Archive for the ‘Science’ Category

Heart to Heart

Monday, August 23rd, 2010

P.Z. Meyers gets a phone call from his doctor’s office.

“We just got the results of your tests from last week. Your heart is a shriveled black lump starved of charity, decency, charm, and kindness,” she said, “a gristly godless clot of marginally functional fibers. You need to go back to Abbott for more tests, and the doctors want to crack your chest and marvel at you.”

“So what else is new? My students are used to that and expect me to be lashing them with fear and pain starting Wednesday…and my black heart is an asset to this job,” I said. “Maybe I can pop in for these tests this weekend. Any chest-cracking can wait for the end of the term and Christmas break, when I wouldn’t be using my heart anyway.”

“No,” she said, “now.”

And I waffled and weaseled and tried to argue with her that this could not be, I had a great deal of work to do right now, and I couldn’t possibly just drop out at the start of the term, and besides, I felt fine. And I bickered, and she exasperatedly told me no way, and I bargained, and then she said, “Here. I’m putting the doctor on.” And the doctor spoke with the voice of Doom and the terrifying tone of I-hold-your-life-in-my-hands-you-dope and she quoth (paraphrased somewhat):

“YOU ARE GOING TO DIE SUDDENLY, ABRUPTLY, WITHOUT WARNING UNLESS WE FIX YOU RIGHT NOW. GO. NOW. DO NOT ARGUE WITH ME.”

“Yes’m,” I said.

Prayers I have none. My wishes are of course useless.

Nevertheless, I wish him well. Tough, bitter, and black hearted he may be, we need him. Liberal politics be damned, he is a crucial warrior for the truth, clear sighted and, may I say it, strong hearted in his field, and we need as many of those as we can get.

Kurzweil Overreaches

Tuesday, August 17th, 2010

No sooner do I disavow P.Z. Meyers than he turns up saying something important. He’s commenting on Priya Ganapati’s Gizmodo article about Ray Kurzweil’s assertion that

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.

Meyers responds

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.

Dammit, and I thought Kurzweil was a schmot guy.

But let me poke a bit on Meyers, too: Simulating the brain down to the protein interactions isn’t going to work, either. The trick is going to be setting up a network of logic gates that can self-organize into a brain under the appropriate stimuli . And, no, we’re not going to understand how it works, either. [Yeah, that link goes to Meyers, too. He knows better.]

Then there’s this from the comments:

[Kurzweil thinks] he’ll be able to resurrect his dead father using DNA recovered from the latter’s grave plus records of his life. IOW, he believes in magic.

Even Jesus can't believe your idiocy.

via SF critic James Nicoll.

Traction

Tuesday, August 17th, 2010

Billy Beck, talking about tractors:

Ladies and gentlemen, this is about managing the immutable reality of mechanical systems. People can bullshit each other — and even themselves — over concepts in all sorts of ways. When concepts are forged in steel, that becomes impossible. You don’t get to bullshit your way around a 5/8″ bolt. You just don’t. When you’re dealing with a flywheel pilot bearing, no mental substitutions — whether from sloppiness or outright psychosis — will suffice: that bearing is only what it is, and your mind had better be right about everything about it.

Robert Pirsig once wrote a very ridiculous book, but he wrote it about a very serious subject.

There is great philosophy in machines.

Accompanied by some heart-warming shop photos.

[Hey, Billy! I've done a couple of head rebuilds, and my question is, where are you getting the gasket sets for this beast?]

This prompted Mike Soja:

I was standing in front of a green hooded idling number of about half the age of Beck’s specimen, while the man I was there to do business with slowly hand pumped diesel into the fuel neck from a large tank out behind his corn crib. Over the rumble, he pointed to the name plate at the prominent place on the nose and asked, “Ever see one of those before?” The plate said, “Deutz”, and I allowed that I hadn’t. He said it was a three cylinder, air cooled.

[He] remarked, “I’d like to buy a new one of these, but they don’t make them anymore.”

I asked, “Did they go out of business?”

“No. They just can’t make them. The government says they have to be water cooled, now.”

And that opened up whole new areas of conversation.

I’ve whacked out about half of that; see the whole thing for the flavor.

I’ve done volunteer teaching of fifth grade science labs. They stopped doing that;it was too damn much trouble, too messy, too loud.

I don’t know how much science got through, but if I managed to get across the faintest glimmer that the universe does what it does, and not what you think it ought to do, I succeeded.

Anybody who thinks economics doesn’t follow that same principle is advocating ruin, death, and chaos.

Why I Can Not Mock

Thursday, August 12th, 2010

I doubt that I will ever believe, as Elizabeth Scalia does, in the God she professes her faith to. I don’t think I can.

But as I have said before, there is a profound and beautiful core of truth to what the Anchoress believes, and I read her every day for the glimpses she vouchsafes us of that beauty.

In a former parish, there was a sister-liturgist who–eager to promote “sensitivity”–decided that the Gloria should be sung with the refrain “Glory to God in the Highest, and peace to God’s people on earth;” she was content to brutalize the ear, change a liturgical prayer that is not supposed to be changed, and disorient the people just a tad, in order that no one should be subjected to that troubling male pronoun, “His.”

I always thought it was a nonsensical point; why go to the trouble of training the people to avoid the “His” in that sung prayer, when it proceed to refer to God as “Heavenly King, Almighty God and Father,” and to Jesus as “only Son of the Father.” And of course, I got into a civil debate with her about it.

“You don’t understand,” she said kindly (because she was a very kind sister) “it’s important that we begin to think of God as having no gender at all, containing aspects of both mother and father, but not limited to our understanding as “Father.”

“Yes, mysticism if fine; I’m a fan,” I said. “But the prayer–which is liturgical and not subject for editing by you or me–makes enough male references throughout that it seems incongruous and silly, to enforce this clumsy and cold “Glory to God and peace to God’s people,” phrasing. It’s ick to my ear. And it puts God at a distance; it’s not intimate.”

To sister’s credit she remained kind but she did buckle down and let me know she wasn’t budging. “There are a lot of people in the world who have had bad fathers, they have bad memories, a lot of people find referring to God as “Father” to be distancing and hurtful. They cannot relate.”

“Well, sister, I happen to be one of those people who had a bad father and carries bad memories, and I like referencing God as Father; I happen to find great comfort and solace in having a Heavenly Father who more than fills the void left by my earthly one.”

She looked stunned. “You are the first person who has ever said that to me; that is not the usual perspective.”

“But don’t you think that’s a perspective worth promoting? Isn’t it a much better thing to tell people whose fathers have failed that they may be consoled by a Father who will never fail? Wouldn’t that be more positive, and ultimately more healing, than wrecking the liturgy to pander to neurotic sadness?”

Read it all.

This is why I continue to read Scalia, but have given up on, say, P.Z. Meyers. There is a profound and beautiful truth to what Meyers teaches as well, a truth arrived at by pathways easier for me to follow than the one illuminated by Scalia, a path that rejects the rigor of faith for a sharper, narrower rigor of another kind. But somehow, somewhere, Meyers has lost sight of that beauty, and has long ago ceased to teach his audience how to find it.

Instead, he wastes his time and talents mocking people like the Anchoress…and, yes, I see much to be mocked about them. I no longer care. Their various blindnesses and failings are trivial compared to their beauties and truths, which science cannot address, and may never be able to address — it is simply not the right tool to do so.

Not at all incidentally, I mind myself of Eric S. Raymond’s definition of “truth” , that truth is what makes the future less surprising. In what sense, you may then reasonably ask, do the Anchoress’ “truths” make the future less surprising? How may her words be unpacked as predictions?

I admit, I’m still struggling with how to express that. But in general, I think that people who think and believe as the Anchoress does are more likely to be, for lack of a better word, decent.

QotD: Humility and Hubris

Wednesday, July 28th, 2010

Just something I needed to make a note of:

Two things, however, are clear about any religion that might derive from cybernetics and systems theory, ecology and natural history. First, that in the asking of questions, there will be no limit to our hubris; and second, that there shall always be humility in our acceptance of answers. In these two characteristics we shall be in sharp contrast with most of the religions of the world. They show little humility in their espousal of answers but great fear about the questions they will ask.

Gregory Bateson, Angels Fear

Blind

Sunday, July 25th, 2010

So, my sister wants new blinds hung in her bedroom. Going by the Big Orange Box instructions, I measure top and bottom width (to check parallelism), diagonals (to check squareness), and height in the middle.

The openings are neither parallel nor square, although they’re not out by much; I’ve seen much worse.

I set about trying to find the widest blind that will fit in each opening. I can’t find an on-line calculator, and when I try to figure out an algorithm myself (while trying to chip the rust off my Python skills), it turns out to be surprisingly difficult. Any given case is straightforward, using Pythagoras, but there seems to be no general solution. And that’s assuming that the top and bottom are parallel and level.

I mention this at the dinner table.

“Why not just measure the old blinds?”

Good question, Mom. Good question.

I’m still piddling about with writing a calculator, just as an exercise. And I’d like to find an online calculator.

Note: the math might be a bit easier if you measure width of the opening top and bottom, length of both sides, true plumb height at both sides, and both diagonals. But I think you can do it with the usual top and bottom width, overall height (assume level), and the diags, and given that those are the measurements most window blinds sites ask for, that would be best.

Inputs and results to the nearest eighth of an inch, please. If you round, round down — a blind that is too large by the height of the drywall texturing, a sixteenth of an inch or less, will not work. Piss off with your sissy millimeters.

A command line calculator is fine by me, but it must work under Windows as well as Unix.

It’s Science: Facts Don’t Matter

Saturday, July 24th, 2010

In fact, facts may actually reinforce opposing assumptions.

It’s one of the great assumptions underlying modern democracy that an informed citizenry is preferable to an uninformed one. “Whenever the people are well-informed, they can be trusted with their own government,” Thomas Jefferson wrote in 1789. This notion, carried down through the years, underlies everything from humble political pamphlets to presidential debates to the very notion of a free press. Mankind may be crooked timber, as Kant put it, uniquely susceptible to ignorance and misinformation, but it’s an article of faith that knowledge is the best remedy. If people are furnished with the facts, they will be clearer thinkers and better citizens. If they are ignorant, facts will enlighten them. If they are mistaken, facts will set them straight.

In the end, truth will out. Won’t it?

Maybe not. Recently, a few political scientists have begun to discover a human tendency deeply discouraging to anyone with faith in the power of information. It’s this: Facts don’t necessarily have the power to change our minds. In fact, quite the opposite. In a series of studies in 2005 and 2006, researchers at the University of Michigan found that when misinformed people, particularly political partisans, were exposed to corrected facts in news stories, they rarely changed their minds. In fact, they often became even more strongly set in their beliefs. Facts, they found, were not curing misinformation. Like an underpowered antibiotic, facts could actually make misinformation even stronger.

More evidence that putting the educated elite in charge of our lives is a bad idea.

My sense is that academics and bureaucrats must be as susceptible to this as anyone else, perhaps even moreso, because they are, effectively, trained to think that they are right, and they are totally isolated from real world consequences if they are wrong. Instead, their assumption that the stupid ignorant mundanes just didn’t take their advice strongly enough, and so they must be forced.

Individuals may well fall victim to the problem, but if they act on false assumptions, they will fail, and they will not be able to force their failure on those around them.

I now propose Moore’s Arrow:

All sources of bias arising from education are arguments for reducing government power.

The only bulwark against this seems to be Popper’s discipline of falsifiability. This demonstrably works, however slowly and unreliably.

Frink: Tool for Thought

Friday, July 23rd, 2010

Frink is a calculator/programming language that keeps track of units. It also has a huge library of custom defined units to cover common calculations. For instance, the unit “water” stands for the density of water.

Here’s one of the example calculations from the documentation:

Fart Jokes

I received one of those endlessly-forwarded e-mails of dubious but “interesting facts” which said “if you fart continuously for 6 years and 9 months, you’ll have enough gas to create the equivalent of an atomic bomb.” Hee hee. Cute. (Thanks to Heather May Howard… being unable to easily calculate the veracity of this statement was one of the primary influences that showed how existing programs were too limited and inspired the creation of Frink.) But I didn’t believe it and wanted to check it. The Hiroshima bomb had a yield of 12.5 kilotons of TNT, which is a very small bomb by today’s standards. How many horsepower would that be?

12.5 kilotons TNT / (6 years + 9 months) -> horsepower
329.26013859711395

Can you produce a 329-horsepower blowtorch of a fart? I doubt it. That’s the power produced by a Corvette engine running just at its melting point. A one-second fart with that much power could blow me 1000 feet straight up. To produce that kind of energy, how much food would you have to eat a day?

12.5 kilotons TNT / (6 years + 9 months) -> Calories/day
5066811.55086559

Ummm… can you eat over 5 million Calories a day? (Again, note that these are food Calories with a capital ‘c’ which are equal to 1000 calories with a small ‘c’.) If you were a perfect fart factory, converting food energy into farts with 100% efficiency, and ate a normal 2000 Calories/day, how many years would it really take?

12.5 kilotons TNT / (2000 Calories/day) -> years
17100.488984171367

17,000 years is still a huge underestimate; I don’t know how much of your energy actually goes into fart production. Oh well. To continue the calculations, let’s guess your butthole has a diameter of 1 inch (no, you go measure it.) Let’s also guess that the gas you actually produce in a fart is only 1/10 as combustible as pure natural gas. What would be the velocity of the gas coming out?

12.5 kilotons TNT / natural_gas / (6 years + 9 months) / (pi (.5 in)^2) 10 -> mph
280.1590446203110

Nobody likes sitting next to a 280-mile-per-hour fart-machine. Lesson: Even the smallest atomic bombs are really unbelievably powerful and whoever originally calculated this isn’t any fun to be around if they really fart that much.

Fart jokes. Sheesh. If Frink isn’t a huge success, it’s not because I didn’t pander to the Lowest Common Denominator.

Frink is the 280-mile-per-hour fart-machine of calculators.

Frink makes it easy to think precisely.

Biter

Friday, July 9th, 2010

I collected this magnificent Chelydra serpentina specimen strolling down the left hand lane of a busy four-lane road a block from my sister’s house.

She was being guarded from traffic by an older woman, and watched by a young Mom and her two little girls, all fascinated and fearful she would be run over, but quite reasonably more than a little scared to pick her up.

OK, OK, I’m a stupid male show-off and a soft touch. I pulled off the main road, went over and picked her up to rescue her. I knew she would thrash, and try to bite and claw, and thus was not surprised into letting go of her.

I’ll note that my grip is not ideal; it would have been safer to hold her further back. But she didn’t get me, and given her size, this was probably the most secure grip.

Mom and Dad were with me, and the woman said she knew of a near-by pond, so I had Dad follow her. We all trooped over to the edge of the pond (a “catch and release” stocked fishing pond in a neighborhood park). I had my fellow rescuer snap a couple of cell-phone pictures for the record, and set the turtle down at the edge of the pond. She sat there for a moment or two — wondering what the catch was, I expect — and then Zoom! right into the water.

You’ll notice I keep calling the turtle “her”. Look closely at the base of the tail in the picture above, and you’ll see a pinkish triangular structure sticking out. It was quite prominent in person, and I assumed it was an penis, erect from aggression.

Wrong. I’ve checked around, and most likely, that was an ovipositor. (I’m trying to get confirmation on this.) Ms. Snappy-snap was probably looking for a place to lay her eggs, or had recently laid them.

For lots of cool info on snappers, check out Chelydra.org.

Whip of the Year, So Far: Anthro Majors

Thursday, July 8th, 2010

Cue letters from anthropology majors complaining that this view of numerolinguistic development perpetuates a widespread myth. They get to write letters like that because when you're not getting a real science degree you have a lot of free time.

The whip is in the roll over text:

Cue letters from anthropology majors complaining that this view of numerolinguistic development perpetuates a widespread myth. They get to write letters like that because when you’re not getting a real science degree you have a lot of free time.

Of course, it’s not just anthropology; see my comment a few posts down about Truth.