Category Archives: Neuroscience

Dendritic Evo-Devo

Remember way back, when I mentioned genetic algorithms in the course of criticizing Michael Egnor? I described, conceptually, a way of using the mechanisms of mutation and selection to discover the structure of DNA, given X-ray crystallography data.

Let a “gene” in the computer’s memory be the spatial locations of molecular units: sugars, phosphates, purines, pyrimidines — the small molecules which Franklin, Pauling et al. knew were the constituents of DNA. We create a “gene pool” of random variations, and then we iterate the genetic algorithm (GA), using as fitness function a comparison between a calculated X-ray diffraction pattern and the X-ray images taken experimentally.

Imagine tossing out a thousand random guesses about what DNA looks like. For each guess, we could calculate what the X-ray diffraction pattern would look like given that particular molecular structure. Most of the time, it won’t look anything like the X-ray pictures we take in the laboratory, but a few of them will by happy accident look a little more like the real thing. This slight preference becomes the starting point for selection. We let our ideas breed, giving favor to those which perform best. The irresistible logic of Darwin goes to work.

(This is a bit of a perspective shift. Instead of thinking like sane people do about DNA carrying genes, we’re considering an abstract sort of gene which defines the shape of a hypothetical DNA structure.)

If we’d invented fast and cheap computers before we knew about DNA — say, in some parallel Sliders world or steampunk fantasy where computers happened five decades sooner — this might well be how scientists would have tried to solve DNA. It requires much less cleverness, and correspondingly more computer time. As I mentioned before, people have applied this method to figuring out molecule shapes, although to my knowledge nobody has tried to “re-solve” DNA this way.

An interesting point: if our “genes” are molecular positions and our “phenotypes” are X-ray diffraction images, then it looks like we’ve got a non-trivial “morphology” between the two. Some “development” has to take place, although it rather happens “all at once.” It might be interesting to look at a GA in which structures are generated by a really non-trivial development process.

How about, say, the growth of neurons?
Continue reading Dendritic Evo-Devo

Brief Vacation-but-not-really

Posting will be light this week. With luck, I’ll get a rerun of some old material I wrote at another site up here Wednesday or Thursday. In the meantime, here’s a lengthy discussion at Russell Blackford’s place about emergent properties and consciousness.

When you’re sated on that, check out Mark Liberman’s “Thou shalt not report odds ratios.” See, this is why the denizens of the science-blogging community should include Language Log in their travels: problems like bad math reporting in science journalism affect us all.

QUICK UPDATE: Isabel has more on the bad math in journalism issue at God Plays Dice.

Nirvana Officially Old

The next time I go out to buy office supplies, I fully expect to hear “Smells Like Teen Spirit” being played over the store PA system. You know why? This is why:

Scientific American has a new “special edition” out, this one covering the psychology and neuroscience of children. And they riffed on the Nevermind (1991) album for the cover art. (I guess that means they covered the cover, didn’t they? Thank you, thank you, I’ll be here all week!)

Never-mind. . . mind, neuroscience. . . see, it all fits together, doesn’t it?

This is about when my mother chimes in saying, “Hah! And now don’t you feel old!”

Remember, it was all the way back in December 1996 when Garth Ennis had a Preacher character reminisce about the days when Nirvana was “everywhere” — and that itself in a flashback, no less. The story with the flashback to the recollection of ubiquitous Gen-X irony (or whatever in blazes that song is supposed to be “about”) is already more than a decade old. Hooray for SciAm driving the point home.

Carnivalia and Blagrolling

Can you believe we’ve made it through sixty-three editions of the Skeptic’s Circle without being struck by lightning, blighted with locusts or dobbsed with leprosy? Rejoice therefore!

One of the many notable entries in this fortnight’s Circle is Steven Novella’s piece on the purported autism-mercury link (hint, hint: there isn’t one, Robert F. Kennedy and Tom Tancredo not withstanding). Dr. Novella also has two good posts on Michael Egnor‘s recent torrid affair with dualism, so if you’d rather get your materialism fix from a Yale University neurologist instead of a physics buff who never learns to lay off the sriracha sauce, there you go.

I’d like to take this moment to give special thanks to all the people who have added Science After Sunclipse to their regular web-surfing experience. In particular, I’ve noticed this little site appearing on some blagrolls in very august company, which makes me happy indeed.

Dialog on the Mind

A recent discussion reminded me of an old joke; adjusted for the current subject, the dialog goes like this.

“You spend all this time attacking creationist claims about ‘the mind,’ but you haven’t put forth your own ideas about what the mind is.”

“The mind is a product of the motion of atoms in the brain, constrained by but not directly predictable from physics and chemistry. To quote the famous philosopher Daniel Dennett, ‘Who are you and how did you get in my house?'”


“Well, that’s what he said when I asked him about it.”

Michael Egnor and Spiritual Pay-Per-View

The weight of evidence, gathered over at least two and a half millennia, indicates that the mind is a product of the brain. Some people find this notion disquieting, and consequently they marshal various arguments to try and dispel the unpleasant conclusion. I haven’t done a quantitative study on which sophistries are the most common, but I have the strong impression that this one is widely used: the soul isn’t “in” the brain, the denier says, any more than television programs are “in” the TV antenna.

This argument would be a whole lot more convincing if damage to different parts of the brain didn’t have different effects, and if imaging of brain activity didn’t show that particular activities and even modes of thought manifest themselves in different, characteristic parts of the nervous system. We’d have to be tuned to a whole premium package of Soul TV channels, each received by its own wet antenna, and each broadcast by its own Ethereal Broadcasting Company — a whole industry of Spiritual Pay-per-View!

The latest devotee of this dubious proposition is — almost inevitably — Michael Egnor.
Continue reading Michael Egnor and Spiritual Pay-Per-View

Michael Egnor: 2400 Years Behind the Times

BPSDBI nearly sprayed my breakfast across my friend’s new flatscreen monitor when I saw the latest from Michael Egnor:

Clearly the brain, as a material substance, causes movement of the body, which is also a material substance. The links are nerves and muscles. But there is no material link between our ideas and our brains, because ideas aren’t material.

Mr. Spock, are your sensors detecting any signs of intelligent life?
Continue reading Michael Egnor: 2400 Years Behind the Times

PZ Myers on the Quantum Mind

This one is worth repeating:

Quantum effects in microtubules are going to be inconsequential relative to ion fluxes and chemical changes in membrane properties and channels, and there is no explained mechanism to regulate quantum effects. It’s like trying to explain the tides by speculating about the dabbling of gnats in estuaries.

The people who talk about this stuff usually seem to have absolutely no knowledge of neuroscience.

For sheer disdain, this might be second only to Patricia S. Churchland‘s remark, “The want of directly relevant data is frustrating enough, but the explanatory vacuum is catastrophic. Pixie dust in the synapses is about as explanatorily powerful as quantum coherence in the microtubules.”

My most extensive essay on this subject can be found here, and a good paper with many references into the literature is A. Litt et al.,Is the Brain a Quantum Computer?” (Cognitive Science, 2006).

Perakh on Barr: Rejoicing in Materialism

Via the Panda’s Thumb comes notice of Mark Perakh’s review of Stephen M. Barr’s Modern Physics and Ancient Faith (2003). I recommend reading the whole review; Perakh demonstrates that Barr’s book, like Ken Miller’s Finding Darwin’s God (1999), offers some lucid descriptions of modern science but devolves into poor reasoning and non sequiturs when it touches notions of faith.

None of Barr’s arguments or Perakh’s counter-arguments are particularly new (which is one sign of how decrepit a business this “natural theology” really is). Barr organizes his book by describing successive “plot twists,” discoveries which supposedly upset the tidy materialism of a century ago. You could guess that quantum mechanics figures prominently; a couple linear operators fail to commute, and people run around saying reality’s been undone. Kurt Gödel also makes an appearance:
Continue reading Perakh on Barr: Rejoicing in Materialism

Recycled Rant: the Quantum Mind

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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Even Though Mom Is Watching

I have to post about Quantum Tantra.

I’m a very ambitious physicist; I was trained at Stanford. I want not merely to find a new particle or equation but to discover an entirely new way of doing science. Quantum tantra aims to put humans in direct touch with nature without the mediation of instruments, without even those instruments called the senses. My needs are simple: I’d like to invent a truly gooey interface that connects my mind to other minds in the Universe. Modern physics is fully erect science; quantum tantra is physics on all fours.

Touching nature directly, and without the senses, eh? Sounds like, ahem, Tanuki-sized bollocks. Honestly, now, who wants to have sex where each motion is too tiny to be detected, and as soon as she observes you getting ready, your wavefunction collapses? (Besides, if there were anything legitimate in this, Richard Feynman would have discovered it already.)

This does, oddly, synchronize with the Attack of the Skinny Vixens which Dr. Joan Bushwell so kindly warns us about. Dr. Bushwell alerts us to this BBC story whose tagline reads, “Scientists are developing a pill which could boost women’s libido and reduce their appetite.” (Gee, I thought we were all supposed to be hunting down the God particle.) According to the BBC, Prof. Robert Millar of the Medical Research Council’s Human Reproduction Unit (in Edinburgh) believes that a pill based on “Type 2 Gonadotrophin-releasing hormone” will ramp up the libido of the human female whilst simultaneously lowering her appetite. Hey, it works with monkeys and shrews!
Continue reading Even Though Mom Is Watching


I seem to have some kind of dopaminergic reward pathway established for blog commenting. Every time I see a new post, I know I’ll either be happy because I agree with it, or I’ll get that little surge from disagreeing vocally! Any time I see a remark about “framing,” I’m either gonna like you or hate your guts, and my natural argumentative streak gives me a positive brain-boost either way.

Trying to find a simple principle which completely covers a complex and heterogeneous set of overlapping problems in which our pious platitudes frequently conflict with one another is, as Sean Carroll says, a mistake. Complex problems, regrettably, often demand complex solutions. If this discussion had, from the beginning, focused on specific and concrete examples, I believe we would have seen much more agreement — and much more productive disagreement!

Blogs are the enkephalins of the masses.

Enough of this. It doesn’t make a difference.

May I remind everyone that Michael Egnor is still saying ridiculous things?

Where Was I When They Were Passing Out the Wit?

Scott Aaronson has a new comment policy:

If you reject an overwhelming consensus on some issue in the hard sciences — whether it’s evolution, or general relativity, or climate change, or anything else — this blog is an excellent place to share your concerns with the world. Indeed, you’re even welcome to derail discussion of completely unrelated topics by posting lengthy rants against the academic orthodoxy — the longer and angrier the better! However, if you wish to do this, I respectfully ask that you obey the following procedure:

1. Publish a paper in a peer-reviewed journal setting out the reasons for your radical departure from accepted science.
2. Reference the paper in your rant.

If you attempt to skip to the “rant” part without going through this procedure, your comments will be deleted without warning. Repeat offenders will be permanently banned from the blog. Life is short. I make no apologies.

It looks like Dave Bacon can now talk about time travel, but my own conspiracy theories will have to wait. But soon, I promise, the real meaning behind supersymmetric quantum mechanics will be made clear. They laughed at me when I suggested that the BPS interpretation of shape invariance may have a non-topological origin. The fools — I’ll show them all!
Continue reading Where Was I When They Were Passing Out the Wit?

Russell Blackford on Human Enhancement

I’m not sure when the idea of “human enhancement” first bubbled up in my brain. It seems to be one of those possibilities which I just grew up with, thanks to a childhood lost in books. In Cosmos, Carl Sagan wrote,

There must be ways of putting nucleic acids together that will function far better — by any criterion we choose — than any human being who has ever lived. Fortunately, we do not yet know how to assemble alternative sequences of nucleotides to make alternative kinds of human beings. In the future we may well be able to assemble nucleotides in any desired sequence, to produce whatever characteristics we think desirable — a sobering and disquieting prospect.

The video version ends with “awesome and disquieting prospect,” by the way. Sagan’s friend Isaac Asimov was a little more cheerful; while dying of AIDS, he concluded the revision of his book The Human Brain with these words:

Man would then, by his own exertions, become more than man, and what might not be accomplished thereafter? It is quite certain, I am sure, that none of us will live to see the far-distant time when this might come to pass. And yet, the mere thought that such a day might some day come, even though it will not dawn on my own vision, is a profoundly satisfying one.

Continue reading Russell Blackford on Human Enhancement