Teaching about genomes using Nessa Carey's book: Junk DNA

Nessa Carey's book about junk DNA is an embarrassment to the scientific community [Nessa Carey doesn't understand junk DNA] [The "Insulation Theory of Junk DNA"].

Today, while searching for articles on junk DNA, I came across a review of Nessa Carey's book published in The American Biology Teacher: DNA. The review was written by teacher in Colorado and she liked the book very much. Here's the opening paragraph,

The term junk DNA has been used to describe DNA that does not code for proteins or polypeptides. Recent research has made this term obsolete, and Nessa Carey elaborates on a wide spectrum of examples of ways in which DNA contributes to cell function in addition to coding for proteins. As in her earlier book, The Epigenetics Revolution (reviewed by ABT in 2013), Carey uses analogies and diagrams to relate complicated information. Although she unavoidably uses some jargon, she provides the necessary background for the nonbiologist.

The author of the review does not question or challenge the opinions of Nessa Carey and, if you think about it, that's understandable. The average biology teacher will assume that a book written by a scientist must be basically correct or it wouldn't have been published.

That's not true, as most Sandwalk readers know. You would think that biology educators should know this and exercise a little skepticism when reviewing books. Ideally, the book reviews should be written by experts who can evaluate the material in the book.

Now we have a problem. The way to correct false information about genomes and junk DNA is to teach it correctly in high school and university courses. But that means we first have to teach the teachers. Here's a case where professional teachers have been bamboozled by a bad book and that's going of make it even more difficult to correct the problem.

The last paragraph of the review shows us what influence a bad book can have,

As a biology teacher who enjoys sharing with students some details that go beyond the textbook or that challenge dogma, I enthusiastically read multiple chapters at each sitting, making note of what I cannot wait to add to class discussions. “Junk DNA” may be a misnomer, but Junk DNA is an excellent way of finding out why.

Oh dear. It's going to be hard to re-educate those students once their misconceptions have been reinforced by a teacher they respect.

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Another failure: "The Mysterious World of the Human Genome"

The Mysterious World of the Human Genome
by Frank Ryan
William Collins, an imprint of Harper Collins, London UK (2015)
ISBN 978-0-00-754906-1

This is just another "gosh, gee whiz" book on the amazing and revolutionary (not!) discoveries about the human genome. The title tells you what to expect: The Mysterious World of the Human Genome.

The author is Frank P. Ryan, a physician who was employed as an "Honorary Senior Lecturer" in the Department of Medical Education at the University of Sheffield (UK). He's a member of The Third Way group. You can read more about him at their website: Frank P. Ryan.

The best TED talk ever

I'm not a fan of TED talks. Comedian Will Stephen has figured them out and he gives a perfect example of everything that's wrong with a TED talk. Watch "How to sound smart in your TEDx Talk."

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The Fermi Paradox: Are we alone in the universe?

All available evidence suggests that we are quite likely the only advanced life form in the Milky Way galaxy. Maybe our planet harbors the only life in the entire universe.

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A DNA quiz

Jerry Coyne discovered a Quiz on DNA. He calls is a so-so quiz on DNA. He says that one question is really, really, dumb. I disagree, I think there are several dumb questions.

I tried it and got a score of 19/19 in just under four minutes. This is misleading since you have to get every question right before continuing on to the next question. I had to anticipate what the authors wanted in order to proceed.

Try the quiz yourself before reading any further. There are spoilers below!

Richard Dawkins makes a mistake when describing why gene trees are evidence of evolution

Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."

There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.

An undergraduate biochemistry lecture converts an atheist to Christianity

I'm reading Creation or Evolution: Do we have to choose? by Denis Alexander in preparation for our discussion next Friday at Wycliffe College on the University of Toronto downtown campus [Discussing the conflict between science and religion with Denis Alexander].

Denis Alexander is a biochemist at the University of Cambridge (UK). I thought I'd share one of the stories in his book.

At the church I attend in Cambridge we baptised an undergraduate in the natural sciences who had come to a personal, saving faith in Christ from a completely atheistic background. As is usual in our church, just before being baptised she explained publicly to the whole congregation how she had become a Christian, telling us she had become convinced there must be a God while sitting through a standard biochemistry lecture, hearing the amazing story of how two meters (about six feet) of DNA are packaged into a single cell. Of course the lecturer was not talking in religious terms at all, but she described to us how the beauty of that engineering feat overwhelmed her as she listened, giving her the deep intuition there must be a God, so leading her onward in he personal pilgrimage to put her trust in this creator God through Christ. Truly natural theology at work!

That got me thinking. I've been describing chromatin and packing in my textbooks since the first version in 1987. There must have been several hundred thousand students who have read my descriptions since then.

I wonder how many I've converted?

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On the (false) significance of a liberal arts education

Joshua Kim posted an article on Inside Higher Education last month (Dec. 8, 2015). The article described his answers to some questions he was being asked in a interview [How Would You Answer These 9 Reimagine Education Questions?].

Here's one of the questions and his answer ...

Question 4: Is there an innovation/idea/movement/methodology that excites you in terms of the future of education?

Yes. A liberal arts education.

Rethinking medical education at the University of Toronto

Watch two medical educators from my Faculty of Medicine at the University of Toronto. They are being interviewed by Steve Paiken of The Agenda. They rightly deplore the traditional lecture style of learning that's common in my university but their solution is more online learning.

The real problem with medical education is that much of the first two years is based on the "memorize and regurgitate" model that we know is ineffective. The best way to change the system is to use evidence-based methods that emphasize student-based learning. The idea is to teach medical students how to access information and how to interpret it rather than have them memorize facts. When teaching biochemistry, for example, it's pointless to ask medical students to take an exam based on structures and pathways that they will forget the day after the exam.

These two physicians are in charge of reforming medical education. They want to please the students by creating a new way of teaching that emphasizes the way "millennials" want to learn. (Short online courses, no lectures.) You'll watch the entire show without hearing any references to the pedagogical literature and what's known to work. Is there any evidence that undergraduate medical students are experts on medical education? (Hint: ... no.)

If this is the wave of the future, I fear that future doctors are not going to be any more informed that the current crop. They will still not be capable of critical thinking.

The way we teach needs to change, but not this way.

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Joe Hanson tells us about evolution

Joe Hanson Ph.D. (Biology) of It's Okay To Be Smart is posting a series of videos on evolution. They're called The 12 Days of Evolution.

The first one is "What Is Evolution Anyway?" You won't surprised to learn that Joe Hanson conflates "evolution" with "natural selection" and fails to mention the most important features of evolution [see What Is Evolution]. You WILL be surprised to learn that Jerry Coyne has the same objections I do! [Twelve Days of Evolution: #1: What’s evolution?]

We need to do a much better job of educating the general public about the meaning of evolution but first we need to educate the teachers. It's okay to be smart but it's not okay to just pretend to be smart.

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Evolution as a foundational concept in biochemistry and molecular biology

The American Society for Biochemistry and Molecular Biology (ASBMB) has been promoting a new way of teaching undergraduate courses. The idea is to concentrate on fundamental principles and concepts rather than on trivial details. The various working groups came up with a list of these fundamental concepts under five main headings: Evolution; Matter and Energy Transformation; Homeostasis; Macromolecular Structure & Function; and Biological Information.

I've discussed the concepts before [ASBMB Core Concepts]. There are problems.

Various committees continue to meet in order to build a "concept inventory" to guide the new curriculum. There have been a series of workshops organized around the main themes. The participants in the workshops are, for the most part, teachers at small universities and colleges. They have lots of experience teaching undergraduate courses but they aren't necessarily experts in the subject material.

I saw this clearly when I attended a session at the last Experimental Biology meeting in Boston last April. The purpose of the meeting was to review the major concepts in Evolution and Homeostasis. I met a great deal of resistance from the workshop leaders when I tried to explain the concepts of neutral alleles and random genetic drift and show them why they were so important when comparing sequences and constructing phylogenetic trees.

INTEGRATING EVOLUTION AND HOMEOSTASIS WITH THE CORE CONCEPTS OF BIOCHEMISTRY AND MOLECULAR BIOLOGY
Symposium Tues. 9:45 am Boston Convention & Exhibition Center, room 256

Chaired: E. Bell

9:45 RCN-UBE: Integrating Evolution and Homeostasis with the Core Concepts of Biochemistry and Molecular Biology J.E. Bell, A. Aguanno, P. Mertz, M. Johnson and K.M. Fox. Univ. of Richmond, Union Col., NY, Univ. of Alabama, St Mary’s Col. of Maryland and Marymount Manhattan. (559.2)

Presenters:
Small Group Work: Integrating Evolution and Homeostasis into the Core Concepts E. Bell, Univ. of Richmond A. Aguanno, Marymount Manhattan Col.

Group Discussion on Core Concept integration with Homeostasis A. Aguanno, Marymount Manhattan Col.

Small Group Work: Question Development Involving Evolution and Homeostasis M. Johnson, Univ. of Alabama

Group Presentations and Discussion on Question Implementation K. Fox. Union Col.

This same group has published some of their findings in the July/August issue of the education journal, Biochemistry and Molecular Biology Education (BAMBED)¹ (Aguanno et al. 2015).

Here are the learning objectives they have developed under the "Evolution" concept.

• central importance of the theory of evolution
• Darwin's theory of evolution
• process of natural selection
• evidence for the theory of evolution
• molecular basis of natural selection

I really think this misses the boat in a biochemistry context where molecular evolution plays such an important role. It will be hard to discuss genome organization and junk DNA, for example, if students don't know about population genetics and random genetic drift. It will be hard to explain (correctly) why different proteins in different species have different amino acid sequences if students don't know about neutral alleles.

I pointed this out to the authors at the meeting and stimulated a discussion about these concepts. The authors, and the other teachers in the room, were pretty certain that the differences in amino acid sequences were all due to natural selection. Most of them had never heard of random genetic drift.

The problem here is that the learning objectives and the "capstone experiences" are being developed by teachers who don't really understand evolution. It is assumed that the best people to work on the new curriculum are experienced teachers but that's demonstrably false. (It applies to the other concepts as well.)

It turns out that biochemistry professors are not as knowledgeable about core concepts as you might imagine.

The authors surveyed 161 teachers in 143 institutions across the USA to find out what are the most important concepts in a biochemistry and//or molecular biology course.

The results, right, indicate that less than 8% of the respondents thought that evolution was an important concept.

This could be due, in part, to the fact that biochemistry courses are often taught by professors who are members of a chemistry department but no matter what the explanation it looks like we have a lot of work ahead of us if we are going to convince our colleagues to make evolution a core concept.

I'm pretty sure that many of the people who teach our introductory biochemistry courses at the University of Toronto don't see evolution as a core concept and don't understand modern evolutionary theory.

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1. Disclaimer: I am on the editorial board of that journal.

Aguanno, A., Mertz, P., Martin, D., and Bell, E. (2015) A National Comparison of Biochemistry and Molecular Biology Capstone Experiences. BAMBED 43:223-232. [doi: 10.1002/bmb.20869]

Nature publishes a misleading history of the discovery of DNA repair

The history of DNA repair is well-known. Here's a quote from "Early days of DNA repair: discovery of nucleotide excision repair and homology-dependent recombinational repair" by W.D. Rupp in 2013 (Rupp, 2013).

This article describes events related to the first papers published in the 1960s describing nucleotide excision repair (NER) and homology-dependent recombinational repair.

Here's are the relevant papers.

Setlow, R.B., and Carrier, W.L. (1964) The disappearance of thymine dimers from DNA: An error-correcting mechanism. Proc. Natl. Acad. Sci. (USA) 51:226–231. [Full Text]

Boyce, R.P., Howard-Flanders, P. (1964) Release of ultraviolet light-induced thymine dimers from DNA in E. coli K-12. Proc. Natl. Acad. Sci. (USA) 51:293–300. [Full Text]

Pettijohn, D, and Hanawalt, P. (1964) Evidence for repair-replication of ultraviolet damaged DNA in bacteria. J. Mol. Biol. 9:395–410. [PubMed]

Lessons not learned from 50 years ago

A few months ago Nature published an article on how to create a science-literate population. There's a letter in the Sept. 17th (2015) issue that addresses this point by reminding readers of another article published 50 years ago (1965).

The title of that older article was "New thinking in undergraduate education." Here's what it said ....

Students are in danger of "spending too much of their time memorizing facts, and [have] insufficient time at [their] disposal to master the principles underlying [their] subject and to develop [their] powers of thought." .... the most important purpose of a university education is to teach [students] to think for [themselves] ... it may on occasion demand a re-examination of the whole approach to a subject in undergraduate courses."

I remember that the biology department where I was an undergraduate (Carleton University in Ottawa) organized a weekend conference to discuss revising undergraduate education in 1967. I spoke about the need to focus on ideas and concepts and get away from boring lectures about facts.

plus ça change, plus c'est la même chose
UPDATE: A reader asked for the references. The letter in the Sept. 17th issue is from Barry S. Winkler [doi: 10.1038/525321f]. The original article from 1965 is in the issue of Feb. 27, 1965 [doi: 10.1038/205835a0]. The 2015 article referred to in the recent letter to Nature is Bradforth et al. (2015).

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Bradforth, S.F., Miller, E.R., Dichtel, W.R., Leibovich, A.K., Feig, A.L., Martin, J.D., Bjorkman, K.S., Schultz, Z.D., and Smith, T.L. (2015) University learning: Improve undergraduate science education. Nature 523:282-284 [PDF]

Best blog post in the past year

3 Quarks Daily is running their annual contest to pick the best blog posts in the past year. The finalists will be picked by popular vote and the winner will be selected from the finalists by Nick Lane. You can review the rules at: Nick Lane to Judge 6th Annual 3QD Science Prize.

The formal description of the prize is "6th annual prize for the best blog and online-only writing in the category of science." This is important because although the rules refer to "blog posts" and "blog entries" it's clear that most of the nominees are more like online poplar science articles than typical blog posts.

Here's a list of the current nominees ...

Jerry Coyne doubles down on his criticism of how evolution is taught in Ontario schools

A few weeks ago, Jerry Coyne got his knickers in a knot because the Ontario school curriculum didn't specifically prescribe the teaching of evolution in the way that he would like [Ontario schools require teaching evolution—except human evolution].

I replied to that post, quoting the Ontario curriculum and pointing out that it was pretty damn good when it comes to evolution [Teaching evolution in Ontario Schools]. The curriculum concentrates on fundamental principles of evolution as they apply to all species. It does not cover any details of the history of life per se. It doesn't specifically mention the evolution of whales, or birds, or any other lineage. It doesn't say which examples have to be included in the classroom instruction. It refers frequently to the fact that humans are not different than any other animals when it comes to biology.

Jerry take this to mean that detailed descriptions of human evolution are specifically excluded and he now claims that this is due to government policy [Ontario school officials respond—or rather, fail to respond—to queries about why they don’t require teaching human evolution].

Teaching evolution in Ontario Schools

In Ontario (Canada) there is a province-wide curriculum that all public schools must follow. This includes the Roman Catholic separate schools that receive money from the province. This post is prompted by something written last month by an anonymous blogger who runs Darwnquixote. He claims that human evolution is not taught in Ontario schools [Be Careful, Evolution is Behind You]. Jerry Coyne picks up on this and launches into a tirade about the Ontario curriculum [Ontario schools require teaching evolution—except human evolution]. Coyne urges everyone to write letters of complaint to the Ontario Minister of Education. (Her name is Liz Sandals and she is an excellent (not perfect) Minister of Education.) Is it true that the Ontario curriculum does not teach that humans have evolved?

I've been quite impressed with the science and technology curriculum as revised in 2008 and I'm hearing good things about the next revision. The teaching of evolution, like all aspects of the curriculum, focuses on understanding the basic concepts and on encouraging students to think for themselves. Students learn about evolution and diversity in the primary grades where the emphasis is on the relationship of humans and other species [The Ontario Curriculum: Elementary: Science and Technology]. In grade 1 they learn that "Plants and animals, including people, are living things" (page 44) and in Grade 2 one of the "big ideas" is that humans are animals (page 58).

What is "PeerWise"?

I came across an interesting article about "PeerWise."

Hardy, J., Bates, S.P., Casey, M.M., Galloway, K.D., Galloway, R.K., Kay, A.E., Kirsop, P., and McQueen, H.A. (2015) Student-Generated Content: Enhancing learning through sharing multiple-choice questions. International Journal of Science Education 36: 2180-2194. [doi: 10.1080/09500693.2014.916831]

Abstract

The relationship between students' use of PeerWise, an online tool that facilitates peer learning through student-generated content in the form of multiple-choice questions (MCQs), and achievement, as measured by their performance in the end-of-module examinations, was investigated in 5 large early-years science modules (in physics, chemistry and biology) across 3 research-intensive UK universities. A complex pattern was observed in terms of which type of activity (writing, answering or commenting on questions) was most beneficial for students; however, there was some evidence that students of lower intermediate ability may have gained particular benefit. In all modules, a modest but statistically significant positive correlation was found between students' PeerWise activity and their examination performance, after taking prior ability into account. This suggests that engaging with the production and discussion of student-generated content in the form of MCQs can support student learning in a way that is not critically dependent on course, institution, instructor or student.

This sounds like a good way to encourage some student-centered learning in large classes. We have several biochemistry classes in our department that could benefit.

Does anyone have any experience with PeerWise?

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The value of critique in science education

One of the most difficult concepts to get across to science educators (e.g. professors in a biochemistry department ) is the idea that students need to be exposed to ideas that you think are incorrect and they need to be given the opportunity to make a choice. It's part of critical thinking and it's part of a good science education. Part of the problem is that there's a general reluctance to even teach "ideas" as opposed to facts and techniques.

There's an extensive pedagogical literature on this but university professors are reluctant to admit that there might be better ways to teach. While browsing this literature, I came across a recent article by Henderson et al. (2015) that makes a good case.

Orac responds to my post on teaching the controvery

Orac didn't like part of my post On teaching alternative medicine at the University of Toronto. Here's what I said a few days ago ...

From an academic pedagogical perspective, there’s nothing wrong with a course that has a reading list emphasizing quack medicine. This is the view that people outside of the university don’t understand. They appear to want to prevent students from ever learning about, or discussing, the anti-vax movement and how to deal with it.

They are wrong.

Orac took this personally and responded in a post of his own [On teaching pseudoscientific controversies in universities…].

Those of you who read the articles and have seen talks by supporters of science-based medicine like Steve Novella and myself will recognize this for the straw man that it is. We never say anything like this, that we want to prevent students from learning about or discussing the antivaccine movement. That is an assertion that is unsupported and, quite frankly, downright risible. So you should understand that I was more than a little pissed off when I read this part of Moran’s post. We never say that we don’t want alternative medicine to be taught or antivaccine views taught. (Indeed, I really wish that pediatrics residency programs, for instance, would do a better job of teaching antivaccine views, so that they don’t catch pediatricians by surprise when parents start expressing them.) What we complain about is the uncritical teaching of these topics, the teaching, for example, of alternative medicine modalities as though they had scientific merit. This is a massive problem in medical academia. I’ve lost track of how many times I’ve reiterated this very point going back at least a decade.

We agree. I wasn't referring to people like Orac who understand how universities should work. I was referring to those people outside of the university community who really do want to ban any mention of alternative medicine at universities. I guess I didn't make that clear.

I'm pretty sure that Orac knows about this crowd. They are totally opposed to the idea of teaching the controversy. They have some very strong views on what's right and what's wrong and they firmly believe that the only views that should ever be expressed in university classes are the ones they agree with.

In the end, my little fit of pique over Prof. Moran’s condescending and dismissive attitude towards those of us who were so outraged by this course being offered by U. of T. aside, we actually (mostly agree). Moran supports “teaching the controversy” with respect to evolution and with respect to alternative medicine. So do I. Where we disagree is over what “teaching the controversy” actually entails. Can Prof. Moran can honestly say that he wouldn’t be the least bit upset if his own department were to offer an entire course on “controversies in evolution” taught by Ken Ham, Casey Luskin, and a Discovery Institute fellow to be named later? That he would approve of such a class as a great way to “teach the controversy”? If he can, I’d say there’s a problem. If he can’t say that, I congratulate him. That’s the correct reaction. In that case, I also point out that he has no business being so contemptuous of our anger over a homeopath teaching a course in alternative medicine as a way of “teaching the controversy.”

As I said in my earlier post, the problem wasn't that an anti-vaccine point of view was being discussed in a university course. The problem was that the course was being taught by someone who wasn't qualified to offer a university course that encouraged critical thinking. That situation has been rectified.

I would love to invite Casey Luskin to come and give a few lectures on Intelligent Design Creationism to my students. It would be far better for them to hear the other side directly from the horse's mouth than filtered through me.

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On teaching alternative medicine at the University of Toronto

There's been a recent kerfluffle about a course called "Alternative Health: Practive and Theory" taught as part of a program in Health Studies at the University of Toronto's Scarborough campus (Toronto, Ontario, Canada).

Most of the readings in the course emphasized non-evidence-based medicine and health. The instructor was Beth Landau-Halpern, a homeopath who warns her patients about the dangers of vaccines [see Beth Landau-Halpern]. She's also the wife of Rick Halpern, the Dean and Vice-Principle of University of Toronto, Scarborough (UTSC). Ms. Landau-Halpern will no longer be teaching and the Dean has resigned [Rick Halpern Resigns].