopeful Models]. Greg says,

The second reason is that the fossil record seems to have the property whereby many species stay roughly similar for long periods of time, then suddenly, there is lots of evolutionary change. You've heard of this, it's called "punctuated equilibrium." If hopeful monsters ... also called saltational (dancing, leaping) evolution ... occurred generally, we might postulate that these moments of dramatic change, these punctuations, are periods in time where for some reason a lot of hopeful-monstering was going on all at once. That would be cool.

Let's be very clear about what punctuated equilibria are and what they aren't. The pattern of punctuated equilibria show that speciation by splitting (cladogenesis) is associated with morphological change. The actual speciation event is relatively rapid (in geological time) and the end result is a morphologically distinct sibling species where the changes were not evident in the population before the split. The most common explanation is that variants in the larger population were enriched in a small founder population that went on to speciate. It's an example of random genetic drift, or possibly selection, but no new mutations have occurred.

What kind of changes are we talking about here? Very small changes. So small, in fact, that it often takes an expert to recognize them in the fossil record. We're talking about the differences between snails in the same genus, or different species of trilobites, or changes in the surface marking of diatoms. We aren't talking about saltations when we look at punctuated equilibria patterns. People who think that the normal pattern of punctuated equilibria represent big leaps in evolution are confusing two different aspects of evolution.

Daniel Dennet wrote a book in 1995 where he tried very hard to destroy the reputation of Stephen Jay Gould. One of the chapters in his book was "Punctuated Equilibria: A Hopeful Monster". Dennet lays out the case for confusion between saltation and puncturated equilibria as follows; "So it seemed to many biologists that Gould was arguing that punctuated equilibrium was a theory of Goldschmidtian speciation through macromutation" (Dennett 1995 p.288). When Gould (and Eldredge) denied any such thing these biologists "scoffed in disbelief. " After all, they knew what Gould had said. Dennet goes on to say,

But did they? I must admit that I thought they did until Steve Gould insisted to me that I should check all his various publications, and see for myself that his opponents were foisting a caricature on him.

Dennett checked, and found that Gould was right. To his credit, he reports that this claim about saltation being part of punctuated equilibria is wrong. Dennett concludes on p. 289-290.

"Punctuated equilibrium is not a theory of macromutation" (Gould 1982, p.88). Confusion on this score still abounds, however, and Gould has had to keep issuing his disclaimers [as has Eldredge, LAM]: "Our theory entails no new or violent mechanism, but only represents the proper scaling of ordinary events into the vastness of geological time" (Gould 1992b p.12).

So this was the false-alarm revolution that was largely if not entirely in the eyes of the beholders.

I'm quoting Dennett here instead of quoting Gould and Eldredge¹ directly because Dennett is one of Gould's fiercest opponents. If Gould's worst enemy can see the truth then why is this myth still being propagated?

I'll close with one of my favorite quotations from Eldgredge (1995 p.99).

Nonetheless, we were accused of being saltationists. Steve Gould wrote two consecutive essays in Natural History in 1977. Among other things, Steve speculated that the recent (sic) discovery of regulatory genes—genes that turn other genes on and off—raised the possibility that mutations in the regulatory apparatus might occasionally have the sort of effect Goldschmidt had in mind with his notion of 'macromutations.' These macromutations had the large-scale effects of the sort he posited for his 'hopeful monsters.' Nowhere in either article did Steve mention punctuated equilibria.

But it was enough, it seems, that he, champion of a new model positing bursts of relatively rapid change, would, a few years later, discuss Goldschmidt in favorable terms. Mayr was one of the first to level the charge that punctuated equilibria was nothing but old saltationism in new guise. Our debt to Mayr's concept of species and speciation, so central to the idea of punctuated equilibria, eventually induced him to do an about face. Mayr came to prefer taking credit for punctuated equilibria rather than seeing it linked to his old nemesis Goldschmidt.

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Dawkins, R. (1996) Climbing Mt. Improbable W.W. Norton & Company, New York.

Dennett, D. (1995) Darwin's Dangerous Idea. Simon & Schuster, New York.

Eldredge, N. (1995) Reinventing Darwin. John Wiley & SOns, Inc., New York

Was Charles Darwin an Atheist?

 
That's the question asked by Irwin Tessman in the January/February 2008 issue of Skeptical Inquirer. Tessman is a Professor Emeritus in the Biology Department at Purdue University. You can see a podcast of his lecture, "A Darwinian View of a Hostile Atheist" at [The Society of Non-Theists at Purdue University].

Tessman is interested in comparing the views of the so-called "militant atheist," Richard Dawkins with the religious views of Charles Darwin. He concludes that their views are not very different. The biggest difference between the two men is that Darwin choose to hide his lack of religion from the public in deference to his wife Emma, who was a devout Anglican.

With the publication of the compete text of Darwin's autobiography in 1958, we now have much greater insight into Darwin's thoughts about religion. Here's how Tessman puts it,

Where does Darwin stand on the matter of a personal God? "The old argument of design in nature, as given by Paley, which seemed so conclusive, fails now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by a man" (Darwin 1958, p.87). Darwin seems to reject the idea of a personal God and, therefore, theism too. His religious views are difficult to pin down (Browne, 2006, p.46), but something close to deism would seem to fit.

Theism is a belief in a personal God, one who responds to prayers and interferes in daily events; atheism is the opposite of theism. Deism is the belief in a God who set the universe in motion whit all the physical laws and both sacred and learned commentaries, but was absent after that. In practice, deism is much like atheism.

There seems to be general agreement that Darwin did not subscribe to the tenets of any organized religion. There is debate over whether he believed in supernatural beings. His Grandfather, father, and brother were non-believers so it's reasonable to suppose that Darwin was too.

He may have been comfortable with agnostic, a term that was invented by his friend Thomas Huxley. This would have been far more acceptable to Emma than atheist. I suspect that if Darwin were alive today he would be an atheist ... unless Emma were also alive.

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Browne, Janet (2006) Darwin's Origin of Species: A biography. Douglas & McIntyre Vancouver/Toronto.

Darwin, Charles (1958) The Autobiography of Charles Darwin, Nora Barlow ed. W.W. Norton and Company, New York.

Junk DNA Poll

 
Just a reminder to vote in the junk DNA poll seen in the left sidebar. Check out A Junk DNA Quiz and comments for more information.

Take the junk DNA quiz in the left sidebar to let me know what you think of your genome. How much of it could be removed without affecting our species in any significant way in terms of viability and reproduction? Or even in terms of significant ability to evolve in the future? In other words, how much is junk?

It's important to register your choice now. You'll get another chance to vote on a similar topic in February and it will be fun to compare the two polls.

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[Image Credit: The junk DNA icon is from the creationist website Evolution News & Views.]

Beware of Terrorists in Canada

 
Friday's Urban Legend: RIDICULOUS

Australia is a small country in the middle of the Pacific Ocean (see map). It is best known for its wild dogs that eat babies, race riots on public beaches, and for 1000 mile long rabbit-proof fences that don't work.

Judging by the buzz on radio stations in Canada, Australia is now becoming known for something else [Crikey! Be careful about Canada…]. It's getting a reputation for extreme stupidity.

The Australian government has a website to inform travelers about foreign countries. Here's what it says about Canada [Travel Advice for Canada].

We advise you to exercise caution and monitor developments that might affect your safety in Canada because of the risk of terrorist attack.

Pay close attention to your personal security and monitor the media for information about possible new safety or security risks.

We advise you to exercise caution and monitor developments that might affect your safety in Canada because of the risk of terrorist attack. Pay close attention to your personal security and monitor the media for information about possible new safety or security risks.

The rating for Canada is "Exercise Caution." This is the same rating that's given to Vietnam, Serbia, Malaysia, United States, United Kingdom, Belgium, Albania, France, and the Netherlands.

Countries receiving the safest rating ("Be Alert to Your own Safety") include: China, Ireland, Japan, New Zealand, Roumania, Hungary, Macau, Norway, and South Korea (Republic of Korea).

Apparently there are some Australians who might want to visit Canada in spite of the terrorists. Not to worry. The Australian government has some additional warnings that will discourage such a foolish trip. The weather in Canada is dangerous ...

Heavy snowfalls and ice in the winter can make driving dangerous. The wind-chill factor can also create dangerously cold outdoor conditions. Transport Canada provides detailed information on road conditions across Canada. You can also get tips for winter driving from the Canadian Automobile Association.

OK, so there's some truth to that statement. If tourists want to visit some parts of Canada in the winter (for skiing) then they should know how to cope with snow.

But the Australian government doesn't stop there. They need to inform their citizens about other common dangers in Canada.

The province of British Columbia in western Canada is in an active earthquake zone.

Alberta and British Columbia are also subject to avalanches. Information on avalanches is available from the Canadian Avalanche Association.

Tornadoes can occur in some areas of Canada between May and September. For more information on tornadoes see Environment Canada's website and the National Hurricane Centre. In the event of a Tornado you should monitor local and international weather on local television and radio.

Bush and forest fires can occur any time in Canada. You should consult local news reports and authorities before visiting forested areas and follow the advice of local authorities.

Scary stuff. I think I'll build a tornado shelter and prepare for bush fires in my neighbourhood. I wonder if there are any other countries where the threat of bush fires is severe? I seem to remember something about suburban houses being destroyed by fires in other countries but never in Canada, to the best of my knowledge.

Australians, you should be ashamed about the terrorist warning for Canada. On the other hand, the weather thingy isn't unusual. All countries have silly advisories about weather on their websites. Here's the one from Canada about Australia [Travel Advice: Australia].

Australia is located in a seismic zone. Canadians should know the address and telephone number of the High Commission of Canada in Canberra in the event of an emergency.

Severe flooding is affecting parts of the country, particularly New South Wales. Rising floodwaters may have an impact on transportation and other services. Travelers should be aware of the increased threat of water-borne disease and take appropriate precautions. Canadians should follow the advice of local authorities and maintain flexible travel plans.

The cyclone season extends from November to April. Cyclones may occur along the coastal areas of Queensland, Northern Territory, and Western Australia. Travellers should keep informed of regional weather forecasts and plan accordingly.

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Creationist Counties in Florida

 
The National Center for Science Education has been following the situation in Florida where the state board of education is revising the science standards. It looks like they will not only keep evolution in the curriculum but specifically mention the dreaded e-word and state that it is a "big idea" around which state standards in biology are organized.

That's the good news. The bad news is that nine country school boards have passed resolutions calling on the state board of eduction "to revise the new Sunshine State Standards for Science such that evolution is not presented as fact, but as one of several theories."

Here are some of the explanations for this bizarre behavior as reported in the St. Petersburg Times.

Dixie County school superintendent Dennis Bennett explained, "We just wanted to get it on the record that we're a Judeo-Christian community and we believe in academic freedom," and Ken Hall, a school board member in Madison County, commented, "We're not asking that evolution not be taught, just that it be taught as a theory, one of several. I'm a Christian. And I believe I was created by God, and that I didn't come from an amoeba or a monkey."

In case anyone wants to avoid those nine counties here they are: Baker, Clay, Hamilton, Holmes, Jackson, Madison, St. Johns, Taylor, and Washington. I've located them on a map for you.

If you live in one of those counties you have my deepest sympathy. Be sure to vote in the next school board elections. In case you're interested, the Canadian counties are all in the south on the west coat below St. Petersburg.

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Tangled Bank #97

 
The latest issue of Tangled Bank is #97. It's hosted at The Inoculated Mind [Tangled Bank 97: The Frozen Bank].

It is interesting to contemplate a frozen bank, clothed with ice of many kinds, with birds not singing on the bushes, with various insects nowhere to be seen, and with worms crawling under the earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have… aw hell, it’s fricken freezing and there’s nothing but ice, snow, and cold air on the banks of Madison, Wisconsin.

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Science in an Age of Endarkenment

 
The University of Toronto Secular Alliance is one of the hosts of tomorrow's talk by David Colquhoun [University of Toronto Secular Alliance].

If you live anywhere near Toronto you should come and hear him speak and support the various groups that are sponsoring the event (University of Toronto Secular Alliance, Centre for Inquiry, Skeptics Canada)

U of T Secular Alliance Presents Professor David Colquhoun, FRS - Friday, January 25th, 2008

SCIENCE IN AN AGE OF ENDARKENMENT - SOME EXAMPLES FROM SCIENTIFIC FRAUD, QUACKERY, RELIGION AND UNIVERSITY POLITICS

Should complementary and alternative medicine be considered alongside evidence-based medicine? What role does it play in today's society? Should unscientific medicine be taught in universities? David Colquhoun tackles these issues and more.

Eminent UK scientist and noted skeptic David Colquhoun, FRS is a professor of Pharmacology at University College London, fellow of the Royal Society, and blogger (Improbable Science). He was recently the centre of controversy surrounding his popular blog, dedicated to exposing alternative medicine and pseudoscientific claims, after criticizing a herbal medicine practitioner about her questionable practices. This herbalist threatened legal action and Prof. Colquhoun was forced to remove his site from the UCL server. After much backlash from the scientific community, his website was revived. A leader in the skeptical community, Prof. Colquhoun will be speaking on issues surrounding alternative medicine, academia, and the intersection between the two.

Dr. Colquhoun's website: http://www.dcscience.net

Friday, January 25th 2008, 7pm-9pm
McLeod Auditorium, Medical Sciences Building, University of Toronto (1 King's College Circle, Toronto)
$7, $4 for students
Tickets available at the door.

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Nobel Laureate: Tom Cech

 

The Nobel Prize in Chemistry 1989.

"for their discovery of catalytic properties of RNA"



In 1989, Thomas R. Cech (1947 - ) was awarded the Nobel Prize in Chemistry for discovering that the ribosomal RNA precursor from Tetrahymena catalyzed its own self-splicing reaction. [Ribosomal RNA Genes in Eukaryotes]. He shared the prize with Sydney Altman who worked RNase P.

The presentation speech was delivered by Professor Bertil Andersson of the Royal Swedish Academy of Sciences.
THEME:

Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

The cells making up such living organisms as bacteria, plants, animals and human beings can be looked upon as chemical miracles. Simultaneously occurring in each and every one of these units of life, invisible to the naked eye, are thousands of different chemical reactions, necessary to the maintenance of biological processes. Among the large number of components responsible for cell functions, two groups of molecules are outstandingly important. They are the nucleic acids - carriers of genetic information - and the proteins, which catalyze the metabolism of cells through their ability to act as enzymes.

Genetic information is programmed like a chemical code in deoxyribonucleic acid, better known by its abbreviated name of DNA. The cell, however, cannot decipher the genetic code of the DNA molecule directly. Only when the code has been transferred, with the aid of enzymes, to another type of nucleic acid, ribonucleic acid or RNA, can it be interpreted by the cell and used as a template for producing protein. Genetic information, in other words, flows from the genetic code of DNA to RNA and finally to the proteins, which in turn build up cells and organisms having various functions. This is the molecular reason for a frog looking different from a chaffinch and a hare being able to run faster than a hedgehog.


Life would be impossible without enzymes, the task of which is to catalyze the diversity of chemical reactions which take place in biological cells. What is a catalyst and what makes catalysis such a pivotal concept in chemistry? The actual concept is not new. It was minted as early as 1835 by the famous Swedish scientist Jöns Jacob Berzelius, who described a catalyst as a molecule capable of putting life into dormant chemical reactions. Berzelius had observed that chemical processes, in addition to the reagents, often needed an auxiliary substance - a catalyst - to occur. Let us consider ordinary water, which consists of oxygen and hydrogen. These two substances do not react very easily with one another. Instead, small quantities of the metal platinum are needed to accelerate or catalyze the formation of water. Today, perhaps, the term catalyst is most often heard in connection with purification of vehicle exhausts, a process in which the metals platinum and rhodium catalyze the degradation of the contaminant nitrous oxides.

As I said earlier, living cells also require catalysis. A certain enzyme, for example, is needed to catalyze the breakdown of starch into glucose and then other enzymes are needed to burn the glucose and supply the cell with necessary energy. In green plants, enzymes are needed which can convert atmospheric carbon dioxide into complicated carbon compounds such as starch and cellulose.

As recently as the early 1980s, the generally accepted view among scientists was that enzymes were proteins. The idea of proteins having a monopole of biocatalytic capacity has been deeply rooted, and created a fundamental dogma of biochemistry. This is the very basic perspective in which we have to regard the discovery today being rewarded with the Nobel Prize for Chemistry. When Sidney Altman showed that the enzyme denoted RNaseP only needed RNA in order to function, and when Thomas Cech discovered self-catalytic splicing of a nucleic acid fragment from an immature RNA molecule, this dogma was well and truly holed below the waterline. They had shown that RNA can have catalytic capacity and can function as an enzyme. The discovery of catalytic RNA came as a great surprise and was indeed met with a certain amount of scepticism. Who could ever have suspected that scientists, as recently as in our own decade, were missing such a fundamental component in their understanding of the molecular prerequisites of life? Altman's and Cech's discoveries not only mean that the introductory chapters of our chemistry and biology textbooks will have to be rewritten, they also herald a new way of thinking and are a call to new biochemical research.

The discovery of catalytic properties in RNA also gives us a new insight into the way in which biological processes once began on this earth, billions of years ago. Researchers have wondered which were the first biological molecules. How could life begin if the DNA molecules of the genetic code can only be reproduced and deciphered with the aid of protein enzymes, and proteins can only be produced by means of genetic information from DNA? Which came first, the chicken or the egg? Altman and Cech have now found the missing link. Probably it was the RNA molecule that came first. This molecule has the properties needed by an original biomolecule, because it is capable of being both genetic code and enzyme at one and the same time.

Professor Altman, Professor Cech, you have made the unexpected discovery that RNA is not only a molecule of heredity in living cells, but also can serve as a biocatalyst. This finding, which went against the most basic dogma in biochemistry, was initially met with scepticism by the scientific community. However, your personal determination and experimental skills have overcome all resistance, and today your discovery of catalytic RNA opens up new and exciting possibilities for future basic and applied chemical research.

In recognition of your important contributions to chemistry, the Royal Swedish Academy of Sciences has decided to confer upon you this year's Nobel Prize for Chemistry. It is a privilege and pleasure for me to convey to you the warmest congratulations of the Academy and to ask you to receive your prizes from the hands of His Majesty the King.

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[Image Credit: Structure of the self-slicing ribosomal RNA precursor from Tom Cech Lab]

Ribosomal RNA Genes in Eukaryotes

 
The "genes" for ribosomal RNAs in eukaryotic genomes are found in separate clusters. One cluster consists of hundreds of copies of the 5S gene. These genes are transcribed by RNA polymerase III [Eukaryotic RNA Polymerases].

The other ribosomal RNA genes are found in an "operon"-like structure that's similar to the bacerial operons [Ribosomal RNA Genes in Bacteria]. Unlike bacterial transcription units, these ones are found in large tandem arrays on eukaryotic chromosomes. There can be hundreds of individual transcription units in a cluster and there can be several clusters. In humans, for example there are five clusters on five different chromosomes and each one has between 50 and 100 transcription units. The large eukaryotic ribosomal RNA genes are transcribed by RNA polymerase I.



There is considerable variation in the size of a transcription unit from one species to the next. This variation occurs in the length of the external transcribed sequences (ETS) that are found at either end of a cluster (open rectangles). There can also be substantial variation in the length of the internal transcribed sequences (ITS)—the ones that will be removed when the precursor is processed. The distance between transcription units can also vary. This region is referred to as the non-transcribed spacer (NTS).

Note that the order of the small (18S) and large (28S) RNAs is the same as in bacteria. Note also that the 5.8S eukaryotic ribosomal RNA is found at the 5′ end of the large RNA. The homologous part of the bacterial RNA is found at the end of the 23S RNA. What's happened in eukaryotes is that a new cleavage site has evolved so that the largest RNA is now expressed in two pieces.

RNA precursors derived from typical transcription units like the one shown above are processed by cutting the RNA at various points to release the mature 18S, 5.8S, and 28S RNAs. The processing steps are well understood. In bacteria, some of the cleavages occur before transcription is terminated but eukaryotic nuclei usually accumulate long precursors that are only processed when transcription terminates. In those species that have nucleoli the nucleolus represents the location of ribosomal RNA genes that are being transcribed.

The electron micrograph shows clusters of ribosomal RNA transcription units being transcribed a high rates in nucleoli. The RNA molecules are splayed out from the DNA like the branches of a Christmas tree. RNAs near the beginning of the gene are short and as transcription proceeds the RNAs get longer and longer until the complete precursor is released at the termination site.

In some species the 28S ribosomal RNA gene contains an intron near the 3′ end. In this case the intron sequence is removed and the two ends of the 28S RNA are joined together to produce the mature ribosomal RNA. The remarkable thing about this splicing event is that it is often autocatalytic. In other words, the precursor RNA folds up all by itself, cuts itself in two places, and rejoins its own ends. No proteins or other molecules are needed for this reaction to occur.



The classic example is the ribosomal RNA transcription unit from the protozoan Tetrahymena thermophilus shown above [Monday's Molecule #59]. The self splicing reaction was characterized by Tom Cech who received the Nobel Prize in 1989 along with Sydney Altman for discovering catalytic RNAs. This particular type of intron is called a group I intron and the mechanism of self-splicing requires a guanosine cofactor. Remarkably, the excised fragment of RNA also has catalytic activity; it can act as an endonuclease cleaving other RNAs.

RNA genes in most species do not have introns.

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Ribosomal RNA Genes in Bacteria

 
Ribosomal RNA is the major component of ribosomes [The Compositon of Ribosomes]. This RNA, by itself, is capable of catalyzing the amino acid joining reaction (peptidyl transferase) during translation but inside the cell the RNA is closely associated with many proteins to form the complete ribosome.



In bacteria (prokaryotes) there are three different ribosomal RNAs called 5S, 16S, and 23S. Eukaryotes have homologous RNAs called 5S, 28S, and 18S ribosomal RNAs. In addition, they have a 5.8S RNA that is homologous to one end of the prokaryotic 23S RNA. (The sizes of eukaryotic RNAs vary considerably and different species might have slightly different names.)

The 5S, 16S and 23S ribosomal RNAs are produced from a single operon in bacteria. An operon is a group of genes that are cotranscribed; that is, they form part of a single transcriptional unit. In this case the parts of the genome that specify each of the ribosomal RNAs are contiguous and the "genes" are transcribed into a single precursor RNA beginning at the promoter (P) and ending at the terminator (t). This large precursor RNA is then cleaved to make the smaller mature ribosomal RNAs. This is one of the problem cases when one is attempting to define a gene [What Is a Gene?].



Bacterial cells need a lot of ribosomal RNA so they usually have multiple copies of the ribosomal RNA operon (rrn). In E. coli for example, there are usually seven different rrn operons called rrnA, rrnB, etc.

In bacterial genomes the operons are located in different parts of the genome—they are unlinked. (By contrast, in eukaryotic genomes they cluster in large tandem arrays.) The example shown above is the rrnC operon in E. coli. The rectangular boxes represent regions that are transcribed into the large RNA precursor. Open boxes are pieces at the ends that are removed by direct cleavage. The purple boxes are internal regions that removed by making two cuts, one on either side.

In this operon there are four transfer RNA genes (tRNA) embedded in the transcriptional unit. These are processed as described in Transfer RNA: Synthesis. The parts of the transcription unit located between the "genes" (i.e., the purple regions) are called "transcribed spacers." When processing is complete the mature 5S, 16S and 23S RNAs are ready to be incorporated into ribosome and the four tRNAs are ready to act in translation.

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Skeptical About Adaptationism

 
Over on Evolution News & Views (a creationist blog) Robert Crowther writes.

Every so often the Darwinists get all riled up about the Scientific Dissent From Darwin list, which lists over 700 PhD scientists who publicly affirm: “We are skeptical of the claims for the ability of random mutations and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian Theory should be encouraged.” As statements go, it’s simple and straightforward. And that perhaps is what concerns Darwinists. People instantly understand what it is saying, what the scientists are courageously endorsing, and why it matters. [Doubts About Darwin Stem from Science Not Religion]

Hmmm ... let's test that claim. I agree with the two statements that are quoted. Does everyone understand why?

I do not agree with the title of the list Scientific Dissent from Darwinism because I don't dissent from Darwinism. In fact, I think that natural selection is a proven mechanisms of evolution and it is immensely important in the evolution of life on Earth. What I don't agree with is the idea that random mutation and natural selection alone can account for the complexity of life.

I suppose that's what Robert Crowther means when he says, "People instantly understand what it [the statements] is saying, what the scientists are courageously endorsing, and why it matters." Right?

Of course not. All intelligent people understand that the purpose of the list is to reveal the ignorance of Intelligent Design Creationists who think that questioning one aspect of evolution is equivalent to belief in God. Some of those 700 people may have been tricked into signing the "Dissent" because they did not instantly understand what it meant to a creationist.

I'm glad we've cleared that up.

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100% Un-deluded

 
One of my readers has designed a T-shirt for atheists. You can buy one at Zazzle.

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Atheism Is Going Out of Business

 
Denyse O'Leary was on the radio this morning on some religious show from Alberta. She was asked how she deals with all the abuse she gets from people who recognize that she's an IDiot. (That's not exactly the way she puts it.)

You can read all of her response on Uncommon Descent, and presumably on three or four other blogs as well [The old order changes, … amid a storm of abuse!].

Canadian Cynic says "I'm just plain running out of punchlines." That's saying a lot.

For those of you who refuse out of principle to view the IDiot's websites, here's part of her insane view of the world.

Look, the fine tuning of the universe for life and discovery has nothing to do with me. Nor am I personally responsible for the fact that the history of life is nothing like what a no-design theory like Darwin’s needs. And a huge freakout of atheist books/blasphemy campaigns won’t change any of that.

Actually, it looks to me like atheism’s Going Out of Business sale. And imagine, that happened in my lifetime …

It’s no surprise if they’re going out of business. They lost an intellectually respected atheist like Antony Flew and their best asset was Richard Dawkins, of whom even atheists tire - in droves now, apparently.

It is true that I benefit from this situation, insofar as my friends’ lives and my life are much less likely to be blighted by religious persecution. But I did not cause the situation. I didn’t fine tune a single aspect of the universe and have never created anything more worthy of note than books and articles, about whose quality critics vary rather widely.

So when anonymous people write abuse, I assume they are venting their own anxiety about a changing order of things, on which it is my job to report. Media pros call what those people do ”shooting the messenger”. Is that caused by poor coping skills and possibly, unhappy lives?

Now do you see why Canadian Cynic has run out of punchlines? What can you say about someone whose view of the world is 180° out of alignment?

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Permission Denied

 
I used to be able to read Shalini's blog Scientia Natura: Evolution And Rationality but now when I try to read a posting I get ...

This blog is open to invited readers only
http://shalinisehkar.com/

It doesn't look like you have been invited to read this blog. If you think this is a mistake, you might want to contact the blog author and request an invitation.

Does anyone else get this message or is it just me? It was one of the best blogs and it would be a real shame to restrict it to invited readers only.

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Out-of-Date Textbooks

 
Linzel of No More Walls is a Canadian high school science teacher. The latest posting is Provincial Curricula - Always behind the Times?. It begins with,

I've always found textbooks to be behind the times. Because of the amount of time it takes to write, edit, publish and distribute textbooks, by the time teachers and students have them they are years out of date. Not to mention the number of years they remain in circulation. I'm not suggesting we move entirely towards the most current thoughts on subject material. Quite often the most recent science research is plain wrong. Fact is students could not comprehend the level of writing and knowledge required.

The fact is though that the material is on the net and is available to be updated immediately. Old webpages can be identified and steered away from. Old textbooks tend to be handed off to other districts and hang around like a bad disease. [Thats overly harsh but it sounded good]

This criticism is directed at high school textbooks and not university textbooks. On another occasion we can discuss whether it applies to my book but for now let's look at the high school textbooks. I think Linzel has misidentified the problem. It's not the fact that textbooks are four or five years old by the time many students are reading them. Basic scientific principles and concepts just don't change quickly enough to make this a problem at the high school level. What we're concerned about is material that's ten or twenty years out-of-date.

There are only two Grade 12 biology textbooks that have been approved by the Province of Ontario [Trillium List]. They are McGraw-Hill Ryerson Biology 12 (2002) published by McGraw-Hill Ryerson, and Nelson Biology 12 (Student Book) (2003) published by Nelson Education Ltd.

Let's look at the first one in order to illustrate the problem. If we check the website [Biology 12] we can find the list of authors. Here they are ...

Leesa Blake
Malvern Collegiate Institute
Toronto, Ontario

Nancy Flood
University College of the Cariboo
Kamloops, British Columbia

Adrienne Mason
Science and Education Writer
Tofino, British Columbia

Meaghan Craven
Professional Writer
Calgary, Alberta

Gord Jasper
Dr. E.P. Scarlett Senior High School
Calgary, Alberta

Grace Price
L'Amoreaux Collegiate Institute
Agincourt, Ontario

Darcy Dobell
Professional Writer
Tofino, British Columbia

Catherine Little
Toronto District School Board
Toronto, Ontario

I think we've identified the problem. How can you have an up-to-date biology textbook if it's not written by biologists? Now, don't get me wrong. I agree that you need to have high school teachers involved in order to make sure the curriculum is being followed, but surely there's more to writing a good biology textbook that just hiring a bunch of high school teachers and professional writers?

Judging by the Table of Contents there's nothing wrong with the material that's covered. There are three chapters on evolution, for example. However, from my experience with university textbooks I can appreciate the complaint voiced by Linzel. It often takes years for modern concepts to reach the second tier of textbooks and the second tier unfortunately includes typical high school textbooks.

There are two obvious solutions.

1. Get more university professors on the textbook writing team, especially those who are teaching introductory university courses.


2. Offer upgrade courses for high school teachers so they can stay on top of the latest principles and concepts. Some people in my department are thinking about this. We'd like to run summer courses for high school teachers.

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Unconvincing Atheist Arguments

 
Not a Blog has a short list of arguments against God that atheists should avoid [Bad Atheist Responses to Christianity]. I've listed them below but you'll have to visit the blog for an explanation. Personally, I'm not convinced that all of them are worthless.

1. There are a lot of gods Christians don’t believe in.


2. If there is a god, He’s obviously not an intelligent designer.


3. The Bible contains numerous inconsistencies.


4. Quoting Isaiah 55:8, “‘For my thoughts are not your thoughts, neither are your ways my ways,’ declares the LORD.” [NIV] is a pretty lousy cop-out.


5. You can’t prove God exists.

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[Hat Tip: Friendly Atheist]

Use the LPC Code to Speed Up Mail Delivery

 
This is a fascinating video. Watch it and learn. Then get yourself on over to Friendly Atheist [Amazingly Helpful Tips] and participate in the discussion. This is related to a number of issues that come up on Sandwalk about how to process information.

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Bias Against Women?

 
GrrlScientist claims that women scientists publish fewer papers than men. She then goes on to offer an explanation [Women, Science and Writing].

The fact is that female scientists do not publish as often as male scientists. Why? Some people have told me that women do not produce scientific results that are of the same high quality as those produced by men (nor do they write life science blogs as well as men, apparently) and that male reviewers can readily recognize when a woman is the lead (or sole) author of an article because "women do science differently from men." Basically, science is still a very sexist community where its female practitioners publish less frequently than men at least partially because of the peer-review system that is in place. I think the commonly used single-blind peer review process is biased against papers whose lead (or sole) author is female, just as the field of science is biased against women in general.

She discusses a scientific study that supports the claim that reviewers are biased against women.

This does not sound right to me. There may be all kinds of reasons why women don't publish as much as men (if it's true) but I doubt very much that reviewers are more likely to reject a paper by a women scientist. For one thing, lots of reviewers are women. For another, why in the world would a male reviewer reject a paper just because the work is done by a female scientist? Do you think this is common practice among the scientists you know? Do you really think that in 2008 there are significant numbers of male scientists who are that biased against women? I don't.

UPDATE: Skepchick joins in with [Are women discriminated against in science?]. Let's not forget that this is the important question. There's no denying that some scientists are sexist, just as there's no denying that some are racist and homophobic. Some of them are even (gasp!) Christians! Does that justify saying that science is racist or science is religious? Of course not. What we should be trying to do is decide whether sexism is rampant among scientists or not. If it is, then we can justify saying that women are discriminated against in science even though we might hesitate to say that gays are discriminated against in science in spite of the fact that some scientists are homophobic.

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Monday's Molecule #59

 

This is an example of a very common molecule found in every cell. It's obviously not a chemical structure but a diagram of something else. You have to give us the common name of this thing and identify the species. You'll be pleased to know that I don't need the systematic IUPAC name for this one.

There's a direct connection between this molecule, the species, and Wednesday's Nobel Laureate. As a matter of fact, the diagram above is from the acceptance speech of the Nobel Laureate. Your task is to figure out the significance of today's molecule and identify the Nobel Laureate who studied it.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate. Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward. The prize is a free lunch at the Faculty Club.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate. Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: We have a winner! Alex Knoll wins a free lunch at the Faculty CLub whenever he's in Toronto. The molecule is the ribosomal RNA transcription unit from Tetrahymena thermophila and the Nobel Laureate is Tom Cech who studied the self-spicing reaction of the ribosomal RNA precursor.

The good news is that every one of the people who responded got it right. The bad news is that there were only eight of you.

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ReGenesis and Scientific Literacy

 
About a year ago I posted an article about ReGenesis, a TV show based on scientific investigation into fictional events such as pandemics, crimes, etc. One of the main consultants on the show is a colleague of mine, Aled Edwards [ReGenesis].

Eva of easternblot has found an online interview with Aled Edwards about the show [ ReGenesis on LabLit]. You can read the entire interview on the LabLit website [ReGenesis guru Aled Edwards].

I like what Aled has to say. He is trying very hard not to let the TV show get dumbed down.

The scientists on this show are more like real scientists than anything else on screen. They have to publish, they make mistakes. We place caveats into the dialogue, trying to convey that on the edge of science, nothing is certain: we deal in hypotheses and uncertainty. The science in the show has real-life ambiguity – there’s no CSI-like wrap-up at the end in many episodes. And there’s an order of magnitude more science on the show than any other I’ve seen on film or TV.

As many of you know, here's a controversy between many scientists and many journalists about how to communicate science. I think Aled Edwards has the correct attitude here. What do the rest of you think? How many have watched the show?

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Predictions of Intelligent Design Creationism

 
Denyse O'Leary gives us nine "predictions" from the IDiots [ Nine predictions, if intelligent design is true]. I present them here without comment. Notice how almost all of them are predictions of what science will not discover and none of them are predictions of what an intelligent designer creationist is expected to do. That's because the essence of Intelligent Design Creationism is anti-science and not pro-designer. Several of the "predictions" are based on Denyse's latest book The Spiritual Brain.

1. No good theory will be found for a random origin of the universe, either by the Large Hadron Collider or anything else. The universe will consistently behave more like a great idea than a great machine.


2. No good theory will be found for a random origin of life, though there will be plenty of huffing and puffing in favour of bad ideas. All theories that exclude purpose and design fail because they leave out the key driver - the purpose that life should come into existence.


3. Complete series of transitional fossils will not usually be found because most proposed series have never existed. Eventually, researchers will give up on ideologically driven nonsense and address the history that IS there. They will focus on discovering the mechanisms that drive sudden bursts of creativity.


4. The environment will prove far more resilient than eco-doomsayers believe. People forget that the Permian extinction wiped out 90% of the marine life forms on this planet. Life seems to want to exist on this planet, even at the South Pole (cf March of the Penguins). Note: I have no time for environment destruction, and personally gave up keeping a car, as the simplest and most economical way to reduce my environment footprint. But I am NOT waiting for enviro-apocalypse!! - I don't believe it will happen. There will be changes. That's all. Not the end of the world or anything like it.


5. No account of human evolution will show a long slow emergence from unconsciousness to semi-consciousness to consciousness, let alone that consciousness is merely the random firing of neurons in the brain. However consciousness got started, it appeared rather suddenly and it permanently separates humans from our genetic kin, however you want to do the gene numbers and however much time researchers spend coaxing monkeys to stop relieving themselves on the keyboard and type something meaningful.


6. Claims that the human brain is full of "anachronistic junk" will be falsified, just as century old claims that there are hundreds of vestigial organs in the human body were falsified. The human body will be recognized as suitable for the purposes for which we exist. (Not in all cases perfect, to be sure, but in general suitable.)


7. No useful theory of consciousness will demonstrate that consciousness is merely the outcome of the random firing of neurons in the brain. All useful theories will accept that the mind and the brain exist in a relationship. Research will focus on delineating the relationship more clearly. That will greatly benefit medical research, especially research on difficult mental disorders such as phobias, depression, etc.


8. No useful theory of free will (human volition) will demonstrate that it does not really exist. Free will (which includes using the mind to help heal bodily injuries) will become an important tool of medicine, especially for helping aging people toward a better quality of life. For example, the fact that a drug only need perform 5% better than a placebo to be licensed for use will encourage the development of mind-based treatments for people who would otherwise be forced to take antagonistic drugs.


9. No useful theory of human psychology will be founded on claims about what happened in the caves of our ancestors (= evolutionary psychology). That is because there are no genes that simply "cause" behaviour in a clinically normal human being. The mind is real and humans create their social environment by mental effort. Information is passed on from mind to mind, not through genes or physiology.

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Gene Genie #24

 
The 24th edition of Gene Genie has been posted at origins genome resources [Gene Genie issue #24: Human genetics (Illumnia conspiracies and Eric Roberts too) provide a light in winter].

Welcome to the 24th edition of Gene Genie!! During these grey winter doldrums, it is all too easy to hunker down and withdraw from the blogosphere into the minutiae of grant writing and lab management (brrr- I haven’t posted in weeks). So it is with true delight that I present and thank our contributors for brightening the season.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

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Changing Minds Through Science Communication

 
There are lots of things going on at the North Carolina Science Blogging Conference but the session I'd most like to have attended was on "Changing Minds Through Science Communication." The speakers were Jennifer Jacquet, Sheril Kirshenbaum, and Chris Mooney.¹

The next best thing to being there is to watch the videotape of the session (below). I must say I'm somewhat underwhelmed. Most of the presentations seemed to be mouthing the same old unsupported platitudes that we've been seeing for the past year, including a shot at Richard Dawkins.

There's was a great deal of talk about getting US Presidential candidates to engage in a science debate sometime in the next few months [Science Debate 2008]. Chris Mooney and Sheril Kirshenbaum spent a lot of time talking about this. How many people think this is a worthwhile way to spend one's time? What are the chances of it happening? If it does happen, will it advance the goal of effective science communication or is there a chance that it will do the opposite? If it doesn't happen, what message will that send about the importance of science?

The goal of the science debate is to use politics and the media to teach the general public about real science (e.g., evolution, global warming, stem cell research etc.) What if the media and politicians trump the process and use the debate to promote anti-science? Going head-to-head with these groups and trying to beat them at the framing game seems a bit naive to me. Am I the only one who thinks this? Since when have candidate debates stuck to scientific facts?

What if a candidate shows up with a list of ten scientists who think that the effects of global warming have been exaggerated, and has ten scientific papers to prove it? What if a candidate says that opposition to stem cell research is based on morality and not atheistic science? What if several of the candidates advocate teaching the controversy in biology class? Aren't we just begging for trouble? Aren't we just giving the kooks an opportunity to refute science during a "science" debate?

There's a good reason why real scientists avoid public debates with creationists. Perhaps science bloggers and science journalists should think about those reasons before promoting a debate on science. They might not get what they're wishing for.

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1. Would it have been impossible to find an active full-time research scientist to participate on this panel? I find it frustrating that scientists are being criticized in a forum like this without being given a chance to present the other side of the case.

Eating Clones

 
We eat cloned organisms every day, but they're plants (e.g., bananas).

Apparently, some people have a great fear of eating cloned animals. Is this irrational fear an "ethical" problem? The underlying question is how do we define an ethical problem? Just because some people incorrectly see a problem where none exists, are we obliged to bow to their definition of "ethics."

Join the discussion on Balblab [Clonal Discrimination].

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The Cloning of Steve Steve

 
Many of our science blogger friends are having a good time in North Carolina at the second North Carolina Science Blogging Conference. I was at the last one and it was lots of fun.

Joshua Rosenau is there and he breaks the news that Steve Steve has been cloned [Scienceblogging]. It has long been suspected that Reed Cartwright had succeeded in cloning Steve Steve but this is the first photographic proof that I'm aware of. As you can see from the photo, some of the cloning attempts were not successful.

I'm waiting to hear the response from the Vatican.

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This ranks among the most morally illicit acts, ethically speaking ...

 
Researchers from Stemagen a private stem-cell research company in California, have created human clones by the same techniques used to clone other mammals. The clones only went through a few cell divisions before being discarded [Ethical storm as scientist becomes first man to clone HIMSELF].

There's nothing remarkable about the science. It's one step toward cloning humans using standard procedures that have been worked out over the past three decades. What's remarkable is the reaction to this announcement. I'm still having trouble figuring out what is the ethical problem here.

I think it's all related to abortion. If you are opposed to allowing a woman to decide what to do with her own body then you're also against stem cell research. The "ethical issue" is mostly confined to religious people (men?) who oppose abortion. At least that's how it appears to me.

Stemagen isn't doing anything wrong; they make this clear on their webpage.

All research at Stemagen is performed in strict accordance with US Federal Regulations for the ethical treatment and protection of human subjects covered in the 45 CFR Part 46 policy issued by the Office of Human Research Protection (OHRP). More specifically, this requires that all research involving human eggs, embryos or human subjects be approved and carefully monitored by an independent Institutional Review Board (IRB) composed of members of the medical and general community, with additional ethical and legal expertise sought when required.

Those who choose to donate oocytes (eggs) and embryos for this type of research do so through informed consents that follow the guidelines for Human Embryonic Stem Cell Research from the National Academy of Sciences (www.nationalacademies.org).

Stemagen's mission is to maintain exemplary standards in human embryonic stem cell research in accordance with the highest ethical and research principles.

This is an important point in so-called "ethical" debates. The scientists are not being unethical and many observers, like me, don't see any ethical problem. Others see an ethical problem as described in the newspaper article.

John Smeaton, of the Society for the Protection of Unborn Children, said: "We have got scientists wandering around in an ethical wilderness, forgetting about matters of justice relating to our fellow human beings.

"We have people creating human beings with the intention of destroying them. That's appalling."

And the Vatican condemned the cloning of human embryos, calling it the "worst type of exploitation of the human being".

"This ranks among the most morally illicit acts, ethically speaking," said Monsignor Elio Sgreccia, president of the Pontifical Academy for Life, the Vatican department that helps oversee the Church's position on bioethics issues.

Here's the issue. At what point does something become an "ethical" issue for society? How many people have to be against something on "ethical" grounds" in order for it to become an ethical problem?

What if their objections are irrational? For example I imagine that US Presidential candidate Mike Huckabee is against stem cell research but his reasons are likely to be as ridiculous as his reasons for opposing same-sex marriage. Does that still count as an ethical problem? It seems to me that elevating stupidity to the level of "ethics" is not the way we want to go.

Why couldn't the headline have been "No Ethical Problem, According to Most Atheists?" Why do we let religious groups define ethics for us? I don't subscribe to their version of ethics, do you?

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Teaching IDiots About Evolution

 
The National Academies (Science, Engineering, Medicine) (USA) have just published their latest book on the evolution/creationism controversy. You can download it for free on their website [Science, Evolution, and Creationism].

The book attempts to define evolution and it doesn't do a bad job of describing a minimal definition that would be acceptable—that is if you only look at the actual definition. Here it is from page 5.

Evolution consists of changes in the heritable traits of a population of organisms as successive generations replace one another. It is populations of organisms that evolve, not individual organisms.

Sandwalk readers will know that this is the kind of definition that I prefer as well [What Is Evolution?]. This sort of definition is neutral with respect to mechanisms. It doesn't matter whether evolution occurs by natural selection, random genetic drift, of something else entirely. That's just as it should be because the explanation of how evolution occurs lies properly in the domain of evolutionary theory. Thus, we can say that evolution is a fact because we see it happening and we have overwhelming evidence that has happened in the past. We can be confident that it is a fact even though we may not be as certain about how it happened.

Once we start committing to an explanation we can no longer talk about facts, in many cases, since the exact mechanism of evolution is often disputed. The National Academies book begins with a wonderful description of Tiktaalik, a fossil animal that shares characteristics of both fish and primitive tetrapods. It is strong evidence in support of the evolution of tetrapods from fish and that lineage is now considered to be a well established fact.

However, it would be wrong to use Tiktaalik as support for a particular mechanism of evolution. The fossil suggests that natural selection is playing a role but random genetic drift is not ruled out. We know from other sorts of data that natural selection and random genetic drift are facts, as well as being part of evolutionary theory, but it's a good idea to draw a distinction between evolution, the process, and theories about how it occurs. This is especially true when trying to explain things to IDiots.

Unfortunately, the authors of Science, Evolution, and Creationism don't do as good a job in this regard as they should have. For example, the (reasonably correct) definition that I quoted above is found at the end of a paragraph that weakens it considerably. Here's the entire paragraph ...

If a mutation increases the survivability of an organism, that organism is likely to have more offspring than other members of the population. If the offspring inherit the mutation, the number of organisms with the advantageous trait will increase from one generation to the next. In this way, the trait — and the genetic material (DNA) responsible for the trait — will tend to become more common in a population of organisms over time. In contrast, organisms possessing a harmful or deleterious mutation are less likely to contribute their DNA to future generations, and the trait resulting from the mutation will tend to become less frequent or will be eliminated in a population. Evolution consists of changes in the heritable traits of a population of organisms as successive generations replace one another. It is populations of organisms that evolve, not individual organisms.

The next paragraph then goes on to describe natural selection. There is no mention of random genetic drift anywhere in the book, although there is a passing reference to the fact that neutral mutations can be fixed. This reference is found on page 29 near the end of the book.

The net result is that evolution the process, is intimately connected to the mechanism of natural selection in this book. Readers will assume that scientists equate evolution with natural selection and use the terms interchangeably.

Why is this a problem? Well, for one thing, it's wrong. Normally that should be a good enough reason to avoid such errors, but these days there's a movement afoot to frame evolution in a way that resonates with the general public. Perhaps it's okay to define evolution as natural selection if it helps educate the average person? I object to such reasoning in the strongest possible terms. The essence of science is being honest and accurate and those goals should never be sacrificed for political gain. It may be easier to avoid confusion by not mentioning other mechanisms of evolution but the end result is that the public is not being educated correctly about evolution. You can't then turn around and complain that the public doesn't understand evolution.

The IDiots are upset about this book. They have found many ingenious ways of criticizing the contents. Here's a perfect example from Casey Luskin [The Facts about Intelligent Design: A Response to the National Academy of Sciences’ Science, Evolution, and Creationism].

I don't have the time, or the patience, to correct everything that's wrong with this article but there's one point I'd like to address. Here's what Casey Luskin says about evolution.

The NAS unscientifically elevates evolution to the status of unquestionable dogma.

The NAS defines evolution as evolution by natural selection and claims that “[t]here is no scientific controversy about the basic facts of evolution,” asserting that evolution is “so well established that no new evidence is likely to alter” it. In doing so, the NAS treats Neo-Darwinian evolution like an unquestionable dogma, not like a science. Such proclamations from the NAS are dangerous because they threaten the prestige of the NAS as an objective and trustworthy voice advising society.

Moreover, the NAS’s claim that there is no controversy over evolution is a bluff, for there is significant scientific dissent from the view of evolution by natural selection. Leading biologist Lynn Margulis, who opposes ID, criticizes the standard Darwinian mechanism by stating that the “Darwinian claim to explain all of evolution is a popular half-truth whose lack of explicative power is compensated for only by the religious ferocity of its rhetoric.”[7] She further observes that “new mutations don’t create new species; they create offspring that are impaired.”[8] In 2001, biochemist Franklin Harold admitted in an Oxford University Press monograph that "there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”[9] Other scientists have gone much further.

Over 700 doctoral scientists have signed a public statement asserting their agreement that they "are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life."[10] But what are these scientists to do when the top scientific organization in the U.S. proclaims that evolution is as unquestionable as the existence of atoms or the heliocentric model of the solar system? Clearly the NAS’s statements threaten the academic freedom of scientists to dissent from Neo-Darwinian evolution.

In the past it has been easy to show that the IDiots are either mistaken or lying when they make comments like this. I've said many times that they deliberately try to confuse people by making it seem as though evolution, the fact, is the same as natural selection, the mechanism. They know full well that there's a difference between controversies over the sufficiency of natural selection and whether evolution, per se, is overwhelmingly support by hard evidence. They know that evolution is not the same as Darwinism and attacks on Darwinism are not the same thing as attacks on evolution.

This rebuttal is now a bit more difficult with the publication of Science, Evolution, and Creationism. Nowhere in the book do the authors deliberately make the distinction between natural selection and evolution and nowhere do they mention any other mechanism of evolution (e.g., random genetic drift). When reading the book, most of us recognize that there are abundant, oblique, references to the fact that the authors are not stupid, but that is only apparent to scientists who know about evolution.

Casey Luskin has taken advantage of this lost opportunity on the part of the National Academies to make it look like they are being dogmatic and forcing everyone to accept Darwinism. When I decided to write about Luskin's silly article, I thought it would be easy to refute what he was saying by referring back to the book. I thought the book would make it clear that evolution is not the same as natural selection. Unfortunately, there's nothing I can quote from the book that explicitly makes that point even though it's there implicitly. That's a missed opportunity that I hope can be remedied in future printings.

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Map That Campus XLII

 
This is one of my favorite challenges in the blogosphere. Can you identify the campus on The Daily Transcript?

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Backwards Bush Countdown Clock

 
Trust me, it's not just Americans who are counting the days.

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Science in an Age of Endarkment

 
Be sure to come to this special event sponsored by the Centre for Inquiry, Toronto. The talk will be given in the auditorium just beside my building. I'll be going to the reception beforehand at CFI—join CFI and you can come too!!!

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SCIENCE IN AN AGE OF ENDARKENMENT: scientific fraud, quackery, religion and university politics

Friday, January 25th, 2008: 7:00 pm - 9:00 pm, MacLeod Auditorium, Medical Sciences Building, University of Toronto (1 King's College Circle, Toronto)

When alternative medicine and academia collide... Featuring a major public symposium with David Colquhoun

Eminent UK scientist and noted skeptic David Colquhoun was recently at the centre of controversy after critiquing the pseudoscientific claims of a homeopathic practitioner. Prof. Colquhoun was asked to remove his site from the UCL server, but after a backlash from the scientific community, his website was revived. He will be speaking about alternative medicine, academia, and the conflicts that arise when the two intersect.

David Colquhoun is professor of pharmacology at University College London and fellow of the Royal Society. He runs a blog called "Improbable Science" (http://www.dcscience.net) dedicated to exposing and debunking pseudoscientific claims.

Dr. Colquhoun will appear at a special reception with food and drinks exclusively for Friends of the Centre from 5:00-6:30pm at CFI Ontario preceding his talk. Contact us at toronto@centerforinquiry.net to find out how you can join.

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[Image Credit: Homeopathy wars in the UK]


[For a short summary of the blogging ban see University College London Restores Professor Colquhoun's Website]

Soybean Genome

 
A preliminary draft of the soybean (Glycine max) genome has been released on the Phytozome website [Glycine max Genome].

The reported size of the genome is 950 Mb (950 × 10⁶ base pairs). This is considerably larger that the genomes of grape (505 Mb), Arabidopsis (157 Mb), rice (389 Mb), and polar (485 Mb).

The larger size suggests a recent polyploidization event in the lineage leading to soybean. The number of genes in the draft sequence is 51,320. This also suggests that many genes are duplicated. (Grape has about 30,000 genes, poplar has about 45,000, rice has 38,000 and Arabidopsis has only 27,029.) Keep in mind that the total number of genes is likely to drop by a considerable amount once detailed annotation gets underway. Nevertheless, it looks like the soybean has a lot more genes than the other flowering plants.

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[Photo Credit: [Photograph]. Retrieved January 18, 2008, from Encyclopædia Britannica Online: bean: soybean]

Brampton Prude

 
Brampton is a city west of Toronto and north of Mississauga, where I live. Heart Lake United Church is trying to attract customers so they put up the sign shown here. I think it's funny.

Nicole Cedrone doesn't agree. She thought it was offensive when she drove by on her way home from the doctor [Church Strips Saucy Sign]. She complained and the sign was removed.

"I have to admit, it is funny, but it's not appropriate for where it is," Cedrone said. "I just think it's offensive."

She said she is glad her 11-year-old wasn't in the car with her to ask, `Mom, what does that mean?'"

Well, the photograph of the "offensive" sign is now prominently featured in The Toronto Star where, hopefully, her 11-year-old son will read it and ask questions like, "Mom, what does 'saucy' mean?" By being such a prude, Nicole Cedrone has ensured that the sign will be viewed by millions and not just a small number of people driving along Sandalwood Parkway. Way to go, Nicole.

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