Archive for April, 2010

Attic, part 19

Tuesday, April 20th, 2010

For a while they just stared at the wall in silence.

“Maybe if we get closer we can figure something out,” Josh suggested. He started walking forward, and they followed.

The wall was farther away than they had thought. As they walked toward it, they began for the first time to understand its true scale. The pieces that made up the wall, which they had at first taken for mere rocks, were actually giant boulders, each easily twice as tall as a person. When they had at last reached the giant construction, it loomed far above them. The rocks at the top of the wall seemed impossibly high up, their jagged outlines framed against the bright cloudless green of the sky.

“What do we do now,” Jenny asked, to nobody in particular. She was surprised when Josh answered.

“We could just go through the door,” he said.

“Very funny,” she made a face. “Anybody else have any ideas?”

Mr. Symarian looked apologetic. “I’m afraid my knowledge does not extend to problems of this sort. Perhaps our demon friend has a suggestion?” He looked down at his shoulder to see that Sid had fallen fast asleep. With one finger he gave the little demon a firm poke. Sid looked around wildly for a moment, then seemed to get his bearings.

With a great show of dignity Sid stood, and looked straight up. “That’s a big wall,” he said.

“Yes, we know that. How do we get through it,” Jenny asked.

“We could just go through the door,” Josh repeated.

Jenny glared at him. She was starting to lose her patience. “It wasn’t all that funny the first time,” she said. “Now if you’ll please be quiet I think we’d all like to hear what Sid has to say.”

“Glad you asked.” The little demon had been giving the wall an appraising look. Now he drew himself up to his full six inches, and paused significantly, until he was sure he had their full attention. “Seems to me that what we got here is what we demons call an impenetrable wall.”

“Oh yes, that’s helpful,” Jenny said sarcastically. “Doesn’t anybody have anything useful to say?”

“This is ridiculous,” Josh said. He strode to the wall, and with one hand he reached out as if to grab one of the enormous boulders. When he pulled his arm back, he was holding the doorknob of a very ordinary looking wooden door. With his other arm he gestured toward the dark passageway within. “Anybody care to go through the door?”

Sid started to laugh. “Like I was gonna say, the best way through an impenetrable wall is to get yourself a path finder.”

When life was simple

Monday, April 19th, 2010

Getting back to why the DNA encoding of amino acids is such a compelling argument for Darwinian evolution…

The diagram I saw in Watson’s book “Recombinant DNA” was a variant on the following table:

You probably learned in school (but forgot) that the twenty amino acids (the building blocks of all proteins — a protein is just a string of amino acids) are Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine and Valine.

You probably also learned (and didn’t forget) that DNA provides instructions for producing these sequences of amino acids. In particular, each amino acid is encoded with a sequence (called a “codon”) of three adjacent base pairs on the DNA chain. Each base pair can be one of four types, usually labeled A, T, G or C (named after the corresponding molecules in your DNA – adenine, thymine, guanine and cytosine).

The only thing that really matters about all this, for our discussion, is what you can see in the above table. Basically, that there are 64 possible codons, because there are 4×4×4 possible ways to put together three base pairs. Any one of these 64 codons ends up encoding either one of the twenty possible amino acids, or else a special instruction to start or stop the process of adding amino acids to the protein.

Of course this code is redundant, since 64 codons is a lot more than 20 amino acids. So there’s generally more than one way to encode a particular amino acid (as you can see in the table).

The thing that struck me when I first encountered this encoding in Watson’s book was that it reminded me of one of those brain-teaser mystery stories where you are told about a crime and you try to figure out how it was done (before the detective gives it away in the end).

The mystery story in this case is all about “what happened when”. The table above clearly shows that at first there was some simpler form of proto-life way back when, which got by just fine with two base pairs. You can see this because there a bunch of amino acids (SER, PRO, ARG, ILE, THR, VAL, ALA and GLY) that never use the third base pair at all.

Furthermore, when the third base pair is the only one that distinguishes between amino acids (as in the case of HIS and GLN), then at most two amino acids ever result, even though that third base pair has the power to identify up to four unique amino acids.

In other words, there is no system at work in how the third base pair is used. In each of these HIS/GLN kinds of cases, at some point an extra amino acid was useful to have around, and some little kluge of a change happened to allow for it.

Note also that the really important structural codes — the ones that signal to start and stop a protein — are mirror images of each other in those first two base pairs. Things start with “AU” and stop with “UA”. It looks as though at some point in the very distant past, back when life was simpler (literally), there might have been a two base-pair version of the codons, with AU and UA as the respective start and stop codes.

Perhaps in some long ago transcription error, the replicating mechanism of one mutant creature started counting by threes instead of twos. But a billion years of variations might have transpired before that ever happened.

The table provides hints to a time even further back, when there may have been only one controlling base pair. Notice the second column of the table — the codons for SER, PRO, THR and ALA. Only a single base pair (the first one) distinguishes between these four amino acids. At some point in the distant past (again, looking at the table) a second base pair proved useful, and the encodings of LEU and ARG split off from PRO. Similarly, ALA split off into VAL and GLY. In each case, new kinds of proteins were now possible.

That tacked on third base pair encodes a lot less than the first two, but then again it never needed to do much. The critical mass of 20 amino acids — sufficient for a huge increase in protein functionality — was finally reached, and the rest (as they say) is history.

There isn’t enough information in the table to give us any precise ordering of events, and yet the history suggested by the encoding of amino acids clearly points to a kind of blind step-wise search: Something happened, then something else happened, and each step was a haphazard refinement of whatever stuff was already around to work with. This is exactly what happens when randomly recombinable elements are run through a fitness function (ie: when one combination happens to survive a tiny better than another).

Like I said the other day, if this structure was all put there by an intelligent God — a structure that clearly suggests the gradual result of fitness-directed evolution — that God must have one hell of a sense of humor.

Attic, part 18

Sunday, April 18th, 2010

“That’s just wrong,” Josh said.

“I’m not certain that ‘wrong’ is an entirely appropriate term in this context,” Mr. Symarian observed dryly.

“It’s physics,” Josh stubbornly continued, “You can’t fight physics. There’s a reason the sky is blue, and not green. Molecules in the air scatter blue light more than they scatter red light…”

“And boys who pop into strange worlds don’t magically burrow their way through densely overgrown forests,” Jenny interrupted. “What, exactly, is your point?”

Josh looked at her, opened his mouth to say something, then apparently thought better of it. At last he said, “I’m guess I didn’t really have a point.”

“Except maybe on the top of your head,” Jenny said, and suddenly two of them found themselves giggling.

“Uh, yo kids,” they heard Sid say, “If you’re about done with the laugh-fest, we got ourselves a problem. And it’d be nice to get a little mind share here.” he gestured with one wing.

They looked to see where he was pointing. Sure enough, a wall was slowly materializing in front of them. And this was no ordinary wall, but a ten foot tall edifice, massive and imposing, that seemed for all the world to be made of solid rock. The great wall, which now looked discouragingly solid, stretched from one horizon to the other, barring the way ahead.

“Now we’ll never get anywhere,” Josh groaned. “What do we do now?”

Antony Flew

Saturday, April 17th, 2010

I read today of the death of Antony Flew at age 87. Mr. Flew was a well known and highly articulate atheist philosopher who in 2004, at the age of 81, suddenly announced that he had changed his mind about the existence of God. To me the most notable thing about this late life conversion to faith was Mr. Flew’s stated reason. Essentially, his argument was that something as complex as DNA could not have occurred without intelligent intervention. The NY Times has quoted Mr. Flew on the subject as follows:

“[DNA research] has shown, by the almost unbelievable complexity of the arrangements which are needed to produce life, that intelligence must have been involved.”

Oh my.

Of all the observed phenomena in the known Universe that Mr. Flew could have chosen as his example, I am astonished that he should have chosen this one. For I had exactly the opposite experience, back when I took it upon myself to learn a bit more about DNA than they had taught me back in high school.

In particular, one day back in 1994 I purchased a copy of Recombinant DNA by James Watson, to learn as much as I could about DNA, ribosomes and genetic replication.

I confess that my motives for this new-found curiosity were not strictly scientific. I had recently fallen madly in love with a beautiful molecular biologist, and I longed to know everything I could about her world. For a while, all things molecularly biological took on a strange romance in my mind. The fact that Watson’s book essentially described the chemistry of sexual reproduction was a further poetic twist that was quite lost on me at the time.

But I digress.

I discovered, as I read this wonderfully written book, a set of facts about DNA and the encoding of amino acids that might as well have been a bright red flashing neon that said “This must be the product of Darwinian evolution!”

In fact, DNA encoding provides such a strong argument for natural selection that if there were a God, the way DNA encodes amino acids would be a demonstration that he/she must be a rather perverse God, possessed either of a nasty and twisted sense of humor or else some sort of deep seated hostility toward humans. Otherwise, he/whe wouldn’t plant evidence (for us humans to find) of his/her own non-existence.

Why does DNA encodimg provide such a strong argument for natural selection? I’ll get to that in two days. Watch this space.

Attic, part 17

Friday, April 16th, 2010

To Jenny it seemed like hours since they had left the little clearing, although there was no way to know for sure. As they went further into the forest, the light seemed to dim. They had tried making small talk near the start of their journey, but it seemed that all conversations petered out within moments. It was as though the forest itself was willing them to silence.

She could barely make out Josh just ahead of her — she realized she was now following him as much by sound as by sight, as he pushed aside branches and leaves to make his way. Every once in a while she would try moving off to the side, to push into a different direction, just to see what would happen. And inevitably she would find that the forest was completely impenetrable in any other direction. At any given moment only one heading was passable — whichever one Josh happened to be using. She wouldn’t have been surprised to discover that the path went only one way. If they tried to double back, she thought, they might very well find that the place where they had just walked was now nothing but a solid thicket of trees.

At some point she realized it was getting lighter. At first she had thought it was her imagination, but now the changing light was unmistakable. She felt a mixture of relief and trepidation when Josh at last led them to the edge of the forest. She followed him through a gap between two trees, and then suddenly they were in the open air. She could hear Mr. Symarian, the demon still perched on his shoulder, come up out of the forest behind them. But it was hard to focus on that — she and Josh were both preoccupied with looking up.

The sky, stretching out above them, was a magnificent shade of green.

A living moment, revisited

Thursday, April 15th, 2010

Recently I’ve been doing something I never used to be able to do. After attending a great theatre or concert or dance performance, I look online afterward, and I usually find an excerpt of that performance somewhere on YouTube. I’m sure most of these recordings are illegal, but there you are.

The videos on YouTube, which are usually of inferior quality (bad lighting, worse sound) don’t really stand on their own. But if you’ve seen the live performance, they take you back to the excitement of the moment, when you saw Placido Domingo or Sutton Foster or Yo Yo Ma or Nellie McKay — the sense of excitement in the audience as everyone realized there was something magical going on this particular evening.

I wonder whether somewhere in here is the answer to the “reality versus cyberspace” debate, for here is a case where the power of the internet to archive and preserve is perfectly meshed with the ability of live performance to capture a living moment.

Attic, part 16

Wednesday, April 14th, 2010

“This is very weird,” Josh said.

“Weirder than a six inch tall cigar smoking demon from Brooklyn?” Jenny asked.

Josh considered this. “Yes, I see your point. But still, what on earth do we do now?”

“No,” Mr. Symarian corrected him. “Not on Earth, I’m afraid. I don’t believe we are meant to return to Earth — or what you would call Earth — until we have completed our mission.”

“Well that’s just great. Anybody know how we’re supposed to do that?” Josh looked around at his three companions, but nobody said a word.

Finally Jenny said, “Anything is better than standing here. Let’s go.” And with that she started off into the woods. She didn’t get very far. “Oh my gosh,” she said, “This is the thickest forest I’ve ever seen. I can’t get more than a few feet into it.”

“Let me try,” Josh said, and he started off in a different direction. Jenny watched in astonishment as he walked right into the woods, as though taking a stroll in the park. “Hey, this isn’t so hard,” he said.

“Sid looked at Mr. Symarian. “Kid’s a pathfinder.”

“A what-finder?” Josh looked confused.

“Our little friend is trying to say,” their teacher explained, “that you always go in the right direction.’

“Wait a second,” Josh looked suspicious. “What happens if I go in a different direction?”

“Look kid, listen to your teacher,” Sid said. “Doesn’t matter which way you go. It’s always the way the path goes. Yeah sure, you can try to change it up, but that’s where the path’ll be. Like I said, you’re a pathfinder. Do I gotta spell it out for you? You — find — paths.”

“Josh,” Jenny said, “Don’t argue with them. Just walk.”

Shrugging his shoulders Josh plunged once more into the brush. Jenny followed, and Mr. Symarian followed her. “Hey!” Sid shouted. “What about yours truly here? What am I, chopped liver?”

“Um,” Jenny said, “Can’t you just fly?”

Sid fanned one of his wings, eyeing it critically. “Nothin’ doing. The wings’re strictly vestigial. They make me look pretty though, don’t they?”

Before they could say anything in reply, Mr. Symarian had scooped the little demon up and deposited him on one shoulder. “I suggest we refrain from dawdling,” he said. “These spells usually contain an element of time. If we do not move with alacrity, I’m afraid we could become permanently mired in this dimension. And then things might become most unpleasant.”

And with that, they plunged onward.

Being a button

Tuesday, April 13th, 2010

Today I saw a very cool talk by researchers from the University of Washington and Microsoft, about an armband that senses vibrations caused by touch. If you wear the armband on your left arm, and then use a finger of your right hand to touch various places on your left arm (or hand or fingers), a computer can analyze vibrations in the armband to figure exactly where you touched.

This means that you can turn your own body into a user interface. For example, you can dial a phone number just by tapping various places on your palm — as though your hand were a numeric keypad. Things get really interesting if you project images onto your arm and hand (eg: through one of those tiny pico-projectors). Then your body effectively becomes a complete computer interface.

The authors gave all kinds of amazing demos, and the audience was impressed by the sheer novelty of it. But things got even more interesting during the question and answer session after the talk. People were clearly engaged by the philosophical implications of turning our own bodies into computer interfaces.

One guy got up to the microphone and asked “How does it feel to be a button?” The speakers didn’t really have an answer to that. I suppose by the time technology has truly turned you into a button, you won’t really notice you’re a button.

In the break afterward, I was chatting with some friends who had also seen the talk. We started musing about how such technologies might change interpersonal relations. For example, body-touch technologies might change the taboos around how and when it is appropriate for one person to touch another.

Imagine if I could use your body as a computer interface, or vice versa. Not only could this be considered an intimate act, but such actions could very well have real consequences. If I let you touch me, and you end up deleting my files, that could be considered a violation of trust.

We may very well be entering a world in which “pushing someone’s buttons” is more than a euphemism.

Attic, part 15

Monday, April 12th, 2010

Sid was pacing back and forth on the desk. “I’m guessing your grandma fell in with a bad crowd, and now some shady operators are using the old gal for their own nefarious purposes.”

“I’m afraid he’s right,” Mr. Symarian said, looking at Jenny sympathetically. “Your grandmother had the power, much as you yourself have. There are forces in other dimensions who will stop at nothing to capture the unwary possessor of such power, and turn its potential toward their own ends. I’m afraid some unscrupulous demons are using your grandmother as an Astral Lens.”

“Did you just say `Astral Lens’,” Josh said. “What is this, a physics class? Are you saying somebody is using Jenny’s grandmother for some kind of demon optics experiment?”

“I only wish it were that benign,” their teacher said. “The power itself is neither good nor evil — it can be turned to any direction. And in the case of your poor grandmother, I am afraid…”

“I won’t let them get away with this,” Jenny interrupted, stamping her foot in anger. “I’m through with being nice. I think maybe it’s time we faced our demons.”

Strangely, in the place where her foot came down, instead of the expected hard wooden floor she felt something soft. Looking down in surprise, Jenny was amazed to see grass beginning to grow around her foot. The grass quickly spread, until it had grown beyond the walls, which had now been replaced by a thick canopy of trees.

They found themselves standing in a small copse in a densely overgrown wood. All except Sid, who was standing on a large rock at about table height. For a long moment the four of them all just looked at each other, too stunned to say anything.

Josh was the first to break the silence. “Toto,” he said, “I have a feeling we’re not in Kansas anymore.”

Sid gave Josh a puzzled look. “Ok, I can deal with the whole being transported to another world thing, seeing as the little gal said she wanted to face those demons. But who the hell is this Toto guy? Him I never heard of.”

People people left left.

Sunday, April 11th, 2010

The other day I mentioned the wonderfully twisted little sentence in the title of this post, courtesy of Gary Marcus. Although arguably grammatical, the sentence does not correspond to the way human brains actually think.

Its meaning, said in a more human-friendly way, is (more or less): “Some people, who were left by some other people, left.” English grammar. with its enormous flexibility, allows us to phrase this more tersely as “People people left left”, but that doesn’t mean anybody actually either talks or listens that way. In other words, if you try to write down formal rules for generating natural language, you will end up generating some sentences that are not really natural speech — in the sense that nobody would ever say them, and nobody would understand them.

Conversely, there are English sentences one might think should be convoluted and hard to understand, but that nobody has any trouble with. In his book The Language Instinct: How the Mind Creates Language, Steven Pinker quotes a great old example:

Daddy trudges upstairs to Junior’s bedroom to read his son a bedtime story. Junior spots the book, scowls, and asks, “Daddy, what did you bring that book that I don’t want to be read to out of up for?”

As a grammatical structure, the kid’s sentence is nested four levels deep, and yet English speakers — including children — generally have no problem understanding it. As Pinker points out, this is because the four nested levels of the boy’s sentence are all different.

In computer science terms, and putting the two examples together, people have no trouble with sentences structured like this: “( [ { < > } ] )” — as in Pinker’s example — but we get stuck on seemingly simpler sentences structured like this: “( ( ) )” — as in the example from Gary Marcus.

In other words, human brains don’t really work as stack machines when creating and understanding sentences. Our brains operate by matching tokens — and those tokens need to all be distinct.

Circling back around to my previous post about Getting to know your robot, I’ve been playing around with software that works with what we know about natural language, as a way to — potentially — bridge the enormous gulf between the way people naturally think and the way computers need to be told how to follow instructions.