I couldn't resist copying this cartoon from Friendly Atheist [Lack of Respect]. It's by Don Addis. Hemant Mehta got it from Freethought Today.

[Photo Credit: Graduate students in the Department of Biochemistry 2007-2008.]
1. Here's an interesting bit of trivia. How many ScienceBlogTM authors have won the free lunch? How many have guessed the correct answer even though they weren't the first to do so? The answers might surprise you.
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.
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.
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).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?
So this was the false-alarm revolution that was largely if not entirely in the eyes of the beholders.
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.
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
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.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.
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.
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.
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.
[Image Credit: The junk DNA icon is from the creationist website Evolution News & Views.]
We advise you to exercise caution and monitor developments that might affect your safety in Canada because of the risk of terrorist attack.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.
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.
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.
The province of British Columbia in western Canada is in an active earthquake zone.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.
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.
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.
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.
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.
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.
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.
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.
[Image Credit: Structure of the self-slicing ribosomal RNA precursor from Tom Cech Lab]
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?