Recently in Resources for Biologists Category

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

The correspondence of Alfred Russel Wallace

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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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In association with the Santa Fe Institute, Melanie Mitchell will teach a free online course called Introduction to Complexity starting on January 28, 2013. Mitchell has been working in complex systems research for years. Her Ph.D. advisors were Doug Hofstadter of Gödel, Esher, Bach fame and John Holland, a towering figure in the study of complex adaptive systems, which is the title of his influential 1975 book. According to the intro video and the course FAQ, it’s is aimed at non-specialists:

This course is intended for anyone with an interest in complex systems. For this introductory course, there are no prerequisites, and no science or math background is necessary. The level will be similar to that of an interdisciplinary undergraduate class, though the topics are broad enough to be of interest to people ranging from high school students to professionals.

To register to earn a certificate of completion, go here. One can watch the course videos without registering, though one won’t take the final nor be able to participate in the student forum.

Hat tip to Sean Carroll.

Free access to some Springer journals through Nov 30

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Here. Hurry before they’re all gone!

Hat tip to Emily Lakdawalla

Fractal-inspired Tree of Life

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

Via The Finch & Pea

Wallace Online

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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

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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

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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

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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”

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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

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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

miller_dvd_webad.jpg

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.

Evolution Matters

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The University of California, San Diego (UCSD), the alma mater of Discovery Institute’s spokesperson Casey Luskin, explores why “Evolution Matters”. In cooperation with UCSD-TV, they bring us a fascinating lecture series:

For 2007-08, the Division of Biological Sciences is launching Evolution Matters: The Diversity of Development. In this series of 5 lectures, held over the course of the year, leading cell and developmental scientists will explore the evolution of plants, animals and humans and will discuss how their research into this field holds promise for finding solutions to key health and environmental issues facing us today.

Educational Website: Grey Matters

Educational Website: Science Matters

Atoms to Xrays

Neil Shubin’s latest book on evolutionary theory is by all standards a great success. It ranks around 200 in Amazon books and first in Evolution Science Books. When I checked the book’s availability in our library system there were close to 40 pending holds.

A sales rank of 200 means 225-250 books per week are sold. Compare this to a rank of 24,000 for Behe’s boo “Edge of Evolution” sold at a bargain price of $6.99 down from $28.00 or 111,550 for the regular priced version. Those numbers translate to few copies per month being sold.

Neil Shubin is a professor of organismal biology at the University of Chicago. He, as part of a team of scientists, discovered the now infamous Titaalik transitional fossil which causes so much consternation amongst Intelligent Design Creationists. His book Your Inner Fish introduces its readers to an exciting overview of how our evolutionary history links us back to a common ancestor with fish. Of course, that’s not where our common ancestry ends.

Why do we look the way we do? What does the human hand have in common with the wing of a fly? Are breasts, sweat glands, and scales connected in some way? To better understand the inner workings of our bodies and to trace the origins of many of today’s most common diseases, we have to turn to unexpected sources: worms, flies, and even fish.

In Your Inner Fish, Neil Shubin tells the story of evolution by tracing the organs of the human body back millions of years, long before the first creatures walked the earth. By examining fossils and DNA, Shubin shows us that our hands actually resemble fish fins, our head is organized like that of a long-extinct jawless fish, and major parts of our genome look and function like those of worms and bacteria.

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