Some freelance science writer named Philip Ball has published an article in the April 25, 2013 issue of Nature: Celebrate the Unknowns.
The main premise of the article is revealed in the short blurb under the title: "On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level, suggests Philip Ball."
What nonsense! We understand a great deal about how evolution works at the molecular level. Perhaps Philip Ball meant to say that we don't understand the historical details of how a particular genome evolved, but even that's misleading.
I've commented before on articles written by Philip Ball. In the past, he appeared to be in competition with Elizabeth Pennisi of Science for some kind of award for misunderstanding the human genome.
SEED and the Central Dogma of Molecular Biology - I Take Back My Praise
Shoddy But Not "Junk"?
Let's look at what the article says ...
Here (below) is my old friend, Keith Yamamoto, talking about taking risks in science. Keith and I were graduate students in Bruce Alberts' lab over 40 years ago. That's him on the left in the photo. I'm the one looking up and the third former graduate student is Glenn Herrick.
Keith and I learned a lot about science from our former mentor. I learned a lot from Keith; for example, he taught me that it is more important to print in your notebook than to use cursive writing. I've been printing ever since. 
Keith also helped me learn that it's sometimes important to fight for a cause even if you know you're going to lose. (He was county coordinator for the George McGovern presidential campaign in 1972.1)
The take-home message in this video is that good scientists need to take risks. It's one of those "motherhood" kinds of statements that every scientist will support but few actually do it. It saddens me to say that today we live in a culture where mundane, data-collecting, science is often more successful than risky science (e.g. ENCODE). Risk entails the possibility of failure and even though you might learn from failure [Bruce Alberts on Learning from Failure], it won't do you much good if you don't get a job or you lose your grant.
So I disagree with Keith when he says that we should encourage risk-taking in young scientists. Some of the best scientists I know took risks and and the work didn't pan out. They couldn't get any papers published and they lost their grants. They were cut out of the system in favor of scientists who could guarantee successful results in their grant proposals. The fact that the results were boring and did nothing to advance our knowledge, wasn't important.
I advise young scientists, post-docs, and graduate students to always have a "safe" project. Don't put all your eggs in the risky science basket. It makes me sad to give that advice.
1. For those of you who weren't born in 1972, Nixon won that campaign and McGovern won only 17 electoral votes (Massachusetts and Washington, D.C).
Here's a short talk from my thesis supervisor on learning from failure. He tells the story of how he failed his Ph.D. oral and how he almost gave up writing his textbook.
I was a gradate student in his Princeton lab from 1969-1974. The most important lesson I learned from Bruce was the importance of knowledge and context. He taught a graduate course called "Macromolecules" where he explained both the basic chemistry and the basic biology. The lesson was clear. You can't do good science unless you see the big picture and understand the fundamentals of your discipline. He reminded us almost every day. As he says in the video ...
Theoretical biology is much more important than my generation had imagined. We were misled by the striking success of the 1953 Watson-Crick DNA model.
I also agree with another comment he makes in the video ...
Both book writing and teaching are really important for creative science, I believe.
Bruce also encouraged us to explore topics outside of our research project. This included Jacques Monod's book "Chance and Necessity: Essay on the Natural Philosophy of Modern Biology" and the writings of the best theoretical biologists of the time. We were encouraged to get involved in politics and society. It was a time of protest and revolution, and scientists had a role to play.
PZ Myers has just given his students a take-home exam. Here's one of the questions [It’s another exam day! ] ...
Question 1: One of Sarah Palin’s notorious gaffes was her dismissal of “fruit fly research” — she thought it was absurd that the government actually funded science on flies. How would you explain to a congressman that basic research is important? I’m going to put two constraints on your answer: 1) It has to be comprehensible to Michele Bachmann, and 2) don’t take the shortcut of promising that which you may not deliver. That is, no “maybe it will cure cancer!” claims, but focus instead on why we should appreciate deeper knowledge of biology.
That first restriction is going to make answering the question a real challenge 'cause you have to take into account the mentality of someone who is not just scientifically illiterate but scientifically anti-literate.
Nevertheless, this is exactly the sort of thing you want your science graduates to know.
More advertising for the Intelligent Design Creationists' tenth or eleventh attempt to destroy "Darwinism" [Darwin's Doubt: The Trailer Is Here!]. They're already offering a 43% discount in order to get you to buy it.
Remember, boys and girls, that scientists aren't allowed to challenge Meyer until the book is published and we have read every page.
It's been a while since I've linked to the Botany Photo of the Day even though I read it all the time.
Check it out. What is that dangling thing coming out of the flower? Does it have a function?
Jerry Coyne has discovered that a course at Ball State University (Indiana) teaches science from a viewpoint that's sympathetic to Intelligent Design Creationism [“Science” course at Ball State University sneaks in religion]. It looks like a really bad course and I'm glad that it's getting a lot of negative publicity. It looks like the instructor is advocating Intelligent Design Creationism.
I defend the right of a tenured professor to teach whatever he/she believes to be true no matter how stupid it seems to the rest of us.1 I'm troubled by the fact that some people are calling for the instructor's dismissal and writing letters to the chair of his department. We really don't want to go down that path, do we? Academic freedom is important and it's especially important to defend it when a professor is pushing a view that we disagree with.
But that's not the only troubling thing about Jerry Coyne's post and the comments it has stimulated. Jerry thinks that it is unconstitutional (i.e. illegal) for a university professor to be advocating religion in a publicly-funded university. He says,
Ball State University, in Muncie, Indiana, is a public university (i.e., part of the state university system). As such, it must abide by the First Amendment to the U.S. Constitution, which has been interpreted as disallowing religious viewpoints (or religiously based theories) in public-school science classes. It is of course kosher to teach courses on the history of religion, or on the relationship between science and religion, but those must not pretend to be “science” courses, and must present balanced views—they can’t push a particular religious viewpoint.
But it’s come to my attention that a science course at Ball State University—actually two courses, because it seems to be cross-listed—is little more than a course in accommodationism and Christian religion, with very little science. It’s my firm opinion that teaching this course at a state university not only violates the First Amendment, but cheats the students by subjecting them to religious proselytizing when they’re trying to learn science.
Is he right? Does the US Constitution really specify that you can't advocate a religious viewpoint in a university classroom?
That's very scary. It probably means that you can't criticize religion either. Does this mean that there's going to be a bevy of lawyers on both sides of the issue examining the content of university courses all across America?
UPDATE:
PZ Myers: I have to disagree with Jerry Coyne
1. There are some limitations, but let's not quibble over details. Teaching that Michael Behe, Ken Miller, Francis Collins, and Bill Dembski might be right don't qualify as exceptions.
Sixty years ago on this day, Nature published three back-to-back papers on the structure of DNA. It was a momentous day for science. Here's how Horace Judson describes it in The Eighth Day of Creations (pp. 154-155)...
The letter to Nature appeared in the April 25 issue. [It was submitted on April 2—LAM] To those of its readers who were close to the questions, and who had not already heard the news, the letter must come off like a string of depth charges in a column sea. "We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest," the letter began; at the end, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." That last sentence has been called one of the most coy statements in the literature of science. According to Watson, Crick wrote it. Wilkins's paper followed, signed also by two of his associates at King's College, A. R. Stokes and H. R. Wilson. It was a restatement of helical diffraction theory, and sprang to life and significance only in the last paragraphs, where Wilkins briefly reported that his x-ray diffraction studies of intact sperm heads and bacteriophage—both, of course, containing a high proportion of DNA—gave patterns that suggested that DNA in living creatures has a helical structure similar to the model just proposed. The note by Franklin and Gosling came next. It was a revision and extension of their draft from the middle of March, in the light of the model. It presented the crucial diffraction photo structure B and analyze that and the other experimental evidence to show—with curt authority—that Franklin's data were compatible with Watson and Crick's structure.
The three papers are ....
Watson, J.D. and Crick, F.H.C. (1953)A Structure for Deoxyribose Nucleic Acid. Nature 171:737-738. [See: The Watson & Crick Nature Paper (1953)] [PDF]
"We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest."
Wilins, M.H.F., Stokes, A.R., and Wilson, H.R. (1953) Molecular Structure of Deoxypentose Nucleic Acids. Nature 171:738-740. [See: The Wilkins, Stokes and Wilson Nature paper (1953)] [PDF]
"The biological significance of a two-chain nucleic acid unit has been noted (see preceding communication). The evidence that the helical structure discussed above does, in fact, exist in intact biological systems is briefly as follows: ..."
Franklin, R. and Gosling, R.G. (1953) Molecular Configuration in Sodium Thymonucleate. Nature 171:740-741. [See: The Franklin & Gosling Nature paper (1953)] [PDF]
"Thus, while we do not attempt to offer a complete interpretation of the fibre-diagram of structure B, we may state the following conclusions. The structure is probably helical. The phosphate groups lie on the outside of the structural unit, on a helix of diameter about 20 Å. The structural unit probably consists of two co-axial molecules which are not equally spaced along the fiber axis, their mutual displacement being such as to account for the variation of observed intensities of the innermost maxima on the layer lines; if one molecule is displaced from the other by about three-eights of the fibre-axis period, this would account for the absence of the fourth layer line maxima and the weakness of the sixth. Thus, our general ideas are not inconsistent with the model proposed by Watson and crick in the preceding communication."
The title of this post is a slight paraphrasing of Theodosius Dobzhansky's famous saying, "Nothing in Biology Makes Sense Except in the Light of Evolution. That was the title of an article he published in American Biology Teacher and that's significant since the main point was to convince teachers that evolution is important.
What applies to biology also applies to biochemistry. Evolution should come up in many places in a typical biochemistry course. The most obvious place is when we teach comparisons of nucleotide and amino acids sequences and the construction of phylogenetic trees. Students have to know the underling concept behind these comparisons. The have to know why some sequences are conserved (negative selection) and why some sequences are variable (fixation of neutral alleles by random genetic drift).
But this isn't the only place where evolution is important. How can you explain why humans need vitamin C and "essential" amino acids without mentioning evolution? How can you teach biochemistry without covering the evolution of biochemical pathways? How do you explain the existence of a complex process like the membrane-bound photosynthesis complexes in chloroplasts without showing how it evolved from simple bacterial examples? Who teaches the information flow section of the course without starting with E. coli and working toward the more complex eukaryotic examples? How do you explain why animals need glucose when most species don't need an external supply of complex carbohydrate? How do you explain why gluconeogenesis is a more primitive pathway than glycolysis? Why are comparative genome studies important in working out metabolic networks? Why does "homology modeling" work?
The American Society for Biochemistry and Molecular Biology (ASBMB) is trying to set up a certification scheme for biochemistry programs in America. The idea is that universities and colleges that meet certain standards would receive a stamp of approval from ASBMB. There would be a nation-wide exam for graduating students and if they pass the exam they get a sort of "certification" that proves they have the minimum skills and knowledge to take jobs that require these skills.
The trick is to define the common skills and knowledge that are needed. I attended two sessions at EB2013 where these criteria were discussed. One was a presentation by the committee in charge followed by some discussion: "ASBMS Certification Program for Bachelor's Degrees in Biochemistry Molecular Biology and Related Majors." The questions in this session were focused on how to get certified and not on what was in the proposal.
The other session was "Promoting Concepts-Driven Teaching Strategies in BMB Through Concept Assessments" but, as it turned out, there was very little chance to discuss the concepts that were being assessed.
You can read the current draft proposal by clicking on the link at ASBMB Degree Certification Program in Biochemistry and Molecular Biology. You might be interested in finding out what a department needs to do in order to be certified.
I'm more interested in what biochemists have to teach. Here's the relevant section ...
Core Concepts and Learning Objectives
An ASBMB-recognized program should be able to relate each element of its BMB curriculum to one or more of the core concepts listed below and their related learning objectives (For reasons of space, sample learning objectives are provided in Appendices II – V):
1. Energy is Required by and Transformed in Biological Systems.
2. Macromolecular Structure Determines Function and Regulation
3. Information Storage and Flow Are Dynamic and Interactive.
4. Discovery Requires Objective Measurement, Quantitative Analysis, & Clear Communication.
The curriculum should present these core concepts in a manner that illustrates the pervasive role that Evolution plays in shaping the form and function of all biological molecules and organisms.
That last sentence is new to me. I've never seen it on any of the slides shown at either of the meetings I attended (EB2012 and EB2013).
It's a welcome addition. But, since most biochemistry courses in America are taught out of Chemistry Departments, I wonder if this will make certification more difficult.
Finally, I can't help but insert a plug for my book. It's the only biochemistry textbook that presents the subject from an evolutionary perspective and it's certainly the only textbook where the pervasive role of evolution is emphasized in every chapter.
The next step will be to help the organizing committee refine and upgrade the "Learning Objectives" for each of the core concepts. These are given in four appendices in the draft document.
Dobzhansky, T. (1973) Nothing in biology makes sense except in the light of evolution. American Biology Teacher 35:125-129.
Having just sat through many talks and read many posters on how to measure what we teach, I'm struck by the overwhelming emphasis on how to measure what biochemists are teaching and the incredible lack of interest in evaluating whether we are teaching the right things.
That's why this image resonated with me. Arthur L. Costa is a retired Professor of Education at the California State University, Sacramento.
[Hat tip: John Wilkins]
Lawrence Krauss says on Facebook ...
six days and counting till the World Premiere of The Unbelievers at Hotdocs International Film Festival in Toronto. An extra screening of the film just added. Stay tuned after that for announcements.
We're going on May 1st. Why not join us?
You can get updates on new posts on Twitter [@larryonsandwalk], on Facebook [Laurence A. Moran], and on Google+ [Laurence A. Moran].
April 21, 2013
Judging the Quality of MOOCs
April 15, 2013
Monday's Molecule #202
April 15, 2013
Why Do We Do Science?
April 16, 2013
Where Do Organisms Get Their Energy?
March 18, 2013
Monday's Molecule #200
September 12, 2012
Does the Central Dogma Still Stand?
August 21, 2012
Designing a New Biochemistry Curriculum
August 7, 2012
Changing Ideas About The Origin Of Life
August 6, 2012
What Does "pH" Mean?
August 3, 2012
On the Evolution of New Enzymes: Completely Different Enzymes Can Catalyze Similar Reactions
July 20, 2012
Better Biochemistry: Good Enough Enzymes
July 13, 2012
Slip Slidin' Along - How DNA Binding Proteins Find Their Target
May 23, 2012
Better Biochemistry: The Perfect Enzyme
Another journalist has written about Massive Open Online Courses (MOOCs). This one is in The New York Times: Two Cheers for Web U!.
Most of these articles about MOOCs are not very good but this one is different. The author expresses some skepticism and hit the nail on the head when he says ...
But the first thing I learned? When it comes to Massive Open Online Courses, like those offered by Coursera, Udacity and edX, you can forget about the Socratic method.
The professor is, in most cases, out of students’ reach, only slightly more accessible than the pope or Thomas Pynchon.
But that's not what I want to talk about today. I want to discuss the quality of these courses and how you might go about judging whether they are truly teaching the subject correctly.
Here's the problem. Too many people, like A. J. Jacobs, the author of today's article, assume that because the lecturer is famous or from a "top" school, the material must be accurate and up-to-date. As A. J. Jacobs puts it ...
On the other hand, how can I really complain? I’m getting Ivy League (or Ivy League equivalent) wisdom free....
With the exception of a couple of clunkers — my plodding nutrition professor might want to drink more organic coffee before class — most of my MOOC teachers were impressive: knowledgeable, organized and well respected in their field.
Students are not in a position to judge whether a professor is "knowledgeable" about the material being covered in a course. In the case of MOOCs, many students just assume that because the professor is from an Ivy League school then he/she knows how to teach an introductory course properly.
That's a very bad assumption as I've shown when I examined the biochemistry material being taught in the MIT courses Where Are the Best University Teachers?. Same is true for the courses at the Khan Academy.
I'm currently in Boston at EB2013 where I'm hanging out with biochemistry and molecular biology teachers and textbook authors. Many of these experts are not household names but they are the experts in their field, which is teaching. If you really want accurate information about the fundamental principles and concepts in biochemistry and molecular biology then you should take the courses they teach. You'll get a far better education than if you listen to professors from big-name research intensive-universities.
The recent ENCODE publicity disaster is just one example of the fact that top-notch researchers don't necessarily understand the fundamentals of subjects that are just outside of their own area of expertise.
Let's try and put a stop to this myth that the best teachers are professors from Ivy League schools. There's very little evidence to support that myth, especially in fields that I'm familiar with: evolution, biochemistry, and molecular biology,
I don't have a lot of time today (I leave for Boston tomorrow) but I can't let this pass.
The complete draft genome of the African coelacanth, Latimeria chalumnae has just been published in Nature (Amemiya et al. 2013). Ceolacanths have long been regarded as "living fossils," a term that persists even though the data have been disputed ever since the first fish were identified 75 years ago. I couldn't believe what I was reading when I saw the press release from the Broad Institute in Boston [Coelacanth genome surfaces]. The author, Haley Bridger of Broad Communications, says ...
An international team of researchers has decoded the genome of a creature whose evolutionary history is both enigmatic and illuminating: the African coelacanth. A sea-cave dwelling, five-foot long fish with limb-like fins, the coelacanth was once thought to be extinct. A living coelacanth was discovered off the African coast in 1938, and since then, questions about these ancient-looking fish – popularly known as “living fossils” – have loomed large. Coelacanths today closely resemble the fossilized skeletons of their more than 300-million-year-old ancestors. Its genome confirms what many researchers had long suspected: genes in coelacanths are evolving more slowly than in other organisms.
“We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at,” said Jessica Alföldi, a research scientist at the Broad Institute and co-first author of a paper on the coelacanth genome, which appears in Nature this week. “This is the first time that we’ve had a big enough gene set to really see that.”
Researchers hypothesize that this slow rate of change may be because coelacanths simply have not needed to change: they live primarily off of the Eastern African coast (a second coelacanth species lives off the coast of Indonesia), at ocean depths where relatively little has changed over the millennia.
This can't be right, I said to myself. Let's check out the actual paper.
Unfortunately, it was right. Here's the figure and here's what the authors say in the results section of the paper.
The morphological resemblance of the modern coelacanth to its fossil ancestors has resulted in it being nicknamed ‘the living fossil.’ This invites the question of whether the genome of the coelacanth is as slowly evolving as its outward appearance suggests. Earlier work showed that a few gene families, such as Hox and protocadherins, have comparatively slower protein-coding evolution in coelacanth than in other vertebrate lineages. To address the question, we compared several features of the coelacanth genome to those of other vertebrate genomes.
Protein-coding gene evolution was examined using the phylogenomics data set described above (251 concatenated proteins) (Fig. 1). Pair-wise distances between taxa were calculated from the branch lengths of the tree using the two-cluster test proposed previously to test for equality of average substitution rates. Then, for each of the following species and species clusters (coelacanth, lungfish, chicken and mammals), we ascertained their respective mean distance to an outgroup consisting of three cartilaginous fishes (elephant shark, little skate and spotted catshark). Finally, we tested whether there was any significant difference in the distance to the outgroup of cartilaginous fish for every pair of species and species clusters, using a Z statistic. When these distances to the outgroup of cartilaginous fish were compared, we found that the coelacanth proteins that were tested were significantly more slowly evolving (0.890 substitutions per site) than the lungfish (1.05 substitutions per site), chicken (1.09 substitutions per site) and mammalian (1.21 substitutions per site) orthologues (P < 10−6 in all cases) (Supplementary Data 5). In addition, as can be seen in Fig. 1, the substitution rate in coelacanth is approximately half that in tetrapods since the two lineages diverged. A Tajima’s relative rate test confirmed the coelacanth’s significantly slower rate of protein evolution (P < 10−20)
The authors make it clear in the discussion that they think of molecular evolution of amino acid sequences only in terms of adaptation.
Since its discovery, the coelacanth has been referred to as a ‘living fossil’, owing to its morphological similarities to its fossil ancestors. However, questions have remained as to whether it is indeed evolving slowly, as morphological stasis does not necessarily imply genomic stasis. In this study, we have confirmed that the protein-coding genes of L. chalumnae show a decreased substitution rate compared to those of other sequenced vertebrates, even though its genome as a whole does not show evidence of low genome plasticity. The reason for this lower substitution rate is still unknown, although a static habitat and a lack of predation over evolutionary timescales could be contributing factors to a lower need for adaptation. A closer examination of gene families that show either unusually high or low levels of directional selection indicative of adaptation in the coelacanth may provide information on which selective pressures acted, and which pressures did not act, to shape this evolutionary relict.
This extraordinary claim flies in the face of everything we know about molecular evolution. Preliminary data from some of these same authors was criticized by Casane and Laurenti1 (2013) earlier this year. I'll quote what they said and leave it up to Sandwalk readers to draw their own conclusions.
Transposing the concept of ‘living fossil’ to the genomic level has led to the hypothesis of genetic stasis (or at least to the idea of a reduced molecular evolutionary rate) that is in sharp contrast with the principles of evolutionary genetics. Genomes change continuously under the combined effects of various mutational processes, that produce new variants, and genetic drift and selection, that eliminates or fixes them in populations. In other terms, the only possibility for genomes to replicate without change implies at least one of the two following conditions: (i) new variants do not appear (i.e. no mutations), and (ii) new variants are systematically eliminated by selection (i.e. no genetic drift and very powerful selection against new variants). Of course we can consider a less extreme case, i.e. a reduced evolutionary rate of the genome, but this still implies a lower mutation rate and/or stronger selection against new variants than observed in other species.
The coelacanth data make no sense. You should be very skeptical.
You should also wonder about the kind of people that Nature asks to review their papers. Reviewers may not be inclined to challenge the data but they should challenge the conclusions and they should ask the authors to address the fact that their interpretation is inconsistent with the modern evolutionary theory.
One other thing, if you look through the names of the authors, you will see several people who should know better than to attach their name to a paper like this. What's going on?
[Photo Credit: This is a photo of a model of a related species Latimeria chalumnae from the Oxford University Museum. (Wikipedia)]
Amemiya, C.T. et al. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature 496:311–316. [doi: 10.1038/nature12027]
Casane, D. and Laurenti, P. (2013) Why coelacanths are not ‘living fossils.’ BioEssays 35:332-338. [doi: 10.1002/bies.201200145]
Some freelance science writer named Philip Ball has published an article in the April 25, 2013 issue of Nature: Celebrate the Unknowns.
