The Trouble With Science

The purpose of a grant, after all, is to facilitate research. But the rationale has become curiously inverted: now the purpose of one’s research seems to be to get a grant ...

Jerry CoyneThis is a post for scientists and those who would be scientists.

Wake up!!! Science is in trouble! If you don't believe me, read How science goes wrong and Trouble at the lab. Both articles were published in the October 19th edition of The Economist.

It likely that you've heard all this before but the magnitude of the problem just hasn't registered with you. Well, it's time to start paying attention.

Jerry Coyne has written an excellent commentary on these articles [Science is in bad shape]. Read it. Now.

These articles and commentaries focus on research but let's not forget teaching. There are far too many science teachers—expecially at the university level—who are doing a terrible job of teaching evolution and biochemistry. (And probably lots of other subjects but those are the ones I'm familiar with.)

We have to do something about this.

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Jukes to Crick on Junk DNA

Dan Graur discovered that the term "junk DNA" was commonly used in the 1960's—long before Susumu Ohno used "junk" in the title of his 1972 paper. This makes a lot of sense. Apparently the term was quite commonly used in Cambridge by people like Francis Crick and Sydney Brenner. (Perhaps you've heard of them?)

Graur found a 1963 paper that refers to "junk" DNA. This is the earliest known refencee to junk in the scientific literature. Read about his sleuthing at: The Origin of Junk DNA: A Historical Whodunnit.

Meanwhile, a person named "ShadiZl" commented on one my posts and pointed me to a letter from Thomas Jukes to Francis Crick in 1979. Jukes, you might recall, was no Darwinian. He was a proponent of Neutral Theory and random genetic drift. The letter is archived on the National Library of Medicine (USE) site under a section devoted to The Francis Crick Papers: Letter from Thomas H. Jukes to Francis Crick.

The letter is interesting because it reveals how casually the "insiders" talked about junk DNA and about the adaptationist misconception even as far back as 1979. This was when Gould and Lewontin published the "spandrels" paper. It also reveals how misguided the creationists are when it comes to the history of junk DNA. They still think that it was "Darwinists" who "predicted" junk DNA based on their view of natural selection. (Do not read this letter if you are irony-deficient. It will only confuse you.)

December 20, 1979

Dear Francis:

I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin.

This additive is so pervasive that if no reason can be found for an evolutionary change, it is necessary to invent one. Kimura points out that one author attributed the pink color of flamingos to protective coloration against the setting sun. This type of thinking carries over into people who sequence mRNA. They claim that differences between rabbit and human globin mRNAs are because each species has its own requirements for secondary structure.

Various people have tried to think up possible functions for the regions of DNA that do not code for anything as far as is known. Roy Britten says that such DNA has a regulatory function.

Actually, the scheme proposed by Britten about ten years ago was that occasionally events of saltatory duplication, took place, so that a great many copies of a short piece of DNA were made. As time went by, the composition of a family of identical copies became changed by drift, until the copies no longer closely resemble each other. Figure 55 of the article by Britten shows a diagram of a sort of "junk DNA generating system". I note that he says on page 105 "the rate of increase in DNA content per cell resulting from saltatory replication alone may prove to be embarrassingly large and a mechanism for the loss of DNA may have to be invoked". I gather that you agree with this.

I quoted you on drift in DNA in a talk that I gave at the symposium for Emil Smith (see enclosure). Your concept of "junk DNA" presumably includes this idea. I shall look forward to hearing more about it, and I have been asked by Die Naturwissenschaften to write an article on silent changes, so I hope I can include mention of your new manuscript when I start to write mine.

With best regards,


Thomas H. Jukes

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Evolution Is Irrelevant to Michael Egnor

The title of this post suggest a story that's about as interesting as the proverbial "Dog Bites Man" story [see Man Bites Dog]. Nevertheless, from time to time it is amusing to see how the creationist mind works.

Michael Egnor is upset about the fact that the American Society for Biochemistry and Moleclar Biology (ASBMB) picked "evolution" as an important concept that should be covered in a biochemistry or molecular biology course. He doesn't like my post: ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution. He decided that he better convince his fellow creationists than biochemists don't know what they are talking about [Is Darwinian Evolution "Indispensable" to Biology?].

Here are some excerpts for your amusement.

Monday's Molecule #220

Last week's molecule was citrate synthase, one of many enzymes that show considerable amounts of structural change during binding. It looks like the "induced fit" mechanism is a general feature of substrate binding and not something that is limited to just a few examples. That part of the question was easy but the second part was hard. Jean-Marc Neuhaus is this week's winner because he has a copy of my book and was able to look up the explanation. The important point to keep in mind when you are thinking about the thermodynamics of biochemical reactions is that most reactions are near-equilibrium reactions where ΔG = 0. In the case of the citrate synthase reaction, ΔG°′ = -31.5 kJ mol^-1, in the direction of citrate formation. What this means is that the equilibrium concentrations of the products are very much higher than the concentrations of the substrates. These concentrations would be closer to being equal if the reaction was coupled to substrate level phosphorylation (e.g. ATP formation). This would be a problem since the concentration of oxaloacetate (substrate) inside the cell is very low. (Because the standard free energy change of the malate dehydrogenase reaction is ΔG°′ = +30 kJ mol^-1) [Monday's Molecule #219]. Jean-Marc lives in Switzerland so I've made arrangements to fly over there to visit him and treat him to fondue at the Pinte de Pierre-à-Bot in Neuchatel.

Today's molecule is one of those molecules that students should never be asked to memorize. It's an intermediate in a very important pathway. Identify the molecule and the pathway. You have to give me the full name and the common abbreviation. Email your answer to me at: Monday's Molecule #220. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

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 email message.)

ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution

Theme

Better BiochemistryTansey et al. (2013) have described the five core concepts in biochemistry and molecular biology. These are the fundamental concepts that all biochemistry instructors must teach and all biochemistry students must understand.

The five core concept categories are:

1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
5. macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]

Darwinists Are Racists?

Intelligent Design Creationists are upset when I call them IDiots. They don't realize that the easiest way to make me stop is for them to stop acting like ... well, idiots.

The IDiots are fond of pointing out that they are all good Christians who would never stoop so low. They are all kind and gentle people who treat their opponents with respect and dignity. That's why they get so upset when we insult them.

Denyse O'Leary and the people who comment on Uncommon Descent have made these points repeatedly. They are the good guys and we are the bad guys when it comes to describing your opponents.

Let's look an example of how Christian IDiots behave. Denyse O'Leary recently wrote a post about The racist implications of Darwin’s theory.

She quotes a passage from Dawrin's The Descent of Man, and Selection in Relation to Sex.

The break between man and his nearest allies will then be wider, for it will intervene between man in a more civilised state, as we may hope, even than the Caucasian, and some ape as low as a baboon, instead of as now between the negro or Australian and the gorilla.

The quote is from page 201.

Denyse then says,

Darwin’s racism was not adopted out of bad will but simply as the logic of Darwinism. That is the point that every Darwinist wants to miss or downplay.

They have demanded that we all understand that the greatest man who ever lived wasn’t a racist and we are all misquoting or misunderstanding him or are bad, bad people or whatever for even bringing this stuff up.

Okay so we’re really awful here at Uncommon Descent. As our name implies, we don’t espouse any theory that says that humans are merely evolved animals or that we must inevitably form separate species as a result of isolation. Heck, we don’t even espouse a theory that says that separate species usually form that way. The evidence is mixed.

His believers are therefore stuck in the awkward position of having to pretend that what is obviously racist isn’t, and denouncing any of us who read the plain sense of it correctly.

Do you see the problem. Those poor IDiots are being criticized unjustly for seeing the obvious; namely, that all Darwinists are racists.

Doesn't your heart go out to them? Poor, poor IDiots.

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Fundamental Concepts in Biochemistry and Molecular Biology

Theme

Better BiochemistryThe American Society for Biochemistry and Molecular Biology (ASBMB) advocates for a concept-driven approach to teaching biochemistry and molecular biology. It set up a number of working groups to flesh out this approach. The results have been published in a series of papers in the latest issue of BAMBED (Biochemistry and Molecular Biology Education). The first paper (Mattos et al. 2013) discussed the strategy [see ASBMB Promotes Concept Driven Teaching Strategies in Biochemistry and Molecular Biology].

The second paper, by Tansey, et al., is the most important paper. It covers the results of a two-year study to define and describe the fundamental concepts that must be taught. The authors begin by explaining why it's important to agree on a core set of fundamental concepts.

Monday's Molecule #219

Last week's molecule was cobalamin or vitamin B12. The structure was solved by Dorothy Crowfoot Hodgkin who won the Nobel Prize in Chemistry in 1964. There have been ten Nobel Prizes for work on vitamins and coenzymes. There were a lot of people who got this one right. The winner is Piotr Gasiorowski. The undergraduate winner is Jacob Toth [Monday's Molecule #218]. That makes four lunches that I owe Jacob. Right now, he's far away (British Columbia) but he may be coming to Toronto to collect. That may cut down on his chances of winning!

Today's molecule is a very common enzyme found in all species (I don't know of any exceptions). It's part of a pathway that's familiar to all biochemistry students. The figure illustrates a classic "induced fit" mechanism of substrate binding where the binding of one substrate creates the binding pocket for the second substrate. In this case, it's the homodimeric animal version of the enzyme showing rotation of the small domain of one of the subunits. Name the enzyme and the reaction it catalyzes.

There's more. In order to win a free lunch you have to explain something else. It's related to the fundamental concepts that all biochemistry students should know. The standard Gibbs free energy change for the reaction catalyzed by this enzyme is ΔG°′ = -31.5 kJ mol^-1. What does that mean if you are trying to understand the reaction that takes place inside the cell? Is there a reason why this reaction isn't coupled to synthesis of ATP? I'm interested in seeing how most Sandwalk readers understand the fundamental concept of reaction thermodynamics.

Email your answers to me at: Monday's Molecule #219. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

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 email message.)

The Accommodationist View of Kevin Padian

In a recent post, I discussed the way Kevin Padian views evolution and why he thinks textbooks misrepresent evolution [see Misrepresentations of Evolution in Textbooks: Definition of Evolution According to Kevin Padian]. Now I want to quote his position on the conflict between science and religion.

Keep in mind that Kevin is President of the National Center for Science Education. He isn't speaking for NCSE in this paper but it's fair to say that his view is quite compatible with those of other members of the NCSE leadership.

Here's what Kevin writes under the subtitle "Avoid pitting science against religion, even though sometimes there are real conflicts" ...

Misrepresentations of Evolution in Textbooks: Definition of Evolution According to Kevin Padian

Kevin Padian is a professor at the University of California, Berkeley and Curator of Paleontology at the University of California Museum of Paleontology. He is also President of the National Center for Science Education (NCSE).

He wrote an article for Evolution: Education and Outreach in which he describes misrepresentations of evolution in textbooks (Padian, 2013). Since he is a prominent leader in the fight against creationism, we need to pay attention when he tells us how evolution should be taught in public schools.

Before examining some of those "misconceptions," let's review some earlier papers in Evolution: Education and Outreach. The very first issue contained an article by John N. Thompson where he defined evolution as ...

Evolution is quite simply heritable change in the genetic structure of a population. There is nothing in this or any similar standard definition of evolution that requires that genetic change in the average size, shape, or any other trait be maintained for a hundred, a thousand, or a million years before it can truly be called evolution. (Thompson, 2007)

Unfortunately, Thompson is under the mistaken impression that natural selection is the only significant mechanism of evolution but that's not the point. The point it that he, and many others, see evolution as a continuous and ongoing process that includes the minor fluctuations that Kevin Padian dismisses.

ASBMB Promotes Concept Driven Teaching Strategies in Biochemistry and Molecular Biology

The latest issue of BAMBED (Biochemistry and Molecular Biology Education) contains a series of articles on "Foundational Concepts and Assessment Tools for Biochemistry and Molecular Biology Educators." The goal is to get teachers to change their way of teaching undergraduate courses in biochemistry and molecular biology.

The first paper is an introduction to "Promoting Concept Driven Teaching Strategies in Biochemistry and Molecular Biology" (Mattos et al, 2013). The authors point out that ASBMB (American Society for Biochemistry and Molecular Biology) has been advocating concept driven teaching strategies for over a decade. What they don't mention is that this advocacy has been remarkably unsuccessful The majority of biochemistry and molecular biology courses are still taught in a memorize-regurgitate format. Most American courses are taught to the MCAT. Understanding concepts won't get you a good grade on the MCAT.

The idea of teaching fundamental concepts is useful if biochemistry and molecular biology are foundational courses designed as prerequisites for more advanced study. That's not how biochemistry is seen in most America colleges. Students usually don't take the course until their junior year and many don't take it until they are seniors! These courses are not generally seen as prerequisites for other courses in the biological sciences.

That's not how it works in Canada where biochemistry is a second year course and it is a prerequisite for many third year and fourth year courses. The importance of concept driven teaching should be more obvious in Canada. It isn't, in my experience. That doesn't mean we don't talk about it—or course we do. We all think that teaching concepts is a great idea. Problem is, we don't do it in our introductory courses.

This is one of the reasons why MOOCs are seen as a viable alternative to in-class biochemistry courses. You can spew out facts for multiple choice exams just as easily on a video as you do in a classroom. If, instead, we were actually teaching a concept driven course using a student-centered approach, then MOOCs would seem ridiculous.

Mattos et al. (2013) report that ASBMB developed a three pronged approach ...

1. Building a network of scientists and educators focused on using and disseminating evidence-based teaching best practices.
2. Fostering both an understanding of the use of appropriate assessment, and the creation of a network of educators focused on defining the foundational concepts of the discipline, identifying key cross-disciplinary principles, and incorporating the appropriate skills necessary for students to succeed in the practice of science into the curriculum and assessment of student outcomes.
3. Promoting best practices in the education of our students by providing appropriate teaching and assessment resources for faculty.

They applied for, and received, a grant from the National Science Foundation (USA) to address these challenges. The results of those studies are ready to be published.

The next paper in this BAMBED issue describes the foundational concepts that all biochemistry & molecular biology instructors have to teach. Can you guess what they are before I post the answer? Put your best guesses in the comments.

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Mattos, C., Johnson, M., White, H., Sears, D., Bailey, C. and Bell, E. (2013) Introduction: Promoting concept driven teaching strategies in biochemistry and molecular biology. Biochem. Mol. Biol. Educ. 41:287–288. [doi: 10.1002/bmb.20726]

Three Senior Fellows of the Discovery Institute Will Discuss Criticisms of Dawin's Doubt on a Radio Show on October 23

Evolution News & Views (sic) will bring together David Klinghoffer and Stephen Meyer to discuss Darwin's Doubt on the Michael Medved show [The Closing of the Scientific Mind: Join Us on October 23 in the Medved Studio for a Special Edition of the Science & Culture Update]. The topic is the "closing of the scientific mind," surely an appropriate topic for three men who are not scientists.

Does science open minds, or close them? A "scientific view" is frequently taken as being basically synonymous with skepticism, questioning, and independent thinking. All good and wonderful things! Yet very often, self-proclaimed paladins of "science" are impatient with genuine skeptics, flee from debate, or find a variety of other creative ways to avoid having to confront challenges to their beliefs.

In the special October 23 edition of the Science & Culture Update on the Michael Medved Show, you'll have a chance to talk about science and skepticism, closed minds and open ones, live in the KTTH radio studio, with Mr. Medved, Darwin's Doubt author Dr. Stephen Meyer, and Evolution News & Views editor David Klinghoffer. All three are Discovery Institute senior fellows.

For the discussion, they'll take as a case in point the critical reception of Dr. Meyer's book, Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, which has sparked furious debate -- and also a great deal of artful dodging of the relevant scientific issues by opponents of the theory of intelligent design. Why are critics of ID so determined to flee from a fair fight?

I think I'm going to try and listen in. I can't wait to hear how Medved, Meyer, and Klinghoffer respond to my scientific critique of Chapter 5: "The Genes Tell the Story?"

• Darwin's Doubt: The Genes Tell the Story?
• The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes
• Stephen Meyer Says That Constant Mutation Rates Are a "Questionable Assumption"
• Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates
• Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates
• Stephen Meyer Says that "Homology" Is a Problem in Molecular Evolution

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John G. West Speaks Out Against Using Derogatory Labels to Describe Your Opponents

John G. West is Vice President for Public Policy and Legal Affairs of the Center for Science and Culture (CSC)—the most important Intelligent Design Creationism propaganda organization. He is upset because some reporters describe Intelligent Design Creationism as a form of creationism. I've taken an excerpt from his post at Attempting to Win the Debate over Intelligent Design through Stereotyping and changed just a few words so you can get the gist of his argument.

The really discouraging thing here is not that some reporters are critical of evolution. It is that so many of them apparently see nothing wrong with preventing evolutionary biologists from defining their own position. This is a very strange way to do journalism, and if journalists started to apply their approach to evolution to other topics, I think it would become manifestly clear how unfair it is. Imagine, for example, a journalist deciding to use "Marxist" as a neutral label for President Obama based on the views of certain right-wing academics and political activists. Would that be regarded as fair or impartial by most journalists? Of course not. What if a reporter redefined Marxist to mean anyone who supports more active government? Would that make applying the term to Obama in a news story more defensible? Hardly. Yet when reporters label evolutionary biologists as "Darwinists," they are essentially doing the same thing.

What is really going on here is censorship. When reporters use as a "neutral" description of evolution a polemical smear invented by its critics, they are effectively silencing evolutionary biologists by not allowing them to speak for themselves. They are poisoning the well so no one will be willing to listen to the actual views expressed by evolutionary biologists. Journalists who write about evolution should re-read the Society of Professional Journalists' Code of Ethics, especially the provisions calling for them to "Support the open exchange of views, even views they find repugnant" and to "Give voice to the voiceless...."

Whatever a news reporter's views on evolution, he or she has a professional duty not to simply spread stereotypes and caricatures. That duty means nothing if it only applies to news coverage of groups and positions with which the reporter agrees. The real test of fairness for reporters is how they treat those with whom they disagree. When it comes to evolution, sadly, many reporters are failing the test.

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October 7-14th Is Quackery Week

The week is half over and nobody told me it's Quackery Week. Perhpas that's because it's only Quackery Week in the USA. The US Senate passed a resolution ...

A resolution designating the week of October 7 through October 13, 2013, as “Naturopathic Medicine Week” to recognize the value of naturopathic medicine in providing safe, effective, and affordable health care.

Don't worry. Orac is on to it with: Naturopaths and vaccines.

But let's not forget that the Canadian College of Naturopathic Medicine makes their students take a course in Homeopathic Medicine and another im Asian Medicine and Acupuncture [Naturopathic "Doctors" Graduate from Convocation Hall on the University of Toronto Campus].

This is one more reason why we have to teach critical thinking in high school and in universities.

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19,853 People Can't Be Wrong ... Can They?

There are days when I think that Canadians will never, ever, become rational, scientifically literate, thinkers. Today is one of those days.

As of right now, 19,853 people have signed a petition asking the Girl Guides of Canada to take GMO ingredients out of girl guide cookies [Girl Guides of Canada: Take all GMO ingredients out of Girl Guide Cookies].

The petition is organized by Maya Fischer and Linda Cirella in Victoria, BC. Here's what they say ...

Our family tries to only buy food that is non-GMO or organic. The reason we're so concerned is because there have been no long-term studies showing that it is safe for people to eat or grow GMO foods. In fact, GMO studies on animals have shown infertility, immune system problems, accelerated aging, faulty insulin regulation, and changes in major organs and the gastrointestinal system. The American Academy of Environmental Medicine actually asks physicians to advise patients not to eat foods with GMO ingredients.

The really sad part is the message that those two women are sending to young girls across Canada. They're saying that science doesn't matter. You can just make up stuff to support your biases and prejudices.

UPDATE: Please read: With 2000+ global studies confirming safety, GM foods among most analyzed subjects in science.

A popular weapon used by those critical of agricultural biotechnology is to claim that there has been little to no evaluation of the safety of GM crops and there is no scientific consensus on this issue.

Those claims are simply not true. Every major international science body in the world has reviewed multiple independent studies—in some cases numbering in the hundreds—in coming to the consensus conclusion that GMO crops are as safe or safer than conventional or organic foods, but the magnitude of the research has never been catalogued.

Still the claim that GMOs are “understudied”—the meme represented in the quotes highlighted at the beginning of this article—have become a staple of anti-GMO critics, especially activist journalists. In response to what they believed was an information gap, a team of Italian scientists catalogued and summarized 1783 studies about the safety and environmental impacts of GMO foods—a staggering number.

The researchers couldn’t find a single credible example demonstrating that GM foods pose any harm to humans or animals. “The scientific research conducted so far has not detected any significant hazards directly connected with the use of genetically engineered crops,” the scientists concluded.

The research review, published in Critical Reviews in Biotechnology in September, spanned only the last decade—from 2002 to 2012—which represents only about a third of the lifetime of GM technology.

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