Recently in Resources for Biologists Category

Avida-ED is educational software that provides an accessible presentation layer on the Avida artificial life platform. The first version was released nine years ago, and today marks Prof. Rob Pennock’s release of version 3, with a formal presentation at Evolution 2016. Avida-ED is geared toward the needs of undergraduate and advanced high school curriculum use.

The new version, Avida-ED Web 3.0, is a web application: it runs in your browser (Firefox or Chrome currently; Safari, Internet Explorer, and Edge have some compatibility issues). To get it, visit the canonical Avida-ED site, or the mirror site. As a web application, Avida-ED Web 3.0 lowers the barriers to use, restoring the ability for those running Linux to use Avida-ED, and giving Windows users access to the latest feature set. While installation is not required, there are installers for MacOS and Windows that set up a local HTTP server and launch a local copy of Avida-ED Web in the default browser. This latter option may be useful for people who expect to be without internet access when they want to use the program. More discussion below the fold.


The September issue of Natural History magazine is devoted almost entirely to essays concerning Alfred Russel Wallace. I usually turn the pages of NH, look at the pictures, and read many of the captions – but I read this issue almost in its entirety (and therefore cannot resist writing about it). Unfortunately, it looks as though none of the articles is available on the Web, but you can get your own copy for $3.95 (US), presumably on the newsstand.

The issue was edited by Richard Milner, head of the Wallace Centenary Celebration. According to the second comment below, he also edited a special issue of Skeptic magazine, and you may request a free copy of either or both magazines by writing Mr. Milner an e-mail.

The first article, by the distinguished naturalist David Attenborough, outlines Wallace’s career. I did not know that, as Wallace returned from South America, his ship caught fire, and he lost all his notes and his specimens; I think I learned that fact 2 more times in subsequent articles. Attenborough outlines how Wallace got the idea of natural selection while studying birds of paradise. As is widely known, he sent an essay to Darwin. Lyell and Hooker arranged to have Wallace’s paper presented alongside a paper by Darwin, who then rushed his own book, On the Origin of Species, into print. Attenborough remarks, “You might have thought there was an embarrassment or perhaps hostility or resentment” between Darwin and Wallace. “Not at all. The two men had great respect for each other, untinged by any sign of jealousy.”

An article by geneticist Andrew Berry goes over some of the same material, though in more detail and more biographically. Berry observes that Wallace’s 1865 definition of “species” is identical to the “biological species concept” that is usually attributed to Ernst Mayr 80 or so years later. There is a certain amount of redundancy in these articles, each of which was written as if the authors thought they would have to stand alone: Berry introduces us to Wallace’s Line, apparently unaware that Attenborough has already done so in the preceding article and Gary Noel Ross will do so later. Wallace originally went abroad, says naturalist Errol Fuller, to earn money by supplying stuffed animals to middle- and upper-class England; evidently such products were in considerable demand at the time, and Attenborough estimates that Wallace collected 110,000 insects, 7500 shells, 8050 bird skins, and over 400 mammals and reptiles. Fuller shows us some stuffed specimens that remain in remarkably good condition today.

But for someone who just wants to look at the pictures, the high point of the issue might be a series of photographs of birds of paradise by Tim Laman with a narrative by Edwin Scholes. An article by Ross describes (sort of) following in Wallace’s footsteps and searching for the golden birdwing butterfly; this article likewise displays excellent photographs, some by the author and including what seems to be a selfie taken from a distance of several meters.

The final article is a reprint of a 1980 article by Stephen Jay Gould. Gould discusses the fact, noted in an earlier article as well, that Wallace and Darwin disagreed on sexual selection, and also on the origin of the human brain. Wallace, according to Gould, took the “hyperselectionist” position that everything that evolved is an adaptation. The brain, however, can do much that it is not adapted to do, like write symphonies. Such reasoning, says Gould, leads Wallace “right back to the basic belief of an earlier creationism that it [Wallace’s hyperselectionism] meant to replace—a faith in the rightness of things, a definite place for each object in an integrated whole.”

If you want to know more, I am afraid that you will have to buy the magazine. And cheer up! The pictures are better in print than on your monitor.

Three years ago I became a chimera. Again. I am also geneticist. Surprisingly, the two are unrelated.

The correspondence of Alfred Russel Wallace


The correspondence of Alfred Russel Wallace is now online. And here’s an interesting “interview” with Wallace, with Wallace’s answers drawn from that correspondence.

Free MOOC course: Introduction to Complexity


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Free access to some Springer journals through Nov 30


Here. Hurry before they’re all gone!

Hat tip to Emily Lakdawalla

Fractal-inspired Tree of Life


For mammals. Click on nodes repeatedly to burrow deeper into it and to access Wikipedia links.

Via The Finch & Pea

Wallace Online


The written works of Alfred Russel Wallace, co-discoverer with Darwin of the principle of natural selection, are now online. The Wallace Online project is directed by John van Wyhe, who also produced the Darwin Online project. Enjoy!

Via the BBC

RationalWiki has posted an exhaustive list of evidence that evolution is a hoax.

Thanks to Mike Klymkowsky for the tip.

Synthese Reminder: Two days left


A reminder that the papers in the special issue of Synthese edited by Glenn Branch and James A. Fetzer are available online free for just two more days, today and tomorrow. After the 31st they disappear behind the Springer paywall. Get ‘em while they’re free!

“Written in Stone” excerpt available


Some years ago I began following the blog of an undergraduate at Rutgers who split his posts between descriptions of work in paleontology and his problems getting a major put together in his preferred field of study. Over the years it has been a real pleasure to watch as Brian Switek, the author of Laelaps (first on Wordpress, later ScienceBlogs and finally on Wired’s network) grew as an up and coming science writer and as a person.

Brian’s first book, Written in Stone: Evolution, the Fossil Record, and our Place in Nature is coming out on December 1, and NCSE has an excerpt. Sadly, it’s not (yet?) available for my Nook (or for the Kindle) so I guess I’ll have to wait a while to read the whole book.

Hat tip to Adrian Thysse.

NSF Center for the Study of Evolution in Action Funded

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William Dembski calls envious attention to the funding (reportedly $25M) by NSF of the BEACON (Bio/computational Evolution in Action CONsortium ) project, a multi-institutional consortium that is intended

…to conduct research on fundamental evolutionary dynamics in both natural and artificial systems, educate a generation of multi-disciplinary scientists in these methods, and improve public understanding of evolution at all levels. The center will unite biologists who study natural evolutionary processes with computer scientists and engineers who are harnessing these processes to solve real-world problems.

Among the researchers associated with the consortium is Joe Felsenstein, who guest posts here on occasion. On a fast run-through of the personnel listing I also see at least four senior people who have been associated with the AVIDA project at Michigan State (Pennock, Lenski, Ofria, and Wilke) and other leaders in both evolutionary biology and computer modeling of evolution. The consortium includes Michigan State University (lead institution), along with the University of Washington, the University of Texas at Austin, North Carolina A&T, and the University of Idaho. I’ll be interested to see what comes out of it, especially given its lofty goals:

BEACON will have a powerful legacy: we will reframe public perceptions of evolution and increase understanding of scientific methods. At the same time, we will produce a conceptual framework to firmly establish evolutionary biology as an experimental science and cement its links to computing in a crossfertilization that enhances both fields.

See also here:

K-12 and general public education.

In this area, BEACON will pursue four main goals:

* Demonstrate the fundamental power and importance of evolution. BEACON will contribute to the pressing national need to bolster U.S. pre-eminence in science and technology by educating people about the importance of understanding, managing and harnessing biological and computational evolutionary processes and deconstructing the false dichotomy of micro- versus macro-evolution.
* Disseminating materials generated by BEACON. Our team includes experts in science education and outreach who will work with all BEACON researchers to adapt BEACON research for use in science classes in schools in ways that address national science standards and goals.
* Increasing participation in science and engineering. We will broaden participation in STEM disciplines by introducing teachers and students from underrepresented groups to the new research opportunities afforded by BEACON’s applied evolutionary tools and research programs.
* Preparing responsible citizens. We will deepen student’s understanding of evolution-related challenges, such as responding to the evolution of infectious diseases and limiting the evolution of antibiotic and pesticide resistance, and have them learn to protect the integrity of the scientific process.

Those are high aspirations.

Smithsonian’s Human Origins Initiative


The Smithsonian Institution has launched a new web site focused on human origins. It includes a good deal of material on the evidence (behavior, fossils, genetics, and dating) and Smithsonian’s research projects, along with what looks like a very useful set of education resources including lesson plans for teachers, a teachers forum, and student resources including an interactive mystery skull interactive exercise (I had trouble with that in Chrome but not in Firefox; apparently there’s a Flash glitch in the interaction of the site with Chrome).

And just to stir the pot a little, the page on the Broader Social Impacts Committee will provide some fuel to the accommodationist/hardliner feud. In particular, notice who is not represented on it.

At any rate, I strongly commend the site to your attention.

Hat tip to ASA Voices.

Evolution: Education and Outreach vol 2 issue 4 online

I missed this earlier, but T. Ryan Gregory reminds us that the new issue of Evolution: Education and Outreach is now online. There’s a broad range of articles and reviews in the issue, and one stands out for me. It’s Douglas Allchin’s article on resources for teaching the evolution of morality. All the articles are linked from Gregory’s post here. I heartily commend it to your attention. That journal is a valuable resource for us all.

NSF’s “The Evolution of Evolution”


The National Science Foundation has announced the opening ot their Evolution of Evolution site. According to the press release,

Going wide and deep, Evolution of Evolution: 150 Years of Darwin’s “On the Origin of Species” provides a uniquely sweeping, at-a-glance explanation of how “Origin” cut an intellectual swath through anthropology, biology, the geosciences, polar sciences and even astronomy, and why it likely will continue to serve as the organizing framework for the sciences into perpetuity.

I’ve not yet gone through the site exhaustively, but I see a number of interesting parts. For example, there’s an interview with Ron Numbers on the impact and interaction of the theory of evolution with astronomy, a nice touch that reminds us that Numbers is an historian of science, not merely of creationism. And it was nice to see David DeVorkin give a shout out in his interview to George Darwin, Charles’ son, who wielded a significant influence on the conception of stellar dynamics in the late 19th and early 20th century. There were more Darwins than just Charles.

I have two minor objections. First, I’m afraid that the ‘silent movie’ conceit in the video interviews might get a little old after the fourth or fifth iteration. And second, the titles/links to video and audio interviews are in ant print, and the whole site seems to be in Flash format, making the text non-magnifiable. Ctrl+ fails. Us old folks will have some trouble with that.

Nevertheless, I recommend it heartily.

New evolution resource site online


There is a wide array of resources on the web about evolution, ranging from public access to technical papers available via PubMed to the excellent Understanding Evolution site operated by the University of California Museum of Paleontology and the National Center for Science Education. The grand daddy of them all, of course, is the TalkOrigins Archive.

Now a new resource has been established by T. Ryan Gregory, evolutionary biologist and blogger at Genemicron. It’s called Evolver Zone, and is “a resource for students, teachers, and researchers with an interest in evolution.”

Evolver Zone is a collection of a wide range of resources on evolution, from online databases to software to teaching resources to multimedia (including games!). I haven’t browsed the whole site yet, but what I’ve seen looks to be very useful, particularly for advanced high school and undergraduate classes. Gregory tells us the site is a work in progress, so check back often for new additions.

Evolution Education: Evolution of the Eye Special Issue

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One of our strategies in the defense of science and the Enlightenment (yes, Ken Miller’s Only a Theory is having an effect on me) has to be to increase the level of scientific knowledge among educators, especially secondary school teachers, and to show how much we actually know about how evolution works to produce complicated organs. One of the canonical complicated organs, the vertebrate eye, is a long-time favorite of creationists and IDists. They happily quote Darwin’s notorious introductory sentence about it:

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.

But then they ignore his answer to the problem in the next sentence:

Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.

Now an outstanding resource to support evolutionary claims about eye evolution is available. A special issue of Evolution: Education and Outreach, which is under the general editorship of Gregory and Niles Eldredge, is available free online. The special issue was edited by T. Ryan Gregory, who also wrote the Introduction to the issue. It includes 11 articles of original research and reviews, three on curriculum possibilities, and a book review. All told it is an excellent resource.

Exploring Life’s Origins

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protocell.jpgThe PT Crew received an email, announcing a breathtaking website called Exploring Life’s Origins. The website displays in stunning graphics and video how scientists are exploring the origins of life. The graphics were made by an NSF Discovery Corps Postdoctoral Fellow named Janet Iwasa, in collaboration with Jack Szostak, and the Current Science and Technology team at the Museum of Science, under an NSF grant. The resources are available under a Creative Commons License which requires attribution, non-commercial use and no derivative works. The website explains in clear and accessible language how science envisions life arose on earth and explains the RNA world, which, despite the wishful thinking of some creationists, has not lost its relevance.

The Howard Hughes Medical Institute has extensive lectures and resources for educators, in fact anyone can order their DVD’s for free. You can also subscribe to their podcasts.

Talks include Ken Miller’s Evolution: Fossils, Genes, and Mousetraps


Leading evolution educator Ken Miller discusses the controversy surrounding the teaching of evolution, presents compelling evidence for evolution and reasons why “intelligent design” is not scientific. The presentation also features Dr. Miller’s responses to questions from a live audience of high school students.

Explore the site, it’s full of interesting information helping anyone appreciate the science of evolution and biology.

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