The second annual Sagan-a-thon is ongoing. Having written last year about Carl Sagan and what I believe his legacy means to us, I thought I’d try something new:
Click for the full image.
Category Archives: Evolution
Cdesign Proponentsist. . . In Song!
Amadan declares, “I Am the Very Model of a C-Design-Proponentsist.”
Anti-Matters
Starting your own journal is a time-honored way to make pseudoscience and outright antiscience look more respectable. Known loonball Paul Cameron did it in order to bolster his homophobia, and the walking dishonesty generators known as “creationists” have done it several times. (Ad hominem? Sure, if you like. But creationism is the morally bankrupt pursuit of the factually wrong, and I lost patience with it quite some time ago.) Now, Jason Rosenhouse reports, they’ve gone and done it again.
These journals invariably founder on their inability to find any scientists willing to write for them. Remember Proceedings in Complexity, Information and Design? It’s been moribund since November 2005. Or how about Origins and Design? That one went belly-up around the turn of the century.
The latest representative of the genre is Anti-Matters. It bills itself as “A quarterly open-access journal addressing issues in science and the humanities from non-materialistic perspectives.â€
Apparently, “non-materialistic” science means attacking evolutionary biology with — wait for it — the Second Law of Thermodynamics! Some bad arguments just never die.
Man, I’m on an emotional roller-coaster here. “Ooh, Jason Rosenhouse has a new post! Joy joy. I wonder what it’s about.” Then I read, and: “Oh. Creationists blathering about the Second Law.
“Now I’m sad.”
On the arXivotubes
If I didn’t have to be modifying and debugging a network-growth simulation today, I’d be reading these papers. The first is not too far from one subject I’m researching right now. Axelsen et al. (arXiv:0711.2208) write about “a tool-based view of regulatory network topology”:
The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for performance based localization on molecular networks. To quantify structure-function relationship we investigate similarities of proteins which are close in the regulatory network of the yeast Saccharomyces cerevisiae. We find that the topology of the regulatory network show weak remnants of its history of network reorganizations, but strong features of co-regulated proteins associated to similar tasks. This suggests that local topological features of regulatory networks, including broad degree distributions, emerge as an implicit result of matching a number of needed processes to a finite toolbox of proteins.
The second, Gaume and Forterre’s “A viscoelastic deadly fluid in carnivorous pitcher plants” (arXiv:0711.4724, also in PLoS ONE), is pertinent to my eventual life goal of building an army of atomic super-plants.
Continue reading On the arXivotubes
Evolution and Turing Machines
I haven’t made any headway on the Grey Lady’s Top 100 Books of the Year, partly because I’ve been too busy reading what comes down the arXivotubes. For example, take Giovanni Feverati and Fabio Musso’s recent e-print, “An evolutionary model with Turing machines” (arXiv:0711.3580, 22 November).
The development of a large non-coding fraction in eukaryotic DNA and the phenomenon of the code-bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code growth) the evolution of a complex code can’t be attained without maintaining a large inactive fraction. To test this hypothesis we performed computer simulations of an evolutionary toy model for Turing machines, studying the relations among fitness and coding/non-coding ratio while varying mutation and code growth rates. The results suggest that, in our model, having a large reservoir of non-coding states constitutes a great (long term) evolutionary advantage.
Taking the broad view, it’s interesting that a large mass of genetic information might not directly code for phenotypic features while still having a long-term adaptive advantage. (Thinking about fitness over multiple generations gives me a headache: the mapping from phenotype to fitness value isn’t constant over time. Cluster a whole bunch of predators together, and they kill off all the prey, changing their environment and thereby making their own phenotype unfit. Some people really care about this; I just know it makes me want to go back to neutrino physics.) A few details of note:
First, Feverati and Musso evolve their Turing machines to specified goals: they want a machine which ends its operation with a tape containing a particular sequence of zeros and ones. In different trials, two distinct goal tapes were used, a tape representing the first 100 prime numbers and a tape holding the bits after the radix point in the binary expansion of π. (These goals were chosen in part because a periodic distribution is an easy thing for a Turing machine to make. I suppose we’re talking about maximizing Kolmogorov complexity, though the authors don’t make that connection explicitly.)
Second, the only form of mutation in their simulation was point mutation. More specifically, they randomly changed each entry in a Turing machine’s description with some probability [tex]p_{\rm m}[/tex]. Gene duplication and other such mechanisms were not implemented. States are added with a certain probability [tex]p_{\rm i}[/tex] per timestep; these states are non-coding until a point mutation elsewhere establishes a call to them.
UPDATE (28 November): A real biologist offers comments below. The number of people who know more than I do about any given subject is awfully impressive!
UPDATE (1 December): More here.
Antidote
John Scalzi’s LOLCreashun contest is going along swimmingly:
Who’s Talking about Judgment Day?
I don’t have a television set — just a projector connected to a computer, which is plenty good for movies but not so great for tapping the airwaves — so my impression of NOVA’s new program, Judgment Day: Intelligent Design on Trial, has been mostly textual. I say “mostly,” because I did see the trailer:
PBS promises us that the whole thing will be available ontube this Friday.
The National Center for Science Education is pleased with Judgment Day, and that’s a recommendation which carries a lot of weight. Still, they’re an awfully Web 1.0 lot over there, so what do we suave cyber-philosophes have to say?
PZ Myers and the Pharynguloids watched the show last night, live-blagging as they went along. Then, this morning, PZ observed that the Discovery Institute’s response was a regurgitation of old whines which managed to miss the point of the program entirely. (EDIT: Tyler DiPietro has some details.)
Greg Laden, who also live-blagged the broadcast (1, 2, 3, 4) has an overview and a couple complaints — nothing fatal; he enjoyed the show, but in a few respects, the producers could have made a good thing even better.
Meanwhile, Dave Bacon is complaining that the biologists are having all the fun. Where are the epic court battles over quantum physics? Come on, you pansy Vedic Shiva-botherers, bring it on!
Continue reading Who’s Talking about Judgment Day?
Spotted on Teh arXivotubes
You know, I’m beginning to like these RSS feeds for the arXiv. Two e-prints just popped up in the “quantitative biology” section which I should look over more carefully:
Continue reading Spotted on Teh arXivotubes
C. proponentsists Caught on Video
If Carl Zimmer says it, it’s gotta be official: cdesign proponentsists is the new term for “creationists.”
For the background to this discovery, see the National Center for Science Education.
Another D-Word Sighting
This is Mark Lawson interviewing Sir David Attenborough on BBC Four.
Remember, Sir David is the most trusted man in Britain.
LAWSON: Have you at any time had any religious faith?
ATTENBOROUGH: No.
Clearly, he’s not going to be trusted in the United States any longer.
One verbal item caught my attention. Lawson, a journalist of English birth and education, employs the word Darwinist.
LAWSON: Your programs clearly are Darwinist, but it’s not something. . . You never seem to actually take on the creationism. For example —
ATTENBOROUGH [overlapping]: Oh, I certainly do, privately, and, and would be happy to do — it’s not the place to do it in the sort of programs I make.
From this single instance, it’s hard to tell whether Lawson equates “Darwinist” with “atheist,” as our American creationists are wont to do, or if he’s closer to the usage observed among certain academics, roughly equating “Darwinism” with “evolutionary biology.”
Posts on Peer-Reviewed Research
Tired of slogging through troll-infested comment threads? Want to reinvigorate your sense of hope for the Internet? Then try blog posts on peer-reviewed research! A week ago, the “Research Blogging Icons” were unveiled, and now, dozens of posts have been marked with these identifiers, indicating that they discuss serious science which has appeared in professional venues. Dave Munger has picked out a sample of ten, and they all look worth reading.
For a wonder, one of my ICCS posts is on the list. Also, I quite enjoyed Kevin Z’s take on the evolution of fireflies. Did you know that the firefly family of beetles, the Lampyridae, contains about 2000 species worldwide, with around 120 represented in North America? And that the species which more closely reflect the ancestral form use pheromone signals, instead of light?
Kevin Z also describes research which has recently been done to understand the costs of flashing lights, both in terms of energy and with regard to attracting predators. And here’s where I kick myself: back in 2005, I wrote a scene for a science-fiction novel which used almost exactly the experimental setup of that predation study, although the goal in the novel was to understand why their flashes had started to synchronize.
Update on the D-Word
Dwight Read is another academic who uses the word Darwinism to refer to evolution by natural selection. During his plenary talk this morning, Read spoke of “Universal Darwinism,” Dawkins’ term for the idea that natural selection is not substrate-specific and can in principle be applied to non-biological things, like cultural memes.
As I mentioned earlier, it’s folklore among the science-blogging community that British academics are more likely to use “Darwinism” in this sense than Americans are. (Over here, hearing the D-word is a pretty sure sign you’re dealing with a creationist, or at least somebody whose knowledge derives too much from creationist sources. I wonder if there’s also a bit of national pride at work.) Read is currently at UCLA, but in 1999 was a visiting professor at the University of Kent, Canterbury.
ICCS: Sunday Morning
The following is my first attempt to liveblog ICCS 2007. I arrived at the Quincy Marriott shortly before 8:30 this morning, having driven south on I-93 from Boston. Unlike the first time I drove out here, I didn’t get lost in Braintree, since I took the left fork at the “Braintree split,” where I-93 undergoes mitosis. These things are important to know.
The morning’s plenary talks began with Diana Dabby (Franklin W. Olin College of Engineering), who spoke about chaotic transformations one can apply to music in order to generate musical variations, as in “Variations on a Theme of Beethoven.” Her scheme begins by breaking the musical performance into a sequence of pitches, denoted [tex]p_i[/tex], and then mapping each [tex]p_i[/tex] to a section of a dynamical trajectory on a chaotic attractor like the Lorentz owl/butterfly mask.
Continue reading ICCS: Sunday Morning
Saucy in the Garden
Kurt Vonnegut, blessed be his memory, once said that science fiction and pornography had one key thing in common: they both portrayed an impossibly hospitable world. Of course, he said that back in the day when John Campbell still held sway over the field, long before Blade Runner, so while pornography stayed where it was, science fiction moved on. Contemplating these matters, I started to wonder if providentialist religion couldn’t be described in the same way. The belief in, as Philip Kitcher says, “a Being who has a great design, a Being who cares for his creatures, who observes the fall of every sparrow and who is especially concerned with humanity” hits that same chord of optimism and ego.
Why am I following this sordid train of thought? Well, because it has a succulent conclusion. Bug Girl points to a reviewer who noticed something we should have remarked upon much earlier. Here is a photograph (by Monica Lam) of Kentucky’s Creation Museum, for which I claim fair use:
What does this tableau of Mr. and Mrs. Adam most strongly resemble?
Continue reading Saucy in the Garden
Language Logged!
UPDATE (31 October): I’ve now heard the D-word in real life.
To my considerable surprise, I found this morning that I’d been Language Logged. I’m glad to hear that Deborah Cameron’s The Myth of Mars and Venus contains a solid critique of evolutionary psychology — in Mark Liberman’s words, “a dissection, and a rather careful and limited one, not a bludgeoning.” After reading what Liberman had to say, I think I erred in my original post on Deborah Cameron and her use of the word Darwinist. I stand by the essential content of what I said before, but in two respects, I goofed. First, I should have called greater attention to the sexism of the news story which first piqued my curiosity; second, I should have been more precise in my claims about “usage.” After saying some nice things, for which I am grateful, Liberman takes issue with this part of what I’d written:
On this side of the Atlantic, hearing a person say “Darwinism” is a red flag that you’re dealing with a creationist or, at least, a person whose knowledge of science derives primarily from creationist claptrap. To me, calling evolutionary biology “Darwinism” makes as little sense as calling all modern music “Beethovenism.” The year is no longer 1859; we understand many things which Darwin did not, although we stand on his shoulders.
In British usage, “Darwinism” is much more synonymous with evolution in general. (Richard Dawkins is a prime example of this tendency.) I find this unfortunate, partly because it slights all the relevant discoveries we have made since, from Mendel’s time to the present day, and partly because it provides unwarranted ammunition to creationists over here. Still, that’s the way they talk.
Instead of talking about general “British usage,” I should have done what I did in my brief follow-up, making explicit that I meant the writings of British evolutionary biologists in particular. Mea culpa! Liberman writes of his searching Google News for “Darwinism,”
Continue reading Language Logged!
Sweet!
Whom does the Internet describe as a “manipulative liar”?
Why, Michael Egnor, of course.