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Evolution, History and Society

Perspectives from a Third Career

Cross post

Posted by admin on July 31, 2016
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“Dr. Science Teacher” nails it regarding belief vs. acceptance.

The best Twitter thread ever

Posted by admin on June 12, 2015
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FRED and R

Posted by admin on July 18, 2012
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Also nothing to do with Evolution, but one of my projects this summer has been to learn the R programming language. This morning I learned how to access data from the Federal Reserve (via FRED) and play with it in R. The result is a somewhat political take on recent economic numbers – I tried to publish an HTML file I generated here, but it didn’t work. However, if you want to see it, it is available here

Ok, so I’m following Evolution 2012 vicariously via Twitter, and clearly the big event of the night has been Rosemary Redfield’s talk, which happened (by coincidence?) to coincide with the release of the paper from her lab (as well as a companion paper from another lab) in Science refuting the “arsenic life” story, which got such a big media splash a year or so ago. When Carl Zimmer posted that the embargo on the paper had been lifted, I immediately went to Science, to find (of course) that the paper, clearly one of interest to the general public, seemed to be behind a paywall. I tweeted my disappointment, and within seconds, Carl responded that it’s available at Arxiv, and much to my delight, it was.

I may be wrong (and I hope not), but I think this is one more nail in the coffin of the Nature/Science/Elsevier model for scientific publishing. Look at it rationally. Here was a study, funded by NASA (i. e. by the public), proposing what is by any standard a revolutionary claim, and which, by the way, is now freely available online. And two studies that directly refute it are hidden behind a publisher’s paywall? Come on. I’m not one to rant about my rights as a taxpayer, but in this case I’m tempted to. What we have is a situation in which the public has funded questionable science, but our ability to judge it is being blocked, first by an “embargo”, and second by the financial interests of a private party. Enough! I know that there are a lot of financial implications of the Open Access model to work through, but the time has past when publicly funded science can be hidden from public scrutiny.

Nothing to do with Evolution

Posted by admin on July 8, 2012
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OK, so I’ve become addicted to using Markdown syntax for virtually everything I do. Indeed, my previous posts on here were composed using that syntax in Textmate, after which I generated HTML from it and copied into WordPress. Imagine my delight to find reference to a WordPress plugin, entitled Markdown on Saved Improved that will allow me to use that syntax directly. I’m still exploring the possibilities, but the purpose of this post is to try it out.

So why Markdown? Here are a few thoughts:

  • It’s easy. With just a short learning curve, one can generate HTML (and other format) documents that can be posted to the web or to other applications.
  • It’s spreading. Most text editors, like Textmateand Text Wrangler (for Mac – I’m sure there are ones for the evil empire as well) have Markdown formatting built in, making generation of decent documents straigtforward.
  • It’s flexible. One can generate code directly from one of the aforementioned editors, or (if more intrepid), one can use one’s own style sheets and embedded HTML code.
  • It liberates me from commercial word processors. I have hated Word for years; since I’ve started using Markdown, I usually only go to it when I need to edit other people’s documents.

There are things that take getting used to. Like HTML, it has some odd ways of dealing with line feeds and paragraph breaks, and generating tables takes some patience. But in my view, for creative writing unimpeded by the vagaries of a full-fledged (and constantly changing) word processor, it can’t be beat. And the plugin is extremely nice – it publishes the html version but saves the Markdown one for editing, so that updating already published documents is a cinch.

Evolution 2012

Posted by admin on July 7, 2012
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I’m sitting here sweltering in Ohio, wishing I was in Ottawa at Evolution 2012. But so be it – I’m attending vicariously via Twitter. For the duration of the meeting, tweets from the conference will be displayed on this site. Enjoy!

Teaching Genetics

Posted by admin on July 6, 2012
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Dr. Rosemary Redfield of the University of British Columbia has published a provocative paper in Plos Biology, suggesting that we reimagine how we teach undergraduate genetics and has asked for comments at her teaching blog. I hope that indeed her paper generates discussion, because based on my experience of having taught in this area for over 30 years, such a discussion, I think. is sorely needed. So herein are a few thoughts to contribute:

  1. Is change needed? Let me state at the outset that I love the historical approach. It is how I was taught, and I never cease to be fascinated by the historical development of genetics as a field, especially as it connected with (and at times seemed to contradict) the development of evolutionary biology. It was how I taught, and for me I think it worked. However, I was hooked by genetics at a very early age, and after an unfortunately (but fortunately brief) excursion into the world of theoretical mathematics, it became my passion. In other words, I was far from the typical undergraduate life science major. Indeed, as a teacher, while I have had my successes with that approach, they have been somewhat fleeting. Thus, if for no other than pragmatic reasons, I’m convinced we need to consider alternatives.
  2. Has Dr. Redfield posed the question correctly? To quote her,“The first goal of a modern basic genetics course should be to provide students with an understanding of genetic principles and processes that will be useful in their non-academic lives.” In other words, should we be academic purists, or (to use a hackneyed word) should we be “relevant”? I would prefer not to view this as a dichotomy, but rather to figure out the best way to be both. That is, how can we convince students that “the stuff is worth knowing” and still provide them with the grounding they would need to pursue advanced studies should they choose for and be comfortable that in making “the stuff” “relevant”, we have not sacrificed rigor?
    To address that, I looked very carefully at Dr. Redfield’s suggested outline, compared it with the text we currently use (which can remain nameless for the moment) and asked myself what was missing from her proposed approach. Without question, a few things are. For example, bacterial and phage genetics are nowhere to be seen. But should they be stand-alone topics, or could they be more effectively subsumed into coverage of key concepts like gene expression and regulation? Conversely, as an evolutionary/population genetics, I am intrigued by the idea of putting variation first. And that is the question that dominates modern genetic research. After all, what is a genome wide association scan if not an application of genomics to the classical population/quantitative genetics quest for understanding of genotype/phenotype relationships?
    I could quibble with some other features – in general, I’d like to see a bit more non-human genetics, and important though it is, I’m not sure cancer genetics can be effectively given the emphasis she suggests. But overall, is there much missing? I don’t think so. And will it be effective in engaging students? I’m hopeful, but that remains to be seen.
  3. Finally, are we giving Mendel the boot? If we define Mendel as Punnett squares and ratios, perhaps. However, I’ve always taken the approach that the key contribution of Mendel was not assortment, segregation, dominance, etc. (after all, they only apply to diploid organisms, a small minority of species), but rather the concept of the particulate gene. If one starts with that approach, then obvious questions follow – what is a gene? How does it work? How is it inherited? How does it explain the diversity of life? These questions are just as central in the era of genomics as they were in the one of wrinkled seeds, white eyes, and tetrad analysis. One may certainly quibble with Dr. Redfield’s proposed trajectory, but it is difficult, I think, to claim that it constitutes some sort of rejection of Mendelism or (as did a comment on a Discovery Magazine blog) a “faux genetics education”.

So in summary, I’m real pleased to see this article published, and if nothing else, I hope it gets teachers, and perhaps most importantly textbook writers, to give serious thought to how we approach the challenge of teaching genetics. We consider it axiomatic that genetics is central to all of biology; if that is true, it behooves us to convey the subject in such a way as to make that point evident to students, not simply because we say it is but because they come to that realization on their own.

The Smithsonian has a Wonderful page on Human Origins; among the many treasures on it is a smart phone app that can transform a person’s picture into a rendition of what s/he would look like as a Neanderthal or as H. heidelbergensis. You can download the app (it’s free) by scanning the QR codes below:

for iPhones and iPads


for Android devices

And the result?


I will admit that I really enjoy TEDTalks, Carl Zimmer’s recent critique notwithstanding. Here’s a good example (albeit one I’m unlikely to show in class).

It’s summertime again, and once again I am not participating in the Summer Reading Program. I did once in the past, and it was actually an enjoyable (although ultimately frustrated) experience. However, in the subsequent three years, I have thought about it and then opted out. Why? I do think the idea is sound – find a book that faculty, staff and incoming students can read in common and use it as the basis for building academic community. Alas, in my experience, that is not what happens. There are at least two underlying flaws in the common approach used, one which has been commented on extensively, the other one less so.

  1. Choice of Book. The National Association of Scholars, an organization with which I have many differences, releases a report every year entitled Beach Books: What do Colleges and Universities Want Students to Read Outside of Class?. Their major thesis, with which I disagree, is that the choices made are based not on quality or literary merit, but rather on political and social content. Quite honestly, that doesn’t bother me – indeed as a scientist who thinks a lot about the societal impact of science, the fact that Rebecca Skloot’s The Immortal Life of Henrietta Lacks was the most commonly selected book in 2011. The NAS report rather contemptuously dismisses the book in stating that “Readers will come
    away from the book having learned new things, but the writing itself is journalistic,
    not intellectual.” I take issue with that statement; to the contrary I think the book raises profound questions that could be used to provoke discussions across many disciplines – biology, political science, sociology, history, and on and on.

    But setting aside the political agenda inherent in the report, there are two features of the report worthy of note. First, it makes the point that there is a bias towards recently published work, often (as is the case at Miami University) that the expectation is that the author will speak at Freshman Convocation. So much for Mark Twain. But most importantly, the NAS did their homework and reported the data – what books were used at a total of 245 colleges and universities in 2011. They break them out in a number of ways (some of them based on political content and thus of questionable objective significance), but the most interesting is their summary of most commonly used books – I’ve extracted it here. I leave the reader to judge this list, but I’ll state my conclusion succinctly – other than Skloot’s book, there is only one that I have read or will read on my own (The Help), and while that is a fine book, it hardly ranks with the great literature of the world. And note also – despite the explosion in high quality science writing of the past few years, that genre is noticeable by its near complete absence (my sophomore students in Evolution loved Neil Shubin’s My Inner Fish, as well as other books on a list I compiled, but these are nowhere to be seen).

    The NAS also provides its own list of recommended books. I’ve extracted both their criteria for making the recommendations, as well as the list that resulted here. I think you’ll find the contrast obvious – I certainly did. And in the interest of providing data (albeit somewhat subjective), I have read (and benefited from) 15 of the 46 recommended books, and I feel guilty about not having read many of the others. And some institutions do buck the trends – Cornell’s program has included such titles as The Grapes of Wrath, The Great Gatsby, Antigone, and Frankenstein (although recent selections may be regressing towards the mean),

    There are other problems in the selection process, one of which is, in my view an excessive concern that the reading will be “too hard”, either for students or (unbelievably) for faculty. I witnessed this first hand at Miami; when in 2008 we used James Bennett’s Beyond UFO’s, an outstanding popular introduction to the astronomy of the solar system, a commonly heard criticism was that it was “too hard”, and that it “contained too much science”. The critics apparently had their impact; the next year the book was Taylor Mali’s What Learning Leaves, a 75 page collection of entertaining but (in my view) rather superficial “slam” poems loosely related to “education”. The book could easily be read in less than an hour, and students had the opportunity not to read it at all, but rather to watch the admittedly highly entertaining Mr. Mali perform them on YouTube.

    So the bottom line on the selection question? Too focused on the recent, a tendency towards the superficial, and lacking in scientific content.

  2. How the books are used Then there is the question as to what is done with the book. At Miami (and at many places), the author speaks, the students break out into faculty-led discussions, and that is basically the end of it. There is no ongoing curricular component associated with it, and there is a complete lack of any sort of assessment of what the students gained from the experience. Indeed, the one time I facilitated a section, when we asked how many had even read the book, about two hands (out of 20) went up. When we asked about reading at least a chapter, a few more did, but one young man asked if reading part of a chapter counted! But of course, that was that science book, which was “too hard”, even for faculty.

    So how do we deal with this? We know that students resist reading, but is that a reason to make it easier for them? I don’t think so; rather, I’d suggest go to the effort to truly incorporate it into our first year programs, and that there be real negative consequences (like grades of F) for students who chose not to make the required effort. I was pleased to discover, by way of a manuscript I reviewed (quite favorably, I would add) that this is what happens at Beloit College. In the fall of 2011, the College used Steven Johnson’s The Ghost Map: The Story of London’s Most Terrifying Epidemic and How It Changed Science, Cities and the Modern World, a history of the 19th century cholera epidemic in London and its role (via the identification of the source on infection as the Broad Street Pump). John Jungck then incorporated it into his mathematics class; his paper describing how he did so can be accessed here. After I reviewed the paper, I read the book and was thrilled by it; on reflection, however, I did not nominate it for use at Miami, in that it was clear to me that given the superficial nature of our program, we could not possibly do it justice. More on the Beloit First Year Initiative is here.

So, if I were to sum up the current state of these programs, I would do so with two words – “wasted opportunity”. By focusing on recent work by living authors, we deprive ourselves of most of the rich canon of world literature. By catering to student’s aversion to reading, we trivialize the process. And by minimizing science in these programs, not only do we do an injustice to the field, but we perpetuate the stereotype of science, for both students and faculty, as that hard stuff that only weirdos care about. Taken together, it means that I will continue to find alternative ways to occupy my summer months.

Have others had different experiences with these programs? If so, feel free to comment. However, I fear that if the trends continue, these programs will do little to enhance students’ academic experiences and will continue to provide fuel to those who (mistakenly, I submit) decry the “liberal bias” and “political correctness” they see as pervasive in American higher education.