Wednesday, December 30, 2009

How Long Does It Take to Recognize an IDiot?


Ken Ham is the man behind Answers in Genesis and the Creation Museum. He's upset with Lawrence Krauss because Krauss has been critical of anti-science creationists in general and the Creation Museum in particular. Ken Ham is particularly upset because Krauss was critical of th Creation Museum before he had actually visited it.
Krauss himself got criticism from some in the secular press because he had not even visited the museum to see it for himself. Presumably because of this criticism, he did come some time later and walked through the Creation Museum exhibits with AiG’s CCO, Mark Looy. Mark actually timed Krauss’s visit. He took a whole 22 minutes to walk through the museum, most of the time asking Mark Looy questions and only occasionally glancing at some of the exhibits. Considering it would take a person nearly one and a half hours to watch the programs in the various theatres, including the Planetarium and SFX theatre, plus take 2 hours to watch all the 50-plus videos in the various exhibits, and a further two hours to read all the signage—it was obvious Krauss wasn’t the least bit interested in researching the content of the museum (as one would expect from a real scientist and well-known anti-creationist commentator), but only visited presumably to tell people he has seen the Creation Museum and thus could comment on it—what a farce!
Now, let's be fair to Lawrence Krauss. He's a very smart guy and I'm certain that it didn't take him 22 minutes to recognize that the museum was a farce. I'm sure he stayed an extra 21 minutes just to be polite to his host.



Thursday, December 17, 2009

Time Magazine's Top 10 Scientific Discoveries


Here's the list of Time Magazine's Top 10 Scientific Discoveries. Given all the hype about The Darwinius Affair last May it's amazing that the discovery of this fossil didn't make the list.

There were several other huge scientific breakthroughs that failed to make the list: proof that Darwin was wrong, the overthrow of evolutionary theory, exposing the fraud of climate change, and the publication of Unscientific America.

There are some real scientific stories that were ignored by Time magazine: the creation of artificial stem cells (continuing), the 150th anniversary of the publication of Origin of Species, Nobel Prizes for telomeres and ribosome structure, and rapid human genome sequencing.

1. Our Oldest Ancestor, "Ardi"
2. The Human Epigenome, Decoded
3. Gene Therapy Cures Color Blindness
4. A Robot Performs Science
5. Breeding Tuna on Land
6. Water on the Moon
7. The Fundamental Lemma, Solved
8. Teleportation!
9. The Large Hadron Collider, Revived
10. A New Planet (or Brown Dwarf?) Discovered

It looks like a bad year for science if this is the best of the best.

In case you've forgotten, here's the top 10 list from last year [2008].

1. Large Hadron Collider
2. The North Pole — of Mars
3. Creating Life
4. China Soars into Space
5. More Gorillas in the Mist
6. Brave New Worlds
7. The Power of Invisibility
8. Cenozoic Park?
9. Can You Spell Science?
10. First Family


Tuesday, December 15, 2009

Does Excess Genomic DNA Protect Against Mutation?

Many eukaryotic genomes have a large amount of "excess" DNA that doesn't have any of the functions we normally assign to DNA (protein-coding, regulatory, origins of replication, centromeres, RNA genes etc.). Many of us think this is junk DNA. It has no function and could easily be dispensed with.

One of the adaptive explanations for this excess DNA is that it protects the functional DNA from mutations. Ryan Gregory thinks this is a serious scientific hypothesis even though he's skeptical. He has a wonderful post that reviews the history of the idea and how the hypothesis should be tested [Does junk DNA protect against mutation?].

The bottom line is that this hypothesis is not taken very seriously by the scientific community for some very good reasons.

First, most spontaneous mutations in the germ line seem to be due to errors in DNA replication. The overall rate of evolutionary change is consistent with the mutation rate of DNA replication + repair, suggesting that it is the dominant form of mutation. This mutation rate is based on the number of nucleotides replicated. What this means is that the rate of mutation in functional DNA is independent of how much other DNA is being replicated. Excess DNA offers no protection from the spontaneous error rate of DNA replication.

THEME

Genomes & Junk DNA
However, the protection hypothesis may be applicable to other kinds of mutation such as those caused by chemicals or ionizing radiation. In multicellular organisms such as animals, fungi, and plants, this possible protection may prolong the lifetime of somatic cells or prevent them from becoming deregulated (e.g., cancer).

The idea is that excess DNA may shield the functional DNA from the effects of these mutagens but this would only work if the excess DNA was specifically organized so that it surrounded the functional DNA and provided physical shielding. There's no evidence that this is the case and, furthermore, it doesn't make much sense. The functional DNA in a nucleus is already shielded by lots of proteins, lipids and membranes so it's unlikely that a bit more DNA is going to make a difference.

Not only that, but some kinds of DNA damage caused by these mutagens will cause strand breakage. What does that mean? It means that the larger the genome the greater the chance that damage will occur. In other words, excess DNA leads to greater rates of mutation, not lower rates of mutation, for those types of mutagens. Ryan Gregory shows results from several studies during the 1970s that establish that fact.

I sympathize with Ryan's call for experimental support of the hypothesis but I'd also like to point out that not only does it not have direct evidence to back it up but it's not even theoretically feasible. It's just a bad hypothesis based largely on a misunderstanding of mutations and how they arise.

Also, the protection hypothesis doesn't pass The Onion Test which is one of the first requirements for an adaptive explanation of junk DNA.


On the Evolution of Homosexuality

 
A reader alerted me to a posting by Greta Christina on The Blowfish Blog.1 She discusses Why Did Gayness Evolve?.

This is not your ordinary posting on the topic. For one thing, she acknowledges that you can only discuss the evolution of homosexuality if there's a significant genetic component. She makes the assumption that there is a genetic component but it is not proven.

From that point on, her analysis of the possible reasons for evolving homosexuality is as good as it gets. Greta Christina avoids the obvious clichés and concentrates on real biology. The words "spandrels" is used a lot.

This is someone who understands evolution. Speaking of understanding evolution, in order to discuss whether homosexuality evolved you need to have a workable definition of evolution. My definition restricts evolution to heritable changes in a population and that's why the discussion of a possible genetic component is relevant.

Some people prefer a different definition of evolution—something like "descent with modification." I wonder how you can discuss the possible evolution of homosexuality using such a definition of evolution? Would it mean that the increased prevalence (and acceptance) of homosexual behavior in ancient societies was an example of evolution?


1. Thank-you Fred.

Thursday, December 10, 2009

Why Are Americans Religious?

 
One of the major questions in 21st century sociology is why are Americans so much more religious than citizens in other industrialized nations. The answer, if there is one, will help us understand why evolution is rejected by so many Americans.

Gregory S. Paul is a writer who has long been interested in this question. His latest contribution is published in the journal Evolutionary Psychology (Paul, 2009).

Paul examined the correlation between religiosity and the Successful Societies Scale (SSS). SSS measures things like crime rates, divorces, mortality rates etc. The United States (U) seems like an outlier compared to other countries.

Does belief in God cause a society to be dysfunctional or are less successful countries more likely to encourage religiosity? Or is there no obvious cause and effect behind this correlation?

You'll have to read the paper to see how Gregory Paul address these questions and how he rules out many possible explanations. I find his conclusion quite intriguing—I never thought of it this way.
Among the prosperous democracies all but the U.S. have adopted most or all of a set of pragmatic progressive governmental policies that have elevated these nation’s societal efficiency, success and security while reducing personal levels of stress and anxiety. These include reduced socioeconomic disparity and competition via targeted tax and welfare strategies, handgun control, anti-corporal punishment and anti-bullying policies, protection for women in abusive relationships, intensive sex education that emphasizes condom use, rehabilitative incarceration, increased leisure time that can be dedicated to family needs, and perhaps most importantly job security and universal health care that make it difficult for ordinary citizens to suffer catastrophic financial failure. Social ills are correspondingly suppressed. As a member of the 1st world the U.S. is an anomalous outlier not only in its religiosity, but in social, economic and political policies as well. Provided with comparatively low levels of government support and protection in favor of less restrained capitalism, members of the middle class are at serious risk of financial and personal ruin if they lose their job or private health insurance; around a million go bankrupt in a year, about half due in part to often overwhelming medical bills. The need to acquire wealth as a protective buffer encourages an intense competitive race to the top, which contributes to income inequality. The latter leaves a large cohort mired in poverty. Levels of societal pathology are correspondingly high. The evidence indicates that the modulation of capitalism via progressive policies is producing superior overall national circumstances compared to the more laissez-faire capitalism favored in the U.S.
       The relationship of religion to these patterns appears to be both passive and active. Starting with the passive, the middle class majorities of western Europe, Canada, Austro-Zealand and Japan apparently feel sufficiently secure in their lives that increasingly few citizens feel a need to seek the aid and protection of a supernatural creator, resulting in dramatic drops in religious belief and activity (Norris and Inglehart, 2004; Paul and Zuckerman, 2007; Zuckerman, 2008). With the implosion of the general religious belief, few subscribe to a fundamentalist world-view that provides the base for creationist opinion,. That there are no major 1st world exceptions to this pattern, and that a significant religious revival has yet to occur in a secular democracy, indicate that the socioeconomic security process of democratic secularization is highly effective even though it is an accidental side effect of progressive economic policies. The universality of the effect is further supported by Asian Japan experiencing the same basic secularization process as the EuroChristian heritage secular democracies. America’s high-risk circumstances, the strong variation in economic circumstances, and chronic competitiveness help elevate rates of social pathology, and strongly contribute to high levels of personal stress and anxiety. The majority of Americans are left feeling sufficiently insecure that they perceive a need to seek the aid and protection of a supernatural creator, boosting levels of religious opinion and participation. The nation’s good ratings in life satisfaction and happiness is compatible with a large segment of the population using religion to psychologically compensate for high levels of apprehension; America’s apparently high level mental illness (Bijl, 2003) may be in accord with this suggestion. The ultimate expression of this social phenomenon is the large minority who adhere to the evangelical Prosperity Christianity and Rapture cultures whose Bible-based world-view favors belief in the Genesis creation story. The results of this study are therefore compatible with and support the socioeconomic security hypothesis of democratic secularization.
Sue Blackmore is intrigued but skeptical [Are we better off without religion?]. She thinks this may be too simplistic and of course she's right. There's no one reason why America is lagging behind other nations in evolving a better society and there's no single explanation for its religiosity.

But I still think Paul's point is worth considering.


Paul, G.S. (2009) The Chronic Dependence of Popular Religiosity upon Dysfunctional Psychosociological Conditions. Evolutionary Psychology 7: 398-441. [PDF]

Friday, December 04, 2009

Quoting Bertrand Russell

 
Jason Rosenhouse has posted a quotation from Bertrand Russell [Quote for the Day]. Like Jason, I am a fan of the great man. Here's my quotation—it's from an essay written in 1940, shortly after Russell was declared unfit to teach at City College in New York.
A man or woman who is to hold a teaching post under the state should not be required to express majority opinions, though naturally a majority of teachers will do so. Uniformity in the opinions expressed by teachers is not only not to be sought but is, if possible, to be avoided, since diversity of opinion among preceptors is essential to any sound education. No man can pass as educated who had heard only one side on questions as to which the public is divided. One of the most important things to teach in the educational establishments of a democracy is the power of weighing arguments, and the open mind which is prepared in advance to accept whichever side appears the most reasonable. As soon as a censorship is imposed upon the opinions which teachers may avow, education ceases to serve this purpose and tends to produce, instead of a nation of men, a herd of fanatical bigots.
 

What Do These Things Have in Common?

 
What do these two images have in common? You'll have to read Ms. Sandwalk's blog to find out [One Month to go]. Next month will be very exciting. I'll be spending all of January in Belgium.




Defining Evolution in Anthropology Textbooks

Here's one of the most interesting articles in the current edition of Evolution: Education and Outreach.
White, J., Tollini, C.D., Collie, W.A., Strueber, M.B., Strueber, L.H., and Ward, J.W. (2009) Evolution and University-level Anthropology Textbooks: The “Missing Link”? Evo. Edu. Outreach 2:722–737 [doi: 10.1007/s12052-009-0176-6]

Abstract: Although studies analyzing the content of evolution curriculum usually focus on courses within the context of a biological sciences department or program, research must also address students and courses outside of the biological sciences. For example, using data solely from biological courses will not fully represent the scope of coverage of evolution in university education, as other fields, like anthropology, also utilize evolutionary principles. We analyzed the content of 31 university-level anthropology textbooks for the following: (1) presence of a definition of evolution in various sections of the textbooks, (2) accuracy and consistency of the definitions provided in the textbook sections, and (3) differences between textbooks for cultural and physical anthropology. Results of this study suggest that anthropology textbooks do not necessarily (1) provide a single definition of evolution or (2) provide an accurate, “baseline” definition of evolution when present. Additionally, substantive differences were observed between definitions provided in different sections within a single textbook, as well as between textbooks written for cultural anthropology and physical anthropology/archaeology courses. Given the inclusion of anthropology courses in general education curriculum at the university-level, we conclude that this situation may further exacerbate the misunderstanding of the basic tenets of evolution that university students have been repeatedly shown to demonstrate. We stress the role of the instructor in choosing textbooks that provide accurate information for students, as well as the responsibility they hold in providing a concise, accurate definition of evolution in social sciences courses.
The authors refer to an earlier study by Linhart (1997) who examined definitions of evolution in biology textbooks.
In our literature search, we were able to locate only one study that directly addressed the coverage of evolution in textbooks. Linhart (1997) focused on textbooks designed for one of the following six courses in the biological sciences: general biology (for majors and non-majors), evolution, genetics, paleontology, ecology, and systematics. He restricted his sample to 50 textbooks that had multiple editions and a sizable market share, and he located at least some of these textbooks using colleagues’ recommendations. He analyzed the content of the glossary entry for evolution in each textbook, as well as the material in any pages listed in an index entry for evolution, and compared these data against a definition of evolution he constructed after reviewing the literature:
Evolution is said to have occurred within a species, lineage, or population when measurable changes in various morphological, physiological, behavioral, or biochemical characteristics can be detected. These characteristics must be at least partly under genetic control. The genetic change(s) can occur as a
consequence of processes such as migration, mutation, genetic drift or bottleneck, natural selection, and nonrandom mating. Genetic changes within different populations of a species can lead to differences among lineages, and sometimes to the origin of new species...Evolution is not a synonym of natural selection. Nor is evolution a process that leads inevitably to increased or improved adaptation, or to greater reproductive success. Evolution does not imply a progressively closer fit between a population and its environment. Finally, evolution does not involve predictable or irrevocable changes from simple to more complex forms or toward some sort of perfection (Linhart 1997: 387).
While he found variation between the textbooks written for the six different courses in his sample, his findings indicated that the majority of all of the textbooks equated evolution with natural selection or adaptation and did not describe evolution in much detail. Linhart (1997) expressed much concern regarding the content of the definition of evolution in these textbooks, arguing that many students will have an inaccurate or incomplete view of evolution unless they are provided with additional material.
I agree with the problems that Linhart outlines and I agree that evolution needs to be defined as a process that involves genetic change and populations. It's very important that evolution should be defined in a way that allows for multiple mechanisms such as natural selection and random genetic drift.

Most of the biology textbooks I've read do an adequate job of defining evolution but I haven't covered as many textbooks as Linhart.

It's disappointing that biology textbooks and anthropology textbooks do such a poor job of defining—and presumably explaining—evolution. Is it any wonder that the general public is scientifically illiterate when we can't even get it right in the textbooks?


Linhart, Y. (1997) The teaching of evolution: we need to do better. Bioscience 47:385–91.

Evolution According to Niles Eldredge

 
I've read all of the books by Niles Eldredge. He's one of my favorite science authors [Good Science Writers: Niles Eldredge]. However, I've never really understood exactly what he means when he talks about evolution. He's not a molecular biologist or a geneticist but does he understand the basics of these disciplines? Does he think of evolution as a branch of population genetics or something else? Does he know about random genetic drift?

Some of these questions have been answered in an article that he co-authors with his son in the latest issue of Evolution: Education & Outreach. This is a journal dedicated to teaching evolution correctly. The article outlines a universal evolution curriculum for all grades from kindergarten to university [Lessons from EEO: Toward a Universal Evolutionary Curriculum].
Abstract We propose a human-centered evolutionary curriculum based around the three questions: Who am I? Where do I come from? How do I fit in? We base our curriculum on our experiences as an evolutionary biologist/ paleontologist (NE) and as a secondary level special education science teacher (GE)—and not least from our joint experience as co-editors-in-chief of this journal. Our proposed curriculum starts and ends with human biology and evolution, linking these themes with topics as diverse as the “tree of life” (systematics), anthropology, Charles Darwin, cultural evolution, ecology, developmental biology, molecular evolution/genetics, paleontology, and plate tectonics. The curriculum is “universal” as it is designed to be taught at all levels, K–16. The curriculum is flexible: “modules” may be expanded and contracted, reordered, or modified to fit specific grade level needs—and the requirements and interests of local curricula and teachers. We further propose that students utilize workbooks from online or printed sources to investigate the local answers to the general questions (e.g., “Who am I?”), while classroom instruction is focused on the larger scale issues outlined in the modules of our curriculum.
I don't like the idea of teaching evolution from a human-centered perspective. Our students are certainly used to thinking of biology only in terms of themselves, but isn't it our goal as educators to teach them that this is wrong?

It's the age-old question of whether the best way of teaching is to cater to student misconceptions or confront them.

A key part of any evolution curriculum is defining evolution. I prefer a scientific definition that allows us to distinguish evolution from other process that may look like evolution. The minimal definition is derived from population genetics and it allows us to recognize that different frequencies of blood groups in different human populations is evolution [What Is Evolution?].

Eldredge prefers a different definition in his evolutionary curriculum ...
What is “evolution?” Evolution is the testable, scientific idea that all species of life on Earth are descended from a common ancestor living billions of years ago since life first began on Earth. You can think of evolution as the history of life on Earth—or even as the fate of genetic information through time.

Module 3: What Is Evolution? How Do Humans Fit into the History of Life?

I've always taught that evolution is a process and that it's distinctly different from the history of life. It's like the difference between gravity and the history of our solar system. The formation of our solar system was a unique event that relied upon, and can be explained by, gravity and other general processes. Similarly, the history of life on Earth is a unique event. It can be explained by evolution and other processes but it's not the same as "evolution."

As far as I know, there are no evolutionary biology textbooks that define evolution as the history of life. The Eldredges are proposing a curriculum that's out of sync with most pedagogical approaches to evolution. Is this a better way to teach evolution? I don't think so.

Module 3 also covers the mechanisms of evolution. Adaptation and natural selection are mentioned but the authors go on to say that natural selection is not the only evolutionary process. The others are: speciation, punctuated equilibria, and mass extinctions.

I've always suspected that Niles Eldredge discounts random genetic drift as a legitimate process of evolution. This confirms my suspicion.

I'm very concerned about the content of this article and it's publication in a journal that's devoted to evolution education. If this is what the experts on evolution education are touting as the ideal curriculum then there are only two possible conclusions: (1) they aren't experts, or (2) I'm dead wrong about everything that I've been teaching.

I'm almost afraid to open up the comments on this posting for fear that (2) is the correct answer.



Wednesday, December 02, 2009

Comparison and Adaptation

 
As most of you know, Richard Dawkins is not a fan of the Spandrels paper by Gould and Lewontin [A Critique of the Adaptationist Programme]. A reader has alerted me to a comment that Richard Dawkins posted on Jerry Coyne's blog.

Dawkins said [I was there ...].
I was there (one of the speakers) at the London meeting of the Royal Society, where the Spandrels paper was first presented (by Gould; Lewontin didn’t come). Before Gould spoke, the talk by Clutton-Brock and Harvey substantially anticipated the Spandrels paper and undermined its central thesis. All of us were eager to hear how Gould would deal with Clutton-Brock and Harvey’s devastating critique of what they guessed (from previous publications) he would say. In the event, Gould totally ignored Clutton-Brock and Harvey, and gave his prepared paper, playing for horse laughs from the gallery, as if nothing had happened. It was the beginning of my disillusionment with Gould, whom I had previously respected. Please, if you read the Spandrels paper, look first at the Clutton-Brock and Harvey paper, in the same volume published by the Royal Society, 1979.
I had not heard of this paper by Clutton-Brock and Harvey and I'm not familiar with their work. Here's the reference and the abstract—it doesn't look to me like a devestating critique of Gould and Lewonton's paper.

Clutton-Brock, T.H. and Harvey, P.H. (1979) Comparison and Adaptation. Proc. R. Soc. Lond. B 205:547-565. [doi: 10.1098/rspb.1979.0084]
It has sometimes been suggested that the term adaptation should be reserved for differences with a known genetic basis. We argue that adaptation should be defined by its effects rather than by its causes as any difference between two phenotypic traits (or trait complexes) which increases the inclusive fitness of its carrier. This definition implies that some adaptations may arise by means other than natural selection. It is particularly important to bear this in mind when behavioural traits are considered. Critics of the 'adaptationist programme' have suggested that an important objection to many adaptive explanations is that they rely on ad-hoc arguments concerning the function of previously observed differences. We suggest that this is a less important problem (because evolutionary explanations generally claim some sort of generality and are therefore testable) than the difficulties arising from confounding variables. These are more widespread and more subtle than is generally appreciated. Not all differences between organisms are directly adapted to ecological variation. The form of particular traits usually constrains the form or value that other traits can take, presenting several obstacles to attempts to relate variation in morphological or behavioural characteristics directly to environmental differences. We describe some of the repercussions of differences in body size among vertebrates and ways in which these can be allowed for. In addition, a variety of evolutionary processes can produce non-adaptive differences between organisms. One way of distinguishing between these and adaptations is to investigate adaptive trends in phylogenetically different groups of species.


Vegetarian Nobel Laureates

I'm sure you've all been dying to know how many Nobel Laureates were vegetarians. Well, here's the answer. It was was on the back of a flyer received by one of the Skepchicks [An Appeal to Chickens and Other Logical Fallacies]. She's asking you to review the front part of the flyer to see how many logical fallacies you can identify.

It's interesting that only one Nobel Laureate won the Noble Prize for Physiology or Medicine. I guess the "logic" behind being a vegetarian isn't as obvious to biologists as it is to writers of fiction.




Name These Geneticists

This is a collection of "geneticists" from the latest issue of Genetics (November 2009). How many can you identify? The correct answers are here.





Tuesday, December 01, 2009

What Can't You Do in the House of Commons?

 
Almost anything goes in Ontario's House of Commons and debates can be rather lively. However, tradition (and House rules) state that you cannot accuse someone of lying. Here's what happens if you break that rule.



Ted Chudleigh is the Conservative MPP for Halton—a district that includes Oakville and Milton. He's ranting about a proposal to harmonize the GST and PST taxes.

Jennifer Smith lives in Milton and she's on the case. A little digging led her to this quotation from a speech by Ted Chudleigh in the House of Commons only 14 months ago [Ted Chudleigh on the HST: What a Difference a Year Makes].
Taxing businesses for their input costs is also a negative thing to do in an economy. It would be far better if we could find a way to harmonize the PST with the GST." (October 2, 2008 - Legislative Assembly Hansard)
Oh, dear. Is it possible that Mr. Chudleigh is a liar? Or is he just a hypocrite?


A Critique of the Adaptationist Programme

The Royal Society of Britain has opened access to a number of classic papers that have been published in Proceedings of the Royal Society. One of them is ...
Gould, S. J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proc. R. Soc. Lond. B 205:581-598. [doi: 10.1098/rspb.1979.0086]

Abstract: An adaptationist programme has dominated evolutionary thought in England and the United States during the past 40 years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an organism into unitary 'traits' and proposing an adaptive story for each considered separately. Trade-offs among competing selective demands exert the only brake upon perfection; non-optimality is thereby rendered as a result of adaptation as well. We criticize this approach and attempt to reassert a competing notion (long popular in continental Europe) that organisms must be analysed as integrated wholes, with Bauplane so constrained by phyletic heritage, pathways of development and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. We fault the adaptationist programme for its failure to distinguish current utility from reasons for origin (male tyrannosaurs may have used their diminutive front legs to titillate female partners, but this will not explain why they got so small); for its unwillingness to consider alternatives to adaptive stories; for its reliance upon plausibility alone as a criterion for accepting speculative tales; and for its failure to consider adequately such competing themes as random fixation of alleles, production of non-adaptive structures by developmental correlation with selected features (allometry, pleiotropy, material compensation, mechanically forced correlation), the separability of adaptation and selection, multiple adaptive peaks, and current utility as an epiphenomenon of non-adaptive structures. We support Darwin's own pluralistic approach to identifying the agents of evolutionary change.
If you haven't read this paper by now then download it and read it carefully. It's the most important paper to read if you are interested in evolution.

Jerry Coyne agrees, "Read the rest; it’s certainly one of the most important papers in modern evolutionary biology." [It’s a spandrel (sort of . . .)!].

He also says,
This paper is famous because the authors were famous, because it’s very well written, but most of all because it posed a direct attack on the “Panglossian paradigm”: the view that sociobiology wants to explain all traits, particularly human behaviors, as the direct products of selection. This paper has been the subject of furious discussion and at least one book. In my view, the paper made some valid points but went overboard in its criticism of the adaptationist program, which, after all, has produced lots of insights about evolution. I knew Gould, who was on my thesis committee, and it always seemed like pulling teeth to get him to admit that natural selection was even a relatively important force in evolution. If pressed, he would, but Gould always preferred (perhaps for political reasons) to emphasize the limitations of selection. Lewontin was not nearly so extreme.
It's true that the adaptationists have produced some valuable insights when the problem they are examining is actually an adaptation. However, this isn't as significant as you might imagine. Think of it like this. Everything looks like a nail when you have a large hammer in your hand. The fact that some things actually turn out to be nails is no excuse for blindly whacking at everything that sticks up.

Gould and Lewontin advocated a pluralist position where many different kinds of explanations should be considered. They note that Darwin himself was not committed to natural selection as the only possible mechanism of evolution.
Since Darwin has attained sainthood (if not divinity) among evolutionary biologists, and since all sides invoke God's allegiance, Darwin has often been depicted as a radical selectionist at heart who invoked other mechanisms only in retreat, and only as a result of his age's own lamented ignorance about the mechanisms of heredity. This view is false. Although Darwin regarded selection as the most important of evolutionary mechanisms (as do we), no argument from opponents angered him more than the common attempt to caricature and trivialize his theory by stating that it relied exclusively upon natural selection. In the last edition of the Origin, he wrote (1872, p. 395):

"As my conclusions have lately been much misrepresented, and it has been stated that I attribute the modification of species exclusively to natural selection, I may be permitted to remark that in the first edition of this work, and subsequently, I placed in a most conspicuous position-namely at the close of the introduction-the following words: "I am convinced that natural selection has been the main, but not the exclusive means of modification." This has been of no avail. Great is the power of steady misinterpretation."




[Hat Tip: Pharyngula: Oldie moldies that are pretty darned fascinating]

On Determining the Structure of a Protein


Michael Clarkson is a biotech postdoc who blogs at Discount Thoughts. One of his recent thoughts is Don't look for "the" structure. He is referring to the fact that the crystal structure of a protein doesn't actually represent the only structure that the protein can adopt.

The figure shown here illustrates one of the problems with referring to the structure of a protein. This is a representation of an NMR structure of bovine ribonuclease A. It shows that various parts of the protein exist in several different conformations. The actual protein structure is a composite of all these structures in equilibrium with each other.

These conformation could be considered "breathing" and you may think they're not important. However, there are many cases where the conformations of a protein are quite different. We are familiar with allostery, where the conformation of a protein changes when it's bound to a ligand, but the are also examples where two very different structures exist in equilibrium in the absence of ligand.

Read his blog posting and keep in mind that proteins are dynamic structures and not static rigid crystals.



FOX News Pie Chart

 
One of Ms. Sandwalk's ancestors was William Playfair who invented the pie chart [Bar Graphs, Pie Charts, and Darwin]. That was in 1786.

FOX News has heard of the concept but they don't quite seem to have mastered the technique.




[Hat Tip: GrrlScientist]

The Cutest of all Invertebrates


Catalogue of Organisms features these cute little animals on "Taxon of the Week."

If you follow the link on that blog to a more detailed overview of the taxon you get a bonus—a description of why Christopher Taylor didn't make it to the International Conference of Arachnology in Brazil.





Wednesday, November 25, 2009

Origin of Species at 150: Day Three

Tuesday November 24, 2009

08:00-09:00 Breakfast

09:00-11:00
Symposium V: Taxonomy
Chair: TBA

09:00-09:40
Mary Winsor (University of Toronto)
"Classification is a Census:" Huxley's Private Quarrel
with Darwin and its Public Consequences

09:40-10:20
Kevin Padian (University of California, Berkeley)
What is "Evidence for Evolution" to an Evolutionist?

10:20-11:00
Richard A. Richards (University of Alabama)
Context and Evidence in the History of Science

11:15-12:45
Session 4.i: Ancient Debates, Ancient Roots
Chair: Charissa Varma

11:15-11:45
P. William Hughes (Carleton University)
Aristotle contra Democritus: Anticipation of the Neutralist-Selectionist
Debate and a Haphazard Route Back to Darwin

11:45-12:15
Andreas Avgousti (Columbia University)
Pre-modern, Modern and Natural Understandings of Man:
Plato, Hobbes, and Evolutionary Theory

12:15-12:45
Robin Zebrowski (Beloit College)
The Evolution of Experience and the Experience of Evolution:
Revisiting Dewey's Analysis of the Influence of Darwin on Philosophy

11:15-12:45
Session 4.ii: The Devil’s Chaplain
Chair: David Smillie

11:15-11:45
Peter Sachs Collopy (University of Pennsylvania)
Naturalizing Calvinism: The Darwinism and Anti-Evolutionism
of George Frederick Wright

11:45-12:15
Stephen D. Snobelen (University of King’s College)
Theological Themes in Darwin's Origin of Species (1859)

12:15-12:45
Christopher diCarlo (University of Ontario Institute of Technology)
The Zing of Perceived Control: Memetic Equilibrium
and the Evolution of Religion

11:15-12:45
Session 4.iii: Laws of Evolutionary Economics
Chair: Mike Thicke

11:15-11:45
André Ariew (University of Missouri-Columbia)
Darwin’s Invisible Hand?

11:45-12:15
Eugene Earnshaw-Whyte (University of Toronto)
Breaking the Bonds of Biology: Natural Selection
in Nelson and Winter's Evolutionary Economics

12:15-12:45
Chris Haufe (Virginia Polytechnic Institute and State University)
Darwin’s “Laws”

12:45-13:30 Lunch Break

13:40-15:40
Symposium VI: Evolution and Development
Chair: Jean-Bernard Caron

13:40-14:20
Manfred Laubichler (Arizona State University)
From Boveri to Davidson and Back

14:20-15:00
Jane Maienschein (Arizona State University)
From Epigenesis to Epigenetics and Back

15:00-15:40
Michael Dietrich (Dartmouth College)
From Goldschmidt to Gould and Back

15:50-17:20 Session 5.i: It's All in the Mind
Chair: Eugene Earnshaw-Whyte

15:50-16:20
Byron Kaldis (The Hellenic Open University)
Species-Qua-Individuals and the Modularity of the Mind: The Saving Grace for Humans

16:20-16:50
Alain Ducharme & Sheldon Chow (The University of Western Ontario
Keeping Darwin in Mind

16:50-17:20
Steve DiPaola (Simon Fraser University)
Darwin, Creativity, and Evoluionary Programming

15:50-17:20
Session 5.ii: International Receptions
Chair: Ari Gross

15:50-16:20
Paranbes Nath (Calcutta University)
Darwin and India

16:20-16:50
Alex Levine & Adriana Nova (University of South Florida)
The Fate of Darwinian Analogies in Latin America:
The Reception of Darwinism in 19th Century Argentina

16:50-17:20
Nolan Heie (Queen’s University)
Albert Kalthoff, Entwicklung and the "World View of Modern Man"

15:50-16:50
Session 5.iii: Fitness
Chair: Ellie Louson

15:50-16:20
Marshall Abrams (University of Alabama at Birmingham)
Individuals have no Fitnesses if Fitness Differences Cause Evolution

16:20-16:50
Kent A. Peacock (University of Lethbridge)
The Three Faces of Fitness

15:50-16:50
Session 5.iv: Language and Logic
Chair: S.J. Patterson

15:50-16:20
Alexander G. Yushchenko (Kharkov State Polytechnic University)
Logics & Ethics of Evolution from the Point of View of Evolutionary Theology

16:20-16:50
Justin Humphreys (New School for Social Research)
Darwin on Language

17:20-18:20
Keynote Address: Brian K. Hall (Dalhousie University)
Charles Darwin, Evolutionary Embryology and Evo-Devo


18:20-19:00 Break

19:00-19:45
Keynote Address: Spencer Barrett (University of Toronto)
Charles Darwin and Current Perspectives on the Evolution and Function of Plant Sexual Diversity


Origin of Species at 150: Day Two

Monday November 23, 2009

09:00-11:00Symposium III: Theistic Evolution
Chair: Michael Bourgeois

09:00-09:40
Bernard Lightman (York University)
Christian Evolutionists in the U.S., 1860-1900

09:40-10:20
Michael Ruse (Florida State University)
Are Science and Religion Compatible and If So, Why?

10:20-11:00
Denis O. Lamoureux (University of Alberta)
Darwinian Theological Insights: Toward an Intellectually Fulfilled Theism

11:15-12:45
Session 2.i: Acceptances and Denials
Chair: David Smillie

11:15-11:45
Fermin Fulda (University of Toronto)
Against Fodor Against Darwinism

11:45-12:15
Stefaan Blanke (Ghent University)
"A million guesses strung together:" Creationist Denial of the Science Behind Evolutionary Theory

12:15-12:45
Daniel A. Newman (University of Toronto)
The Rhetoric of Probability: How Darwin Overcame the Argument from Design

11:15-12:45
Session 2.ii: Historical Receptions
Chair: Jaipreet Virdi

11:15-11:45
John Court (University of Toronto)
Darwinian Evolution's First Fifty Years of Impact
on Botany at the University of Toronto. 1859 to 1909

11:45-12:15
David M. Steffes (Arizona State University)
Population Ecology and Evolution: Darwin's Origin and the
Modern Synthesis of the 1940s and 50s

12:15-12:45
Kevin Pent (York University)
Julian Huxley's 'Apogee of Species': Darwin's 'Man' Comes of Age

11:15-12:45
Session 2.iii: A Brave New Darwin
Chair: Chris Belanger

11:15-11:45
Peter Fedor (Comenius University)
Advances in Artificial Intelligence in Species Identification

11:45-12:15
Wybo Houkes (Edinhoven University of Technology)
Hypothesis Testing in Artefact Evolution

12:15-12:45
Laura Landen (Queen's University)
Natural Selection, The Intentional Stance, and Mirror Neuron Research

12:45-13:30 Lunch Break

13:40-15:40
Symposium IV: Species
Chair: Ronald de Sousa

13:40-1420
John Beatty (University of British Columbia)
Darwin on Species

14:20-15:00
Kevin de Queiroz (Natural Museum of National History; Smithsonian)
Charles Darwin and the Evolution of the Species Concept

15:00-15:40
Marc Ereshefsky (University of Calgary)
Mystery of Mysteries: Darwin and the Species Problem

15:45-16:45
Keynote Address: Michael Ruse (Florida State University)
Is Darwinism Past its “Sell-By” Date?

16:45-18:15
Session 3.i: Naturalism
Chair: Curtis Forbes

16:45-17:15
Jason Marsh (University of Western Ontario)
Darwinism and Divine Hiddenness

17:15-17:45
Khaldoun Sweis (Olive-Harvey College)
Philosophical Paradoxs of Darwin Evolutionary Naturalism

17:45-18:15
Maarten Boudry (Ghent University)
Methodological Naturalism as an Intrinsic Property of Science:
A Grist to the Mill of Intelligent Design Theory

16:45-18:15
Session 3.ii: Reconstructing Darwinism
Chair: Erich Weidenhammer

16:45-17:15
Peter Gildenhuys (Lafayette College)
Putting the Struggle for Existence to Work

17:15-17:45
Katharine Browne (University of Toronto)
A Darwinian theory of Games

17:45-18:15
Sarah Winter (University of Connecticut Storrs)
Species as Value: Biosemiotics in Darwin's Origin and Saussurian Linguistics

16:45-18:15
Session 3.iii: Applying Darwinism
Chair: Mike Stuart

16:45-17:15
Marion Blute (University of Toronto at Mississauga)
Darwinism in the Social Sciences Today

17:15-17:45
Howard M. Huynh (Acadia University)
In the Footsteps of Darwin: The Value of Scientific Collecting in
Biodiversity Research and Conservation

17:45-18:15
Joel Velasco (Stanford University)
The Tree of Life: From Darwin to Today

18:15-19:15
Keynote Address: Evelyn Fox Keller
(Massachusetts Institute of Technology)
Darwin as the Newton of a Blade of Grass


Origin of Species at 150: Day One

The conference on Origin of Species at 150 was sponsored by The Institute for the History & Philosophy of Science & Technology, The Department of Ecology and Evolutionary Biology, and The Department of Philosophy at the University of Toronto.

Here's the schedule for the first day.

Sunday November 22, 2009

08:00-09:00 Breakfast

09:00-10:00
Keynote Address: Alison Pearn (Darwin Correspondence Project)
Cast of Thousands: Charles Darwin's Life in Letters

10:00-12:00
Symposium I: Gender, Evolution, and Sexual Selection
Chair: Joan Steigerwald

10:00-10:40
Lisa Lloyd (Indiana University)
Bias in Evolutionary Explanations of the Female Orgasm

10:40-11:20
Marlene Zuk (University of California, Riverside)
Sex and the Scala Naturae

11:20-12:00
Erika Milam (University of Maryland, College Park)
Negotiating Choice: Animal Minds and Human Instincts
in the History of Sexual Selection

12:00-12:30 Lunch Break

12:45-13:45
Session 1.i: Reassessing Themes and Sources
Chair: Michael Cournoyea

12:45-13:15
Scott Sinclair (St. Louis University)
Three American Philosophers’ Response to Darwin

13:15-13:45
Fred Wilson (University of Toronto)
Replacing an Old Paradigm: Intelligent Design and Natural Selection; Hume, Mill, and Darwin

12:45-14:15
Session 1.ii: Social Perceptions
Chair: Jaipreet Virdi

12:45-13:15
Eleanor Louson (University of Toronto)
Nature, Projected: Evolutionary Theory in Wildlife Documentaries

13:15-13:45
David Smillie (University of Toronto)
Evolution and Popular Culture: Darwin on the Box

13:45-14:15
Ian Hesketh (Queen’s University)
Of Apes and Ancestors: Myth and the Cultural Memory of the Oxford Debate of 1860

12:45-14:15
Session 1.iii: Species and Sexuality
Chair: Sebastián Gil-Riaño

12:45-13:15
Masoud Hassanpour Golakani (Macquarie University)
The Spiral Valve Intestine of the Australian Lungfish, a Primitive Characteristic

13:15-13:45
Eugene S. Morton (Hemlock Hill Field Station)
Sexual Conflict and Brood Desertion in Blue-Headed Vireos: How Females Won

13:45-14:15
Jerome Goldsten (San Francisco Clinical Research Center)
The Neurobiology of Sexual Orientation: A Tribute to Charles Darwin

14:30-16:30
Symposium II: Ecology
Chair: Richard Landon
(Coffee/Tea Service Provided)

14:30-15:10
Joan Roughgarden (Stanford University)
Darwin and Ecology

15:10-15:50
Gene Cittadino (New York University)
Reflections on Darwin and Ecology: The History of a Tenuous Relationship

15:50-16:30
Gregory Cooper (Washington and Lee University)
The Darwinian Character of Evolutionary Ecology

16:40-17:40
Keynote Address: James Moore (University of Cambridge)
Darwin’s Progress and the Problem of Slavery

18:00-19:30
Special Presentation
Re: Design: A Dramatisation of the Correspondence between Charles Darwin and Asa Gray (Produced by the Menagerie Theatre Company)


150 Years Ago


On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life was published 150 years ago on November 24, 1859. The publisher, John Murray, had already taken orders for 1,500 copies so the initial printing of 1,250 copies was sold out immediately.
Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate study and dispassionate judgment of which I am capable, that the view which most naturalists entertain, and which I formerly entertained—namely, that each species is independently created—is erroneous. I am fully convinced that species are not immutable; but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are descendants of that species. Furthermore, I am convinced that Natural Selection has been the main but not the exclusive means of modification.



Tuesday, November 17, 2009

Monday's Molecule #144: Winner?

 
The creature is the spirochete, Treponema pallidum. This bacteria causes syphilis. The Nobel Laureate is Julius Wagner-Jauregg who discovered a way to treat the lethal form of dementia that develops in the late stages of the disease.

There were only three people who got the right answer. All of them were ineligible. There is no winner this week!




This is another one of those times when there's no "molecule" that provides a clue to a Nobel Laureate.

Your task is to identify this creature and the reason why it's important. There are three Nobel Laureates who might be associated with the creature but two of them have already been covered. The last name of the this week's Nobel Laureate does not begin with the letters "E" or "D". Who is it?

The first person to identify the "molecule" and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Alex Ling of the University of Toronto, Bill Chaney of the University of Nebraska, Linda Zhang, a former student at the University of Toronto who will soon be on her way to graduate school at the University of Hong Kong and Kirill Zaslavsky, a Neuroscience student at the University of Toronto.

Dima, and Bill have agreed to donate their free lunch to an undergraduate. Consequently, I have two extra free lunches for deserving undergraduates. I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

THEME:

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

Correct responses will be posted tomorrow.

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



Should Intelligent Design Creationism Be Taught in Schools?

 
PZ Myers and someone named Jerry Bergman debated the question; "Should Intelligent Design be Taught in The Schools?." Bergman said "yes" and PZ said "no."

You can read summaries of the debate on Greg Laden's Blog [Bergman vs. Myers Debate: Should Intelligent Design be Taught in The Schools?] and on Kittywhumpus [I thought it went really well, until he brought up Hitler]. PZ has posted a summary on Pharyngula [That Bergman-Myers debate].

By all accounts it was a rout. PZ won the day for keeping Intelligent Design Creationism out of the classroom. It was like shooting fish in a barrel.

I'd like to debate PZ on this topic. I think Intelligent Design Creationism has to be brought up in the classroom. It's the major misconception that students have and to ignore it is stupid. You have to address the issues that students are confused about or you aren't educating. It's one thing to say that Intelligent Design Creationism isn't science when you are outside of the classroom but unless the students hear it in the classroom you are wasting your time.

We are never going to make progress against scientific illiteracy unless we recognize the elephant in the room and deal with it. Study after study has shown that the misconceptions of students aren't changed when you just present them with facts. They will readily incorporate those facts into their distorted worldview and that's exactly what happens when we teach evolution to creationists.

They need to be shown why their worldview is wrong and this means bringing up in class all the problems with Intelligent Design Creationism. Like it or not, that means teaching Intelligent Design Creationism in the science classroom even if the goal is to refute it.

Astrology is a good analogy. One way to teach critical thinking is to have a lesson on astrology where you explain what's wrong with it and why it doesn't work. You don't ban it from the classroom because it's bad science—you bring it into the classroom because it's bad science and students need to hear why.

If you don't do that, many students will continue to think that astrology is real and before you know it you've created another generation of citizens who don't understand science.

The thing that Intelligent Design Creationists should fear the most is that we actually will confront it in the classroom and expose it for the nonsense it is. They're safe as long as we tip-toe around it. That leaves them free to teach their nonsense in Sunday school without fear of ever being contradicted.

(I'm well aware of the Constitutional arguments in America. If someone like PZ wants to argue that Intelligent Design Creationism should be taught in US schools but the Constitution forbids it, then I'm prepared to agree with him. The debate I want is whether it should be taught in schools that don't have such a silly law. Should it be taught in Canadian schools? I say yes.)


Genetic Load, Neutral Theory, and Junk DNA

The average human newborn has about 130 new mutations that were not found in either parent [Mutation Rates]. These mutations accumulate as a natural result of errors in DNA replication between the time that the zygote is first formed and the time that the sperm and egg cells are produced for the next generation.

A species cannot afford to accumulate deleterious mutations in the genomes of its individuals. Eventually the number of "bad" mutations will reach a level where most genes have multiple "bad" alleles and it becomes impossible to produce offspring.

This phenomenon is referred to as genetic load. It means that species can only survive if the genetic load is below some minimum value. A good rule of thumb is that there can't be more than 0.1 deleterious mutations per individual per generation but in actual populations this value can be a bit higher. [UPDATE: This should be one (1) deleterious mutation per generation.]

How do you reconcile this with the known mutation rate in humans? If there are, on average, 130 mutations per individual per generation, then hardly any of these can be deleterious if the species is to survive.

This is one of the arguments in favor of Neutral Theory. Most mutations are neither deleterious nor beneficial. They are simply neutral with respect to natural selection.

Let's think about a typical protein-encoding gene.1 The coding region is about 2,000 base pairs in length and consist of 666 codons. More than half these codons can be mutated to a new codon encoding a different amino acid without severe effects on the function of the protein.2 These are called amino acid substitutions. Of the "essential" codons, many can tolerate mutations that create synonymous codons. Putting these facts together suggests that only about 20% of mutations to protein encoding regions are detrimental. The rest are effectively neutral.

This partially explains why we can tolerate 130 mutations per individual per generation. If only 20% were detrimental then the genetic load is reduced to about 26 mutations per generation.

That's still unacceptably high. It leads to the idea that a large percentage of our genome must be unaffected by mutations. In other words, genes represent only a small percentage of our genome and mutations can freely accumulate in the rest without detrimental consequences.

In order to bring the genetic load down to acceptable levels, the number of genes has to be less than 40,000 according to the arguments made in the 1960s. We now know that we have only 20,000 genes. Most of them encode proteins and the coding regions of those genes make up about 40,000,000 bp or about 1.3% of our genome [Junk in Your Genome: Protein-Encoding Genes].

Recall that only 20% of mutations in coding regions are likely to be detrimental. That means that the effective target size for detrimental mutations is about 20% x 1.3% = 0.26% of our genome. Out of 130 mutations, only 0.3 per individual per generation will be detrimental.3

Since we are diploid organisms, the 130 mutations in the zygote are spread out over two copies of our genome but almost all of them will be in the chromosomes coming from the father. Every zygote inherits one complete set of chromosomes with hardly any mutations while the other set has less than one detrimental mutation.

Because a large percentage of gene mutations are neutral, and because most of our genome is junk, we can easily tolerate 130 mutations per individual per generation without going extinct.

Creationists will never understand this because: (a) they believe that modern evolutionary theory is all about "Darwinism" and Darwinian evolution doesn't recognize neutral mutations and random genetic drift, and (b) they can't admit to junk DNA because that's the opposite of what intelligent design would look like.


1. Similar arguments apply to genes that make functional RNAs and not proteins.

2. Over the course of several billion years of evolution it is unusual to see more than 30% sequence similarity between homologous genes. I realize that this is a somewhat circular argument but it's still a good one.

3. There are lots of other regions of the genome where mutations can be detrimental. I don't mean to imply that only protein encoding regions can be affected by mutations. Collectively, these other regions don't make up more than a few percent of our genome and they can tolerate many mutations [Genomes & Junk DNA]

Monday, November 16, 2009

Genetic Load

 
If the average rate of deleterious mutations is about 1 per individual per generation then the species can't survive. It means that most offspring will carry a mutation. This is an intolerable genetic load for a species.

In fact it's worse than that. Simple calculations suggest than even a rate of 0.1 deleterious mutations per individual will spell doom for the species. This is a well-known limitation and it was widely used in developing several key components of evolutionary theory and in explaining the size and composition of eukaryotic genomes.

The average total mutation rate in humans is about 130 mutations per genome per generation. Scordova concludes that this proves Intelligent Design Creationism [Nachman’s Paradox Defeats Darwinism and Dawkins’ Weasel]. It does no such thing. It proves once again that a little knowledge is a dangerous thing—especially in the mind of an IDiot.


Monday's Molecule #144

 
This is another one of those times when there's no "molecule" that provides a clue to a Nobel Laureate.

Your task is to identify this creature and the reason why it's important. There are three Nobel Laureates who might be associated with the creature but two of them have already been covered. The last name of the this week's Nobel Laureate does not begin with the letters "E" or "D". Who is it?

The first person to identify the "molecule" and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Alex Ling of the University of Toronto, Bill Chaney of the University of Nebraska, Linda Zhang, a former student at the University of Toronto who will soon be on her way to graduate school at the University of Hong Kong and Kirill Zaslavsky, a Neuroscience student at the University of Toronto.

Dima, and Bill have agreed to donate their free lunch to an undergraduate. Consequently, I have two extra free lunches for deserving undergraduates. I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

THEME:

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

Correct responses will be posted tomorrow.

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


The Hat Gene

 
Humans have always had a urge to cover their heads with various forms of headgear. There must be a hat gene in our genomes and it probably evolved in the human lineage after it split from chimpanzees. Chimps don't wear hats.

If you believe this then you've probably fallen for the idea that FOXP2 is a gene for language and that there's a gene for God/religion. See The hunt for the Hat Gene for a good discussion of where you're going wrong.


Bill Maher on Vaccination

 
Bill Maher has attempted to clarify his position on vaccination [Vaccination: A Conversation Worth Having]. His blog is a lot like his TV show. It's a confusing, rambling, attempt at justifying an indefensible position using (attempted) humor, sarcasm and anecdote as a substitute for rationalism.

The question is whether vaccinations are good or bad. It's a strictly scientific question with a well-known scientific answer.

As far as I can tell, these are Bill Maher's main reasons for opposing vaccinations.
  1. You wouldn't need to have vaccinations if you had a healthy immune system to begin with. (And I'm sure he has some opinions on what you should eat to ensure a healthy immune system.)

  2. The success of vaccinations has been exaggerated by the medical community but he's not accusing anyone of a conspiracy.

  3. Vaccines have bad things in them and they may be harmful to healthy people.

  4. Vaccinations are supported by drug companies and you need to be skeptical about anything that's supported by large for-profit corporations.
I'm just trying to represent an under-reported medical point of view in this country, I'm not telling a specific pregnant lady what to do. With unlimited air time, I would have, for example, added to my discussion with Dr. Bill Frist on October 2 that, yes, any flu or health challenge can be dangerous when you're pregnant, and if your immune system is already compromised by, for example, eating a typical American diet, then a flu shot can make sense. But someone needs to be representing the point of view that says the preferred way to handle flus is to have a strong immune system to begin with, and getting lots of vaccines might not be the best way to accomplish that over the long haul.

Now, sometimes its OK to fuck with nature -- I believe "intelligent design" is often anything but intelligent; that "God's perfect universe" is actually full of fuck ups and design flaws, like cleft lips and Down Syndrome -- so correcting nature is sometimes the right thing to do. And then, sometimes its not. For me, the flu shot is in the "not" category.

In addition, my audience is bright, they wouldn't refuse a flu shot because they heard me talk about it, but if they looked into the subject a little more, how is that a bad thing? If they went to the CDC Web site and saw what's in the vaccine -- the formaldehyde, the insect repellent, the mercury -- shouldn't they at least get to have the information for themselves?
Instead of setting up this straw man of me not understanding germs or viruses, let's have a real debate about how much we should use vaccines and antibiotics. Of course it's good that we have them in our arsenal, but isn't the real skeptic the one who asks if these powerful but toxic methods do harm to what actually is a a very good defensive system, the one you were born with?

Also, I have never said there was a medical conspiracy. In fact, when Howard Dean asked me that, my response was "I wouldn't call it a conspiracy." Any more than there's a conspiracy for the Pentagon budget to be obscenely bloated and operated largely for the corporate welfare of defense contractors. If these are conspiracies, they're mostly legal ones that happen in plain sight. (Good time here to plug the hostess' book, Pigs At the Trough, it's all in there!) I have, in fact, used the phrase "medical-pharmaceutical-food industry" complex in comparing it to Eisenhower's famous depiction of a "military-industrial complex."
I believe in science and I believe in studies to determine the truth. I also believe Senator Ron Wyden of Oregon was correct when he said recently on MSNBC: "If you've got a checkbook in this town, you can get just about any set of facts you want." So if I remind you of a conspiracy theorist, you sometimes remind me of Britney Spears when she said "we should just do whatever the president says to do, and not ask questions and just support him." The medical community can be brutal on dissent, which would hold more weight if I thought this was a terribly healthy country, which it isn't. Health care is one sixth of our economy, and we spend way more on it than any other nation. The elephant in the room of the health care debate is that we are going to have a high health care bill every year no matter what law they pass because we're sick -- we need a lot of drugs and services.

Am I a conspiracy theorist if I suggest that since the network's nightly news broadcasts are sponsored almost entirely by prescription drug ads, that you might have to hold your breath a long time before you hear the alternative point of view to using pharmaceuticals to cure all our ailments?

Is it conspiracy theory to believe that American medicine too much treats symptoms and not root causes of disease? I always ask my friends when they go to the doctor for something, "Did your doctor ask you what you eat?" The answer is almost always 'no,' and a lot can be cured with diet and a healthier lifestyle. (And a lot can't. I also understand the role of genetics and generations of artificial selection). But Americans don't want to hear that, so doctors don't push it. It's easier and more profitable to write a prescription for Lipitor. They're not bad people, and at the end of the day, you can't make someone eat right. I like and respect all the M.D.s I've had over the years, and for the record, I have a naturopath doctor and I have a Western doctor. I would make an analogy to Republicans and Democrats: in both politics and health, I don't commit to either party because I'm on the side of the truth, whoever has it. In both cases, I'm an Independent.
This last quotation is the most revealing of all. Bill Maher listens to his naturopath doctor and feels competent to distinguish the truth when his quack doctor disagrees with evidence-based medicine (e.g. "Western" medicine).

In addition to falling for quackery, Bill Maher is making an elementary error in logic. Yes, it's true there are problems with modern medicine and the influence of drug companies, especially in the USA. But that's not to be confused with a rational discussion about the value of vaccinations. The scientific judgment about whether vaccinations are good or bad is independent of any opinions you might have about conspiracies, imagined or otherwise. The real question isn't about drug companies, it's whether you accept science or quackery.

The scientific evaluation of vaccination takes place in many countries throughout the world, including those with socialized medicine. They have all concluded that vaccinations are a proven technology that prevents disease.


[Hat Tip and Thank-you to esaul]

Friday, November 13, 2009

timmyme

 
Ms Sandwalk just got an iPhone. She's thrilled by all the things it can do and I'm happy for her. However, most of the things an iPhone does are not important to me. I already have a camera and I'm not interested in iTunes. My Samsung flip phone works just fine, thank-you very much.

Up until last week, getting an iPhone was the last thing on my mind. It was a waste of money as far as I was concerned.

Then I learned about a wonderful app called timmyme [Tim Hortons coffee locator comes to the iPhone]. This little program allows you to find the nearest Tim Hortons no matter where you are in the civilized world.

I have to have an iPhone. To hell with the cost.


Where do we come from? Where are we going?

 
This is the runner-up in Discover magazine's "Evolution in Two Minutes" contest. It was selected by PZ Myers [The Winner: Evolution in Two Minutes].

I seem to be one of the few people who think this is a horrible way to teach the public about evolution. I guess that's why I'm a curmudgeon.

I think we can do much better. I think we should do better.




The Theory of Evolution

 
Here's one of the submissions to Discovery Magazine's "Evolution in Two Minutes" contest. It's the one chosen by viewers [The Winner: Evolution in Two Minutes].

I wish we could stop talking about "The" theory of evolution. There's really no such thing and the term conjurs up thoughts of evolution being only a theory. A better term is evolutionary theory.1 A short description of modern evolutionary theory would include population genetics, the major mechanisms of evolution (natural selection and random genetic drift), and the latest theories of speciation. More sophisticated versions of evolutionary theory might include punctuated equilibria, lateral gene transfer, symbiosis, neutral theory, group selection, kin selection, species sorting and molecular phylogeny.

But before you can talk about any of these things you have to define evolution so that we all know what we're talking about. The consensus scientific definition of evolution—the fact, not the theory—is: "Evolution is a process that results in heritable changes in a population spread over many generations" or some related variation of that statement [What Is Evolution?].

The makers of these videos are free to select a definition that is not the consensus scientific definition but why would they do that? Is it a good idea to use another definition to teach the general public about evolution? What purpose does that serve?




It's OK to talk about The theory of natural selection or The theory of punctuated equilbria.

Thursday, November 12, 2009

Three Options

 
Here's a multiple choice question from Barry Arrington on Uncommon Descent [Is a Modern Myth of the Metals the Answer?].

He's concerned about the "fact" that "Darwinism" leads to immorality.
There are three and only three options.

1. We can continue to fill our children’s heads with standard Darwinian theory (which Dennett rightly calls “universal acid”), understanding that at least some of them are going to put two and two together and realize that the acid has eaten through all ethical principles – and act accordingly.

2. We can try to come up with a secular noble lie. “OK kids. You might have noticed that one of the implications of what I just taught you is that your lives are ultimately meaningless and all morals are arbitrary, but you must never act as if that is true because [fill in the noble lie of your choice, such as “morality is firmly grounded on societal norms or our ability to empathize with others”].

3. We can teach our children the truth – that the universe reveals a wondrous ordered complexity that can only be accounted for by the existence of a super-intelligence acting purposefully. And one of the implications of that conclusion is that God exists, and, reasoning further, He has established an objective system of morality that binds us all, and therefore the moral imperatives you feel so strongly are not just an epiphenomenon of the electro-chemical states of your brain.

Looking around I see that for the last several decades we have tried options one and two, and we have gotten what we have gotten. I vote to give option three a run.
Tough choice. I guess I'll opt for #2 although I don't think that telling children the truth about where morality comes from is a lie.

And correct me if I'm wrong, but haven't we already tried #3? It didn't work out very well, did it?


Wednesday, November 11, 2009

Nobel Laureate: Johannes Fibiger

 

The Nobel Prize in Physiology or Medicine 1926

"for his discovery of the Spiroptera carcinoma"


Johannes Andreas Grib Fibiger (1867 - 1928) won the Nobel Prize for "proving" that gastric tumors could be caused by a nematode, Spiroptera carcinoma (now called Gongylonema neoplasticum). Unfortunately, later work showed that the nematode was not the cause of cancer, although it may contribute to a worsening of the symptoms.

This is one of the worst mistakes that the Nobel Prize committee has ever made in awarding a science prize. How did it happen?

Fiberger is rightly celebrated for his many important contributions to experimental medicine and for pioneering a modern version of clinical trials. When he learned of the work of Katsusaburo Yamagiwa, who induced cancer in rabbits by treating their skin with coal tar, he promoted Yamagiwa's results in Europe. Many people believe that Yamagiwa should have received the Nobel Prize.

Here is the entire Presentation Speech. The work sounds like something that deserves a Nobel Prize, doesn't it?
THEME:
Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

Few diseases have the power of inspiring fear to the same degree as cancer. However, who would be surprised at that? How many times is this affliction not synonymous with a long, painful and grievous illness, how many times is it not equivalent to incurable suffering? It is therefore natural that we should strive to throw light upon its nature; but the road to this discovery is both long and difficult. Cancer always, in fact, presents the investigator with a number of obscure and unsolved problems. Thus the cause of cancer has for a long time baffled the penetrating studies of the most tireless research workers. Fibiger was the first of these to succeed in lifting with a sure hand a corner of the veil which hid from us the etiology of the disease; the first also, to enable us to replace with precise and demonstrable theories the hypotheses with which we had had to content ourselves.

For example, it had been thought for a long time that a causal connection existed between cancer and a prolonged irritation of some sort, mechanical, thermal, chemical, radiant, etc.; this supposition was supported by the incidence, sometimes verified, of cancer as an occupational disease. Cancer occurring in radiologists, chimney sweepers, workers in the manufacture of chemical products, establish so many examples of cancerous infection that one might believe they were provoked by radioactive or chemical irritation. However, each time experiment was resorted to in an attempt to provoke cancer in animals by irritants of this nature, it failed, and the animals refused to contract the disease.

Others, with all the more reason, sought to find in cancer the work of microparasites, for true neoplastic epizootics were thought sometimes to have been established in the animal world. But research into the pathogenic agent, the «cancer bacillus», and the experiments attempting to inoculate the disease had remained fruitless. Cancer has been equally attributed to other parasites, and notably to the worm. But, just as the attempts to provoke cancer, whether by inoculation or by irritation remained unproductive, in the same way it proved impossible to demonstrate experimentally that the disease was attributable to worms. These authorities who continued to support this thesis were, moreover, frequently considered to be fantasts. Because of the failure of attempts to establish, by experiment, the accuracy of any theory, there was no clear idea concerning the cause of cancer, and such in general was the position of this question. Then it was, in 1913, that Fibiger discovered that cancer could be produced experimentally.

It is of the greatest interest to follow Fibiger along the laborious path of his research. The first idea of his discovery, which was to make his name celebrated the world over came to him in 1907: he recorded in three mice in his laboratory (originating from Dorpat), a tumour, unknown until that time in the stomach; in the centre of the neoplasm he noted the presence of a worm belonging to the family of Spiroptera.

Fibiger did not succeed at first in proving a relationship existing between the formation of the neoplasm and the worm. The attempts to provoke a cancer in healthy mice by making them ingest neoplastic tissue from diseased mice, and containing worms or eggs, failed completely. Fibiger then had the idea that perhaps this worm, like many others, underwent part of its evolution from an egg to an adult individual in another animal, which served as an intermediate host. After numerous and vain attempts to find again mice attacked by the tumours seen in 1907 - he unsuccessfully examined more than 1000 animals - Fibiger eventually discovered in a sugar refinery in Copenhagen mice who exhibited in considerable numbers the type of tumour he was seeking; in these tumours he found once again the worm he had observed in 1907. The factory was at this time infested with cockroaches, and Fibiger was then able to establish that the worm in its evolution used these cockroaches as intermediate hosts. The cockroaches ingested the excreta of the mice, and with them the eggs of the worm. These developed in the alimentary tract of the cockroaches into larvae, which, like the trichina, were distributed into the muscles of the insects where they become encapsulated. The cockroaches were in their turn eaten by the mice and in the stomach the larvae transformed into the adult form.

By feeding healthy mice with cockroaches containing the larvae of the spiroptera, Fibiger succeeded in producing cancerous growths in the stomachs of a large number of animals. It was therefore possible, for the first time, to change by experiment normal cells into cells having all the terrible properties of cancer. It was thus shown authoritatively not that cancer is always caused by a worm, but that it can be provoked by an external stimulus. For this reason alone the discovery was of incalculable importance.

But Fibiger's discovery had a still greater significance. The possibility of experimentally producing cancer gave to the particular research into this illness an invaluable and badly needed method, lacking until this time, allowing the elucidation of some of the obscure points in the problem of cancer. Fibiger's discovery also gave remarkable impetus to research. Whereas research had, in many respects, entered upon a period of stagnation, Fibiger's discovery marked the beginning of a new era, of a new epoch in the history of cancer, to which the fruitful research made by him gave fresh vigour. From his discoveries we have continued to march forward and have gained valuable ideas as to the nature of this illness.

It is thus that Fibiger has been and will remain a pioneer in the difficult field of cancer research. «To my mind», says the famous English expert on cancer, Archibald Leitch, to name only one of the numerous critical commentators on Fibiger's research, «Fibiger's work has been the greatest contribution to experimental medicine in our generation. He has built into the growing structure of truth something outstanding, something immortal, quod non imber edax possit diruere.» It is for this immortal research work that Fibiger is today awarded the Nobel Prize for Medicine for 1926.


The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.