11 June 2012

The biology of Prometheus

The debut of Prometheus spawned a surprisingly large amount of attention in my scientific social network this weekend. This proves that scientists are not attracted by circus afros, I guess.

I’ve reviewed the film on its artistic merits on Sunday Matinee, my movie review blog.But I thought it would be fun to talk about some of the biology in the film. I’ll leave the astronomy (which I have my suspicions about) to others.

Spoilers ahead, so discussion continues below the fold:

At the heart of Prometheus are two ideas. First, that Earth was visited in the ancient past by an alien race (nicknamed “the engineers”) that created humans.

At first glance, this idea belongs only to pseudoscience and fiction. The “ancient astronaut” angle owes a lot to Erich von Däniken’s Chariots of the Gods. “Aliens messing with human evolution” has been well explored in science fiction, not least in 2001: A Space Odyssey.

A weaker version of the “aliens making humans,” is bandied about as a speculative hypothesis. Panspermia (pan = everywhere) is the idea that life is abundant throughout the universe, and life on Earth was seeded by extraterrestrial impacts. Comets are often mentioned as possible “seed carriers” for life to our solar system.

For many (including myself), panspermia is an unsatisfying hypothesis because it doesn’t provide any insight into the origin of life; it just moves it off world. I had a discussion with a panspermia advocate on Usenet who said, “Life is a miracle,” which seemed to me to be an unusually honest admission. Miracles have never found a place in science, and to the extent that panspermia treats life as a miracle, it’s not science.

The second big idea is that the engineers didn’t just start the ball rolling on life, but had a very specific outcome in mind. A big moment in Prometheus is that the engineer’s DNA is an “exact match” for human DNA. This is used as the definitive proof that the engineers’ created humans.

If aliens created humans, how would we know? Would it be as simple as ordering up a galactic paternity test?

Detecting the difference between the evolved and the constructed is... not simple. This is the problem faced by Creationists and Intelligent Design. They claim that they have methods of detecting design in biological organisms, except that instead of the designer being Prometheus’s engineers, they see the designer as God. One potential criterion for distinguishing the designed from the evolved is “specified complexity.” So far, biologists have not found “specified complexity” useful, but the question of distinguishing the “built” from “biological” is a good one.

Distinguishing the designed from the evolved could increasingly be a relevant problem as synthetic biology progresses. Researchers have been able to build viruses from scratch for a decade now. We had the first organism with an artificial genome a few years ago. There, the team at the J. Craig Venter Institute deliberately implanted “watermark” in the DNA sequence of the bacteria.

Not everyone might be so helpful as to sign their work, however. How could you determine if a flu virus was a natural mutation versus one that was deliberately built in a lab? You probably couldn’t, as far as I can tell. There’s no way to tell DNA made in a lab apart from DNA made in an organism. It’s all atoms.

Prometheus is hazy on the details of how the aliens created humans. The opening scene shows one of the engineers dying on a barren planet (presumably Earth [Update: Director Ridley Scott says it may well not be.]), with DNA molecules swirling off into the waters. It’s not clear when this was supposed to have happened, although the barren landscape implies that it’s before any life formed on Earth.

The film is also hazy on what they mean by an “exact match” of DNA. But the haziness lets me indulge in some fun hand-waving.

It would be completely illogical for the “exact match” to mean that the detailed DNA sequence of engineers is the same as humans. Engineers – huge, alabaster white, and hairless – are obviously a different species. They are arguably as different in their morphology from humans as humans are from chimpanzees. Those differences in phenotype would require differences in genotype, and quite substantial ones.

A more plausible explanation for “exact match” might be that the engineers use DNA as their genetic material, as we do. Indeed, if we did find alien life, “Do they have DNA?” would be one of the first questions we’d want to answer.

In E.T. – The Extra-Terrestrial, a scientist comes in after E.T. is captured, announcing, “He’s got DNA.” The scene was meant to show the difference between Eliott’s concern for E.T. as a friend and the scientists treating E.T. as a specimen. But even though I wasn’t even in university yet (I wouldn’t get out of high school for another two years), I always understood why someone would want to know the answer to that question if they met an alien. Because that would be a big f’in’ deal.

Right now, we have no idea what range of molecules could be used for inheritance. On this planet, we have two closely related nucleic acids, DNA and RNA. Earlier this year, Pinheiro and colleagues made a whole series of other chemicals – six, to be exact – that could potentially transmit genetic information, which they called XNAs.

Our DNA uses two pairs of nucleotides – A, T, C, and G – to carry instructions. Last year, Yang and colleagues added new bases that could be used in a DNA code. Three pairs instead of two.

Given that we know of at least eight different molecules already that could serve as carriers of genetic information, and that we are not limited to the same four pairs of chemicals to carry out the actual coding, to find two species on different planets both using DNA and both using A binding to T, and C binding to G would be... remarkable.

But we could go a step further in similarity. The genetic code that DNA uses to code for proteins is almost universal to most species on this planet. Where there are differences, they seem to be minor modifications from the common code.

It appears that much of the code is arbitrary. There is no particular reason why UGA should be one of three codes for “You’re done making the protein, now stop!” Why couldn’t UGA code for part of a protein instead of stop? Why are there three “stop” codes instead of two, or four, or one?

Although some have suggested that some features of the genetic code have been optimized through evolutionary processes in some way, to find a species on another planet that used DNA, with the same genetic code as life on this planet, would be very strong evidence of a connection between the two species.

This wouldn’t clinch the case, though. There would still be an alternative hypothesis to rule out: convergence. It is possible that there is something particularly efficient about DNA and that particular code that we currently do not understand. This seems unlikely, but then again, we don’t have aliens that we can compare our molecules to.

I doubt that the writers of Prometheus went through this much agony in trying to determine how one would prove that an alien race created humans. Because they don’t let the one biologist in the film get a simple historical fact right.

At one point, the biologist in the film mentions that the discovery of aliens messing with human evolution would overturn “three centuries of Darwinism.”According to the movies’ timeline, it is set very late this century, which would mean that On the Origin of Species would be closer to 200 years old than 300 years old.

While the writers may not have gotten everything right about about biology, they arguably did get something right about biologists. At least one biologist I know admitted that she probably would have “bought it” the way the scientist in the film does, because she’s far too curious about new life to leave well enough alone...

External links

Stealing fire
Curly haired mafia hour and half Google Plus hangout on Prometheus


jebyrnes said...

Favorite commentary quote so far: "I think the entire film was a scathing indictment of the current failure to teach STEM subjects in school and the dumbing down of evolution and introduction of ID into the school curriculum. After all, it shows a group of people two generations or so from now who are at the top of their fields to be selected for a mission that explores the very meaning of existence of life on earth and yet they all act like they just escaped from Mike Judge's Idiocracy." from boingboing

Karl said...

"Three centuries of Darwinism" isn't wrong -- you have the 19th, 20th, 21st = 3 centuries.

Really though, the idea that you can "create humans" without creating all their associated microbial life is wrong, considering the sequence similarities. That really would be "overturning Darwinism."

Zen Faulkes said...

Karl: True, but I don’t think that’s a normal way most people think of centuries. It would sound weird if I talked about The Rolling Stones or The Human League creating music for “two centuries”.

It’s hard to tell what the filmmakers meant... just like much of the rest of Prometheus.

Lenoxus said...

Karl wrote: Really though, the idea that you can "create humans" without creating all their associated microbial life is wrong, considering the sequence similarities. That really would be "overturning Darwinism."

For certain definitions of "create", this isn't necessarily true. For example, there's a sense in which humans created dogs. Also, parents are often said to "create" their children – this becomes relevant to the film when Shaw reminds Halloway about her infertility after he suggests that it seems like "anyone" can "create life". (He should have replied with something like "Well, in the sense I was using, no human can create life yet, but I apologize for my insensitive choice of words.")

I like to think that if I were that bespectacled biologist in the debriefing scene, then instead of saying something silly about centuries of Darwinism, I would ask "What do you mean by 'create'?" As usual, the movie doesnt quite answer the question, especially if we are to accept that the planet at the beginning is not Earth. I personally hope it isn't, since the notions of a very humanlike entity existing before life on Earth, sans time travel, is nonsense. You might as well have aliens that speak Pig Latin.

On another forum, someone suggested a much better explanation for the film's events than whatever its creators probably have in mind: the pale humanoids are actually humans, either evolved or genetically modified by some other aliens who visited those ancient cultures and took a few specimens. After that, who knows what happened, but at least this idea keeps biology and logic in effect.