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Friday, January 30, 2015

Stephen Fry blows it by assuming he knows the mind of god

This video is making the rounds and a lot of atheists are wetting their pants over Stephen Fry's response to the question of what he would would say to "he, she, or it" if he encountered god when he dies.

My questions would be "Who are you? Which groups of humans (if any) got it right when making up a religion? Tell me about yourself and why you didn't reveal yourself to me."

That's not what Stephen Fry would do. He makes the assumption that he knows the mind of god and attacks the god for not being nice to humans. In other words, he accepts the problem of evil and assumes that the god he is facing gives a damn about some obscure species on a minor planet in one of billions of galaxies. Later on Stephen Fry concedes that he could be talking to the Greek gods or some other gods but by then it's too late.

The god he is addressing may or may not have done any of the things in the Bible. If he isn't that god then he will know that Stephen Fry is attacking a strawman. If he is the god of the Bible then presumably he/she/it had his/her/its reasons for doing apparently evil things and Stephen Fry is about to get educated about the real mind of god. That may turn out badly for Stephen Fry.

If you ever run into any real gods I'd advise you not to mess with them.

Many of my atheist friends think that Fry's response is fantastic because he really shocks the interviewer, Gay Byrne [Stephen Fry on God]. That's naive. Most intelligent Christians have developed some very good rationalizations concerning the problem of evil. They've heard it all before and they know how to respond. One of the classic responses is that cannot they know the mind of god. But Stephen Fry knows the mind of god and this is puzzling because Fry is an atheist.

American scientists think science education is a problem

The results of the latest PEW/AAAS survey are getting a lot of attention [Public and Scientists’ Views on Science and Society]. Most people focus on the fact that the American public doesn't accept evolution and anthropogenic climate change. That's not news.

The real issue is what can we1 do about it. Alan Leshner, Chief Executive Officer of AAAS and Executive Publisher of Science, thinks he has the answer. Here's what he writes in an editorial "Bridging the opinion gap" ...
Speaking up for the importance of science to society is our only hope [my emphasis, LAM], and scientists must not shy away from engaging with the public, even on the most polarizing science-based topics. Scientists need to speak clearly with journalists, who provide a great vehicle for translating the nature and implications of their work. Scientists should also meet with members of the public and discuss what makes each side uncomfortable. In these situations, scientists must respond forthrightly to public concerns. In other words, there needs to be a conversation, not a lecture.
Isn't that insightful? Here we are in 2015 and nobody ever thought of that before now! Can you imagine how much better off we'd be if scientists have only started speaking up 40 years ago, or even 10 years ago?

Scientists have been engaging with the American public about evolution for half a century and it has not worked. They've also been speaking to journalists.2

Fortunately, there are some people who have gone way past these naive views and actually thought seriously about the problem. Here's are the results of two questions from the survey.
  • Only 16% of AAAS scientists and 29% of the general public rank U.S. STEM education for grades K-12 as above average or the best in the world. Fully 46% of AAAS scientists and 29% of the public rank K-12 STEM as “below average.”
  • 75% of AAAS scientists say too little STEM education for grades K-12 is a major factor in the public’s limited knowledge about science. An overwhelming majority of scientists see the public’s limited scientific knowledge as a problem for science.
I agree with those scientists. We are part of the problem because we are not doing a very good job of educating students in the ways of science. The long term solution is to do a far better job of teaching about science. We should not be graduating students from university who reject evolution and climate change. We should not be giving out degrees to students who fall for pseudoscience gobbledegook like homeopathy and astrology. If we do that then we are not doing our job as educators and survey results like these are not going to change in the forseeable future.

Now, to be fair, Alan Leshner recognizes the problem even if he's wrong about the solution.
The public's perceptions of scientists' expertise and trustworthiness are very important, but they are not enough. Acceptance of scientific facts is not based solely on comprehension levels. It can be compromised whenever information confronts people's personal, religious, or political views, and whenever scientific facts provoke fear or make people feel that they have no control over a situation. The only recourse is to have genuine, respectful dialogues with people. Good venues are community clubs, science museums, science fairs, and religious institutions. Working with small groups is more effective than working with large groups.
Perhaps he and some other scientists can sit down in small groups with Republican members of Congress and change their minds. Maybe you could do it in their churches. (Remember to be respectful when dialoguing with John Boehner.) Meanwhile, I believe that's not the "only hope." I think educating our young people is a better investment in time and effort even though it won't pay off for a generation.

1. I say "we" because the same problems exist in Canada.

2. Maybe Alan Leshner should have a little chat with Elizabeth Pennisi.

Thursday, January 29, 2015

My community is outraged over trash

My community (Peel Region, west of Toronto, Ontario, Canada) is changing the way it collects trash so it put out a pamphlet to advise citizens of the upcoming changes. Here's the cover.

It's a little chilly right now to be putting out the garbage with no clothes on but even in the summer I'll probably throw on a shirt. I might consider the naked method but only if it were very late at night or if I were as good-looking as the guy in the picture.

At least two members of the community are outraged. Can you guess why?

Peel’s ‘naked man' trash pamphlet sparks outrage

Check out My Secret Atheist Blog for more pictures of naked men.

Wednesday, January 28, 2015

Vision and Change

A few years ago the AAAS (American Association for the Advancement of Science) sponsored a study of undergraduate education in the biological sciences. The study groups published a report in 2011 called Vision and Change in Undergraduate Biology Education: A Call to Action. Since then a number of disciplines, including biochemistry and molecular biology, have been trying to encourage university teachers to implement these proposals. So far, the "call to action" has pretty much fallen on deaf ears. Most professors are reluctant to admit that their teaching needs improvement and they are reluctant to read this report or any other part of the pedagogical literature.

“Scientists should be no more willing to fly blind in their teaching than they are in scientific research, where no new investigation is begun without an extensive examination of what is already known.”

Bruce Alberts, NRC, 1997
What could be wrong with this?
The time has come for all biology faculty, particularly those who teach undergraduates, to develop a coordinated and sustainable plan for implementing sound principles of teaching and learning to improve the quality of undergraduate biology education nationwide. The stakes are too high for all biologists not to get involved with this national call for change.
The main recommendations are that we should concentrate on teaching fundamental concepts and principles and not facts and that we should adopt a student-centered form of learning.
The recommendations discussed in this report include the following action items aimed at ensuring that the vision of the conference becomes an agenda for change:

1. integrate Core Concepts and Competencies throughout the Curriculum
  • Introduce the scientific process to students early, and integrate it into all undergraduate biology courses.
  • Define learning goals so that they focus on teaching students the core concepts, and align assessments so that they assess the students’ understanding of these concepts.
  • Relate abstract concepts in biology to real-world examples on a regular basis, and make biology content relevant by presenting problems in a real-life context.
  • Develop lifelong science-learning competencies.
  • Introduce fewer concepts, but present them in greater depth. Less really is more.
  • Stimulate the curiosity students have for learning about the natural world.
  • Demonstrate both the passion scientists have for their discipline and their delight in sharing their understanding of the world with students.
2. Focus on student-Centered Learning
  • Engage students as active participants, not passive recipients, in all undergraduate biology
  • Use multiple modes of instruction in addition to the traditional lecture.
  • Ensure that undergraduate biology courses are active, outcome oriented, inquiry driven, and relevant.
  • Facilitate student learning within a cooperative context.
  • Introduce research experiences as an integral component of biology education for all students, regardless of their major.
  • Integrate multiple forms of assessment to track student learning.
  • Give students ongoing, frequent, and multiple forms of feedback on their progress.
  • View the assessment of course success as similar to scientific research, centered on the students involved, and apply the assessment data to improve and enhance the learning environment.
"Appreciating the scientific process can be even more important than knowing scientific facts. People often encounter claims that something is scientifically known. If they understand how science generates and assesses evidence bearing on these claims, they possess analytical methods and critical thinking skills that are relevant to a wide variety of facts and concepts and can be used in a wide variety of contexts.”

National Science Foundation, Science and Technology Indicators, 2008
The evidence is in. Whether or not we should change is a no-brainer.

The other two recommendations have to do with implementation .... this is the tough part.
3. Promote a Campuswide Commitment to Change

4. Engage the Biology Community in the implementation of Change
Notice that MOOCs and online learning are not prominent objectives in Visions and Change. You have to wonder why AAAS isn't inviting the members of these study groups to give plenary lectures at their 2015 meeting instead of the President of Coursera [see President of Coursera to give plenary lecture at AAAS meeting]. Maybe they've changed their minds since 2011?

Evidence-based teaching

A lot of people have spent a lot of time and effort studying undergraduate education. Why not pay attention to what these experts have to say? There's a good book on the subject published by the National Academies (USA). It's called Reaching Students: What Research Says About Effective Instruction in Undergraduate Science and Engineering (2015).1

Here's are some excerpts from the Preface.
This book is based on the 2012 NRC report on DBER [discipline-based education research], as well as on interviews with expert practitioners who have successfully applied findings from DBER and related research in their classrooms, departments, or institutions. The goal is to summarize the most salient findings of the NRC committee and the experience of expert practitioners about how students learn undergraduate science and engineering and what this means for instruction. This book presents new ways of thinking about what to teach, how to teach it, and how to assess what students are learning. To encourage instructors and others to apply this information in their institutions, it also includes short examples and longer case studies of experienced practitioners who are implementing research-based strategies in undergraduate science and engineering courses or across departments or institutions. Although these findings could apply to a variety of disciplines, this book focuses on the disciplines addressed in the NRC study-physics, astronomy, biology, chemistry, geosciences, and engineering.

This book is intended for anyone who teaches or plans to teach undergraduate courses in science and engineering at any type of higher education institution or who is in a position to influence instruction at this level. Throughout the book, the term “instructor” is used broadly to refer to the full range of teaching staff—tenured, non-tenured, or adjunct faculty; lecturers and similar teaching positions; and postdoctoral scholars or graduate students with teaching responsibilities. Although many of the strategies and ideas in these pages are geared to instructors, others with an interest in science and engineering education will find suggestions for encouraging or supporting research-based instruction. These other audiences might include department heads; faculty development providers; provosts, deans, and other higher education administrators; leaders of professional societies and associations for science and engineering; and those with policy roles in higher education or science education.
There's lots of interesting stuff in this little book but the main emphasis is on teaching fundamental concepts rather than facts and on student-centered learing (active learning).

The report recognizes that university lecturers need to change the way they are teaching and it won't be easy.
Throughout the chapters you will find concrete examples and case studies that illustrate how skilled instructors and leaders from various disciplines and types of institutions have used findings from DBER and related research on learning to design and support instruction in their classrooms, departments, or institutions. These examples may inspire, intrigue, challenge, or provoke you. Whatever your reaction, the examples are intended to encourage reflection and discussion about effective ways to help students learn science and engineering.

This type of reflection is not always easy. Instructors may be unaware of this body of research. Even if they aware, they may be disinclined to change teaching methods that are familiar or ubiquitous in their departments and seem to be working, at least for some students. Departmental and institutional cultures may also present obstacles to changing practice, as discussed in later chapters.

On a positive note, however, as a scientist or an engineer you already have the intellectual tools and experience needed to examine students’ learning and your own teaching from a research perspective. Every day, you tackle research problems in your discipline, consider various strategies to solve those problems, try out a strategy, and revise that strategy based on the results. Why not apply this same mindset to your teaching? The research is there, and so are a variety of curriculum materials, professional development opportunities, and other resources. With some effort, the rewards will be there, too—better educated students, greater professional satisfaction, and a brighter outlook for society.

1. You can download the book for free. All you have to do is sign in.

President of Coursera to give plenary lecture at AAAS meeting

The American Association for the Advancement of Science holds a meeting every February. This year the meeting is in San Jose, California. There are four plenary lectures [Plenary Lectures 2015]. Three of them will be given by prominent researchers who will be talking about science. The fourth is by Daphne Koller, President and co-founder of Coursera.

Coursera is a for-profit company offering "universal access to the world’s best education." What they mean by "best education" is MOOCs offered by professors at the "top" universities. There's no evidence to support the claim that the best undergraduate courses for the general audience are those given by professors at Stanford, MIT, Princeton, and Harvard. Indeed, there's quite a bit of evidence that this isn't true.

Daphne Koller is going to talk about The Online Revolution: Learning Without Limits. Keep in mind that at the end of every article published in Science (AAAS publication) there's a small notice stating that, "The authors declare no financial conflict of interest" or statements that clearly spell out the conflicts.

Why is AAAS asking someone to give a plenary lecture about selling online courses from someone with a clear financial interest in promoting her company?

Science education is important and there's plenty of evidence that universities are graduating students who don't understand science and aren't capable of critical thinking. There are hundreds of people whose main research interest is pedagogy and especially science education. They have proposed solutions to the problem and suggestions on how we should change the way we teach. Very few of them think that MOOCs are the answer and very few of them are trying to market their ideas for profit [ Reaching Students: What Research Says About Effective Instruction in Undergraduate Science and Engineering (2015)].

Why not ask some of those experts to address the AAAS meeting and possibly explain what's wrong with canned videotaped lectures? MOOCs are just ways of transferring the way we teach now to the mass market. But what if the traditional way we now teach (lectures) is wrong? Isn't that a question that the delegates at San Jose ought to think about?

Here's Daphne Koller giving a TED talk. Near the end she talks about the importance of "active learning" (student-centered learning). I'm a big fan of student-centered learning. She implies that having students take online courses from "top" educators is consistent with active learning but she's wrong. It's the exact opposite. In my opinion, it's a step backwards and by promoting MOOCs we are going to make it more difficult to convince professors to change the way they teach. Instead, the ones who are good at delivering traditional lectures will bring in money for themselves and their universities.1 They will be getting the kudos and the teaching awards instead of those who are paying attention to evidence-based methods and trying to improve undergraduate education.

Here's another video. It's an interview with Daphne Koller from June 2013. Listen to the first few minutes and you'll hear a different view of active learning. Here, she explains the concept of the "flipped classroom" where students watch online videos and then come to class to participate in "something that's much more engaging and stimulating, active learning" (4 mins). There's nothing wrong with that except that students could read a textbook instead of watching a video. The important part of the learning is what happens in the classroom and not what happens in the textbook or the taped lecture.

She also explains how they are going to make money (5-6 mins).

Daphne Koller is very fond of repeating the myth that the best courses are the ones taught at the top research universities. (She happens to be a teacher at one of these universities.) I bet she can't prove it unless she's talking about very specialized upper level courses.

1. For-profit companies like Coursera offer kick-backs to the professors and schools that contribute courses.

Saturday, January 24, 2015

Learn biology with Eric Hovind

If you want to learn biology, I suggest you take this course taught by Eric Hovind. It's a good illustration of the importance of MOOCs and how they are eventually going to replace professors at universities.

Friday, January 23, 2015

About half of all cancers are just bad luck. It's not your fault.

There's been a lot of talk recently about a paper claiming that two thirds of all cancers are due to bad luck [Bad Luck of Random Mutations Plays Predominant Role in Cancer, Study Shows]. The take-home message was that you could get cancer even if you ate "healthy," took lots of vitamins, didn't smoke, and went to the gym every day. That's not what people wanted to hear.

But scientists have known for decades that many cancers are due to random mutations that just happen. These cancers are not hereditary and are not caused by the environment. There's nothing new here.

That didn't stop a number of people from criticizing the article and some of the criticisms were justified. Nevertheless, what the article showed was that cancers tended to occur more often in tissues with lots of cell divisions (and DNA replications). That's exactly what you expect if random mutations due to replication errors are the cause of the cancer mutations.

David Gorski of Science-Based Medicine sorts it all out for us [Is cancer due mostly to “bad luck”?]. Please read his lengthy article if you want to understand the issues. David Gorski concludes ...
It’s understandable that humans crave explanation, particularly when it comes to causes of a group of diseases as frightening, deadly, and devastating as cancer. In fact, both PZ Myers and David Colquhoun have expressed puzzlement over why there is so much resistance is to the concept that random chance plays a major role in cancer development, with Colquhoun going so far as to liken it to ” the attitude of creationists to evolution.” Their puzzlement most likely derives from the fact that they are not clinicians and don’t have to deal with patients, particularly given that, presumably, they do have a pretty good idea why creationists object to attributing evolution to random chance acted on by natural selection and other forces.

Clinicians could easily have predicted that a finding consistent with the conclusion that, as a whole, probably significantly less than half of human cancers are due to environmental causes that can be altered in order to prevent them would not be a popular message. Human beings don’t want to hear that cancer is an unfortunately unavoidable consequence of being made of cells that replicate their DNA imperfectly over the course of our entire lives. There’s an inherent hostility to any results that conclude anything other than that we can prevent most, if not all, cancers if only we understood enough about cancer and tried hard enough. Worse, in the alternative medicine world there’s a concept that we can basically prevent or cure anything through various means (particularly cancer), most recently through the manipulation of epigenetics. Unfortunately, although risk can be reduced for many cancers in which environmental influences can increase the error rate in DNA replication significantly, the risk of cancer can never be completely eliminated. Fortunately, we have actually been making progress against cancer, with cancer death rates having fallen 22% since 1991, due to combined efforts involving smoking cessation (prevention), better detection, and better treatment. Better understanding the contribution of stochastic processes and stem cell biology to carcinogenesis could potentially help us do even better.

Is Intelligent Design Creationism winning the debate in the scientific community?

Back in 1998 the Intellignet Design Creationists published the Wedge Strategy. They set themselves several goals including some twenty year goals that they hoped to achieve by 2018 (three years from now). They are ...
  • to see intelligent design theory as the dominant perspective in science
  • to see design theory applications in specific fields, including molecular biology, biochemistry, paleontology, physics and cosmology in the natural sciences, psychology, ethics, politics, theology, and philosophy in the humanities, to see its influence in the fine arts
  • to see design theory permeate our religious, cultural, moral, and political, life
They aren't even close to achieving the first two goals but I think it's fair to say that they are well on their way to achieving the third goal in the United States. I don't think they've had much success in other countries. Perhaps readers in Europe, India, Africa, and China could let me know if design theory has permeated their culture and their politics?

Casey Luskin has recently posted a progress report in Evolution News & Views (sic) [In the Darwin Debate, How Long Before the Tide Turns in Favor of Intelligent Design?]. He's very optimistic. He lists thirteen (13) recent victories for Intelligent Design Creationism and concludes ...
Don't expect a revolution overnight. We are in this for the long haul, recognizing that it can take time for the truth to slip past the checkpoints that the Darwin lobby sets up to keep the public uninformed. In the end, though, I'm optimistic because the fundamentals of ID -- the science underlying the inference to design in nature -- are sound. The truth will win out, though it may tarry in doing so. Or to put it another way, the tide of ID is already well on its way in. We need to focus on telling people about it.
They'd better hurry. There's only three years left.

Sunday, January 18, 2015

80% of Americans support mandatory labels on food containing DNA

A recent survey reports that 80.44% of Americans believe that there should be mandatory labels on food containing DNA [Food Demand Syrvay]. Slightly more (82.28%) think there should be mandatory labels of food produced with genetic engineering.

It's easy to mock the respondents for being scientifically illiterate but that's not fair. The real idiots are the people who asked the question.

Ilya Somin has been thinking about what should be said in this mandatory label [Over 80 percent of Americans support “mandatory labels on foods containing DNA”]. Here's one possibility ...
WARNING: This product contains deoxyribonucleic acid (DNA). The Surgeon General has determined that DNA is linked to a variety of diseases in both animals and humans. In some configurations, it is a risk factor for cancer and heart disease. Pregnant women are at very high risk of passing on DNA to their children.
Can anyone think of foods that would not carry this warning? What do you eat if you want to avoid DNA?

Did you notice that 87% of Americans want labels on meat to identify the country of origin? Is that because they don't know where New Zealand lamb comes from? Or is it because they want to make sure they're getting genuine Canadian bacon?

Francis Collins rejects junk DNA

Francis Collins is the Director of the National Institutes of Health (NIH) in the USA. He spoke recently at the 33rd Annual J.P. Morgan Healthcare Conference in San Francisco (Jan. 12-15, 2015). His talk was late in the afternoon on Tuesday, January 13, 2015. You can listen to the podcast on the conference website [J.P. Morgan Healthcare Conference].

The important bit is at the 30 minute mark where he comments on a question about junk DNA. This is what Francis Collins said last week ...
I would say, in terms of junk DNA, we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu's, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that's where the epigenome gets involved, and is teaching us a lot.
What seems like "hubris" to Francis Collins looks a lot like scientific evidence to me. We know enough to say, with a high degree of confidence, that most (~90%) of our genome is junk. And we know a great deal about the data that Collins is probably referring to (ENCODE)—enough to conclude that it is NOT saying what he thinks it says.

It would be bad enough if this were just another confused scientist who doesn't understand the data [see Five Things You Should Know if You Want to Participate in the Junk DNA Debate] but he's not just any scientist. He's a powerful man who talks to politicians all the time and deals with the leaders of large corporations (e.g. the J.P. Morgan Conference). If Francis Collins doesn't understand the fundamentals of genome science then he could mislead a lot of people.

Collins has many colleagues surrounding him at NIH and other agencies in Washington. These scientists also make important decisions about American science. I'm assuming that he reflects their opinion as well. If not, then why aren't they educating Francis Collins?

Hat Tip: Ryan Gregory

Friday, January 16, 2015

Functional RNAs?

One of the most important problems in biochemistry & molecular biology is the role (if any) of pervasive transcription. We've known for decades that most of the genome is transcribed at some time or other. In the case of organisms with large genomes, this means that tens of thousand of RNA molecules are produced from regions of the genome that are not (yet?) recognized as functional genes.

Do these RNAs have a function?

Most knowledgeable biochemists are aware of the fact that transcription factors and RNA polymerase can bind at many sites in the genome that have nothing to do with transcription of a normal gene. This simply has to be the case based on our knowledge of DNA binding proteins [see The "duon" delusion and why transcription factors MUST bind non-functionally to exon sequences and How RNA Polymerase Binds to DNA].

If you have a genome containing large amounts of junk DNA then it follows, as night follows day, that there will be a great deal of spurious transcription. The RNAs produced by these accidental events will not have a biological function.

Thursday, January 15, 2015

Richard Lewontin and Tomoko Ohta win the Crafoord Prize in Biosciences

"for their pioneering analyses and fundamental contributions to the understanding of genetic polymorphism"
It is the great irony of modern evolutionary genetics that the spirit of explanation has moved more and more towards optimal adaptation, while the technical developments of population genetics of the past 30 years have been increasingly to show the efficacy of non adaptive forces in evolution.

Richard Lewontin
"A natural selection" Nature May 11,1989 p.107

The ‘neutral theory’ proposed that most evolutionary changes at the molecular level were caused by random genetic drift rather than by natural selection. Note that the neutral theory classifies new mutations as deleterious, neutral, and advantageous. Under this classification, the rate of mutant substitutions in evolution can be formulated by the stochastic theory of population genetics. Kimura's theory was simple and elegant, yet I was not quite satisfied with it, because I thought that natural selection was not as simple as the mutant classification the neutral theory indicated, and that there would be border-line mutations with very small effects between the classes. I thus went ahead and proposed the nearly neutral theory of molecular evolution in 1973. The theory was not simple, and much more complicated, but to me, more realistic, and I have been working on this problem ever since.

Tomoko Ohta
Current Biology, August 21, 2012

HatTip: Jerry Coyne (student of Lewontin): Dick Lewontin and Tomoko Ohta nab the Crafoord Prize

The Nature of Science (NOS)

There is a growing recognition among teachers that we need to teach the "Nature of Science" (NOS). Ideally, this should begin in the primary grades and extend all the way through university. Teaching about the nature of science should not be restricted to students who major in science. Every student should learn about the nature of science.

This is not controversial. I'm not aware of anything in the recent pedagogical literature that argues against teaching the nature of science. What's controversial is how to describe what science is all about.

Wednesday, January 14, 2015

How did the zebra get its stripes? (again)

The National Geographic has just posted an article on Why Do Zebras Have Stripes? New Study Makes Temperature Connection. Here's part of it ...
A leopard may not be able to change its spots, but some zebras change their stripes. Zebras in warmer places have more stripes, a new study shows, which might help answer an age-old question: Why stripes?

The answer probably comes down to keeping zebras cool and fending off disease-causing insects that are more common in hotter climates, researchers reported Tuesday in the journal Royal Society Open Science.

All three species of zebra have bold black and white stripes that stand out among more drab-looking African grazers, like buffalo and antelope, especially against a plain savanna background. And standing out would seem to make a zebra more likely to become a lion's lunch.

This "stripe riddle" has puzzled scientists, including Darwin, for over a century. There are five main hypotheses for why zebras have the stripes: to repel insects, to provide camouflage through some optical illusion, to confuse predators, to reduce body temperature, or to help the animals recognize each other.
There's a fifth possibility: maybe there's no reason at all and stripes are just an evolutionary accident.

The last time I addressed this issue was in 2012 [How Did the Zebra Get Its Stripes?]. At that time I quoted the famous Spandrel's paper where Gould and Lewontin wrote ...
... the rejection of one adaptive story usually leads to its replacement by another, rather than to a suspicion that a different kind of explanation might be required. Since the range of adaptive stories is as wide as our minds are fertile, new stones can always be postulated. And if a story is not immediately available, one can always plead temporary ignorance and trust that it will be forthcoming ....
That's exactly what's happening in the National Geographic article. After almost 100 years of speculation, nobody has come up with a good adaptive explanation of zebra stripes. They never consider the possibility that there may NOT be an adaptive explanation.

Stephen Jay Gould wrote about this problem more than 30 years ago [How the Zebra Gets Its Stripes]. He pointed out back then that stripes are almost certainly due to small changes in just a few genes that alter the timing of differentiation in early embryology. He rails against adaptationist thinking then says ...
For many reasons, ranging from probable neutrality of much genetic variation to the nonadaptive nature of many evolutionary trends, this strict construction [vulgar Darinwism] is breaking down, and themes of unity are receiving attention.... One old and promising theme emphasizes the correlate effects of changes in the timing of events in embryonic development. A small change in timing, perhaps the result of a minor genetic modification, may have profound effects on a suite of adult characters if the change occurs early in embryology and its effects accumulate thereafter.
The point is that the prominence of stripes on zebras may be due to a relatively minor mutation and may be nonadaptive. That's a view that should at least be considered even if you don't think it's correct.

Gould was being very optimistic when he suggested that the old ways were breaking down.

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. Lon. B Biol. Sci. 205: 581-598. [PubMed] [doi: 10.1098/rspb.1979.0086]

Looking for Spandrels

I've just assigned the Spandrels paper to the students in my molecular evolution class. A few of them will have read it already but most haven't. It's such an important paper that it should be required reading for every undergraduate in the biological sciences.

I've mentioned this before on Sandwalk (see links below). While searching through my old posts I came across one from 2008 titled In Search of Spandrels. I'd forgotten about it completely. It reproduced a post that I wrote for on Aug. 20, 1998. Nobody knows about these days but some of us have fond memories. (It still exists.) Here's what I wrote 17 years ago. It was a different era.
I recently found myself in the catacombs of the library archive far away from the stress of students writing their summer exams. It was very peaceful. It was also a place where creationists never go.

I must confess that my primary motivation for being there was work avoidance—I hate marking exams—but there was another reason as well. My secondary mission was to retrieve a pristine copy of the "Spandrels" paper so I could hand it out to my students. (My own copy had some embarassing margin notes that weren't fit for young eyes.)

There were many bound volumes of the Proceedings of the Royal Society of London (Series B). Did you know that this journal goes back over one hundred years? (That's even before I was born.) Did you know that you have to look in the stacks under "R", for "Royal", and not "P", for "Proceedings"? Did you ever wonder why librarians do that? My own theory is that they really don't want us to take out their books so they make it as difficult as possible to find something.

I was looking for volume 205 (1979). As usual, it was on the bottom shelf; way down at the level of my shoes. I had to get down on one knee and that's a lot of work. But at least volume 205 wasn't missing. With trembling hands I flipped the pages looking for the sacred text. Would it be there or would the pages have been cut out with a razor blade? Chances were good—pre-med students don't read about evolution.

Yes! There it was: "The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptionist programme" by S.J. Gould and R.C. Lewontin. They even spelled "programme" correctly! Off I went to the photocopy machine. Off I went to buy a new photocopy card. Back I came to the photocopy machine. Let's see now ... how much magnification will I need to fill an 8x11 page so I don't have to close the damn lid every time I copy a page? 125% should do it. Wrrrrr .... flash .... swish .... splat.

Maybe 120% would work ...

At last, page 598 was perfect. (Anyone want extra copies of the references from this paper?) I worked my way forward to page 581 fending off the librarian who insisted that I had to close the lid or I would ruin the photocopier—and my eyes (I'm not sure which was more important to her).

I was lucky there were three or four students to distract her. Behind my back I heard some mumblings about "eccentric" and "stubborn" but unfortunately I couldn't see exactly what was going on.

Hope I didn't miss anything interesting.

I knew that Gould had presented the paper at a meeting in London in December, 1978. Lewontin wasn't there because you have to fly to get to England and Lewontin thinks that if humans were made to fly then we would have evolved wings. So, who else was at the meeting? Did they publish papers in the same issue of the journal? Let's see ...

My thoughts were interrupted by some shouting in the line behind me. Guess I'd better get away from the photocopier. The machine seems to be making people angry.

Off I went to find a desk to sit down at. Found one. Off I went to the photocopier to retrieve my photocopy card. Back I came to the desk.

Someone was there. Found another desk. It had a banana peel on it.

Cool. All the papers are here. The meeting was called "The Evolution of Adaptation by Natural Selection" and it was organized by John Maynard Smith and R. Holliday. Orgel has a paper on evolution in vitro. The Charlesworths write about sex in plants. There's a paper by Maynard Smith on game theory and the evolution of behaviour. George Williams was present (more about him later). And guess who else? - Richard Dawkins!

The Dawkins' paper is titled "Arms races between and within species" (R. Dawkins and J.R. Krebs). It goes on and on about the adaptive significance of arms races and the optimization of animals. I bet the Gould talk was not well received by Dawkins in 1978. :-)

The Williams paper is very interesting ("The question of adaptive sex ratio in outcrossed vertebrates"). He examines two popular theories of the adaptive control of sex ratio (why there are 50% males and 50% females). After looking at the detailed models and the available data he concludes,
Evidence from vertebrates is unfavourable to either theory and supports, instead, a non-adaptive model, the purely random (Mendelian) determination of sex.
Good for him. I wish I could have been at the meeting. Maybe there was a discussion. Flipping to the back of the book I find a petulant summary of the meeting written by A.J. Cain. You can tell he's really annoyed at something that went on in the meeting,
Ever since natural selection appeared on the scene, there have been those who voiced an a priori and dogmatic dislike of it. One classic example is George Bernard Shaw ... I suspect from my own work that natural selection may have been very much more important than anyone has realized up to now. If so, can these emotional and other rejections of it, or, more generally, the tendency of the human race to take a non-objective view of evolution and kindred topics, be explained by natural selection?

There is a possible evolutionary explanation, as yet untested, and no other scientific one that I know of.
Whew! The discussion must have been exciting. Let's see, it should be right at the end. Ah, here it is,
[It has not been possible to include the general discussion in this publication.]

Gotta go, the banana peel is making me ill—it looks like it's been here since the day before yesterday. Is that a fruit fly? Off I go.

Back again. (Forgot my pen.) See ya.

Larry Moran

What Does San Marco Basilica Have to do with Evolution?

A Critique of the Adaptationist Programme

An Adaptationist in Piazza San Marco

The Spandrels of San Marco and the Panglossian Paradigm

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

Sunday, January 11, 2015

Why can't we teach properly?

The popular press usually screws up whenever it writes about universities and education. This time they got it right. Richard Pérez-Peña published an article in The New York Times a few weeks ago about new ways of teaching science [Colleges Reinvent Classes to Keep More Students in Science]. It was reprinted in The New York Times supplement that arrives with my Sunday copy of the The Toronto Star. The new title is Colleges Try to Enliven Science Teaching. (I don't have a link.)

The opening paragraphs set the tone ...
Hundreds of students fill the seats, but the lecture hall stays quiet enough for everyone to hear each cough and crumpling piece of paper. The instructor speaks from a podium for nearly the entire 80 minutes. Most students take notes. Some scan the Internet. A few doze.

In a nearby hall, an instructor, Catherine Uvarov, peppers students with questions and presses them to explain and expand on their answers. Every few minutes, she has them solve problems in small groups. Running up and down the aisles, she sticks a microphone in front of a startled face, looking for an answer. Students dare not nod off or show up without doing the reading.

Both are introductory chemistry classes at the University of California campus here in Davis, but they present a sharp contrast — the traditional and orderly but dull versus the experimental and engaging but noisy. Breaking from practices that many educators say have proved ineffectual, Dr. Uvarov’s class is part of an effort at a small but growing number of colleges to transform the way science is taught.

Thursday, January 08, 2015

Evolutionary biochemistry and the importance of random genetic drift

I urge you to read an important paper that has just been published in PNAS.
Lynch, M., Field, M.C., Goodson, H.V., Malik, H.S., Pereira-Leal, J.B., Roos, D.S., Turkewitz, A.P., and Sazer, S. (2014) Evolutionary cell biology: Two origins, one objective. Proc. Natl. Acad. Sci. (USA) 111:16990–16994. [doi: 10.1073/pnas.1415861111]
Here's the bit on random genetic drift. It will be of interest to readers who have been discussing the importance of drift and natural selection in a previous thread [How to think about evolution].

Do you think Lynch et al. are correct? I do. I think it's important to emphasize the role of random genetic drift and I think it's true that most biochemists and cell biologists are stuck in an adaptationist mode of thinking.
A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection. Leaving no room for doubt on the process, this narrow view leaves the impression that the only unknowns in evolutionary biology are the identities of the selective agents operating on specific traits. However, population-genetic models make clear that the power of natural selection to promote beneficial mutations and to remove deleterious mutations is strongly influenced by other factors. Most notable among these factors is random genetic drift, which imposes noise in the evolutionary process owing to the finite numbers of individuals and chromosome architecture. Such stochasticity leads to the drift-barrier hypothesis for the evolvable limits to molecular refinement (28, 29), which postulates that the degree to which natural selection can refine any adaptation is defined by the genetic effective population size. One of the most dramatic examples of this principle is the inverse relationship between levels of replication fidelity and the effective population sizes of species across the Tree of Life (30). Reduced effective population sizes also lead to the establishment of weakly harmful embellishments such as introns and mobile element insertions (7). Thus, rather than genome complexity being driven by natural selection, many aspects of the former actually arise as a consequence of inefficient selection.

Indeed, many pathways to greater complexity do not confer a selective fitness advantage at all. For example, due to pervasive duplication of entire genes (7) and their regulatory regions (31) and the promiscuity of many proteins (32), genes commonly acquire multiple modular functions. Subsequent duplication of such genes can then lead to a situation in which each copy loses a complementary subfunction, channeling both down independent evolutionary paths (33). Such dynamics may be responsible for the numerous cases of rewiring of regulatory and metabolic networks noted in the previous section (34, 35). In addition, the effectively neutral acquisition of a protein–protein-binding interaction can facilitate the subsequent accumulation of mutational alterations of interface residues that would be harmful if exposed, thereby rendering what was previously a monomeric structure permanently and irreversibly heteromeric (8, 36–39)1. Finally, although it has long been assumed that selection virtually always accepts only mutations with immediate positive effects on fitness, it is now known that, in sufficiently large populations, trait modifications involving mutations with individually deleterious effects can become established in large populations when the small subset of maladapted individuals maintained by recurrent mutation acquire complementary secondary mutations that restore or even enhance fitness (40, 41).

1. Note the brief description of how irreversibly complex structures can evolve. This refutes Michael Behe's main point, which is that irreversibly complex structures can't have arisen by natural processes and must have been designed. We've known this even before Darwin's Black Box was published.

Wednesday, January 07, 2015

The problem of the origin of life has been solved and creationists are terrified

You learn something new every day. Today I learned that a young physics professor at MIT has figured out how life originated without god(s). Salon let's us know about this amazing discovery: God is on the ropes: The brilliant new science that has creationists and the Christian right terrified.
The Christian right’s obsessive hatred of Darwin is a wonder to behold, but it could someday be rivaled by the hatred of someone you’ve probably never even heard of. Darwin earned their hatred because he explained the evolution of life in a way that doesn’t require the hand of God. Darwin didn’t exclude God, of course, though many creationists seem incapable of grasping this point. But he didn’t require God, either, and that was enough to drive some people mad.

Darwin also didn’t have anything to say about how life got started in the first place — which still leaves a mighty big role for God to play, for those who are so inclined. But that could be about to change, and things could get a whole lot worse for creationists because of Jeremy England, a young MIT professor who’s proposed a theory, based in thermodynamics, showing that the emergence of life was not accidental, but necessary. “[U]nder certain conditions, matter inexorably acquires the key physical attribute associated with life,” he was quoted as saying in an article in Quanta magazine early in 2014, that’s since been republished by Scientific American and, more recently, by Business Insider. In essence, he’s saying, life itself evolved out of simpler non-living systems.
Jerremy England's ideas are too complex for me. Watch this video to see for yourself.

Should politicians and lawyers ban the teaching of some subjects in public schools?

The Scottish Secular Society (SSS) was upset that creationism might be slipping into some schools in Scotland. They petitioned the Scottish government requesting that teaching creationism be banned in public schools in Scotland.1 Government officials refused on the grounds that there were already mechanisms in place to ensure that students received a proper science education [Schools creationism ban rejected by Scottish Government].

The official said,
Safeguards include; school managers having oversight of curriculum planning and resources; local authorities with robust complaints procedures, independent school inspections and the development of curriculum materials through a collegiate approach that provides for early identification of any inappropriate material.
This seems like the proper approach to me. Governments can set up mechanisms to create standardized curricula and that should include descriptions of what should be taught in each grade. They can even pass a law saying that all schools have to adhere to the guidelines.

I don't think they should be responding to pressure groups that want to ban the teaching of certain subjects. Most of us would react strongly to any government that banned teaching of sex education, evolution, communism, Islamic culture, feminism, gun control, or post-modernism.2 We should also be wary of banning other subjects even though we are certain that they are wrong—subjects such as Young Earth Creationism. If you give politicians the right to ban teaching of certain subjects then don't be surprised if it backfires.

It's best not to give them that power in the first place but to rely instead on curricula and standards that are developed by educators and enforced by educators. Mistakes will be made but it's better in the long run to do it that way than to have education influenced by the power of lobbyists and pressure groups and petitions.

Jerry Coyne disagrees. He thinks that the Scottish government should have banned the teaching of creationism [Scotland refuses to ban teaching of creationism]. This is one of those issues where Jerry and I strongly disagree. He wants to fire teachers who teach creationism and he wants government to pass and enforce laws that prohibit the teaching of certain subjects.

Here's the letter he wrote to Fiona Robertson, the director of Scotland’s Learning Directorate.
Dear Ms. Robertson,

As an American professor who teaches evolutionary biology, I was deeply disappointed to read in The Herald of Scotland that your country’s education directors refuse to ban the teaching of creationism to schoolchildren....

As the author of a popular book on the evidence for evolution (Why Evolution is True), I am fully aware of the massive evidence for evolution and the complete absence of evidence for any creationist views, which invariably stem from Biblical literalism. Creationism is thus a purely nonscientific view based on religion, and I’m saddened that Scotland won’t take even a minimal stand to ensure that its children are not indoctrinated with such bogus "science". The truth of evolution, I’ve found, is not only fascinating, based as it is on mountains of diverse but congruent evidence, but also deeply enlightening, showing us how our own species, and other species as well, came to be. It is the true story of our origins.

I hope that Scotland, like England and Wales, will have the resolve to explicitly establish some guidelines about what Tim Simmons, head of the Curriculum Unit, called "well-established science." Without an explicit statement that creationism is not well-established science, schools are at the mercy of whatever their teachers want to impart about the origins and diversity of organisms.

Thank you for your consideration.
Jerry Coyne
Department of Ecology and Evolution
The University of Chicago
Chicago, IL 60637 USA
I don't agree with Jerry Coyne. I'm all in favor of teaching evolution and proper science but I'm also in favor of teaching students why things like creationism, astrology, and homeopathy are wrong and why the Loch Ness monster doesn't exist.

It's a bit ridiculous to pass laws banning the teaching of every single thing that "is not well-established science."

It's true that "schools are at the mercy of whatever their teachers want to impart" but the way to fix that problem is to change the views of society, and teachers, about evolution and creationism. There isn't much evidence that simply banning certain subjects will actually change whether students believe them or not. If that were true, then we would expect that the students of Dover Pennsylvania have now come to accept evolution and reject creationism.

1. I'm using "public" school in the North American sense to refer to schools that are open to the public and supported by government funding.

2. I'm a bit ambivalent about banning post-modernism.

Tuesday, January 06, 2015

The textbooks are wrong about protein synthesis according to a press release from the University of Utah

A recent paper in Science provides evidence that when protein synthesis is stalled a protein called Rqc2 ("conserved from yeast to man") catalyzes the addition of random amounts of alanine and threonine the the C-terminus of the proteins that's about to be destroyed (Shen et al., 2015).

Here's the editorial summary of the work ...
During the translation of a messenger RNA (mRNA) into protein, ribosomes can sometimes stall. Truncated proteins thus formed can be toxic to the cell and must be destroyed. Shen et al. show that the proteins Ltn1p and Rqc2p, subunits of the ribosome quality control complex, bind to the stalled and partially disassembled ribosome. Ltn1p, a ubiquitin ligase, binds near the nascent polypeptide exit tunnel on the ribosome, well placed to tag the truncated protein for destruction. The Rqc2p protein interacts with the transfer RNA binding sites on the partial ribosome and recruits alanine- and threonine-bearing tRNAs. Rqc2p then catalyzes the addition of these amino acids onto the unfinished protein, in the absence of both the fully assembled ribosome and mRNA. These so-called CAT tails may promote the heat shock response, which helps buffer against malformed proteins
This is mildly interesting. We've known about ubiquitin ligase for decades but this is a different way of tagging proteins for destruction.

We'll have to see if this work stands up to verification but even if it does, it's not going to make it into the textbooks.

Let's see what the University of Utah Press Office has to say ...
Defying Textbook Science, Study Finds New Role for Proteins

Open any introductory biology textbook and one of the first things you’ll learn is that our DNA spells out the instructions for making proteins, tiny machines that do much of the work in our body’s cells. Results from a study published on Jan. 2 in Science defy textbook science, showing for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints – DNA and an intermediate template called messenger RNA (mRNA). A team of researchers has observed a case in which another protein specifies which amino acids are added.

"This surprising discovery reflects how incomplete our understanding of biology is,” says first author Peter Shen, Ph.D., a postdoctoral fellow in biochemistry at the University of Utah. “Nature is capable of more than we realize." ...
Mathew Cobb, writing on Jerry Coynes blog, explains why this isn't really a big deal [CAT tails weaken the central dogma – why it matters and why it doesn’t]. Let me just add that the synthesis of peptides with defined sequences in the absence of mRNA and ribosomes has been described in most textbooks since the 1980s. The best examples are the peptides involved in pepditogylcan synthesis (cell walls) and peptide antibiotics.

Here's a figure from my book.

What this means is that the statement, "... showing for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints – DNA and an intermediate template called messenger RNA (mRNA)" is simply not true.

We really, really, need to do something about university press releases.

Shen, P.S., Park, J., Qin, Y., Li, X., Parsawar, K., Larson, M.H., Cox, J., Cheng, Y., Lambowitz, A.M., Weissman, J.S., Brandman, O., and Frost, A. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Science 347:75-78. [doi: 10.1126/science.1259724 ]

Guilt by association

There are many common fallacies that can easily make your argument invalid. The Intelligent Design Creationists seem to posses an uncanny ability to use each and every one of them. Here's a good example of guilt by association, heavily laced with ad hominem.

It's a documentery called The Biology of the Second Reich) by John West and colleagues. John West is one of the bigwigs at the Discovery Institute. The IDiots see this sort of propaganda as support for Intelligent Design Creationism and evidence against evolution.

The IDiots are excited about the fact that this documentary just won a prize in the "Best Documentary Short" category of the Los Angeles Cinema Festival of Hollywood! [Congratulates to John West as Biology of the Second Reich, "Best Documentary Short," Scores Big Recognition!]. I'm pretty sure the prize is based on the quality of the production and not on the accuracy of the information in the documentary. This is typical of most awards for documentaries and nonfiction books.

Monday, January 05, 2015

If you take away religion, you can't hire enough police

Here's a Harvard Professor, Clayton Christensen, telling us with a straight face that democracy in the USA requires religion because in the absence of religion people won't choose to obey laws. He ends with, "If you take away religion, you can't hire enough police."

It makes me wonder how much critical thinking goes on in his classes at Harvard Business School. Do Harvard students let him get away with this crap?

Sunday, January 04, 2015

A lesson on genetic load

The genetic load argument is one of the five things you should know if you are going to participate in the junk DNA debate.

Dan Graur has written an excellent summary of the genetic load argument from the perspective of population genetics. He links to it from his blog: If @ENCODE_NIH is right, each of us should have 7 x 1045 children.

Read it.

Is that really all they've got?

Last week I alerted you to seven of the top ten evolution stories according to IDiots [Is that all they've got?. Now it's time for the top three stories .... hang on to your hats.

#3. #3 of Our Top Ten Evolution Stories of 2014: Cosmos Finale Takes One Last Shot at the Privileged Planet Thesis

#2. #2 of Our Top Ten Evolution Stories of 2014: Now with More Doubt! Meyer's Landmark Is Back in a New Edition, Replying to the Critics

And the number one proof of Intelligent Design Creationism in 2014 is ....

#1. Happy New Year! Our #1 Evolution Story of 2014: New Paper from Biologic Institute, "Shared Evolutionary History or Shared Design?"

At this rate real, science will probably survive through most of 2015.

A physiologist thinks about evolution

Denis Noble is a physiologist at Oxford University (now Professor Emeritus). He is famous for his work on the physiology of the heartbeat and he is touted as one of the founders of systems biology.

Denis Noble wrote a book on evolutionary theory called The Music of Life. It's featured on The Third Way, a website created by James Shapiro to promote his version of a paradigm shift in thinking about evolution. All the usual suspects are represented on that site.1

Here's how the book is described on that website ....
What is Life? Decades of research have resulted in the full mapping of the human genome - three billion pairs of code whose functions are only now being understood. The gene’s eye view of life, advocated by evolutionary biology, sees living bodies as mere vehicles for the replication of the genetic codes.

But for a physiologist, working with the living organism, the view is a very different one. Denis Noble is a world renowned physiologist, and sets out an alternative view to the question - one that becomes deeply significant in terms of the living, breathing organism. The genome is not life itself. Noble argues that far from genes building organisms, they should be seen as prisoners of the organism.

The view of life presented in this little, modern, post-genome project reflection on the nature of life, is that of the systems biologist: to understand what life is, we must view it at a variety of different levels, all interacting with each other in a complex web. It is that emergent web, full of feedback between levels, from the gene to the wider environment, that is life. It is a kind of music.

Including stories from Noble’s own research experience, his work on the heartbeat, musical metaphors, and elements of linguistics and Chinese culture, this very personal and at times deeply lyrical book sets out the systems biology view of life.
I haven't read this book and I don't intend to read it. Having listened to a lecture by Denis Noble (below) I don't think I'm going to learn anything more by buying the book.

I urge you to watch the lecture. It's the plenary lecture at the International Conference of Physiological Sciences in November, 2012. Denis Noble is the President of the International Union of Physiological Sciences. The lecture is only 30 minutes long but it gives you a good introduction to the way many scientists from outside the field of evolutionary biology are thinking about evolution (and the Central Dogma of Molecular Biology). It's not a very pretty picture.

If you want a brief summary of what's wrong with this lecture see Jerry Coyne's blog website post: Famous physiologist embarrasses himself by claiming that the modern theory of evolution is in tatters.

1. For more on James Shapiro see: The Third Fourth? Way
Evolution: a View from the 21st century
Reply to Laurence A Moran’s review of Evolution: A View from the 21st Century
James Shapiro Responds to My Review of His Book
James Shapiro Never Learns
James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle"
Revisiting the Central Dogma in the 21st Century.

Saturday, January 03, 2015

Thinking critically about the Central Dogma of Molecular Biology

Our department is preparing to review our undergraduate courses and programs. Part of the review will be to examine our fundamental goals and objectives and determine if we are meeting them. In preparation for this exercise, I've been going over some papers that have been sitting around my office.

One of them concerns teaching the Central Dogma of Molecular Biology (Wright et al., 2014). It was just published last year. The authors have discovered that students have a "weak conceptual understanding" of information flow. Here's how they describe it in the abstract.
The central dogma of molecular biology, a model that has remained intact for decades, describes the transfer of genetic information from DNA to protein though an RNA intermediate. While recent work has illustrated many exceptions to the central dogma, it is still a common model used to describe and study the relationship between genes and protein products. We investigated understanding of central dogma concepts and found that students are not primed to think about information when presented with the canonical figure of the central dogma. We also uncovered conceptual errors in student interpretation of the meaning of the transcription arrow in the central dogma representation; 36% of students (n = 128; all undergraduate levels) described transcription as a chemical conversion of DNA into RNA or suggested that RNA existed before the process of transcription began. Interviews confirm that students with weak conceptual understanding of information flow find inappropriate meaning in the canonical representation of central dogma. Therefore, we suggest that use of this representation during instruction can be counterproductive unless educators are explicit about the underlying meaning.

Thursday, January 01, 2015

Most popular Sandwalk post in 2014

Lot's of people are publishing year-end summaries of their blog activity. It got me to wondering which of my posts was the most popular in 2014.

The result was a surprise ...

August 18, 2014: John Wilkins discusses the "Demarcation Problem"
One of the most fascinating things about philosophy is the fact that philosophers still can't agree on the major issues even after debating them for hundreds of years. For example, they still can't, as a discipline, agree on whether there are good arguments for the existence of gods. Many universities have theologians who masquerade as philosophers and publish in philosophy journals....