Friday, June 29, 2012

Adaptation vs Drift at Evolution Ottawa 2012

I've been looking over the program for the First Joint Congress on Evolutionary Biology to be held in Ottawa, Canada next week [Evolution Ottawa].

The talks are divided into sessions with six short presentations per session. Here's the list of sessions with the words "adaptation" or "selection" in the title.
Adaptation 1
Adaptation 2
Adaptation 3
Adaptation 4
Adaptation 5
Adaptation 6
Adaptation 7
Adaptation 8
Adaptation 9
Adaptation 10
Adaptation and Evolutionary Genetics
Sexual Selection and Mating Systems 1
Sexual Selection and Mating Systems 2
Sexual Selection and Mating Systems 3
Sexual Selection and Mating Systems 4
Sexual Selection and Mating Systems 5
Sexual Selection and Mating Systems 6
Sexual Selection and Mating Systems 7
Sexual Selection and Mating Systems 8
Sexual Selection and Mating Systems 9
Sexual Selection and Mating Systems 10
Sexual Selection and Mating Systems 11
Sexual Selection and Mating Systems 12
Sexual Selection and Mating Systems 13
Sexual Selection and Mating Systems 14
Sexual Selection and Mating Systems 15
Mating Systems and Sexual Selection 1
Mating Systems and Sexual Selection 2
Adaptation and Experimental Evolution 1
Adaptation and Experimental Evolution 2
Sexual Selection and Experimental Evolution
Adaptation and Gene Flow
Adaptation and Genomics
Adaptation and Evolutionary Ecolgy 1
Adaptation and Evolutionary Ecolgy 2
Adaptation and Evolutionary Ecolgy 3
Adaptation and Evolutionary Ecolgy 4
Adaptation and Evolutionary Ecolgy 5
Natural Selection in the Wild: from Genotype to Phenotype
Here's the list of sessions with "Random Genetic Drift" or Neutral" in their titles.
Isn't that strange? There are many more neutral alleles than beneficial alleles and random genetic drift is overwhelmingly the most common mechanism of evolution. I guess most evolutionary biologists have a huge bias toward studying adaptation. One can't help but wonder how many studies were abandoned when the investigators discovered that they couldn't prove natural selection was involved.

Why weren't those studies completed and published as examples of random genetic drift?

There are more than one thousand talks being given at this meeting and only five (5) have the word "drift" in their title—and one of those is about education!


Thursday, June 28, 2012

What's Wrong with Michael Ruse's View of Accommodationism?

Michael Ruse wrote a book called Science and Spirituality: Making Room for Faith in the Age of Science (2010). It's a defense of accommodationism—the position of atheists who maintain that science and religion are compatible because they are different ways of knowing. Ruse is one of the main proponents of Methodological Naturalism, which postulates that science is restricted, or limited, to investigations of the natural world. Since religion deals, by definition, with the supernatural world, it falls outside the domain of science and is, therefore, compatible with science. This leads Ruse to define several criteria of Christianity that are immune to scientific investigation [The Essence of Christianity].

This position used to be overwhelmingly accepted by the majority of scientists and philosophers, especially in America. It has become the standard view of most professional scientific organizations and of The National Center for Science Education (NCSE). It's a convenient way for atheist scientists and religious people who are mostly accepting of science to avoid conflict as they make common cause against the extreme creationists.

But that view is now being challenged and it's no longer acceptable to claim that it represents the only view of science. That's what the good guys did during the Dover trial a few years ago but it wouldn't work today because there are dozens of prominent philosophers of science who would argue against such a limitation of science.

One of them is Peter Slezak of the School of History and Philosophy, University of New South Wales, Sydney, Australia. He recently wrote a review of Ruse's book: Michael Ruse: Science and Spiritutality: Making Room for Faith in the Age of Science (Slezak, 2011).

Much of the conflict depends on definitions and Slezak clearly endorses a much broader view of science than Ruse. Here's how Slezak challenges the view that science has limits.
This is a widely held and obviously appealing line to adopt for those, like Ruse, who are committed to the scientific enterprise and its claims. However, I will suggest that, despite its appearance of open-minded ecumenicalism, the posture faces insuperable intellectual difficulties. In wishing to leave room beyond ‘‘the allowable scope of science’’ (p. 235), Ruse is effectively endorsing a traditional demarcation between science and metaphysics in order to restore respectability to some claims in the latter category. However, this recidivist project does not properly address the hegemonic nature of the scientific enterprise. This conception is expressed in the final remarks of Bertrand Russell’s (1935) book Religion and Science. Aside from questions of value that lie outside the realm of truth and falsehood,

Russell says:
Whatever knowledge is attainable, must be attained by scientific methods; and what science cannot
discover, mankind cannot know (1935, p. 243).
The title of Freud’s (1927, 92) book The Future of an Illusion refers to religion and ends with the exactly the same sentiments: ‘‘an illusion it would be to suppose that what science cannot give us we can get elsewhere’’. These expressions of a positivist conception are less dogmatic than they appear because they may be understood as statements of the openmindedness of science rather than its opposite. That is, ‘‘science’’ doesn’t exclude anything simply because the honorific label is used for anything worth believing. That is, if there are any rational grounds for a proposition, it will become included within the domain of established science. Or, rather, perhaps we should say that it will be included on the spectrum of claims ranging across ‘good, bad and bogus’ to use the sub-title of Gardner’s (1981) book. The point is captured in Laudan’s (1983) account of the ‘‘Demise of the Demarcation Problem’’ since he shows that ‘‘the problem of demarcation … is spurious’’ and the heterogeneity of beliefs and activities means that there are no lines to be drawn (see Special Issue of Science & Education, 2011, volume 20, 5–6). In particular, this means that the claims of religion fall somewhere on the spectrum, arguably nearer the bogus end. However, this means that they are subject to the usual criteria for deciding what is worth believing, which is, in any case, clear enough from the nature of the claims as we will note presently.
Ruse and his allies believe that any attempt to step outside the limits of science constitute a venture into metaphysics and this is not science but something else. Peter Slezak rejects this argument ...
Plantinga (1991, 8) suggests that the question of the clash between faith and reason is ‘‘enormously difficult’’ requiring ‘‘penetrating grasp of the relevant theological and philosophical issues’’ as well as the complex science. However, this is sheer bluff since the arguments don’t depend on any such arcane knowledge. Thus, citing Plantinga, Ruse (p. 183) seeks room for claims alongside and independent of science on the grounds that there are alternative ‘‘world views’’ and, therefore, a choice between two ‘‘metaphysical’’ options— naturalism and theism. The air of reasonableness and even profundity in this stance produces a vacant illusion of explanation but disguises sophistry. First, even if we are to talk this fancy philosophical way with Plantinga, it remains obscure why the Christian theistic ‘‘metaphysics’’ is the only alternative to the ‘‘naturalistic’’ one. One could presumably find or invent many others that would have equal status as alternatives to naturalism by virtue of having nothing to recommend them. Does Plantinga think that Mexican metaphysics based on the theology of Quetzalcoatl deserves equal consideration with his Christian variety?

The very idea that we can transcend what Ruse calls the ‘‘limitations of a science based knowledge’’ (p. 10), or that we have a choice between alternative ‘‘metaphysics’’, is an illusion. There is no alternative to our best theories other than worse ones. Naturalism is just the picture provided by our current science and is, therefore, the best we’ve got. Pretentious philosophical talk of ‘‘metaphysical’’ options can’t change the fact that naturalism is the only game in town since it is simply the totality of our theories in physics, chemistry, biology, neuroscience, geology and so on. Does Christian metaphysics provide a better account of quantum physics, cosmology or the structure of DNA?
Slezak is going to be accused of scientism or, at the very least, naturalism. The accommodationists will claim that the leap to naturalism is overstepping the limits of what science can or cannot claim. That's not true. Science teaches us that the scientific approach works and that most things have a naturalistic explanation. It follows that any claim of a valid a non-naturalistic explanation must have at least as much to recommend it or else it is nothing more than hand-waving.


Slezak, P. (2011) Michael Ruse: Science and Spiritutality: Making Room for Faith in the Age of Science Sci & Educ 21:403-413. [DOI 10.1007/s11191-011-9373-0]

Tuesday, June 26, 2012

Guess Where We're Going Tonight?

I hope Neil Diamond sings Sweet Caroline, we know the actions better than this crowd does! See you at the Air Canada Centre at 8pm!




Monday, June 25, 2012

Monday's Molecule #175


If you look closely, you'll see that today's molecule is an unusual variant of a very common cell component. Your task for today is NOT to give this molecule a specific name but rather to describe it in general terms and identify three (3) ways in which it differs from the more common molecules. Finally, you have to tell us where these molecules are found.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: This is a typical bacterial membrane lipid found in archaebacteria (Archaea) and in some gram-negative bacteria. It differs from the glycerophospholipids in eukaryotes and other bacteria in three ways. (1) The backbone molecule (a three carbon glycerol molecule) is sn-glycerol-1-phosphate, a stereoisomer of the more common backbone sn-glycerol-3-phosphate, found in other lipids. (2) The long fatty acid chains are attached to the glycerol moiety by an ether linkage, rather than an ester linkage. (3) The hydrocarbon chains of the fatty acid chains are composed of isoprenoid units methyl units. Today's winner is Raul A. Félix de Sousa (again).


Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa


Sunday, June 24, 2012

Do the IDiots Understand Evolution?

David Klinghoffer noted recently that an anthropologist, Richard Leakey, and some lawyer named Jonathan H. Adler seem to be using different meanings of the word "evolution" [For Richard Leakey and So Many Other Darwin Advocates, Evolution Is a Word that Can Mean Anything]. It doesn't seem to matter to Klinghoffer that one of those men is a scientist and the other isn't.

Picking up on the point that evolution is a word that can mean anything, Joshua Youngkin1 adds his 2 cents [On the Useful Instability of the Word "Evolution"].
David's concern, I think, is that Darwinists use the term "evolution" in various and even conflicting ways in order to occasionally serve less-than-noble purposes. It's almost as if Darwinist usage of the term "evolution" is sometimes meant to keep skeptics and even the public guessing, as if to avoid a fair fight on the evidence about a stable, commonly understood set of propositions. Why would anyone want to do that?
The meanings of the word "evolution" can be found in evolutionary biology textbooks and at many places on the web. You can read two of my contributions at What Is Evolution? and Evolution Is a Fact and a Theory. It seems to me that many evolutionary biologists are making a very serious effort to define their terms.

Some of the IDiots actually get it as I pointed out a few weeks ago [All IDiots Believe in Evolution!]. That was in response to a posting by johnnyb who said ....
So what is one to do? Well, thankfully, our friends the evolutionists have given us a way out. In their zeal to claim consensus on the “fact of evolution,” they have had to steamroll together such a large diversity of opinion into the single term “evolution”, that the word “evolution” no longer has the grand meaning it used to. The only real meaning everyone can agree on is “change in allele frequency over time” – and that is a definition that literally everyone can agree with.
Apparently his fellow IDiots didn't get the memo.

It doesn't take a lot of effort to recognize what evolutionary biologists mean when they use the word "evolution." You have to be really stupid to imagine that they are deliberately using different meanings in in different contexts for the sole purpose of confusing the IDiots. As you can see, the IDiots are quite capable of confusing themselves without our help.

Speaking of deliberate obfuscation ... I wonder why they continue to refer to "Darwinists" when they've been told hundreds of times that this is not a synonym for "evolutionary biologists"? Is that for a "less-than-noble purpose" or is it just because the IDiots are stupid? I think we know the answer to that one.

I have some sympathy for bloggers who are ignorant but I don't like liars. However, the people I really hate are the hypocrites.


1. Joshua Youngkin is a lawyer who works for the Discovery Institute. He's probably an expert on the meaning of the word evolution.

Tuesday, June 19, 2012

A Tribute to Stephen Jay Gould

Stephen Jay Gould died ten years ago on May 20, 2002. Last month there was a conference in Venice, Italy, that celebrated his legacy [Stephen J. Gould's Legacy: Nature, History, Society]. I wish I could have attended because all the main characters were there (Richard Lewontin, Niles Eldredge, Elisabeth Lloyd, and many more).

Ryan Gregory gave a talk on A Gouldian view of the genome and he has posted the video of his presentation (see below). I urge you to watch the whole thing but, if you only have a few minutes, then watch the beginning where Ryan describes the important lessons that Gould taught us.

Monday, June 18, 2012

Evolution Ottawa July 6-10 2012

I'll be going to this meeting next month. Let me know if you'll be there and we can arrange to meet for lunch, dinner, beer, or coffee. We'll definitely be doing a poutine run into Quebec and a walk to Byward Market to get beaver tails.

This is the year Canada celebrates it's victory over the USA in the war of 1812. You can thrill to the spectacle of the changing of the guards on Parliament Hill and see the fearsome redcoats up close. Americans (the losers) are welcome! :-)
Welcome to the site of the First Joint Congress on Evolutionary Biology (aka ‘Evolution 2012’), to be held in Ottawa, Canada’s capital city. This landmark event will bring together five of the world’s largest academic societies devoted to the study of ecology and evolutionary biology: the American Society of Naturalists (ASN), the Canadian Society for Ecology and Evolution (CSEE) the European Society for Evolutionary Biology (ESEB), the Society for the Study of Evolution (SSE), and the Society of Systematic Biologists (SSB). This event merges the traditional ‘Evolution’ meeting, the joint annual meeting of the ASN, SSE and SSB, with both its European and Canadian counterparts (the biennial ESEB congress and annual CSEE meeting). This will be the first time that these five societies have met together, creating a truly international event that spans the fields of ecology and evolution. The meeting will be the premier showcase in 2012 for the presentation and discussion among peers of the latest, leading-edge research in ecology and evolution, and will also be an important forum for outreach and education.
I'll also be attending two workshops on Friday July 6th.
EVO101
Science educators in the Ottawa area are invited to join evolutionary biologists and other science educators at the First Joint Congress on Evolutionary Biology for “EVO 101”, a one day workshop on evolution and using evolutionary data in the classroom. Come learn about exciting research in the field of evolution and attend sessions featuring hands-on activities designed to facilitate the integration of ecological and evolutionary data into your curriculum.

Workshop to include: Talks by scientists and educators and hands-on activities demonstrating effective and fun ways to teach evolution; FREE teaching resources and other give-aways for participants; an opportunity to meet and chat with professional evolutionary biologists who both study and teach evolution; attendance at the Gould Award Lecture, given by the recipient of the Stephen Jay Gould Prize, awarded annually by the Society for the Study of Evolution to recognize individuals whose sustained and exemplary efforts have advanced public understanding of evolutionary science and its importance in biology, education, and everyday life in the spirit of Stephen Jay Gould.
Communicating Science to Society
Whether you need to learn the basics or fine tune the dark art of science communication, this half day workshop is for you. Come for insider advice from a group of North America’s top science communicators. The session will open with evolutionary ecologist Tom Sherratt talking about his experience with the media and why he does it. The panellists will introduce an area of journalism and discuss their experiences with interviewing researchers. Then the panel discussion will expand on some of the challenges scientists face and the practical communication solutions. Finally a break-out session will allow for an interactive round table letting participants choose a topic of particular interest (how to give an interview, how to pitch a science book to a publisher, 101 for scientists using social media). The workshop will conclude with a networking session between fellow science communicators and the panellists. By the end, delegates can expect to have built a strategy as to how to effectively approach and handle different media opportunities (such as TV, radio, print & social media) and also leave with a handout of useful tips.

Hosts: Peter Calamai (Adjunct Research Professor, Carleton University School of Journalism and Communication; founding member of the Canadian Science Writers' Association) and Richard Webster (Science & Communications Officer for Row to the Pole and Biology Ph.D. candidate, Carleton University)
Speakers:

  • Carl Zimmer (NYT columnist & author of A Planet of Viruses and many other best sellers)
  • Penny Park (Producer of CBC’s Quirks & Quarks and Discovery Channel’s The Daily Planet. Now Executive Director of the Science Media Centre of Canada)
  • Elizabeth Howell Ottawa Business Journal, freelance science journalist and social media expert
  • Tim Lougheed Freelance science journalist
  • Tom Sherratt Evolutionary ecologist, Carleton University
This second workshop is unusual because there's an actual scientist presenting! :-)


Monday's Molecule #174

This is a rather unusual molecule but it's found in many species. You need to identify the molecule AND tell us why it was a significant discovery.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is pyrrolysine, an amino acid found in the proteins of some species of archaebacteria many species of bacteria. Pyrrolysine is made from lysyl-tRNA synthesized in the cytoplasm and attached to a specific pyrrolysyl-tRNA by a specific pyrrolysyl tRNA synthetase. Pyrrolysine is subsequently incorporated into protein during translation. It is inserted at a specific codon (UAG) and counts as the 23 amino acid. The 21st amino acid is N-formylmethionine and the 22nd amino acid is selenocysteine. Today's winner is Raul A. Félix de Sousa who responded before I remembered to turn on comment moderation so I had to delete his response.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa


Friday, June 15, 2012

What Kind of People Take Vitamins?

"There's a sucker born every minute."

David Hannum
(frequently attributed to P.T. Barnum)
For normal healthy people there's no evidence that vitamin supplements are necessary, or helpful, in any way [Good Food, Bad Food]. Megadoses of vitamins may be harmful [A bad week for the nutritional supplements industry].

So, why would anyone fork out good money for vitamin supplements?

Biochemistry instructors should make sure students understand the difference between science and pseudoscience. That's why I inserted boxes like this one in the latest version of my textbook.
Whatever happened to vitamin B4 and vitamin B8? They are never listed in the textbooks but you’ll often find them sold in stores that cater to the demand for supplements that might make you feel better and live longer.

Vitamin B4 was adenine, the base found in DNA and RNA.We now know that it’s not a vitamin. All species, including humans, can make copious quantities of adenine whenever it’s needed (Sections 18.1 and 18.2). Vitamin B8 was inositol, a precursor of several important lipids (Figure 8.16 and Section 9.12C). It’s no longer considered a vitamin.

If you know anyone who is paying money for vitamin B4 and B8 supplements then here’s your chance to be helpful. Tell them why they’re wasting their money.


Thursday, June 14, 2012

The 10,000 Mile Diet

This article, Shop locally, eat globally? , appeared in today's edition of our university bulletin. I thought it was worth posting a link because, unfortunately, many of my relatives, friends, and colleagues think you can support a large city by only eating food grown within one hundred miles (161 kilometers).
Pierre Desrochers knows how to serve up controversy. When an acquaintance mentions she follows a 100-mile diet to help the environment, Desrochers calmly asks how much energy it takes to heat an Ontario greenhouse.

When a colleague lauds local food as more nutritious than products shipped thousands of miles, Desrochers politely points out that the diet of a 19th-century German peasant consisted of lentils and peas.

Now, the University of Toronto Mississauga geography professor has published a controversial new book that goes beyond polite mealtime conversation and pits what Desrochers calls the “romanticism” of local eating, or locavorism, against the realities of a global food-supply chain.

Desrochers is the co-author of The Locavore’s Dilemma: In Praise of the 10,000-mile Diet, in which he argues that we should stop obsessing about how many miles our food has travelled to get to our dinner plate.

“Three centuries ago most people were eating local food,” Desrochers says. “Why do we think the world moved away from that? There are significant benefits—particularly, environmental and economical—in collaborating to produce food in the best geographic locations.”


Wednesday, June 13, 2012

Richard Harter 1935 - 2012

I just heard from Dave Greig that Richard Harter died over a month ago [Richard Harter 1935 - 2012]. He was a long time contributor to talk.origins having been there since it was called net.origins in the early 1980s. Richard was a staunch defender of science and evolution and a vocal opponent of stupidity (aka creationism). Here's how he describes the phenomenon that is talk.origns [Evolution, Creationism, and Crackpots].
I discovered the usenet news groups circa 1983. In those days there was no big 8 hierarchy; everything was net.this and net.that. One of the hot groups was net.origins, now talk.origins, the designated dumping grounds for creationism/evolution flame fests.

Some usenet newsgroups are models of decorum, where specialists in sundry topics urbanely discuss their specialties. Some are havens of nattering wherein recipes and small talk are exchanged. Such newsgroups represent usenet at its best as a civilized expression of the electronic personal free press. How boring.

There are newsgroups which are open cockpits wherein all and sundry engage in electonic eye-gouging, leaving bodies scattered about the floor, bodies which miraculously arise to gouge and rabbit punch in return. Much more entertaining. Unfortunately such entertainments pall after a while. The same things are said by the same people endlessly. When one flamer departs he or she is replaced by a clone, another mindless dweeb screaming invective into the electronic night air. There is no content, merely an exchange of prejudices and emotion.

The talk.origins group is, to my taste, a happy combination of meat and sauce. To be sure there are no end of flames. However there is much content also. It all has to do with the subject matter. Talk.origins is supposed to be the arena where creationism and evolution are debated. That happens. However it is a happy hunting grounds for cranks and crackpots who come to be told that they are idiots. They revel in it for, finally, someone is listening to them.

The nifty thing about talk.origins is that you can get a real education by reading the group -- the crackpots are not only told that they are idiots, people cite chapter and verse to show where they are in error. Biologists, archaeologists, paleontologists, and the like post there. There is also a good deal of offbeat humor. For your delectation I have prepared a potpourri of essays and materials drawn from talk.origins.

Richard was born in South Dakota and he moved back there in 2000. He never stopped reminding us that South Dakota actually exists and people actually live there. He died of complications from myelodysplastic syndrome (MDS) [Why couldn't I have something simple, like pneumonia].

There's lots more where that came from. Check out Richard Harter's World while it's still active. I especially like his detailed analysis of one of the most difficult problems in all of science: The Seat Stays Up. His summary of everything related to Piltdown Man is a classic.1

The motto on his web page is appropriate ...
I don't worry about dying.
It's not going to happen in my lifetime.

UPDATE: talk.origins remembers Richard Harter

UPDATE: I'm told that Richard's website will be preserved at Richard Harter's World.


1. I hope someone copies it before it disappears.

Sunday, June 10, 2012

Visiting John Hawks

I'm in Madison Wisconsin. What in the world does one do In Madison? Well, there's the State Legislature (beautiful), the free zoo, and a boat ride on the lake.

But all those pale in comparison to the main attraction ... visiting John Hawks of John Hawks Weblog. I found him in a lab full of bones at the at the University of Wisconsin, Madison.


Saturday, June 09, 2012

Delusions

I know I shouldn't pick on David Klinghoffer and the other IDiots at Evolution News & Views but, believe it or not, this is the best the IDiots have to offer.

I just can't resist posting this quotation from his latest post at: The Stubbornness of Their Ignorance.
Forget for a moment about who, Darwinists or Design advocates, is actually right. If you took a sample of ID folks and a sample of Darwin people, specifically those who have felt confident enough in their views to write about them for publication, and then quizzed each group about what arguments their opponents offer, there's no question that those from the ID community would know better what their opposites in the debate say.

Just look at ENV as a convenient illustration. We strive to keep up with toughest challenges, such as they are, from evolutionists. Now look at the competing Darwin blogs. Guys like PZ Myers & Co. concentrate their fire on naïve young-earth creationists. Jerry Coyne and his colleagues in the Darwin-defending business are careful to stay unaware of the very serious challenges to Darwinism from ID.
Wrong!

As it turns out, most of us know more about Intelligent Design Creationism than the average IDiot. As for evolution, I've yet to meet an IDiot who even comes close to understanding it, although Michael Behe and Michael Denton come pretty close.

Klinghoffer and his friends are deluding themselves if they think we don't know what they are saying and they are even more delusional if they think they understand evolution. We've proven time and time again that they don't.

Are we surprised? No, because the one thing all IDiots have in common is the God delusion—the biggest one of all.


What Do Aromatic Compounds Have to Do With DNA Stability?

Jacqueline of skepchick tells us at: 2D Molecules that Form Our 3D World.


My Review of Shapiro's Book Is Finally Published!

I wrote a review of Evolution: A View from the 21st Century for NCSE (National Center for Science Education). It was finished last September but NCSE delayed publication until they fixed up the website for Reports of the National Center for Science Education.

Here's the Table of Contents of the latest issue. All articles are free!

Shapiro threatens to respond to my review if he doesn't like it. I'm certain he won't like it. I'm looking forward to seeing how he responds to my criticisms, especially concerning his lack of knowledge of the history of evolutionary theory and his confusion about the meaning of the Central Dogma of Molecular Biology.


Carnival of Evolution #48

This month's Carnival of Evolution (48th version) is hosted by a developmental biologist at the University of Minnesota (Morris). He blogs at Pharyngula: Carnival of Evolution 48: The Icelandic Saga
I must begin by apologizing for my tardiness, especially since John Wilkins managed to post the last one on time. I was traveling in the 2½ weeks preceding the deadline for CoE, and the combination of spotty internet access, extreme jetlag (British Columbia to Germany to Iceland, where the sun hovered around the horizon all night long, just messed me up), and of course, the incredible distractions of exotic foreign lands, meant that I was disgracefully dilatory in putting it all together.

The next Carnival of Evolution (July) has no host. If you want to volunteer, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution.


Thursday, June 07, 2012

Kirsty Duncan MP Objects to "Bias" in the Working Group on CIHR Funding of a Clinical Trial on "Liberation Therapy"

The previous post mentioned a recently published article on "liberation therapy" that referred to it as something akin to faith healing. It criticized the decision by Canada's CIHR to fund a clinical trial on the procedure. One of the authors of that article was Barry Rubin who served on the working group that recommended the trial.

This prompted a letter from Liberal MP Kirsty Duncan to Dr. Alain Beaudet, President of CIHR [MP lists concern with CIHR expert]. This is a blatant example of political interference and it should not be tolerated. Duncan should be reprimanded in Parliament.
Dear Alain,

Hello and warm wishes.

I am writing to you in order to bring an urgent issue to your attention. As you know, Dr. Barry Rubin is a member of CIHR's expert working group to study CCSVI. According to CIHR's website, the working group's mandate is: "The scientific expert working group will make recommendations on further studies including, if appropriate, a pan-Canadian interventional clinical trial that would evaluate the safety and efficacy of venous angioplasty in patients with MS, and will provide advice on the protocols to expedite such a trial (e.g. inclusion/exclusion criteria)."

Dr. Rubin is the fourth author on an article, 'The "Liberation Procedure" for Multiple Sclerosis: Sacrificing Science at the Altar of Consumer Demand', in the May, 2012 Journal of the American College of Radiology, Volume 9, Issue 5, Pages 305-308.

Alain, you and I have discussed conflict of interest numerous times before-both at committee and in correspondence. Surely, a member of the scientific expert working group publishing such a paper questioning clinical trials is in conflict with the group's mandate.

It is absolutely imperative that all members of the expert working group be independent, but equally important, be seen as independent, and not to have taken a position. Dr. Rubin can no longer be seen to be an independent judge of the scientific literature, as demonstrated by the conclusion of the paper.

Let me quote from the article, "Although some would agree that a randomized, blinded clinical trial is necessary to settle the issues raised in the controversy surrounding this procedure, others would agree that not all controversial procedures require such an expensive approach. Funding trials of a procedure that has minimal basis in rational, empirical knowledge seems questionable. At this point, the procedure rests in the same category of "medical" management as chelation therapy for atherosclerosis (which failed just such a trial), treatment of breast cancer with laser photodynamics, Laetrile for cancer, and other unproven therapeutics found in the retail sphere. When consumerism and patient advocacy groups pressure the scientific and political establishment, reasonable accommodation is warranted. The question is, What is reasonable? It may be that the operators believe in the therapy as much as the understandably desperate patients. The subsidiary question is, When is healing 'faith healing'?"

I will not comment on the science-or lack thereof-of the above.

It is extremely important to note that the first author of the paper, Dr. Michael Brant-Zawadzki of Hoag Memorial Hospital is being credited with prompting the FDA warning this past week.

There are important questions that need investigation. How did Dr. Brant-Zawadski and Dr. Rubin make contact? Were you apprised that Dr. Rubin was writing the article? Did you read the article pre-publication? When was the article accepted for publication? Were you or other officials at Health Canada and CIHR apprised of the FDA alert, and if so, when? Does CIHR support Dr. Rubin's behaviour? Are you concerned that the FDA alert-and this article-will prejudice/affect the ethical board reviews for CCSVI clinical trials? What action will be taken, as clearly this is a conflict of interest?

There is real concern amongst the CCSVI community that while the government fast-tracked Tysabri-a drug which was known to cause PML, and has now infected 232 people and killed 49 people-, and Gilenya, a drug which has now killed 11 people, and is currently under review in Canada (by the way, I am still waiting to hear from Paul Glover about the process for Health Canada's review of Gilenya)-, the government has been reticent about clinical trials for venous angioplasty, which is performed for Budd-Chiari syndrome, May-Thurner syndrome etc. across this country. Now a key panellist has not only come forward, but also published a paper with tremendous hyperbole, "sacrificing science at the altar", and members of the CCSVI community are concerned that a parallel process is being created-one in which the government says it will undertake clinical trials, while a key player appears to work actively to prevent this.

In closing, Dr. Haacke, Dr. McDonald, and Dr. Zamboni were not included in the August 26th, 2010 joint CIHR-MS Society meeting. The explanation given for their not being included in the meeting was that their work would be discussed, and including them might bias the discussion. Now, we have a member of CIHR's expert working group publishing and questioning clinical trials. Clearly, his position may bias the discussion.

Alain, this is extremely serious, and so, I look forward to hearing from you at the earliest time possible regarding Dr. Rubin's inclusion in the scientific expert working group.

Yours very truly,

Kirsty (Duncan)
Kirsty Duncan does not understand how science works and she does not understand that advocates of quack medicine are the ones who are "biased" against real science. It's not the scientists on the working group who caused the problem.


Canadian Government Allocates Funds to Investigate "Liberation Treatment" for Multiple Sclerosis: Sacrificing Science at the Altar of Consumer Demand

The Canadian Institutes of Health Research (CIHR) is the main funding agency for health research in Canada. Most of the research in my department is funded by CIHR grants and the number and size of those grants has been shrinking, with disastrous consequences for my colleagues.

Chronic cerebrospinal venous insufficiency (CCSVI or CCVI) is the name of a condition invented by an Italian doctor named Paolo Zamboni. He claims that it is the cause of multiple sclerosis. He also claims to have developed a procedure called "liberation treatment" or "liberation therapy" that will alleviate the symptoms of MS. It involves opening up some of the veins in a patient's neck in order to improve blood flow. He has been treating patients from all over the world for the past few years.

As you might have guessed, the treatment at his clinic is not free.

There has been enormous pressure on the Canadian and provincial governments to fund this treatment for MS patients, who otherwise have no hope of a cure. So far, most provinces have refused to pay for the treatment. In August 2010, CIHR announced that it would not fund research into something that does not exist [CIHR makes recommendations on Canadian MS research priorities].
Ottawa (August 31, 2010) – On Thursday, August 26, the Canadian Institutes of Health Research (CIHR), in collaboration with the MS Society of Canada, convened a meeting of leading North American experts in multiple sclerosis (MS) to identify research priorities for Canada in this area. Today, at a press conference in Ottawa, CIHR President Dr. Alain Beaudet announced the outcomes of the discussions and shared the recommendations he has made to the Honourable Leona Aglukkaq, Minister of Health.

"There was unanimous agreement from the scientific experts that it is premature to support pan-Canadian clinical trials on the proposed "Liberation Procedure," said Dr. Beaudet. "There is an overwhelming lack of scientific evidence on the safety and efficacy of the procedure, or even that there is any link between blocked veins and MS."
This is the right decision. Money is scarce and it would be criminal to devote any of it to quackery at the expense of legitimate scientific research.

But there's a catch.

Wednesday, June 06, 2012

Casey Luskin "Explains" Intelligent Design Creationism

Casey Luskin is upset with a philosopher named Christopher Pynes. Paynes had the audacity to suggest that one of the key features of Intelligent Design Creationism is ... creationism. According to Paynes, "supernaturalism is a necessary component of ID: there must be a designer" [AD HOMINEM ARGUMENTS AND INTELLIGENT DESIGN: REPLY TO KOPERSKI].

Luskin wants to remind everyone that Intelligent Design Creationism has nothing to do with a creator/designer [Professor Pynes Rails Against the "Straw-Man Fallacy" while Attacking a Straw-Man Version of Intelligent Design]. According to Luskin (a lawyer), Intelligent Design Creationism is a purely scientific theory that relies on: (a) proving that evolution is wrong, (b) detecting the creator/designer by examining nature.

On the primary1 grounds that it's always good to know your enemy, I present to you the best scientific grounds for Intelligent Design Creationism.
  • Studies of physics and cosmology continue to uncover deeper and deeper levels of fine-tuning. Many examples could be given, but this one is striking: the initial entropy of the universe must have been fine-tuned to within 1 part in 10(10^123) to render the universe life-friendly. That blows other fine-tuning constants away. New cosmological theories like string theory or multiverse theories just push back questions about fine-tuning, and would, if true, simply exacerbate the need for fine-tuning. This points to high levels of complex and specified information (CSI) in the cosmid architecture of the universe--information which in our experieince only comes from intelligence.
  • Mutational sensitivity tests increasingly show that DNA sequences are highly fine-tuned to generate functional proteins and perform other biological functions. Again, this is high CSI--which in our experience only comes from intelligence.
  • Studies of epigenetics and systems biology are revealing more and more how integrated organisms are, from biochemistry to macrobiology, and showing incredible fine-tuned basic cellular functions. The integrated nature of organismal body plans shows CSI throughout biological systems--in our experience, only intelligence can generate tightly intregrated multi-component blueprints.
  • Genetic knockout experiments are showing irreducible complexity, such as in the flagellum, or multi-mutation features where many simultaneous mutations would be necessary to gain an advantage. This is more fine-tuning--and in our experience, irreducibly complex machines arise only from intelligence.
  • The fossil record shows that species often appear abruptly without similar precursors, which represents mass-explosions of high CSI--something which requires an intelligent cause.
  • There have been numerous discoveries of functionality for "junk DNA." Examples include recently discovered functionality in some pseudogenes, microRNAs, introns, LINE and ALU elements. Intelligent design predicted this data.
If all of these things were true, then you'd predict that scientists would be flocking to church on Sundays. You'd also expect that the scientific literature would be full of papers proving the existence of God. It would be the most remarkable discovery in the history of humans.

A key part of Intelligent Design Creationism—the part that Casey Luskin is leaving out—is to explain why it has been so remarkably unsuccessful after 200 years of trying. That part has to do with the huge Darwinist conspiracy that forces scientists to tow the line and stick with atheistic Darwinism in spite of all the scientific evidence against it. If you read the blogs, you'll see that attacking scientists and Darwinism is the dominant theme. The "scientific" "evidence" for Intelligent Design Creationism is almost never mentioned.

Most of us scientists don't realize that we are part of such a conspiracy because we have been brainwashed into believing in evolution. However, a few god-fearing souls have seen the truth. Some of them are lawyers (Casey Luskin, Philip Johnson), some of them are philosophers, some of them claim to be mathematicians, and a few think they are scientists (Michael Behe, Jonathan Wells). The one thing they all have in common is that they are all IDiots.


1. The secondary grounds are to keep a record of the June 2012 "facts" because they will change soon enough.

Tuesday, June 05, 2012

Graduation Day

June is graduation month at the University of Toronto. There are various classes graduating every morning and afternoon for several weeks. (We have more than 70,000 students on three campuses, counting undergraduates, graduates, and enrollment in professional faculties.)

Today it's the turn of medical students. About 215 students just received their M.D. degrees. I'll be glad when it's all over 'cause the lineups at Tim Horton's1 are horrible.



Starbucks too, but I don't care about them.

Monday, June 04, 2012

A Platypus Describes Humans

Ryan Gregory invents The Platypus Fallacy to illustrate an important concept in evolution. Here's how a platypus describes humans. See if you can spot the problem.
The lineage of which humans are a part is a very ancient offshoot of our mammalian family tree, so it was 166 million years ago that we last shared a common ancestor with humans, and that puts them somewhere between mammals and reptiles, because they lack a lot of specialized characters that we have gained but the ancestral amniote also lacked; for instance, they have no electroreception, no bills, no webbed feet, and no venom. So we can use them to trace the changes that have occurred as we went from being a reptile, to having fur to making milk to having our specialized features.


Bruce Alberts Talks About Science Literacy

Bruce Alberts was president of the National Academy of Sciences (1993-2005), author of The Molecular Biology of the Cell, and winner of the Gairdner Award for his work on DNA replication. He was my Ph.D. supervisor. He is currently editor-in-chief of Science magazine. He has been interested in science education and science literacy for many decades so when he makes a comment about science education, it's worth listening to.

Here's a quote from a recent interview in PLoS Genetics [Scientist Citizen: An Interview with Bruce Alberts].
You look at the current political system in the US. It's incredibly depressing. These kinds of statements that “scientists only believe in climate change so that they can get a grant.” This kind of stuff couldn't be said if we actually had a population that understood what science is. We have a fantastic scientific community, and if we don't unleash them and give them credit for working on these things, then I don't think our country is going to prosper.

Every ten years the Academy publishes a booklet called “Science, Evolution and Creationism” [available online], and before the last one in 2008, the Academy hired one of the companies that put people behind a one-way mirror and interview them to see what they think about some new product. But this question was, “How do they think about science and creationism?”

And the staggering message from these college-educated adults is that they don't see any difference between science as a belief system and religion as a belief system. So basically, the preacher tells them what religious people believe, the scientists tell them what scientists believe, and [they think] “I can choose either one.” And the reason they can say that is that they don't understand what we call “science as a way of knowing”. That it is not a belief system, that it is an evidence-based community process.

This is just unbelievable, that our American public can determine our future without understanding the fundamental issues about scientific facts. If the population isn't prepared to deal with these kinds of issues, to think rationally and respect evidence, then I think the country is really in danger.
Like I say, science is a way of knowing that involves evidence and rationality. Now you know where I got that from.


The photo was taken at Bruce's 70th birthday party. It shows him with his first three graduate students: Keith Yamamoto (left), me (second from right), and Glenn Herrick (right).

Monday's Molecule #173

This is an easy one. We talked about this molecule in our lunch time seminar just a few minutes ago. It binds to lots of proteins.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is malonyl-ACP where ACP stands for acyl carrier protein. The winners are Bill Chaney and Matt McFarlane. One other person got it right but didn't specify what "ACP" stood for. The most common error among those who came close was to call it malonyl-CoA.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane


Friday, June 01, 2012

Cornelius, Meet Johnnyb

Cornelius Hunter doesn't like anything about evolution. He especially doesn't like us to say that Evolution Is a Fact.

Here's the latest from Cornelius [When I Pointed Out the Evolutionary Tree Has Failed Two Professors Gave Me Pushback ].
If you are new to the evolution debate you might wonder why evolutionists do not simply acknowledge the painfully obvious fact that evolution is not a fact. It is not as sure gravity and in fact there are significant questions and problems with evolution. Why don’t evolutionists admit to the truth of how the science bears on their theory?

The answer is that evolution is not about the science. At issue here is not merely the status of another scientific theory. Evolutionists won’t be swayed by the evidence because doing so—and confessing that evolution is not overwhelmingly supported by the evidence—would immediately expose evolutionists to all kinds of possibilities which they simply cannot accept. An evolutionist can no more change his mind than could a cultist. Evolution is underwritten by a religious worldview—it is a metaphysical theory, not at scientific theory. As such it may lose every battle, but it cannot lose the war.
Contrast this with what Johnnyb said a few weeks ago on Uncommon Descent [see All IDiots Believe in Evolution! ].
So what is one to do? Well, thankfully, our friends the evolutionists have given us a way out. In their zeal to claim consensus on the “fact of evolution,” they have had to steamroll together such a large diversity of opinion into the single term “evolution”, that the word “evolution” no longer has the grand meaning it used to. The only real meaning everyone can agree on is “change in allele frequency over time” – and that is a definition that literally everyone can agree with.

In other words, even if you are a young earth creationist, if your professor asks if you believe in evolution, the legitimate answer is “yes”. Given the common definition of “evolution,” the only thing they are really asking with that question is, “do you believe in genetics?”
Cornelius Hunter and Johnnyb really should get together and agree on the facts.


Turn Right! Turn Left!

If you're driving on a two lane highway and a head-on collision seems imminent, you should turn right. This probably doesn't work in England.

Phil Plait of Bad Astronomy tells us that the Andromeda Galaxy is on a collision course with our Milky Way Galaxy [Hold on tight: in 4 billion years, we’re due for a galactic collision!]. What should we do? We don't know whether the Andromedons drive on the right side of the road or the left. Which way should we turn to avoid the collision?