Header image alt text

Evolution, History and Society

Perspectives from a Third Career

Introduction – December 2017

Posted by admin on November 15, 2017
Posted in Uncategorized  | No Comments yet, please leave one

Having let this site sit moribund for a couple of years, I’m hoping to be a little more active, now that I am entering my fourth career, that of professor emeritus. Posts, when they occur, will probably a bit more general in nature, but I will attempt to stick to the themes of genetics, evolution and history. There are actually 40 days left until that career commences, so don’t expect much until after Christmas, when I will be spending more time working on this, as well as my more technical site Population Genetics: Applying Theory to Data.

Migrating away from Dropbox

Posted by admin on November 17, 2017
Posted in Uncategorized  | No Comments yet, please leave one

Step one of this process is complete. I’ve managed to move my mapped photos to github. I have a love-hate relationship with that platform, but at least personal sites at github.io are free. The result can be seen here

Cross post

Posted by admin on July 31, 2016
Posted in Uncategorized  | No Comments yet, please leave one

“Dr. Science Teacher” nails it regarding belief vs. acceptance.

The best Twitter thread ever

Posted by admin on June 12, 2015
Posted in Uncategorized  | No Comments yet, please leave one


FRED and R

Posted by admin on July 18, 2012
Posted in Uncategorized  | No Comments yet, please leave one

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.

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
Posted in Uncategorized  | No Comments yet, please leave one

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
Posted in Uncategorized  | No Comments yet, please leave one

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

iPhone

for Android devices
Android

And the result?

Heidelbergensis