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Tuesday, July 10, 2012

Rosie Redfield at Evolution Ottawa 2012

Rosie Redfield gave a talk on Sunday night. She described the work she did on the so-called "arsenic-incorporating" strain of bacteria that was made famous in a NASA press release and a subsequent Science paper last year [Arsenic and Bacteria] [Arsenic-associated bacteria (NASA's claims)] ["This Paper Should Not Have Been Published"].

You might recall that Rosie was among the first scientists to point out the flaws in the original paper and this led to a delay in its publication. When it finally was published there were several critical comments—including one from Rosie—that appeared in the same issue.

Rosie obtained the GFAJ-1 strain and tested its growth characteristics. She determined that it absoltutely required phosphate for growth and growth stopped when the phosphate in the medium was depleted. The strain did tolerate high levels of arsenic in but there was no evidence that it could replace phosphorus.

Rosie purified DNA from cells grown in the presence of arsenic and sent it to her collaborators. There was no arsenic in the DNA. (Carl Zimmer takes you through a blow-by-blow summary of Rosie's talk at Live-blogging Arsenic Life].)

The work was submitted to Science and the paper was accepted for publication It was due to be published on July 26th which meant that, under the conditions imposed by Science, Rosie wasn't allowed to talk about her work until then. Rosie informed Science that she intended to violate the embargo and describe her results at this meeting. Science responded by moving the publication date forward and posting the paper on their website at 8pm Sunday night [Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells]. Carl Zimmer was watching the website as Rosie spoke and at one point in her talk she turned to Carl to ask if the paper was up—it was.

The audience recognized that this was a major victory for open science. As the moderator put it at the end of her talk, you can mess with NASA, you can mess with Science, but don't mess with Rosie Redfield!

There are two papers being published in Science. The other one [GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism] says essentially the same thing as Rosie's paper.

The bottom line here is that the original paper by Wolfe-Simon et al. (2011) was deeply flawed and should never have been published by Science. More importantly, the latest results show that Felisa Wolfe-Simon was dead wrong when she claimed at the NASA press conference that GFAJ-1 incorporated arsenic into its DNA. You can watch her say this in the video I posted at: The Arsenic Affair: No Arsenic in DNA!.

You may be wondering how NASA and the authors of the original paper are handling this issue. In spite of the fact that they held a public press release and in spite of the fact that Felisa Wolfe-Simon was interviewed multiple time in the press and even gave a TED talk, they maintain that the only proper forum to discuss criticism of their paper is in the peer-reviewed literature! (I hate hypocrites.)

When Wolfe-Simon heard that Rosie's paper was in press she said [Arsenic-based life finding fails follow-up] ...
Wolfe-Simon, who says she can’t comment in detail until Redfield’s results appear in a peer-reviewed journal, wrote in an email that her original paper never actually claimed that arsenate was being incorporated in GFAJ-1’s DNA, but that others had jumped to that conclusion. “As far as we know, all the data in our paper still stand,” she wrote. “Yet, it may take some time to accurately establish where the [arsenic] ends up.”
She's right about the fact that the original paper never actually said that arsenic replaced phosphorus in DNA but it did strongly imply that this was the logical conclusion. However, in her press conference, Wolfe-Simon explicitly talked about arsenic replacing phosphorus in DNA and nobody who listened to that talk could have come away with any other impression. You didn't have to "jump to that conclusion" after hearing the presss conference.

So what are they saying today? Read Rosie's blog at: NASA's cowardly responses to their #arseniclife FAIL. And here's what Wolfe-Simon is saying, quoted at: New Studies Say No, Life Can't Live on Arsenic Alone.
These Science authors have made it clear that they are convinced they have tightly shut the door on arsenic incorporation into biomolecules. Yet, low amounts of arsenic incorporation may be challenging to find and unstable once cells are opened," she writes, "so may merit comprehensive and systematic efforts with other assays and conditions.
I don't think it's reasonable to expect Wolfe-Simon to apologize but I do think the scientific community should continue to apply pressure on NASA.

Here's a very good account of what happened and why NASA should be ashamed: Scientist in a Strange Land. It also expresses some sympathy for Felisa Wolfe-Simon.


Photo courtesy of Seanna Watson.

Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) A bacterium that can grow by using arsenic instead of phosphorus. Science. 332:1163-1166. Published online 2 December 2010; published in Science magazine Jun 3, 2011 [doi: 10.1126/science.1197258]

Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) Response to comments on "A bacterium that can grow by using arsenic instead of phosphorus". Science. 332:1149. [doi: 10.1126/science.1202098]

Saturday, July 07, 2012

Beaver Tails

Tonight a bunch of us went for dinner at a pub in the Byward Market area of Ottawa just a short walk from the conference centre. Afterward we ate Beaver Tails.

There were fifteen of us. Four of Ryan Gregory's graduate students, three people I met at the evolution education session, Bjørn Østman, Ford Denison (This Week in Evolution), Carl Zimmer, Steve Watson, Seanna Watson, Ryan Gregory, and Joe Felsenstein.

Everyone liked Beaver Tails. I had chocolate and banana.

We talked about evolution, blogging, science writing, and Rosie Redfield ('cause she wasn't there!).


Quantitative Trait Evolution

I'm at Evolution Ottawa 2012 and this afternoon I went to a session on New phylogenetic methods for quantitative trait variation.

I attended two talks.

Introduction and asymptotic behavior of trait evolution models under drift and stabilizing selection by Cecile Ane.

Placing fossils on molecular phylogenise with Brownian motion or Ornstein-Uhlenbeck models of continuous trait evolution by Joe Felsenstein.

It was interesting to be exposed to this kind of theoretical population genetics but I really didn't understand a single thing.

There were more than 200 people in the audience listening with rapt attention. They're a lot smarter than me. It was embarrassing.

There's one thing Joe said that I understood, and it was very impressive. He referred to a paper "published by me." Nowadays, almost everyone would say, incorrectly, "published by myself."


That's a photo of one of the speakers. Can you guess which one?

Communicating Science to Society

I attended a workshop on Communicating Science to Society at Evolution Ottawa 2012. The workshop was hosted by two science writers, Peter Calamai and Richard Webster and there were about one hundred people at the session.

The goal was ...
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.
The panelists were ....
  • 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
I've been to half a dozen of these meetings at various conferences. The main theme is always the same. It consists of a bunch of science journalists telling scientists how we should help them (the journalists) make a living at science writing. We are told repeatedly that they have deadlines and editors and that they have to write about science in a way that appeals to the general public. We are told that if we want our research to be publicized then it has to to be cool and sexy and if it isn't then the science writers will help us "frame" it in a way that appeals to the public.

At this meeting, the emphasis was all about deadlines and writing about the latest papers from your labs. The science writers thought that we all wanted to get our latest hot results on the front pages of the newspapers. That's just not true. It's not what science is all about and it's not what we need in order to increase public awareness of science. (To his credit, Carl Zimmer seems to understand this better than other science journalists.)

What we need is not more splash about the latest Nature paper on the evolution of mimicry in insects. What we need is more articles on what evolution is and why it's so important. If science writers were really in the business of communicating science to the public then that's what they would be writing about. That, and topics like; what is DNA, how do genes work, what's in your genome, what causes speciation, why bacteria are important etc. etc.

The public needs to know the basics and they need to appreciate excitement of understanding what life is all about. They need Biology 101, not some senior level course that focuses on the latest research. That kind of science writing doesn't have to be done in a hurry before the embargo expires and it would be a much more useful way of communicating science to society.

Just once, I'd like to attend a meeting like this where the science journalists admit that they have been remarkably unsuccessful at educating the general public about science. Instead of telling us how to fit into the current failed system, I'd like them to ask us how they can change the way they write about science in order to advance science literacy.

I don't think that's ever going to happen. As a general rule, science writers seem to think that they are the experts on communicating science to the general public and all they need to do is teach us scientists how to work the system and tell people what they want to hear. It never occurs to them that the system is broken and that's why we have a scientifically illiterate society.


Evolution and Poutine

A bunch of us are attending Evolution Ottawa 2012. We set off to find the best poutine in the region and ended up at Jean Burger in Wakefield Quebec—about 30 minutes north of Ottawa.

Here's the group enjoying "French cuisine." From top left to right there's Bjørn Østman, Seanna Watson, Steve Watson, Ryan Gregory, Rosie Redfield, and Jerry Coyne.


Jerry really liked the poutine. Rosie ... not so much ... although she did say it wasn't as bad as she expected. For the record, it was the best poutine I've ever had so the trip was worth it.


Afterwards we drove into Wakefield and visited the bakery for dessert. I've been going to this bakery for 50 years—my favorite ski hill is nearby.


We talked about a lot of things, especially science, skepticism, and blogging.


Wednesday, July 04, 2012

Another IDiot Book: Science and Human Origins

The IDiots at Disco (Discovery Institute) have published another book. This time the authors are Ann Gauger, Douglas Axe, and Casey Luskin. Gauger and Axe are scientists so this book is supposed to be about science. Unfortunately, Casey Luskin is a lawyer which pretty much negates the authority of Gauger and Axe.

The book has been thoroughly reviewed by Paul McBride on Still Monkeys. McBride is a graduate student studying evolution in New Zealand. Read the reviews at ...

Science and Human Origins - Chapter 1 review
Science and Human Origins - Chapter 2 review
Science and Human Origins - Chapter 3 review
Science and Human Origins - Chapter 4 review
Science and Human Origins - Chapter 4 review: Part 2
Science and Human Origins - Chapter 5 review

Wanna know the bottom line?

1. Common descent is still alive and well.
2. Natural selection still works.
3. The human fossil record still demonstrates evolution.
4. Junk DNA still exists.
5. There's no evidence for Adam and Eve.

Here's how Paul McBride sums up his review.
Science and Human Origins has to be described first and foremost as being anti-evolution rather than pro-intelligent-design, or pro-science. If it offers solace to those seeking evidence against evolution for their faith, the solace should be as incomplete as the arguments made in the book.
This is a common criticism. Most IDiot literature is nothing more than a misguided attack on evolution. It's increasingly rare to see any defense of intelligent design. Perhaps that's because it's indefensible?


Carnival of Evolution #49

This month's Carnival of Evolution (49th version) is hosted Mousetrap: ecology and evolution footnotes. Read it at: Carnival of Evolution catch 49
Evolutionary studies are rich both in concepts and methods but not dis-integrated. As you will see, there is a common theme. Have fun.

The next Carnival of Evolution (August) will be hosted by Teaching Biology. If you want to volunteer to host others, 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.

Tuesday, July 03, 2012

Biochemists on Abbey Road

Jerry Coyne posted the photograph on the right and said, "If you don’t know what happened a few minutes after this picture was taken in 1969, you are either way too young or have no knowledge of rock history" [Music history about to be made]. I agree but, unfortunately, there are way too many people who are way too young. You can't blame them for not knowing what was about to happen.

I've been on that crosswalk dozens of times because it's right near a house in St. John's Wood where I once stayed while in London. Here's a photograph (below) of the owner of that house along with some of his friends. You don't have to be very old to have been around when this photo was taken but you do have to have some knowledge of the history of biochemistry and molecular biology.

How many of you can name all the scientists in this photo? (No peeking at the comments.)



Sebastian Thrun Will Change Education

John Hawks is a big fan of online education. He posted a link to a Wall Street Journal article about online education [Online education and Silicon Valley]. The article, Sebastian Thrun: What's Next for Silicon Valley?, is mostly about a Stanford professor and Google employee, Sebastian Thrun.
The entrance to his building is littered with the gaudy red, blue, yellow and green bicycles that Googlers tool around on. I'm at the secret headquarters of the not-so-secret Google X, where the way-out-there projects of the search giant turn into reality. The gregarious play master, Sebastian Thrun, leads us into a well-worn conference room. The chairs are a shade of green not found in nature and the disrupting clang and cheers from a rousing foosball game waft in through the door. Mr. Thrun, 45 and slight in stature, is sporting a gray T-shirt of a local start-up and speaks softly with German-English diction.
Thrun and his Google colleague, Peter Norvig, taught an online course on artificial intelligence that attracted a huge number of students. Apparently there were 23,000 students who completed the course. That's amazing. But there's more ...
Mr. Thrun's cost was basically $1 per student per class. That's on the order of 1,000 times less per pupil than for a K-12 or a college education—way more than the rule of thumb in Silicon Valley that you need a 10 times cost advantage to drive change.

So Mr. Thrun set up a company, Udacity, that joins many other companies attacking the problem of how to deliver the optimal online education. "What I see is democratizing education will change everything," he says. "I have an unbelievable passion about this. We will reach students that have never been reached. I can give my love of learning to other people. I've stumbled into the most amazing Wonderland. I've taken the red pill and seen how deep Wonderland is."
How in the world do you pay attention to 23,000 students and give them a grade that reflects what they learned for only $23,000? The only way you could do that is to have all assignments and tests evaluated electronically and that's no way to teach properly. (You also need very cheap servers, internet access, and software and Thrun and Norvig have to work for free.)

Udacity is a for-profit company. How will it make money? [Ex-Stanford Teacher’s New Startup Brings University-Level Education To All].
Classes are currently focused on computer science since that’s what the team already knows how to teach. Examples include: Building a Search Engine and Programming a Robotic Car. As one of the inventors of Google’s self-driving car, Sebastian is perfectly suited to teach a class on how to program one. Udacity plans to expand to other subjects with the goal of building a full university online.

All classes are currently free, and the goal is to keep it that way. When asked how it will make money, Sebastian pointed out that recruiting good technical talent is something that companies pay for. Udacity knows who the best students are and could pass them along to companies looking for new hires.
Somehow I doubt that Udacity will be offering courses in philosophy, French, or art history. I don't even think they'll be teaching biochemistry since very few of our undergraduates move directly from a Bachelor's degree to jobs in biotech or pharmaceutical companies.

Sebastian Thrun thinks he's going to "democratize" education but, if he succeeds, what he's really going to do is dumb down and cheapen education. The only thing in his favor is the fact that today's universities are doing the same thing so creating online courses is probably no worse that what students are currently getting in the classroom. If someone can offer the same quality of "education" for much less money then what's the point of attending classes?



Was the Origin of Life a Lucky Accident?

Nick Lane has written a very nice article in the June 23, 2012 issue of New Scientist: Life: is it inevitable or just a fluke?.

Nick Lane is a biochemist who works on the origin of life at University College London (UK). He's also a science writer who recently won the Royal Society Prize for Life Ascending: The Ten Great Inventions of Evolution. His new book will be called, CHASM: The Outlandish Origins of Complex Life.

Lane is one of the main proponents of the "Metabolism First" view of the origin of life. The idea is that life began with the evolution of an energy source much like the main source of energy in today's cell. The energy is derived from a gradient of proton concentration across a membrane. This was first discovered by Peter Mitchell (chemiosmotic theory) and it was one of the most important discoveries in biochemistry—although most people, including most biochemists, haven't got a clue what it's all about [Ode to Peter Mitchell] [Why Are Cells Powered by Proton Gradients?] [Metabolism First and the Origin of Life ].

The ability to generate usable energy in this manner could have arisen near thermal vents in the ocean where the gradient exists between the alkaline interior of small cavities in the rock and the external seawater. The energy was then used to build up small organic molecules such as sugars and amino acids. Early metabolism arose when pathways for the simple molecules of life evolved using simple inorganic catalysts and/or simple peptide catalysts. "Metabolism First" is a much more reasonable scenario, in my opinion, than "Prebiotic Soup" [More Prebiotic Soup Nonsense].

If this view is correct then the origin of life depends only on the presence of simple chemical systems that create an energy producing gradient and this is likely to happen on many planets. However, the leap from simple cells to complex cells may have been the rate-limiting step in the evolution of sentient beings.

Lane suggests that large complex cells with large genomes could only have arisen if they discovered an abundant source of energy. That happened when some simple bacteria formed an endosymbiotic relationship with bigger cells to create a new life form with mitochondria [Energetics and genetics across the prokaryoteeukaryote
divide
]. This unique event was not inevitable. It happened only once in the history of life—about 2 billion years ago. This sort of lucky accident may never occur on other planets so it may just be a fluke that sentient beings evolved on Earth.

We may be alone in the universe.


Monday, July 02, 2012

Monday's Molecule #176

Today's molecule has a common name and a much less common systematic (IUPAC) name. You need to supply both names in order to win. You also need to tell us what this molecule does.

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 dextromethorphan [(+)-3-methoxy-17-methyl-(9α,13α,14α)-morphinan]. It's a cough suppressant (DM). The first person with the correct answer is DR but unless he/she posts his/her name and status (undergraduate?) in the next 24 hours the prize will got to Raul A. Félix de Sousa.

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
July 1: Raul A. Félix de Sousa


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