SGU Episode 380

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SGU Episode 380
27th October 2012
(brief caption for the episode icon)
SGU 379                      SGU 381
Skeptical Rogues
S: Steven Novella
B: Bob Novella
J: Jay Novella
E: Evan Bernstein
Quote of the Week
The Web is great for finding a list of the ten biggest cities in the United States, but if the scientific literature is merely littered with wrong facts, then cyberspace is an enticing quagmire of falsehoods, propaganda, and just plain bunkum. There simply is no substitute for skepticism.
Samuel Arbesman
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Introduction

You're listening to the Skeptics' Guide to the Universe, your escape to reality.

S: Hello and welcome to the Skeptics' Guide to the Universe. Today is Wednesday, October 17, 2012, and this is your host Steven Novella. Joining me this week are Bob Novella,

B: Hey, everybody.

S: Jay Novella,

J: Hey guys.

S: and Evan Bernstein.

E: Here I am. How's everyone?

J: Hello.

B: Good, thanks.

S: Rebecca is preparing for her paranormal road trip, which, by the time this show goes out, will have been done.

R: She claims she just got her driver's license about a week ago in preparation for this trip.

B: Oh, boy.

E: I'm not sure driving halfway down the United States is the best way to—

J: I think it's gonna be hysterical. I mean, could you imagine all the things that she's gonna say. Like, all the comments that she's gonna come out with?

E: Yeah, like "what's that red octagon that says 'stop' mean?" (laughter)

J: "What does the sign that says 'stop' mean?" Yeah.

S: And she'll have two British guys with her giving her directions. (laughter)

E: They'll say "Turn left, I mean right!"

B: "You're on the wrong side of the road!"

E: Could you imagine?

This Day in Skepticism (1:07)

S: We have a couple of interesting "This Day in Skepticism" or science news. The first is October 27, 1780 was the first astronomical expedition of the United States. Observers left from Harvard College in Cambridge, Massachusetts to Penobscot Bay

B: Penobscot

S: Yeah, Penobscot. They were led by Samuel Williams and they were there to observe an eclipse that was occurring that year. Interestingly, this was, we were fighting a war with Britain at the time. But the British Navy allowed the scientists into the Bay and to set up their equipment so that they could observe the eclipse.

B: That's cool.

J: Yeah.

S: But there was a hitch. According to the expedition's calculations they were trying to view totality. But they found that they were outside of the path of totality and a sliver of the sun was still visible even during the maximal eclipse.

E: Aghh! What a drag!

J: So, totality meaning a complete solar eclipse.

S: Yeah, one hundred percent blocked—

E: One hundred percent in the line.

S: But still, they made their observations.

B: Somebody screwed up.

S: It was successful to that extent.

E: But it was only, it was the first expedition, you know. I mean, that's pretty good for the first one.

S: For the U.S., yeah.

E: Yeah, for the U.S. They got better at it.

J: What else you got, Steve?

S: And, in 1891, Philip B. Downing invented something very important and was awarded a U.S. patent for . . . do you know?

J: Yes, the stuffing for pillows.

S: He made a design improvement to the street mailbox. He developed that little

J: The flag?

S: opening, the flap, doohicky, so you know how you can drop the letter in but you can't reach in there and pull letter out. And also obviously protects the letter from the rain and from the weather.

J: Oh you mean the thing, when you're doing a drop-off of mail for the post office and you slip it in the slot and then you can't reach your hand in there.

S: Yes.

E: Because there's a piece of metal, like an L-shaped piece of metal, that would block you.

S: Right.

E: It would hold the letter until you put it down and then the letter slides down safely depositing it into the box.

S: Correct.

E: Unfortunately, it does not protect against, say, bags of dog poop that get put into the mailbox.

B: (disgusted noise) How lame.

E: But you know, bad senses of humor.

J: Do people do that?

E: What I'm saying is that people have been known to throw all sorts of objects in there. Garbage and clothes . . .

S: Yeah, it just keeps you from taking stuff out.

E: Right.

S: Invented in 1891. Still used today. A lot of longevity for that particular invention.

News Items

Genetic Logic Circuit (3:34)

• Washington University in St Louis: A complex logic circuit made from bacterial genes

S: Well Jay, you're gonna tell us about building computers, sort of, out of bacteria.

J: Sweet. Yeah, how impressive is that idea? But, put simply, at its core, a computer processor does some very basic things that some scientists believe that they might be able to duplicate in bacteria. So a computer processor, as we know it, the kind that we have in our cell phones and our laptops and everything, manages a gigantic number of logic gates that are made out of electrical wiring, transistors and integrated circuits. Logic gates have served us well. Every device we own, like I said, has at least one of these in them, including your car, if you have a modern car, it has a lot of processors in it. And I'd to thank Jesus and Al Gore for both of things.

B: Oh, jeez. Oh, Gore.

J: Logic gates compare the bits or the ones and zeroes in which computers encode information. So every logic gate has two or more inputs and one output. The output depends on the input and the operation the gate performs. And then, as you string logic gates together you can get to very complicated pieces of logic that determine the outcome of events and different, lots of different things. The interesting thing is that logic gates can be made out of tons of different things. So, you could actually make a logic gate out of a series of pipes with plumbing and water going through it. You could make logic gates out of wooden levers and whatnot. You can make them large mechanical logic gates.

S: It reminds me of a discussion about artificial intelligence and consciousness, you know.

B: ____________'s Room?

S: Yeah, you think about having a computer brain that has the complexity and processing power of a human brain and it seems intuitive that it can be consciously aware. Think, okay, but what if you had, like as you say, like your logic gate, was people using a slide rule, but you had seven billion of them and you had some way of coordinating and communicating among those people, and let's just say for hypothetical purposes you can get to the point where, although very slow, you can actually have a powerful supercomputer comprised of people using slide rules. Could that be conscious? It still could process the same information that a silicon or whatever computer can. So it's an interesting thought experiment. I think the answer is no, but I think substrate does matter in that context. But it does, it is dependent on this notion that anything could be a logic gate as long as you fit the minimum criteria of you have different inputs, one output, and you have some logic to it.

J: Well, to continue on, this was a very interesting bit of research that's being done. There's two people: Tae Seok Moon and Christopher Voigt, who's a Ph.D. And they're working on building logic gates out of genes. How cool is that, guys?

E: That's very cool.

S: Yes.

B: Sounds a lot better than water pipes.

J: they made the largest genetic-based circuit to date. So this is what's going on. Moon is the lead author of an article that describes the project in the October 7 issue of Nature and it's called Genetic Programs Constructed From Layered Logic Gates in Single Cells. The tiny circuit constructed from these gene gates could someday be components of engineered cells that will monitor and respond and interact with their very small local environment. The specialized bacteria could do powerful and specific things. This is what they were talking about in the article. They can clean up pollutants, they can excrete out bio-fuels. They can be infection-control bacteria that might bustle around and kill pathogens. There's dozens of other things that you could get bacteria to do that would be very helpful, beneficial: fighting disease. You know, just doing all sorts of different things. One of the things that they were discussing is there's a couple of gates that are typical in all computing and anything that deals with a logic gate. There's an "AND" gate, and an "OR" gate, right? They're two very different and specific things. So an AND gate, for example, turns on only if all its inputs are on. So if it has two or more inputs, if all of them are saying yes, the logic gate is opened. OR gate turns on if any of its inputs are on. So if one or more of its inputs is in the on state, the gate opens. And to simulate these in genes, Moon had to find a gene that would, say, be an AND gate, its activation would have to be controlled by two or more molecules, not actually input, so the molecules, these binding molecules, would actually become the input of the gate. If you

E: Right.

J: If you can follow what I'm saying. If both molecules are present, then the gate would be turned on. And relax, Bob, not that kind of turned on.

B: Ha ha.

S: If I can, Jay, so, the proteins are, they bind to promoter regions of DNA. So these are regions of DNA that regulate whether a gene is turned on or not. Whether the gene gets transcribed and turned into protein. All you need to do is find a gene that has two or more promoter sites. If all of those promoter sites need to be bound in order for the gene to make the protein, then you have an AND gate, essentially, and the output is the production of the protein.

J: That's right. So an example of this is salmonella bacteria, or better known as the thing that causes food poisoning. And I've had it, and it's terrible. But anyway

S: Can I just say when I read that I'm like the organism that cause food poisoning, as if there's one. It's one of many bacteria that can cause food poisoning.

E: Good point.

J: You're right, of course, Steve. But this is the big one. That's the one everyone knows.

S: Yeah.

J: That's why they used it. The circuit Moon eventually built consisted of four sensors for four different molecules, like Steve was describing, that fed into three two-input AND gates. Does that make sense?

S: Yeah.

J: And if all four molecules were present and all three AND gates turned on, and the last one produced a reporter protein that fluoresced red so that the operation of the circuit could be easily monitored. That's cool. I mean that's the biological gate is showing you that it's working. I thought that was really really interesting.

E: Right down to the indicator light. That's very cool.

J: Yeah, I know, right? Hey, your genes are blinking. Someday Moon imagines a synthetic bacteria, bacterium, that might detect four different cancer indicators and in the presence of all four, release something to kill the tumor.

S: Yeah. So you're actually programming the cell as like a drug-delivery system. It will be able to detect with multiple inputs a situation in which the drug should be released. Very likely to be a cancer cell.

J: So another thing, there are lots of things in their way to make this work, but, one of the ones I found most interesting is this idea that biological circuits could accidentally cross-talk with each other or get confused if they were in the region of another one and part of that problem is that biology is really unorganized in a way. Meaning that, you know, with electrical wiring the precision is incredible. But in biology there's lots of things floating around. Even inside of a cell and everything there's lots of moving parts and stuff like that.

S: It's messy. I mean, even evolution. Receptor sites, et cetera, are not clean. It's not like a hundred percent on or off. There's lots of related proteins and related receptors and there's gonna be some cross-reactivity. It's not clean.

J: Yeah, they call that cross-talk, and Moon had to eliminate this. And one way that he did it was he took three different strains of bacteria and he took pieces of each one of them. And then what he did was, he prompted the bacteria to reproduce and he hand-picked the ones that were least likely to cross-talk but still functioned. So basically he was looking, as he was forcing these things to reproduce, he was hand-selecting the mutations that were in his benefit, which another cool thing.

B: So he was creating this selective pressure himself.

J: Yeah.

B: Forcing the evolution of the bacteria in the direction that he wanted, which could be slow, but an effective way of going about doing it.

J: Yeah. Yeah, but I would find that probably to be common in situations like this where they're looking for mutations that have different properties and whatnot. Yeah, that's the way to make it happen. Moon said:

"We're not trying to build a computer out of biological logic gates. You can't build a computer this way. Instead, we're trying to make controllers that will access all the things biological organisms so in simple programmable ways. I see the cell as a system that consists of a sensor, a controller (which is the logic circuit), and an actuator. This paper covers work on the controller, but eventually the controller's output will drive an actuator, something that will do work on the cell's surroundings."

So, like Steve said, this is all about not just detecting things, but actually reacting to the environment and doing things on that level. Very very small immediate fast-moving level.

B: Steve, you're saying, if the output is the creation of a protein, how does that speak to how fast this thing is gonna go about doing its business?

S: Yeah, obviously it's not going to be doing it at computer speeds.

B: Right.

S: (garbled) –this isn't going to be a computer. But that could still be fast in biological terms.

B: Yeah, especially if you've got many many cells or bacteria doing the, performing this task. It wouldn't take long for something significant to build up.

S: Right. Right. So we'll see. Like any new idea, we can sit here and speculate about how it might be used, but how it actually gets used is probably going to be very different. But it is a neat basic concept.

Efficient Language (13:26)

• PNAS: Language learners restructure their input to facilitate efficient communication

S: Lets go on to the next news item, this one really caught my interest. We talk about language a lot on the show, I mean this is a podcast made of words so language is important.

E: (chuckles)Yep, pendantic!

S: Yes, I have a bit of a fascination with this. This is a study looking at how people react to artificial languages, so they had their subjects, they made, it was a very small artificial language that they made up for the study, and they wanted to se how the subjects would spontaneously alter or change the language depending on various situations. But, before I tell you the results, I'll give you a bit of background, there is a few different hypotheses or theories about why languages are structured the way they are, and specifically why certain patterns or structures seem to recur in many different or even disparate languages. One possibility is that modern languages all have a common root. If you went back far enough in time two seemingly disparate languages may have evolved from the same root language, that's one possibility. Another possibility is that there is something inherent in the way our brains work that guide languages in certain directions and the third related to that, it there is some inherent logic to language that asserts itself over and over again as languages evolve. So this study was really, was partly addressing that question, are these patterns that we see in languages the same because there's a logic to how people see and use languages and that is in fact what they found. So, what this study shows, again, kind of makes sense, but it may seem like this is an obvious outcome, but when you put it into the context of our different theories of language it makes more sense. What they found is that when the subjects were presented with ambiguous situations, where the artificial language could not unambiguously describe the scene that they were being told to describe in the artificial language, they would add details, they would change the form of words in order to make it unambiguous. But they wouldn't do it otherwise. Specifically, they used, the variable here is case. Case is the different forms of nouns that vary depending on what role the noun is playing in the sentence.

E: For example.

S: I'll give you some examples. So in English actually, we do not use case very much. There's only a few cases in English. The main one that we use is the genitive case, or possessive case. English has really just three cases: nominative, oblique and genitive. But other languages have many different cases. They might have a different form of the noun for when the noun is doing the action, when the action's being done to them,

E: Which gender is saying it. Or to which gender it's referring?

S: No, that's different. That's gender. That's different than case. So, I can run through them: there's nominative case, when the noun is the subject; accusative case when it's a direct object of a verb; dative case indicates indirect object of a verb; ablative case is movement from something, so if you're going from your house, that's the ablative case; genitive, which is possessive; vocative case is addressee, like, how you doing tonight, Evan; locative case, you know, where—at home; and instrumental indicates an object used in performing an action: you mop the floor with a mop. So in English we don't use forms of the noun to indicate all those cases. We use word order or prepositions. With, of, to. But other languages don't use word order, they have a fluid word order. So like if I say "Evan hit Bob." In English that means Evan hit Bob. In other languages that word order would mean nothing. And it could as easily mean that Bob hit Evan as Evan hit Bob. And you would know by the nouns you used for Bob and Evan which one was doing the action and which one was having the action done to him.

B: Well that explains some weird ways that people learn language, English as a second language, the way they construct sentences. Because it's a new concept to them, and sometimes I try to make sense of why they used that particular word order. And that explains some of what I've heard. Interesting.

S: Oh, yeah, absolutely. If your hear Chinese speakers who, for whom English is a second language and they haven't quite mastered it, they don't know quite how to use prepositions properly 'cause they don't use prepositions. Or they don't quite get the word order correct. 'Cause they're not used to thinking in word order and prepositions, and that's how we think about language. And we would be lost in a language that had a fluid word order until we mastered all those cases that don't even exist in English. So what this means is that different languages found different solutions to the same problem of unambiguously indicating who is doing what in a sentence. Case, preposition, word order. Those are different solutions. So what the researchers did is they gave, in the artificial languages they created, word order was fluid. So the speaker had to use case in order to indicate the different purpose that the noun was serving in the sentence. So what they found was that the speakers used case only when it was necessary to make the sentence unambiguous. But then dropped it when it wasn't necessary. So they interpreted that to mean that there are . . . what they felt they did was they demonstrated there are two sort of logical imperatives in how people use language and they extrapolated this to how language evolves over time. That we have a tendency to make language unambiguous and efficient. And we will use the most efficient construction that is still unambiguous. Obviously we don't always do this all the time, but that's sort of the tendency within language to do that. And that explains how languages evolve over time. We tend to shorten sentences. We tend to swallow consonants, like, people make fun of the way we say the double "t's" or the double, say "hi'en" instead of "hidden," you know, or "wri'en" instead of "written."

B: So we're just being efficient, that's all.

S: Yes. Well, this is a natural tendency in languages over time. You tend to swallow syllables, you tend to shorten words. If you don't lose any meaning, or if there's, if the resulting shortened sentence or word is just as unambiguous as the longer version, then there's no impediment to doing that. And therefore we'll do it. We'll take the shortcut. So language becomes efficient over time, but we also make changes in order to make it unambiguous. We'll add cases or prepositions or whatever. You find some strategy to render it unambiguous as well.

E: Well, sure, 'cause you want people to understand the point you're trying to drive home.

S: Yeah, but you don't want to say one more syllable than you absolutely have to.

E: Exactly. Efficiency.

J: Why's that?

B: Well I think you can think of it as

E: Time is short.

B: like a genetic propensity to be more efficient but unambiguous at the same time and our languages reflect that.

S: Yeah. Exactly. And so the authors also talk about the fact it's, you know we talk about being pedantic and keeping true to the correct original form, if you will, of a language, when in fact, they say, it's good for languages to change over time. As languages evolve over time they become more efficient and unambiguous, let them change over time.

E: Oh, boy.

S: Yeah.

E: I betcha some people are gonna disagree with that.

S: Well, I think, we've said as much before, ourselves. You know, that languages are living things left to change, but you have to balance that against a certain amount of stability in the language so that people know what other people are saying. When I've thought about this, when I'm going to be pedantic it's when there is, it's for the purpose of unam . . . unambiguity(?) Is that a word? Is when you're confusing different forms of the word or different uses of a word that actually obscure the meaning. As opposed to "this is just the right way to do it."

B: Okay, yeah. That makes sense.

E: Hey, Bob, I'm sorry I hit you earlier in Steve's example. I hope it didn't hurt too badly. (laughter)

B: I'm over it.

Closest Exoplanet (22:01)

• Independent: Scientists find Earth-like planet Alpha Centauri Bb in neighbouring star system but rule-out possibility of life thanks to its 1,500C surface

Alien Hacker (30:34)

• Slate: U.K. Will Not Extradite Alien-Hunting Hacker With Asperger’s Who Broke Into NASA, Military Computers

Who's That Noisy? (43:17)

• Answer to last week - revealed in three weeks

Questions and Emails

Zombie Bite (44:36)

Hey Guys, I got a fun Medical Question for you all and maybe a little bit more aimed towards Dr. Novella due to his medical background. If you've seen the new season of the Walking Dead (spoilers), in the first episode the old guy gets bitten on the leg and the main character decides to amputate his leg because he thinks it's like a venomous snake bite. The rationale is even though they all know they're all infected already, that zombie bites cause a secondary infection that makes you sick and you die thereby allowing the primary infection to turn you into a zombie. Is the choice to amputate really stupid even if the infection was like a venomous bite? You would think they made a relatively moderate problem of a huge bite into an enormous problem given that there's going to be massive blood loss now, chance of incidental infection, and well....the old guy is really old and he probably can't take the shock of getting his leg hacked on repeatedly by a handaxe. If they intended to cauterize the amputation later, wouldn't it have been better to just cauterize the huge bite wound instead and hope that would be enough? It seems like anything they could do to help the amputation they've could have done to the bite wound and it wouldn't have been as bad. Dr. Novella has talked about in medicine that usually treatments have risks but the benefits outweigh the risks. In this case I'm wondering if the Amputation is causing more damage than it's helping, given their fictional situation. Thanks, Henry Loo

Announcements

SGU Nominated For The 2012 Stitcher Award (54:46)

• The Stitcher Awards

Science or Fiction (55:17)

S: Item number one. The hagfish can rapidly produce as much as 20 liters of slime as a defense against predators. Item number two. The oldest fossil hagfish is 300 million years old and shows remarkable similarity to modern hagfish, demonstrating unusual evolutionary stability. Item number three. Molecular analysis has confirmed that hagfish are transitional between vertebrates and invertebrates. And item number four. Hagfish are the only creatures known to have a skull but no vertebral column.

Skeptical Quote of the Week (1:09:45)

The Web is great for finding a list of the ten biggest cities in the United States, but if the scientific literature is merely littered with wrong facts, then cyberspace is an enticing quagmire of falsehoods, propaganda, and just plain bunkum. There simply is no substitute for skepticism.

J: Samuel Arbesman!

References