The vacuity of Stephen Meyer

Via Sandwalk, here is Stephen Meyer explaining the central concepts of his theory: it’s all about the origin of information.

It’s a ridiculous argument. He constantly repeats this mantra of “digital information”: I don’t think he knows what he’s talking about. He also likes to claim that he’s using an accepted scientific argument, of using only known, extant processes and extrapolating to the past; which is fine, except that he pretends ignorance of the fact that we know of natural processes that increase the amount of information in the genome without intervention by any intelligent agent.

He has this silly syllogism that he trumpets in his book, Signature in the Cell:

  1. Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.

  2. Intelligent causes have demonstrated the power to produce large amounts of specified information.

  3. Intelligent design constitutes the best, most causally adequate, explanation for information in the cell.

Point #1 is false, except for the trivial loophole of “specified” information, a term he never defines. Point #2 is true. However, Point #3 fails because he hasn’t shown that his first premise is true.

This is all the Discovery Institute has got: blindly repeating the same lies over and over again.

No difference, no point

Why do horrible things happen to faithful people?

The religious run a protection racket. The key thing about that is that no actual protection is offered, only threats.

Warning: anyone who tells that really, really stupid story about a man in a flood praying for rescue will be disemvoweled. It’s a stupid story that makes excuses for the inaction of their deity, and I’ve heard it a few hundred times too often.

(via Joe.My.God)

SETI built on GIGO

I’ve never been a fan of SETI, the search for extraterrestrial intelligence. It’s like playing the lottery obsessively, throwing down lots of money in hopes of a big payoff, and I don’t play the lottery, either.

I’d really like to know if Seth Shostak is innumerate enough to play the lottery, though, because his recent claim that we stand a good chance of discovering extraterrrestrial intelligence within 25 years. All right, bring it: let’s see your evidence for such a claim.

“I actually think the chances that we’ll find ET are pretty good,” said Seth Shostak, senior astronomer at the Search for Extraterrestrial Intelligence Institute in Mountain View, Calif., here at the SETIcon convention. “Young people in the audience, I think there’s a really good chance you’re going to see this happen.”

Shostak bases this estimation on the Drake Equation, a formula conceived by SETI pioneer Frank Drake to calculate the number (N) of alien civilizations with whom we might be able to communicate. That equation takes into account a variety of factors, including the rate of star formation in the galaxy, the fraction of stars that have planets, the fraction of planets that are habitable, the percent of those that actually develop life, the percent of those that develop intelligent life, the fraction of civilizations that have a technology that can broadcast their presence into space, and the length of time those signals would be broadcasted.

Reliable figures for many of those factors are not known, but some of the leaders in the field of SETI have put together their best guesses. Late great astronomer Carl Sagan, another SETI pioneer, estimated that the Drake Equation amounted to N = 1 million. Scientist and science fiction writer Isaac Asimov calculated 670,000. Drake himself estimates a more conservative 10,000.

The Drake Equation? That’s it? I hate the Drake Equation. It’s seven arbitrary parameters plugged into a simple formula, of which we have reasonable estimates of one (the rate of star formation), growing evidence of values for another (the number of planets around each star), and the other five are complete wild-ass guesses, most of them dealing with biology and culture, and we’ve got astronomers who know next to nothing of either inserting optimistic values. When biologists amend the values to something more reasonable, the likelihood of intelligent life plummets. Not that their wild-ass guesses are necessarily more accurate (although they are based on the history of life on this one planet), but it does say something that the equation can yield results that vary by six orders of magnitude, depending on who does the calculation.

It’s a useless formula. You can’t calculate anything from a formula in which almost all of the variables are complete unknowns, and it’s also meaningless in that no matter what result we acquire from empirical evidence, it can all be retrofitted to the magic formula. I really don’t understand the appeal of the Drake Equation, except that it turns our ignorance into a pseudo-sciencey string of fake math…but smart people ought to be able to recognize garbage.

I can’t really make a prediction here, unlike Shostak, who seems willing to gamble everything on promises he doesn’t have to worry about fulfilling. He could win the lottery. But I’m not going to place any bets on it.

Ray Kurzweil does not understand the brain

There he goes again, making up nonsense and making ridiculous claims that have no relationship to reality. Ray Kurzweil must be able to spin out a good line of bafflegab, because he seems to have the tech media convinced that he’s a genius, when he’s actually just another Deepak Chopra for the computer science cognoscenti.

His latest claim is that we’ll be able to reverse engineer the human brain within a decade. By reverse engineer, he means that we’ll be able to write software that simulates all the functions of the human brain. He’s not just speculating optimistically, though: he’s building his case on such awfully bad logic that I’m surprised anyone still pays attention to that kook.

Sejnowski says he agrees with Kurzweil’s assessment that about a million lines of code may be enough to simulate the human brain.

Here’s how that math works, Kurzweil explains: The design of the brain is in the genome. The human genome has three billion base pairs or six billion bits, which is about 800 million bytes before compression, he says. Eliminating redundancies and applying loss-less compression, that information can be compressed into about 50 million bytes, according to Kurzweil.

About half of that is the brain, which comes down to 25 million bytes, or a million lines of code.

I’m very disappointed in Terence Sejnowski for going along with that nonsense.

See that sentence I put in red up there? That’s his fundamental premise, and it is utterly false. Kurzweil knows nothing about how the brain works. It’s design is not encoded in the genome: what’s in the genome is a collection of molecular tools wrapped up in bits of conditional logic, the regulatory part of the genome, that makes cells responsive to interactions with a complex environment. The brain unfolds during development, by means of essential cell:cell interactions, of which we understand only a tiny fraction. The end result is a brain that is much, much more than simply the sum of the nucleotides that encode a few thousand proteins. He has to simulate all of development from his codebase in order to generate a brain simulator, and he isn’t even aware of the magnitude of that problem.

We cannot derive the brain from the protein sequences underlying it; the sequences are insufficient, as well, because the nature of their expression is dependent on the environment and the history of a few hundred billion cells, each plugging along interdependently. We haven’t even solved the sequence-to-protein-folding problem, which is an essential first step to executing Kurzweil’s clueless algorithm. And we have absolutely no way to calculate in principle all the possible interactions and functions of a single protein with the tens of thousands of other proteins in the cell!

Let me give you a few specific examples of just how wrong Kurzweil’s calculations are. Here are a few proteins that I plucked at random from the NIH database; all play a role in the human brain.

First up is RHEB (Ras Homolog Enriched in Brain). It’s a small protein, only 184 amino acids, which Kurzweil pretends can be reduced to about 12 bytes of code in his simulation. Here’s the short description.

MTOR (FRAP1; 601231) integrates protein translation with cellular nutrient status and growth signals through its participation in 2 biochemically and functionally distinct protein complexes, MTORC1 and MTORC2. MTORC1 is sensitive to rapamycin and signals downstream to activate protein translation, whereas MTORC2 is resistant to rapamycin and signals upstream to activate AKT (see 164730). The GTPase RHEB is a proximal activator of MTORC1 and translation initiation. It has the opposite effect on MTORC2, producing inhibition of the upstream AKT pathway (Mavrakis et al., 2008).

Got that? You can’t understand RHEB until you understand how it interacts with three other proteins, and how it fits into a complex regulatory pathway. Is that trivially deducible from the structure of the protein? No. It had to be worked out operationally, by doing experiments to modulate one protein and measure what happened to others. If you read deeper into the description, you discover that the overall effect of RHEB is to modulate cell proliferation in a tightly controlled quantitative way. You aren’t going to be able to simulate a whole brain until you know precisely and in complete detail exactly how this one protein works.

And it’s not just the one. It’s all of the proteins. Here’s another: FABP7 (Fatty Acid Binding Protein 7). This one is only 132 amino acids long, so Kurzweil would compress it to 8 bytes. What does it do?

Anthony et al. (2005) identified a Cbf1 (147183)-binding site in the promoter of the mouse Blbp gene. They found that this binding site was essential for all Blbp transcription in radial glial cells during central nervous system (CNS) development. Blbp expression was also significantly reduced in the forebrains of mice lacking the Notch1 (190198) and Notch3 (600276) receptors. Anthony et al. (2005) concluded that Blbp is a CNS-specific Notch target gene and suggested that Blbp mediates some aspects of Notch signaling in radial glial cells during development.

Again, what we know of its function is experimentally determined, not calculated from the sequence. It would be wonderful to be able to take a sequence, plug it into a computer, and have it spit back a quantitative assessment of all of its interactions with other proteins, but we can’t do that, and even if we could, it wouldn’t answer all the questions we’d have about its function, because we’d also need to know the state of all of the proteins in the cell, and the state of all of the proteins in adjacent cells, and the state of global and local signaling proteins in the environment. It’s an insanely complicated situation, and Kurzweil thinks he can reduce it to a triviality.

To simplify it so a computer science guy can get it, Kurzweil has everything completely wrong. The genome is not the program; it’s the data. The program is the ontogeny of the organism, which is an emergent property of interactions between the regulatory components of the genome and the environment, which uses that data to build species-specific properties of the organism. He doesn’t even comprehend the nature of the problem, and here he is pontificating on magic solutions completely free of facts and reason.

I’ll make a prediction, too. We will not be able to plug a single unknown protein sequence into a computer and have it derive a complete description of all of its functions by 2020. Conceivably, we could replace this step with a complete, experimentally derived quantitative summary of all of the functions and interactions of every protein involved in brain development and function, but I guarantee you that won’t happen either. And that’s just the first step in building a simulation of the human brain derived from genomic data. It gets harder from there.

I’ll make one more prediction. The media will not end their infatuation with this pseudo-scientific dingbat, Kurzweil, no matter how uninformed and ridiculous his claims get.

(via Mo Constandi)

I’ve noticed an odd thing. Criticizing Ray Kurzweil brings out swarms of defenders, very few of whom demonstrate much ability to engage in critical thinking.

If you are complaining that I’ve claimed it will be impossible to build a computer with all the capabilities of the human brain, or that I’m arguing for dualism, look again. The brain is a computer of sorts, and I’m in the camp that says there is no problem in principle with replicating it artificially.

What I am saying is this:

Reverse engineering the human brain has complexities that are hugely underestimated by Kurzweil, because he demonstrates little understanding of how the brain works.

His timeline is absurd. I’m a developmental neuroscientist; I have a very good idea of the immensity of what we don’t understand about how the brain works. No one with any knowledge of the field is claiming that we’ll understand how the brain works within 10 years. And if we don’t understand all but a fraction of the functionality of the brain, that makes reverse engineering extremely difficult.

Kurzweil makes extravagant claims from an obviously extremely impoverished understanding of biology. His claim that “The design of the brain is in the genome”? That’s completely wrong. That makes him a walking talking demo of the Dunning-Kruger effect.

Most of the functions of the genome, which Kurzweil himself uses as the starting point for his analysis, are not understood. I don’t expect a brain simulator to slavishly imitate every protein, but you will need to understand how the molecules work if you’re going to reverse engineer the whole.

If you’re an acolyte of Kurzweil, you’ve been bamboozled. He’s a kook.

By the way, this story was picked up by Slashdot and Gizmodo.

Rule of thumb: Never trust an organization with “family” in the name

The Australians are having an election, and one of the parties is the Family First Party — a Christianist group — and another is the Australian Sex Party, which would have my vote just for the name, if I were Australian. And after watching this debate between the two, I am confirmed in my bias.

I’m a bit disillusioned with Julia Gillard, who’s a bit too quick to throw away principles to pander for votes (which probably means she’ll get elected). Fiona Patten, though, seems quite nice and forthright. And I like their ads.

Now if only the US had a party like that…

You can buy anything on eBay, I guess

There ought to be some regulation of the kind of fraud some people peddle online. I’m tempted to try this one: BOOTY ENHANCEMENT Spell Cast by Powerful Wiccan Witch (note: bikini-clad bottom on display at that link), just to see what happens. Except that I know what will happen: nothing. Less than nothing, actually, since we’re changing diet here and I expect my booty will be shrinking — the TrophyWife™ has actually put together a flavorful, low calorie, non-fat menu for me that looks pretty good already.

But then…the magic spell is only $8.95!

And this is the most dismal statistic of all:

99.8% Positive feedback

* Consistently receives highest buyers’ ratings
* Ships items quickly
* Has earned a track record of excellent service

She’s got precisely ONE negative evaluation in her entire eBay history, from someone whose butt apparently failed to plump up. Suckers swarm over this stuff.

I’m in the wrong business.

Oh, look: Rebecca Watson beat me to this one.

Ghoul visits Vancouver

This is a good way to do it: when the fortune-telling, pseudo-necromancer John Edward showed up in Vancouver to do his ridiculous cold-reading act, CFI met his deluded followers with information and honesty. It was a sad spectacle; many of the attendees were desperate, bereaved people, there for a little hope and getting fleeced instead (tickets were $200!)

It sounds like they did everything just right. The only reservation I have is…where were the media? This is the kind of event where contacting a few newspapers and television and radio stations beforehand, and publicizing the protest, is an essential force multiplier — and the news media love a controversy. They’re planning another event when the odious James Van Praagh, another phony speaker to the dead, comes to town, and getting a newspaper op-ed or a minute on television can provoke in interesting ways.

The only thing that might make be break my boycott of the HuffPo is…

…is an article by Vic Stenger. He addresses that weird old canard that “absence of evidence is not evidence of absence”, which has always struck me as bogus. Of course it is! It is just evidence of variable strength, from laughably weak (I have no evidence of a teapot in orbit around the sun, which isn’t a very strong case since no one has looked for an orbiting teapot, and it’s a tiny target in a vast volume anyway) to extremely strong (there are no dragons in my backyard; I have looked, and there are no large firebreathing reptiles gnawing on virgins back there).

I wonder if the source of this cliche isn’t a different claim, that absence of evidence is not proof of absence…which is actually mostly true (still, there is no way to claim there are dragons in my backyard) and also entirely irrelevant, since science doesn’t deal in proof. And since most of the wackjobs who cite the aphorism can’t tell the difference between proof and evidence anyway, they probably think it means the same thing.

My lost weekend

Now that it is over, I can say what happened — sometimes people freak out over this kind of thing, and there were no real worries here.

On Friday, as I do every day, I went out for a walk for about an hour — I strolled down to the Stevens County Fair, on an unpleasantly muggy early afternoon, and then walked back home…and I was almost there when I felt a peculiar tightness in my chest. That’s odd, I thought, I wasn’t exerting myself that much. And then I felt a slow ache building in my left arm.

If you have any familiarity with physiology and medicine at all, you know that is a very bad sign. I was about equidistant from home, where I briefly thought I would just go, lie down, and feel the odd weak ache go away, and the Stevens County Medical Center, where I would go if I were sane and taking the problem seriously. Sanity won handily, since I had a father who had his first heart attack in his early forties, and after a series of more heart attacks, would die in his mid-fifties. So I turned right and walked two blocks to the medical center (if I’d been entirely sane, I probably should have whipped out my cell phone and called them, but it was such a mild pain, and I was so close…).

Anyway, it turns out that if a 50ish man walks into a hospital and mentions chest pains radiating into the left arm, there is a kind of automatic freak-out response that I’m sure saves lives. I was flat on my back on a bed with an IV needle in a vein and a nitroglycerin pill under my tongue in about 30 seconds, and then I was hooked up to an EKG and surrounded by doctors and nurses. The ache was also gone right after that, but then I was completely in their control, and was wheeled right up into a hospital room for 24 hours of observation, which because it was a weekend, turned into several days of observation and tests and getting blood drawn every four hours and being awakend at 2am for more tests, all while being wired up to telemetry widgets.

It made for an epically boring weekend.

The good news, though, is that there was no sign of a heart attack, and even when they subjected me to a stress test (no fun at all for a sedentary professor) the pains did not return. The bad news is that all my bad habits were exposed and measured, and it turns out I have moderately high blood pressure, which is already responding to drugs, and a few little cardiac abnormalities that they’re going to check out more thoroughly later this week with an angiogram. So I’m OK! Don’t start the deathwatch yet!

It could have been worse. Mainly what I got was slapped upside the head with a warning, this time.

The main consequences are that I’m going to be taking pills everyday, and that I have to change my diet to more cardboard and blandness, which the TrophyWife™ has grimly seized upon as an excuse to take over all the cooking at home, and stick me with the dishwashing job. I think it also means that when I’m off giving talks and joining in the post-event celebration at the local bar, I’ll be eschewing the greasy bar food for a salad. Damn.

Oh, well, this is the price we pay for the accidents of family history. I got a brain and an appreciation of learning from both my parents, but my mother’s iron constitution passed me by, and instead I got my father’s heart. I’m not complaining, though, since it was the heart of a romantic poet; we all know how fragile those things are, but I wouldn’t trade it in for anything.

Oh, and for everyone reading this: if you feel some persistent twinge that you suspect might be a sign of some problem, but you think maybe if you just lie down for a bit and the symptom will go away, don’t. Get it checked out, even if it does mean you get to spend a weekend in a bed surrounded by beige walls.