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, 1997What 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
  courses.
• 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, 2008The 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?

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How to become a better teacher (not)

Here's a video by Dr. Lodge McCammon. He has a website: lodgemccammon.com. Here are his credentials.

Dr. Lodge McCammon is an educational innovator. His career began in 2003 at Wakefield High School in Raleigh, North Carolina, where he taught Civics and AP Economics. McCammon received a Ph.D. from NC State University in 2008 and continued his work by developing innovative practices and sharing them with students, teachers and schools across the world. McCammon is a musician who spends much of his time in the recording studio composing curriculum-based music. His songs and related materials can be found in Discovery Education Streaming. He is also an education consultant who provides professional services, including keynote speeches, presentations, curriculum development, and a variety of training programs.

Watch the video and discuss. I think you can guess what I think. I reject one of the basic premise; namely that online courses are taught by the very best teachers. How do we know who is the best teacher just by watching videos?

Here's a question for your consideration. It concerns "reflective teaching." Imagine that you record yourself teaching an incorrect version of the citric acid cycle or a flawed version of the Central Dogma of Molecular Biology. How many times do you have to watch that video to recognize that what you are teaching is wrong? Is it more than three? Less than ten?

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Evolution: A Course for Educators: Week One

I'm taking a MOOC! It's called Evolution: A Course for Educators. The principle instructors are Joel Cracraft and David Randle of the American Museum of Natural History in New York (USA).

Welcome to Evolution: A Course for Educators! We’re excited to have almost 13,000 students enrolled in the course and look forward to spending the next four weeks together as we learn about the Tree of Life, natural selection, the history of life, and human evolution, as well as how to incorporate an exploration of these issues into your classrooms.

You can earn a "Verified Certificate" by paying $29.00.

Do Graduate Students Understand Evolution?

 
The other day I was discussing how to teach evolution with one of my colleagues and the discussion turned to the presumed distinction between students who were really interested in science and everyone else. My colleague claimed that students who were science oriented probably managed to acquire a good understanding of evolution in spite of the fact that some undergraduate courses weren't doing a very good job of teaching the subject.

I pointed out that my impression was different. I suggested that most Professors in our department don't have a firm grasp of one of the most fundamental concepts in biology (evolution), and neither do our graduate students. I reminded my colleague of the times when we cringe at graduate student presentations when the topic of evolution comes up.

Ryan Gregory must have felt the same way since he was prompted to do a survey of graduate students in science departments at Guelph University. The result is published in BioScience. You can read about it on Ryan's blog: How well do grad students grasp evolution?.
Here's the press release...

Science Students Could Brush Up On Darwin, U of G Study Finds

October 01, 2009 - News Release

Even students pursuing advanced degrees in science could brush up on their knowledge of evolution, according to a new study by University of Guelph researchers.

The finding reveals that there is room for improvement in how evolution is taught from elementary school up, said Ryan Gregory, a professor in Guelph’s Department of Integrative Biology, who conducted the research with former student Cameron Ellis.

The study was published today in BioScience. It’s particularly timely, given that this year is the bicentennial of Charles Darwin’s birth and the 150th anniversary of publication of On the Origin of Species, which underpins understanding of the diversity of Earth’s organisms and their interrelations.

“Misconceptions about natural selection may still exist, even at the most advanced level,” Gregory said.

“We’re looking at a subset of people who have spent at least four years, sometimes even six or seven years, in science and still don’t necessarily have a full working understanding of basic evolutionary principles or scientific terms like ‘theories.’”

Many previous studies have assessed how evolution is understood and accepted by elementary, high school and undergraduate students, as well as by teachers and the general public, Gregory said. But this was the first to focus solely on students seeking graduate science degrees.

The study involved nearly 200 graduate students at a mid-sized Canadian university who were studying biological, physical, agricultural or animal sciences. About half of the students had never taken an evolutionary biology course, which is often not a prerequisite.

The researchers found that the vast majority of the students recognized the importance of evolution as a central part of biology. Overall, they also had a better understanding of evolutionary concepts than most people.

“That was encouraging, especially because it was across several colleges — it wasn’t just the biology students,” Gregory said.

But when the students were asked to apply basic evolutionary principles, only 20 to 30 per cent could do so correctly, and many didn’t even try to answer such questions. Of particular interest to Gregory is the finding that many students seem less than clear about the nature of scientific theories.

“This is telling us that traditional instruction methods, while leading to some basic understanding of evolution, are not producing a strong working knowledge that can be easily applied to real biological phenomena.”

Gregory has studied evolution-related topics for years and recently co-organized a workshop designed to improve how the subject is taught in public schools. He is also associate editor of Evolution: Education and Outreach, a journal written for science teachers, students and scientists. He recently created Evolver Zone, a free online resource for anyone interested in evolutionary biology.
He is also helping bring an evolution-inspired art exhibit to U of G this month. “This View of Life: Evolutionary Art in the Year of Darwin, 2009” highlights diverse artists’ views of Darwin’s ideas and evolution in general. It runs Oct. 9 to 30 in the science complex atrium.

Some of us know what the problem is. What are we going to do about it? How are we going to convince professors that evolution education has to change when most of them don't even recognize there's a problem because their own views of evolution are flawed?

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What is bioethics? Is Margaret Somerville a bioethicist or a Roman Catholic apologist?

I had an interesting conversation with a student the other day. She's studying "bioethics" at the University of Toronto. This is a program run by the Deptment of Philosophy.

I asked her to define "bioethics" and she couldn't. To her credit, she immediately recognized that this wasn't right. If she's taking an entire program in bioethics she ought to be able to explain what it was all about. She was then joined by her friend, who is also majoring in bioethics. My colleague, Chris DiCarlo also joined us. He's a philosopher writing a book on ethics.

We described a scenario where I wanted to end my life and Chris was willing to help me. Neither of us have an "ethical" problem with that decision. So why is assisted suicide thought to be a problem for bioethics? If some people don't want to participate in euthanasia then nobody is going to make them? Where's the problem?

Does it only become a bioethical problem if some people want to impose their views on others? In this case, the people who are personally opposed to euthansia want to pass a law preventing me from ending my life with the help of my friend. Our students were puzzled by this discussion. Even though they have taken many courses on bioethics, nobody had ever raised this issue. Isn't that strange? You would think that any program run by a Department of Philosophy would emphasize critical thinking. Sadly, this turns out to be rare whenever the topic of bioethics comes up.

Shame on The University of Vermont

 
The University of Vermont will be awarding an honorary degree to Ben Stein, the man behind the movie Expelled. Here's the press release from the University of Vermont [Ben Stein to Deliver Commencement Address]. Notice that they don't mention the movie. That's no excuse.

The multi-talented Ben Stein, actor/comedian/lawyer/economist/presidential speechwriter/filmmaker, will address the graduates and receive an honorary degree at the University of Vermont's 205th commencement ceremony on Sunday, May 17.

Popularly known as the host of Comedy Central's seven-time Emmy award winning game show, "Win Ben Stein's Money," and for an iconic classroom scene in the film Ferris Bueller's Day Off, Stein is also an accomplished writer who has published 30 books and written for publications ranging from the Wall Street Journal and The New York Times to E! Online and New York Magazine. Stein earned his undergraduate degree with honors in economics from Columbia University and went on to graduate as valedictorian of his class from Yale Law School. He has taught at American University, the University of California at Santa Cruz and Pepperdine University in subjects ranging from political and social content of mass culture to securities law. Along with his academic and entertainment achievements, Stein has as served as a trial lawyer for the Federal Trade Commission and as White House speechwriter for presidents Nixon and Ford.

The University of Vermont offers a Major in Biochemistry. Before enrolling, students need to check out the courses to see if they encourage critical thinking and to see how evolution is presented.

The University of Vermont has every right to award honorary degrees to anyone they want. That's what academic freedom is all about. The downside is that the University of Vermont will be judged by who they choose to get an honorary degree. That judgment is not going to be favorable.

UPDATE: Ben Stein has decided that he has another commitment that will prevent him from receiving the honorary degree from the University of Vermont [Stein backs out].

Having been involved in selecting honorary degree recipients, I can assure everyone that you don't make public announcements until the candidate has agreed. Thus, it looks very much like Ben Stein and the university have made a joint decision that inviting Stein to accept an honorary degree was a mistake.

I'm glad the University of Vermont came to its senses.

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Does the University of Toronto really care about undergraduate education?

My university, the University of Toronto (Toronto, Canada), is huge. We have 60,000 undergraduates making it one of the biggest universities in North America. You'd think that undergraduate education should be a very high priority.

The university publishes an online "newspaper" called the Bulletin every Tuesday and Thursday. It's basically a PR ploy to advertise everything that's great about the University of Toronto. There was a time in the past when the Bulletin had editorials that were critical of university practice and policies but I haven't seen anything like that in years.

The latest issue has a link to an article by the President of the University, Meric Gertler. The title of the article is: Job Ready: U of T is developing new programs to help students succeed after graduation. I want to discuss two things in that article. The first is whether the university really is committed to the goals of undergraduate education (this post). The second is What does "liberal arts education" mean in the 21st century?.

Sex, genes & evolution

 
With a title like that how could you not want to read John Logsdon's new blog? Yesterday was his first post but I'm looking forward to lots more in the near future [Sex, Genes & Evolution].

John is a molecular evolutionary biologist in the Biology Department at the University of Iowa. He has published a number of papers with W. Ford Doolittle from the time he was at Dalhousie University in Nova Scotia. These include several papers with Arlin Stoltzfus on the evolution of introns. The Stoltzfus/Logsdon papers from this era were among the best papers to refute the intron-early hypothesis formerly championed by their mentor, Ford Doolittle. One of the things this demonstrates is that it's possible to disagree with your boss and survive!

Their chief target at the time was the Gilbert lab. John Logsdon was one of the participants in the famous online BioMedNet debate on The Origin and Evolution of Introns in November 1996—back in the time before blogs. This was mostly a debate between members of the Ford Doolittle lab and the Gilbert lab. Unfortunately, the transcript is no longer available. It was required reading in most molecular biology courses in the late 1990's. (I wish we had more debates like that.)

The Logsdon lab is interested in sex in protists, specifically the evolution of genes involved in recombination and meiosis (e.g., RAD51). John participates in a larger project that is trying to define the eukaryotic tree of life. As most of you know, the relationship of protists is controversial and the collaborative project intends to try and resolve the controversies. It not going to be easy to figure out the early history of eukaryotic evolution. This is a problem that has perplexed evolutionary biologists for several decades.

The Iowa biologists' goal is to sequence nine genes (actin, α- and β- tubulin, cob, EF-1 a , Hsp70, Hsp90, RPB1, SSU rRNA) from at least 200 different protists [ Assembling the Tree of Eukaryotic Microbial Diversity and Eu-Tree].

I'm excited about this project because they're looking at the best gene (HSP70). I hope he won't be disappointed to learn that my undergraduates have already solved the problem [The Evolution of the HSP70 Gene Family]. But all is not lost, those other genes might make a minor contribution to understanding evolution.

Welcome to science blogging, John.

Now, why not jump right in and describe your favorite hypothesis for why we have sex? I'm guessing you're a fan of repair, right?

The Demise of the Squiggle

Fritz Lipmann is often credited with discovering ATP but that's not correct. He won his Nobel Prize for discovering Coenzyme A [The Nobel Prize in Physiology or Medicine 1953].

However, it's fair to say that Lipmann made some of the most important contributions to our understanding of ATP as an energy currency. His classic 1941 paper in Advances in Enzymology was entitled "Metabolic Generation and Utilization of Phosphate Bond Energy." In that paper he introduced the concept of an energy-rich phosphate bond designated by a squiggle (~). Thus ATP could be represented as

AMP~P~P
to show that it had two such high energy bonds. The cleavage of either bond is accompanied by a large release of energy that's available to do work. The idea that ATP contained some special bonds with high energy was very attractive and the concept ruled in biochemistry textbooks for several decades. Indeed, there are still many courses and websites that still use the squiggle.

The concept is extremely misleading and came under attack by many biochemists in the 1950s and 60s. According to these biochemists, the correct way of looking at ATP as an energy currency is to recognize that the overall reaction of hydrolysis is associated with a large negative Gibbs free energy change.

ATP + H₂O → ADP + P_i          ΔG°′ = -32 kJ mol^-1

It's the system, including reactants and products, that is associated with the large negative free energy change. The only reason ATP is useful as an energy currency is because the concentration of ATP is maintained at high levels relative to ADP + P_i inside the cell. As a matter of fact, the actual Gibbs free energy change in vivo is closer to -48 kJ mol^-1.

If the system were allowed to reach equilibrium then ΔG°′ = 0. Think about what this means. At equilibrium those ~P "high energy" bonds are still being broken but there's no useful energy being produced.

Does this mean that the strength of a chemical bond depends on the relative concentration of reactants and products? Of course not. What it means, in the words of someone who knew Friz Lipmann, is that his understanding of basic thermodynamics was rudimentary.

The arguments over the proper way to think about ATP raged back and forth in the scientific literature for over thirty years. For the most part Lipmann did not participate in the squiggle debates, he left his defense to others. It's fair to say that there was no knock-out blow that ended the fight. Gradually people began to realize that the squiggle—and the concept of a high energy bond—were unfortunate at best and possibly misleading to the point of being counter-productive. The squiggle has been dropped from most (all?) textbooks.

So, how do we explain the fact that ATP hydrolysis is associated with a large release of energy under conditions found inside the cell? If it's not because of some special "high energy" bond, then what is it? See Why Is ATP an Important Energy Currency in Biochemistry?.

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Here's a couple of articles on the history of the squiggle:

Fritz Lipmann

Power, Sex, Suicide: Mitochondria and the Meaning of Life: The elusive squiggle (p.80>)

Here are some websites that still refer to "high-energy" bonds and still use the squiggle. It's interesting that most of these sites include a modest disclaimer, stating that there's no such thing as a "high-energy bond" but they then go on to talk about high energy bonds using the squiggle notation.

Rensselaer Polytechnic Institute

Columbia University

University of Connecticut

Online Textbook: Department of School Education, Govt. of Tamil Nadu, India

[I am indebted to my colleague Byron Lane for explaining the history to me. He was a post-doc in the Lipmann lab during the 1950s where he was in a position to observe the debate first-hand. Byron kindly gave me copies of the relevant papers. Our discussion began when we realized that the kinds of scientific debates that were common in the past are no longer occurring even though there are many controversies bubbling beneath the surface. We don't know why. Does anyone?]

Silent Mutations and Neutral Theory

 
This is a post about the quality of science writing and what can be done about it. I'm picking on an article in SEED magazine here but it's not because SEED is any worse than the competition. It's partly because SEED makes claims about raising the quality of science writing and science education. For example, this statement from a SEED press release seems to indicate that they aspire to better science writing than the competition [Seed Media Group Adds Scientific and Political Pundits to Editorial Team] and certainly their commitment to science bloggers suggests the same aspiration.

As part of its growth strategy, Seed Media Group will develop original science content aimed at a general audience for distribution across a number of media channels, including magazines, books, newspapers, online, topical blogs, digital, film and television. Seed Media Group's endeavors will present science in the same culturally articulate and accessible style that earned Seed a prestigious UTNE Independent Press Award in 2004 and the support of leading advertisers.

It's reasonable, in my opinion, to expect that SEED will live up to this billing. They've certainly made a major step in that direction by hiring PZ Myers to write a monthly science column. The science in his first two contributions is impeccable. As we will see, it raises the question of whether you need to be a scientist in order to get the science right. I hope that's not true.

I'm not going to criticize PZ's articles. Instead, I want to examine another article published in the March 2007 issue of SEED. (That's the one with the "TRUTH" prominently displayed on the cover!) The article in question is titled The Sound of Silence and it's written by Lindsay Bothwick, an experienced science writer with a M.Sc. from McGill and a Masters degree in journalism from Ryerson University here in Toronto. She's a senior editor at SEED so I'm assuming she can take criticism.

The article talks about silent mutations in protein-coding regions. The focus is on a recent Science paper showing that some silent mutations affect the activity of a protein. The point I will make is that the SEED article is very misleading and misrepresents the state of knowledge in this field.

Before getting into the article, let me give you some background.

The most common kinds of mutations are those where one nucleotide is substituted for another. For example, a G or an A or a T replaces a C. This substitution usually results from an error during DNA replication.

If the mutation (allele) persists in a population, it's called a single nucleotide polymorphism or SNP (pronounced snip). The term polymorphism means that there are at least two different alleles segregating in the population. Often these are the original "wild-type" allele and the new mutant allele.

We now recognize that genomes within a population are very heterogeneous. Polymorphism is common. This level of variation was discovered in studies during the 1960's and it's much higher than most scientists thought prior to 1960.

There are three explanations that can, in theory, account for this high level of polymorphism

First, if we think about SNP's, they can represent a transient phase of fixation by natural selection. In this case, one of the alleles is rapidly replacing the other and we just happen to catch it in the act. Back in the days when natural selection was the only game in town it was thought that this transient stage would be rare so populations were not expected to show much variation.

Polymorphism can also be explained by balancing selection. This is when the population has to maintain several different alleles because there is selection for heterogeneity. The classic example is the mutation for sickle cell anemia. When a person is homozygous for the mutant allele they exhibit the symptoms of anemia but when heterozygous they are resistant to malaria. Balancing selection is not common and it can't explain the variation that was discovered in the 1960's.

The third explanation was that the variation is mostly neutral. The idea here is that the majority of mutations are not being acted upon by natural selection. They are not being removed by purifying selection; they are not being maintained by balancing selection; and they are not rising to fixation under positive selection. It was the discovery of significant polymorphism in populations that gave rise to Neutral Theory in the first place ((Kimura, 1968, King and Jukes, 1969).

Neutral mutations will eventually become fixed or be eliminated from the population and the change in frequency is due entirely to random genetic drift. Drift is a much slower process than natural selection so there will always be large numbers of neutral alleles in the process of becoming fixed or extinct.

Neutral Theory and random genetic drift explains variation and it also explains molecular evolution and the (approximate) molecular clock. There are no other explanations that make sense and nobody has offered a competing explanation since Motoo Kimura (1968) or Jack King and Thomas Jukes (1969) published their papers almost fifty years ago. (Aside from occasional nitpicks, of course. There are always scientists who like to show that some mutations that were thought to be neutral are actually beneficial or deleterious. None of them have mounted a serious claim that most variation or most of molecular evolution can be explained by natural selection.)

The history of variation and the competing explanations were well covered by Lewontin in his 1974 book The Genetic Basis of Evolutionary Change. (Lewontin published the classic 1960's papers that revealed extensive within population variation.)

Long-held assumptions about "silent" genetic mutations have been torn down, challenging a fundamental evolutionary theory.

Lindsay Borthwick
SEED
March 2007This brings me to the article in the March issue of SEED [The Sound of Silence]. It begins with a conclusion that's all too common in popular science writing these days,

Scattered throughout the human genome are thousands of mutations that biologists have treated mostly as footnotes. They're hardly few in number—in coding regions of the genome, there are as many as 15,000—but biologists regard them as mutations that simply don't change the way a cell functions. Both in name and effect, they have been accepted as "silent." Now, however, new discoveries are showing that silent mutations appear to play an important role in dozens of human genetic diseases, a fact that is forcing biologists to discard a long-held evolutionary theory and to reexamine the very rules governing the transfer of information from DNA to proteins.

What's going on here? Has there been some extraordinary new discovery that's about to overthrow evolutionary theory and the "rules" of information flow? I will attempt to show that this rhetoric is completely unjustified. It presents a misleading picture of the state of modern science.

The author is talking about silent mutations. These are mutations in the coding region of a gene that alter a codon without changing the amino acid. The genetic code is redundant because there are 64 possible codons and only 20 amino acids. This means that several amino acids have multiple codons. For example, there are six codons for leucine (Leu): TTA, TTG, CTT, CTC, CTA, and CTG. If an original TTA codon is mutated to CTA then it still specifies leucine and this is a silent mutation.

The concept of codon bias has been known for almost forty years and it's an important part of all university courses in molecular biology. Some codons are more efficient than others during translation because the levels of various tRNAs in a cell are not identical. A rare codon will be translated less efficiently because the tRNA that binds to it will not be recognized as frequently as the codon for more abundant tRNAs. There are published codon usage tables for most species showing the preferred codons in that species. Highly expressed genes will preferentially use the codons recognized by the abundant tRNA species. All students know what these tables mean. It means that not all silent mutations are neutral. (It's on the exam!)

This is only one possible reason for silent mutations not being neutral. The various possibilites were discussed by Jukes back in 1980 when he revisited the evidence for neutral changes (Jukes, 1980)) . He gave some specific examples and then addressed the theoretical problem,

The question arises, are these silent changes actually neutral, or have they taken place for adaptive reasons, such as the requirement for a specific secondary structure in mRNA, or a preferential use for certain transfer RNAs in regulating the rate of synthesis of a protein?

For some results the answer is that the silent changes really are neutral, although in a few cases there is evidence of adaptation. The point is that these issues have been recognized and dealt with for decades.

The existence of a few exceptions to a rule does not invalidate the generality. That's an important point. It's one that all science journalists need to grasp. There are no absolute, inviolate, rules in biology. The generalities are all about relative frequencies. Are most silent mutations neutral or are most subject to natural selection?

As Jukes put it 27 years ago,

The neutral approach to molecular evolution is a proposal to prove a negative, which is something like trying to show that a given substance is not a carcinogen. The counterrresponse to the publications by Kimura (1968) and King & Jukes (1969) has been quite strong. Any exceptions to neutrality are usually taken as disproof of it, and many authors have cited such exceptions for this purpose. We have, indeed, developed evidence for such exceptions ourselves, because a theory should be challenged by those who have postulated it.

For example, the finding that synonymous codons for each amino acid are not use in equal amounts in β-hemoglobin mRNA has been cited as disproof of the neutral model, as if such a departure from randomness in a single gene were pertinent.

As the old expression goes, "those who are ignorant of history are doomed to repeat it." It helps a lot to be aware of the history of biology and the contributions of those who developed our current understanding. Modern science writers often fail to understand that there's not much that's new in biology these days. In this case, it's just not true that biologists were too stupid to recognize that some silent mutations weren't neutral. There was no "orthodoxy" that all silent mutations were neutral and, therefore, no orthodoxy has been overturned.

Silent mutations have no impact on the amino acid sequence of proteins and, therefore, were not expected to change their function.

Lindsay Borthwick
SEED
March 2007The SEED article goes on to describe the results of experiments done by Kimchi-Safaty et al. (2007). They presented evidence that a cluster of three silent mutations in the MDR1 gene led to a slow down in translation and subsequent misfolding of the protein. Lindasy Bortwick then writes, "Through a series of elegant experiments, the team put to rest the idea that silent mutations were neutral." Of course, they did no such thing. They merely added one more data point to something that we already knew; namely, not all silent mutations are neutral.

Borthwick closes with,

Most fundamentally, the involvement of silent mutations in disease undermines the neutral theory of molecular evolution. This theory, posited by Motoo Kimura in the late 1960s and a powerful influence ever since, asserted that the vast majority of mutations were neutral, having no effect on the fitness of an organism, and spread through a population by chance. The fact that silent mutations are not harmless anomalies of nature means that they are not neutral. In contrast, some, if not all, silent sites must be subject to the forces of Darwinian natural selection.

The theme of the article is that neutral theory is in big trouble. This point is emphasized in the highlighted quotations that are prominently displayed on page 35 (see the two boxes above). That's totally wrong and it distorts the modern consensus among knowledgeable scientists. Neutral Theory is alive and well, thank-you very much. It can easily accommodate one more example of a non-neutral mutation.

I believe that science writers have an obligation to get the concepts right and I believe they shouldn't misrepresent the science they're supposed to be presenting in a "culturally articulate and accessible style" to a general audience. A layperson reading this article would go away with the impression that a decades old concept has just been overthrown by a single paper published in Science. That's irresponsible journalism.

Jukes, T.H. (1980) Neutral Changes Revisited. In The Evolution of Protein Structure and Function, pp. 203-219.
.
Lewontin, R.C. (1974) The Paradox of Variation. in Evolution Mark Ridley ed., Oxfrod University Press, Oxford UK.

Kimchi-Sarfaty, C., Oh, J.M., Kim, I.W., Sauna, Z.E., Calcagno, A.M., Ambudkar, S.V., and Gottesman, M.M. (2007) A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315, 525-528.

Kimura, M. (1968) Evolutionary rate at the molecular level. Nature 217, 624-626.

King,J.L. and Jukes,T.H. (1969) Non-Darwinian evolution. Science 164, 788-798.

Style vs substance in science communication: The science writer perspective

I want to address a recent article on science writing: When editors and scientists meet: communicating science without dumbing it down. The author is Alex Ip and the article is a commentary on a panel session about science writing at the ScienceWriters2021 conference held in early October [Editing experts: How to help scientists meet journalism standards].