Evolution, Pseudoscience

Enhanced Circumlocution Techniques

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Lately, there’s been a bit of a dust-up over at the ScienceBlogs schizophrenic hive mind over some statements by Mitt Romney. During the course of the kerfluffle, I started thinking about the slippery way words work, and how oddities in our relationships to words affect the way we interpret them. As the fracas was dying down, a related post zinged my way from a different quarter which motivated me to ramble about the whole affair.

It began with Michael Luo writing the following at the New York Times political blog “caucus.”

“I believe that God designed the universe and created the universe,” Mr. Romney said in an interview this week. “And I believe evolution is most likely the process he used to create the human body.”

He was asked: Is that intelligent design?

“I’m not exactly sure what is meant by intelligent design,” he said. “But I believe God is intelligent and I believe he designed the creation. And I believe he used the process of evolution to create the human body.”

Is this a good sign or a bad one? More exactly, does it signify a move from very bad to less so? Well, tough to say — I don’t think “close reading” is a very useful tool to apply to politicians’ statements. (If this were a letter from Thomas Pynchon, then yes, we should scrutinize it for every nuance of meaning, yet Romney is not a future Nobelist but rather an embryonic Nixon.) Whether a man can be an ally in the struggle for reason and critical thought depends not only upon his ideas, but upon the man himself.

As a person who is moderately informed about biology, I grow nervous when I hear people single out “the human body” for preferential treatment as the desired end product of the evolutionary process. Remember in Calvin and Hobbes when Calvin described the prehistory of Earth from 4.5 billion years ago until today and then announced, “Now, in 1988, there’s me. The acme of evolution!” Satire, almost twenty years ahead of its target. Remember Prometheus, sculpting humans out of clay and stealing fire because all the good tricks had been given to the other animals? The only noteworthy difference between the Greek story and the modern myth is that like Bill Watterson, the Greeks recognized how feeble our bodies are without feral claws and feline night-vision.
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Chaos Theory, Classical Mechanics, Plectics, Statistical mechanics, Topology

Chaos, Phase Transitions and Topology

Ben has suggested the following paper as a target for our discussion. We should, he says, have the necessary background by the end of the summer.

As the abstract says, the paper is divided into two main parts:
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About this Blag, Group Theory, Seminar Announcements, Seminar Summaries

Group Theory Homework

One reason I call this site a “blag” and not a “blog” is that I’m always late.

For example, I’m finally typing up the group-theory homework assignment which Ben gave last Monday (and which will be due next Monday). During our seminar over in BU territory, we discussed the relations among the Lie groups SU(2) and SO(3) and the manifolds S3 and RP3. Problems will be given below the fold.

Also, Eric will be discussing statistical physics this afternoon at NECSI.
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Astronomy, Popularization, Wobosphere fun

Eta Carinae

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I remember a time when it seemed like I was the only person in the world who knew that stars we could see in the night sky might one day go foom, letting us read at night or, possibly, destroying the habitability of our planet. Of course, I couldn’t have been alone in knowing this, since I found out about it by reading books by other people, but in the dark times of Web 0.1, before writers and scientists were people who listened to music and got in spats with one another, it was easy to feel alone while exploring the heavens.

And now, look, everybody who reads the Washington Post knows about Eta Carinae, thanks to Joel Achenbach:

I dropped by NASA headquarters last Monday to hear about the relatively nearby and extremely massive star that might explode at any moment. Remember the name: Eta Carinae. Sounds like an Italian opera singer, or maybe a snazzy little sports car. It’s a monster of a star — something like 120 times the mass of the sun, and roiling, heaving, spewing out gobs of star stuff in what may be the prelude to a cataclysmic bang, a supernova unlike any seen before.

If it blows, you might be able to read a book by its radiance at night — unless it fires a narrow beam of gamma rays right at us, in which case all bets are off. One astrophysicist on hand said, “It would probably destroy all the ozone in the atmosphere.” Similar to what we tried to do ourselves, before we banned those nasty chlorofluorocarbons. Eta Carinae would be like a giant can of 1950s hairspray. Not a pleasant picture.

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Transhumanism

Deep Quandaries of Metaphysics

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Some questions can be asked in a single sentence, yet despite (or perhaps with the aid of) their brevity, they probe the deepest passages of meaning and the darkest abyssals of mystery. For example, “Will super glue stick to teflon?”

Last night, while drinking down beverages flavored with improbable syrups, Joshua and I came up with another: “What happens when an alien facehugger attaches to a zombie?”

I hope everyone appreciates the profundity of these conundra.

And just think, without the Internet, you probably would never have heard of them. Makes you wonder what else you’ve been missing all these years.

Most Christians happily disavow Baal and the Flying Spaghetti Monster without reference to monographs of Baalian exegesis or Pastafarian theology.

— Richard Dawkins

For the record, I think Predator vs. Alien vs. Night of the Living Dead came up when we were talking about Kaavya Viswanathan. “If they had hired me to write an inspiring book for teenage girls about a young woman who goes to Harvard,” I said, “I would have had her meet the admissions interviewer in chapter 1. The interviewer says she’s got good grades, but she needs more extracurricular activities. So, in chapter 2 — fast forward through the clubs and the senior prom — she gets into Harvard and her parents drive her to Cambridge in their Range Rover. Then, in chapter 3, she gets bitten by a vampire, and the biotech lab in Roxbury explodes, releasing a zombie-making virus all over Boston. So, young Emerald and her friends have to use her growing vampire powers to fight the legions of undead moaning their way up Massachusetts Avenue. . . and that’s why they don’t hire me to write inspiring books for teenagers.”

Astronomy, Cosmology, Popularization, Quantum mechanics, String Theory

A Quarter of Everything

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I have just two quibbles with this New Yorker article on the Large Hadron Collider to which Scott Aaronson directed my attention. First, throughout her informative story, Elizabeth Kolbert consistently abbreviates “Large Hadron Collider” as “L.H.C.” I’ve yet to see anybody in the physics community use the periods when they write “LHC.” Is this some official policy which we, the project’s website and the rest of the Internet just are too lazy to follow? Or are these strange little dots the product of a New Yorker in-house style guide demanding their presence based on some holier-than-Sinai rule about tiny ink specks? If the latter is the case, the foolish prescriptivist responsible needs an introduction to my friend the clue-by-four.

My second and marginally more serious complaint involves the following passage from page five:
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Pseudoscience, Wobosphere fun

The Skeptical Garden of Forking Paths

The 60th Skeptic’s Circle is up at Infophilia. Our Sunclipse contingent is represented by these three posts. Lots of good stuff is on offer; I particularly enjoyed Conspiracy Factory’s anecdote about anecdotes, and Bronze Dog’s take on vibrational woo struck a chord with me.

Thank you, thank you, I’ll be here all week!

Infophile clearly put some serious effort into this Circle. The end result, a fine example of hypertext fiction bent to pedagogical purposes, indicates that he truly appreciates the quantum feminist perspective:

The lurch and the jump of a browser’s deterritorialized journey through a hyperlinked text simultaneously problematizes connectivity, perspective and the nature of multidimensional space even as it explores them. […] Luce Irigaray has asked, “What do we call a gap that is full?” (qtd in Joyce, 1995, 207) and in the webbed space of hyperlinked fiction the pregnant gaps between the nodes are at least as important as the textual nodes themselves. The nodes exist in conjunction with the dynamic space of the journey and cannot be discussed in isolation. This information gap can only be travelled through and never visited directly because it is the interpolation of space and nonspace. It is mnemonic space: the fleeting space between the moment of remembering and forgetting. This is not the white space of the printed page, but instead the full, noisy gap of the cyberspatial leap through sensual and perceptual space. These gaps are felt, not seen.

Transparency, Wobosphere fun

The Algorithm Finds Brooke Shields

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It looks like those zany Englanders need some lessons in drawing muted post horns:

The Alphabet of Brooke Shields

This graffito has been puzzling people all throughout London. First described by Londonist, it remains enigmatic. Sightings throughout the Greater London Above area are tabulated here. (Something odd also seems to be happening with Frozen Indigo Angel, which sounds an awful lot like a codename Charles Stross would invent for a Bob Howard novel.) Metro.co.uk writes,

So do you have any theories? Do you know what Alphabet of Brooke Shields means? Tell us in the comments, please. We’re going mad here. In this puzzle wrapped in an enigma wrapped in Brooke Shields, only one thing is certain — if it turns out to be just some rubbish viral marketing for a band or a perfume or a robotic dog or something, we’re all going to be very upset indeed.

I’m torn. Does this topic require more Neverwhere jokes (“Brooke Shields” is actually a warrior princess fording rivers in London Below) or more The Crying of Lot 49 references? (Weird “Alphabet” Still Teasingly Elusive. Don’t Ever Alphabetize The Horn.)
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Favorites, Popularization, Wobosphere fun

Cosmos 2.0

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I expect that by now we’ve all learned to be a little wary of X 2.0, just like we wonder what’s being oversimplified when we see “the New X” or, worse yet, “X is the new Y.” We know that anything 2.0 should be approached with curiosity, skepticism and a sense of humor. Such is the spirit I would like to evoke for the following post, which I’m recycling from this Memoirs of a Skepchick comment.

The subject was brought back to my attention, oddly enough, by the Time Magazine list of most hoopla-ed people about which I already ranted. In addition to bashing my head against my desk thanks to the Dawkins profile, I happened to check Neil deGrasse Tyson‘s write-up (authored by Michael Lemonick). I could only think that Lemonick exaggerates Tyson’s name-recognition factor and meme-market capitalization. He fits Tyson neatly into the “next Carl Sagan” slot, but in my humble (cough, cough) estimation, Tyson has a fair way to go. As I mentioned a few days ago, the subject of “science superstars” came up during my breakfast chat with PZ Myers. Not long after I arrived, before the others showed up, we got to talking about how one invents a scientist persona for the mass media. Adam Bly, Seed Magazine’s founder and Editor-in-Chief, appears to be taking Sagan as his archetype. Notice that we’re all still looking for “the next Carl Sagan,” not somebody who is “bigger and badder and sexier than Neil deGrasse Tyson.” In other words, I wish Tyson were as famous as Lemonick makes him out to be.

(I was also a trifle irked by Lemonick’s statement that Sagan guest-starred on Johnny Carson’s show while Tyson trades jokes with Jon Stewart and Stephen Colbert. Apples and tangerines! Three decades ago, was satire the only channel of intellect TV provided?)
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Bad Math, Neuroscience, Pseudoscience, Quantum mechanics

Recycled Rant: the Quantum Mind

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This is a topic which seems to come up with depressing regularity, so I figure I should put my stance on the record. The bulk of this post is recycled from a Memoirs of a Skepchick comment thread.

For various reasons, I am extremely skeptical of the notion that consciousness could be rooted in quantum phenomena. Of course, the entire world is quantum, in a sense: it’s the principles of quantum mechanics which determine the properties of materials out of which the world is made. Like Democritus of Abdera said twenty-five hundred years ago, “Nothing exists save atoms and the void”, and quantum physics constitutes the rules by which atoms play.

The challenge, then, is not to say “all is quantum” (a statement with no more content, by itself, than saying “all is love”). In what way do the strange and esoteric mathematical descriptions of the atomic and sub-atomic world build up the everyday stuff with which we are so familiar? This is a deep problem, one with many mysteries left to resolve, and physicists spend lots of time worrying about it. One thing which we do know is that when you put a lot of quantum particles together, at a certain point they stop acting in the quantum way and become better approximated by Newton’s laws of classical mechanics. This is odd, because if you put a pile of classical pieces together, you get a bigger classical object! Newton’s laws reproduce themselves at higher scales, but the quantum laws do not.

It’s a bit like discovering that all the ordinary houses on your ordinary street are made of bricks from Faerie.
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Evolution, Information Theory, Network theory, Seminar Summaries

Info Theory and DNA/Evolution

We’re reviewing the IEEE papers.

After reviewing the first batch of papers, we came up with some questions to answer in the future, in order of difficulty/open-ness:

1. Given the robustness of a code (e.g. due to a many-to-one codon->AA mapping), can we calculate bounds on the channel capacity of such a code? How does the empirical R (info transmission rate) of the codon->AA code compare with the empirical C (channel capacity, e.g. from mutation rates)?

2. How does the length/entropy/complexity of code-bits (e.g. parity bits, non-message bits used for error correcting) relate to the complexity of the error-correcting task, and e.g. the entropy and length of the data-bit sections (e.g. the actual message you’re sending) to satisfy R≤C?

– Is the von Neumann entropy,
[tex]H = {\rm Tr\,} \rho\log\rho = \sum\lambda_i\log\lambda_i [/tex]
where {λ} are the eigenvalues of the matrix, useful for discussing network robustness? (There’s a paper where they use Kolmogorov-Sinai/Shannon entropy to do this, which Blake has somewhere…) If so, then can we apply this to a genetic-regulatory network, and tie in the error-correcting or homeostatic abilities of such a network with VNE or other network metrics?

Next week:

We meet Monday at BU for group theory. Ben will be discussing SU(2) and SO(3) from Artin. Friday, Blake will present on the symmetry-breaking-in-genetics paper, and possibly on the information-theoretic considerations for BLAST.

BLAKE SEZ: I believe the paper which caught my eye was L. Demetrius and T. Manke (15 February 2005) “Robustness and network evolution — an entropic principle” Physica A 346 (3–4): 682–96.

Evolution, Quantum mechanics

Favorite Paper Title of the Day

J. D. Bashford, I. Tsohantjis, P. D. Jarvis (3 February 1998). “A supersymmetric model for the evolution of the genetic code” PNAS 95 (3): 987–992.

The application of group theoretical methods to spectroscopy is today part of the accepted set of techniques for the analysis of many body systems in physics. In the present paper, we consider models for the symmetries of the genetic code by using the classical Lie superalgebras. We claim that, beyond the physical language of spectroscopy in which the method is couched, the group theoretical technique is indeed able to give a succinct account of many of the currently understood aspects of the evolution of the genetic code and the observed degeneracy structure of the codon-amino acid correspondences. We present one particular model, based on the Lie superalgebra A(5,0) ≅ sl(6/1), which has many natural structural features for this purpose that conform with observation. We argue that the model is susceptible to numerical verification by using the wealth of data that are available on biologically important molecules related to DNA.

See related and citing articles in Google Scholar.

Evolution, Pseudoscience, Transparency

The Edge of Evolution

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UPDATE (31 May 2007): For more on this topic, see Mark Chu-Carroll’s review, my follow-up and this list of reviews.

Yet more fallout from Time Magazine’s lamentable choice to have a fraud write their profile of Richard Dawkins:

Michael Behe’s mealy-mouthed description of Dawkins offers an interesting tidbit of news: he’s got a new book in the pipeline. Called The Edge of Evolution: The Search for the Limits of Darwinism, and due out this June, it promises a level of dreck not seen since Darwin’s Black Box (1997).

I have little doubt that the pro-fact sector of the Blagopelago will drown The Edge of Evolution in scalding, scathing, witty and above all factually correct reviews. To get the process started, I’d like to look at the laudatory quotes which currently praise this book which is almost certain to be a waste of paper.
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Popularization, Quantum mechanics, String Theory

Press Release from AdS/CFT Territory

The good folks at Princeton have been beavering away at the esoteric, abstrusely mathematical yet infinitely tantalizing relationships between string theories and gauge theories. The latter are the rather well-respected mathematical descriptions of how the bits and pieces of atomic nuclei interact; the former is what you get when you look at the dawn of time, the centers of black holes and the other places where our understanding throws up its hands, and you jump in with both feet. Or, at least that’s what string theory was, back in 1997 or so.

Today, we’ve come to recognize that physics has a strange property: ideas you invent in one place pop their heads up where you never expected. Thus, supersymmetry — a mathematical concept invented in the 1970s to make string theory look a little more like the real world — branched off to become its own field of inquiry. In trying to figure out the implications of supersymmetry, Ed Witten and company invented supersymmetric quantum mechanics, which (among other things) gives you a wickedly delightful insight into all the problems professors use to torture their undergraduate physics students in Quantum Mechanics I.

The journey from string theory to SUSY QM leaves behind the essential “stringiness” of the original theory, but over the past several years, we’ve seen a whole slew of results which suggest that the math invented to quantize gravity, break the hearts of black holes and hold the Big Bang in our hands is also applicable to other, more accessible situations. Does this mean that string theory is the right path to quantizing gravity and all the rest? No, not necessarily. Does it mean that we can get our teeth into the equations and use experiments to see if at least some of our ideas work? Yes. Is knowing about this arena of activity a key part of understanding what physicists are doing today? Again, the answer is yes.

You can really hear the writer stretching for metaphors in the ScienceDaily story based on Princeton’s press release: “Between the two road sections lay a seemingly unbridgeable mathematical gulf”, etc. If you look at the paper which provoked this release, or even its abstract, you can appreciate why the press office’s language gets so tortured:

In two remarkable recent papers the planar perturbative expansion was proposed for the universal function of the coupling appearing in the dimensions of high-spin operators of the N=4 super Yang-Mills theory. We study numerically the integral equation derived by Beisert, Eden, and Staudacher, which resums the perturbative series. In a confirmation of the anti–de Sitter-space/conformal-field-theory (AdS/CFT) correspondence, we find a smooth function whose two leading terms at strong coupling match the results obtained for the semiclassical folded string spinning in AdS5. We also make a numerical prediction for the third term in the strong coupling series.

Clear as a kegger in a mud pit.

The press release tries to draw a layman-friendly picture, as I mentioned. At a slightly higher level of mathiness are Barton Zwiebach’s String Theory for Pedestrians lecture videos. (Yes, that’s the same Zwiebach who taught the class and wrote the book.) The AdS/CFT correspondence stuff appears in the second and third lectures of the three-lecture series.

(Tip o’ the string theorist’s beret to Peter Steinberg.)

"no matter how gifted, you alone cannot change the world"