Science & SF Tidbits: Oct 21, 2012: Sequencing Martian DNA, Animal Language, Anthropology SF

More bioscience and science fiction bits from around the web:

• Genome Hunters Go after Martian DNA - Technology Review »

It's a race: two biotech companies - J Craig Venter's Synthetic Genomics and Jonathan Rothberg's Ion Torrent - want to send a DNA sequencing machine (made by their company, of course) to Mars. Both companies are adapting their hardware for Martian conditions, and are testing them in Mars-like Earthly sites like the Mojave Desert.

The advantage to sequencing the DNA of Martian microbes while on the planet, rather than sending the sample back to Earth - is that it makes contamination from Earthly life less likely. The experiment would have an incredibly high payoff, if any DNA were found to be sequenced.

Undaunted by the lack of any evidence that Mars currently hosts microbial life, Venter is already talking about reconstructing Martian organisms from their DNA sequence in a super-secure laboratory on Earth.

"People are worried about the Andromeda strain," says Venter. "We can rebuild the Martians in a P-4 spacesuit lab instead of having them land in the ocean."

I'm pretty sure this is a publicity stunt, but it's a fun one to think about the possible results if it were actually successful.

• Is language unique to humans? » BBC Future

Parrots, bonobos, dolphins and even dogs can learn to understand human words and sentences. But is that language? Maybe not, if you think of language as a method of computation rather than a means of communication.

"What makes human language unique is not that it allows us to communicate with each other, but that it allows us to do so with infinite variety. A monkey can scream to warn its troopmates of an approaching predator, or alert them to a cache of tasty food, but it can't communicate something like "doesn't that hawk have a funny looking beak?" or "with a little salt, this fig would taste divine"."

• How to Read Like a Science Nerd » New York Times Magazine

Science writer Maggie Koerth-Baker shares her book recommendations with The New York Times and recommends a science fiction classic:

“Lilith’s Brood,” by Octavia Butler, is the best book about an alien invasion that I have ever read. It’s smart, and it’s deeply human, and (as a former anthropology major) I think it should be on the required-reading list for anyone interested in cultural anthropology.

I agree with her recommendation. Butler's Lilith's Brood (also known as the Xenogenesis Triology) should be required reading for all SF fans, not just anthropology enthusiasts. It asks the uncomfortable question of whether alien takeover might actually be for our own good.

Image: Parrot Culture by Marendo Müller. Public Domain.

Kurt Vonnegut: War, Anthropology, and Atheism

This is a look at another SF authored who was interviewed by the Paris Review. The interviews with  Aldous Huxley and William S. Burroughs took place in the early 1960s. Now we jump ahead more than a decade to a 1977 interview with Kurt Vonnegut.

The Paris Review's interview with Kurt Vonnegut starts out with a discussion of Vonnegut's experiences as a infantry scout in during the Second World War.  His experience as a prisoner of war during the firebombing of Dresden formed the basis for his 1969 novel Slaughterhouse Five - at least for the parts that weren't set in a zoo on the planet Tralfamador.

Before the war Vonnegut studied chemistry at Cornell University for several years. When he enlisted in the Army, he was transferred to the Carnegie Institute of Technology where he studied mechanical engineering. His studies were interrupted by the war.

After the war was over, Vonnegut went back to school to study anthropology as a post-grad at the University of Chicago. As he describes it, anthropology influenced his opinion of religion and his own atheism:

After the war, I went to the University of Chicago, where I was pleased to study anthropology, a science that was mostly poetry, that involved almost no math at all.

[. . .] [Anthropology] confirmed my atheism, which was the faith of my fathers anyway. Religions were exhibited and studied as the Rube Goldberg inventions I’d always thought they were. We weren’t allowed to find one culture superior to any other. We caught hell if we mentioned races much. It was highly idealistic.

Those views would influence the depiction of the fictional island dictatorship of San Lorenzo in his Hugo-winning 1963 novel Cat's Cradle. The government of San Lorenzo promotes (by prohibiting) a made-up religion to control its population. 

Apparently a poor student, Vonnegut left the anthropology program without completing his degree.  Luckily one of the University of Chicago's deans was apparently a fan, and got Cat's Cradle accepted in lieu of Vonnegut's rejected thesis in 1971.  

Twenty years [after leaving the University of Chicago], I got a letter from a new dean at Chicago, who had been looking through my dossier. Under the rules of the university, he said, a published work of high quality could be substituted for a dissertation, so I was entitled to an M.A. He had shown Cat’s Cradle to the anthropology department, and they had said it was halfway decent anthropology, so they were mailing me my degree

According to Vonnegut it was a "piece of cake".

Several characters in Cat's Cradle were inspired by the scientists he met while working in the public relations department of General Electric in Schenectady, New York.  Even the idea for the novel's compound "ice-nine", supposedly came from Nobel-prize winning GE scientist Irving Langmuir.   The way Vonnegut tells it, he wasn't even the recipient of that suggestion:

[H.G.] Wells came to Schenectady, and Langmuir was told to be his host. Langmuir thought he might entertain Wells with an idea for a science-fiction story—about a form of ice that was stable at room temperature. Wells was uninterested, or at least never used the idea. And then Wells died, and then, finally, Langmuir died. I thought to myself: “Finders, keepers—the idea is mine.”

Even if Wells had used the idea in a story, I doubt it would have turned out anything like Vonnegut's version.

Read the whole interview for more of Vonnegut's reminiscences and thoughts on writers and writing.

Tomorrow: Ray Bradbury

Science in Science Fiction at Comic-Con

Update: Script PhD has a transcript of the Mad Science panel! Some of the topics of bio-interest include brain scanning, legal issues regarding the children of clones, where they get their science ideas and the role of science advisors.

There's also this quote from Fringe writer Glen Whitman on why they like to base their plots on biology:

Fringe is a horror show, partly. Creepy and gross is easier with biology and virology, than astrophysics, usually.

Update 2: Science Not Fiction has the scoop on the Unlocking Arkham panel.

Update 3: I've embedded video of the Mad Science panel below. There are more recaps linked here.
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For those of you willing to brave the crowds at Comic-Con (and lucky enough to have been able to purchase a ticket before they sold out) you might be interested in the Mad Science: Science of Science Fiction panel on Thursday, from 6pm-7pm:

... explore science as a double-edged sword – it's ethically and morally neutral in and of itself, but science depends on who wields it and how. [. . . It will be ] a lively and fun discussion on science used for good vs. evil."

• The moderator is Phil Plait of Bad Astronomy
  
• Jaime Paglia — co-Executive Producer of Eureka
• Kevin Grazier — Battlestar Galactica and Vituality science advisor. From his bio: "Grazier earned B.S. degrees in Computer Science and Geology from Purdue University, and a B.S. in Physics from Oakland University, as well as M.S. degrees in physics from Purdue and Geophysics and Space Physics from UCLA. He did his Ph.D. in Planetary Physics at UCLA." Grazier currently is a scientist at NASA's Jet Propulsion Laboratory.
  
• Jane Espenson — major scifi writer/producer: Firefly, Dollhouse, Battlestar Galactica, Star Trek: The Next Generation and many other shows
  
• Rob Chiappetta and Glenn Whitman — writers for Fringe
• Ricardo Gil da Costa — cognitive neuroscientist at the Salk Institute for Biological Studies and consultant for Fringe

The panel is co-sponsed by Discover Magazine and the Science and Entertainment Exchange.

Sounds like it should be interesting and entertaining. Maybe someone will post video? Here's the video:



There are a few other events of science in SF interest on the Thursday schedule:

5:30-6:30 The Physics of Hollywood Movies— Join physics instructor Adam Weiner (author of Don't Try This at Home! The Physics of Hollywood Movies) for an interactive presentation employing basic physical principles and a sense of humor in analyzing scenes from favorite Hollywood science fiction, superhero, and action movies, from Iron Man to 2001: A Space Odyssey, and actually learn the physics behind them—both good and bad!

6:30-7:30 The Anthropology of Star Trek – Daryl Frazetti (Department of Anthropology, Lake Tahoe Community College, where he teaches a course by the same name), Ian Morris (UCSB student), John Stivers, Jacob Hurd, and Kanan Miller (Lake Tahoe Community College students) discuss the anthropological themes in the Star Trek universe. Select themes include such topics as politics, religion, identity, technology, the cultural role of the individual, and the anthropological concept of "race." A brief discussion on the subculture of fandom is also included, along with the cultural impact of Trek. Audience participation is encouraged. This presentation spans the franchise and explores the relationship between Star Trek and society throughout the past four decades.

6:30-7:30 Unlocking Arkham: Forensic Psychiatry and Batman's Rogues' Gallery – Arkham Asylum holds some of Gotham City's most disturbed criminals. But do they truly belong there? From the vantage point of a forensic psychiatrist utilizing real-world psychiatric diagnostic criteria, panelists explore the mental disorders of the Dark Knight's Rogues' Gallery, with in-depth analyses of The Joker, Two-Face, Riddler, The Ventriloquist, Mad Hatter, and Mr. Zsasz, among others. Learn as three psychiatrists explain the meaning of such terms as "psychotic," "not guilty by reason of insanity," and "psychopathy." Bring your questions, and join the fun as experts unlock Arkham Asylum and possibly set free some of its "inmates"! Panelists include H. Eric Bender, M.D., University of California, Los Angeles; Praveen Kambam, M.D., University Hospitals/Case Medical Center, Cleveland, Ohio; and Vasilis K. Pozios, M.D., University of Michigan, Ann Arbor.

Tags:science fiction, biology, Comic Con

Ursula Le Guin and Anthropology

There was an interesting profile of Ursula Le Guin in today's LA Times. Le Guin's parents were both prominent anthropologists, and their work has in turn influenced her own.

Le Guin's early years help explain her abiding concern: Is there such a thing as a stable human nature? She grew up in Berkeley, the daughter of Alfred Kroeber, a founder of modern anthropology, and Theodora Kroeber, author of "Ishi in Two Worlds," about an American Indian who had outlived his tribe. Her childhood, which included summers at a family ranch in Napa, was full of reading, storytelling and visits from European intellectuals and Native Americans.

"I was privileged," she says, "to know the kind of people that most American kids, most bourgeois white kids, don't." She was raised "as irreligious as a jack rabbit."

Eric Rabkin, who teaches at the University of Michigan, sees her work as profoundly shaped by her exposure to alien cultures as well as her father's ambition to find as specifically as he could the time and place from which Western civilization had sprung. "There's a kind of romance to that view," Rabkin says. "That once upon a time, the worst antagonisms were merely inter-familial -- that basically we're all alike and trustworthy. And I believe she grew up in a family in which that was considered not a fantasy but a scientific fact."

[Note that I added the links to the excerpt above.]

While most of Le Guin's science fiction would be considered of the "soft" rather than "hard" variety, that doesn't mean that there is no science - or technology - in her work, as she aptly points out in this rant:

How can genuine science fiction of any kind lack technological content? Even if its principal interest isn't in engineering or how machines work — if like most of mine, it's more interested in how minds, societies, and cultures work — still, how can anybody make a story about a future or an alien culture without describing, implicitly or explicitly, its technology?

Nobody can. I can't imagine why they'd want to.

Its technology is how a society copes with physical reality: how people get and keep and cook food, how they clothe themselves, what their power sources are (animal? human? water? wind? electricity? other?) what they build with and what they build, their medicine - and so on and on. Perhaps very ethereal people aren't interested in these mundane, bodily matters, but I'm fascinated by them, and I think most of my readers are too.

Read the whole essay. I can't help but think that her ability to clearly explain how silly it is to limit "technology" to modern shiny gadgets has something to do with the anthropology in Le Guin's background. It's excellent food for thought.

Tags:science fiction, anthropology, Ursula Le Guin

Arthur C. Clarke (1917-2008)

It was reported today that Arthur C. Clarke has died at the age of 90. Clarke wrote many science fiction classics: Childhood's End, Against the Fall of Night, The Fountains of Paradise, Rendezvous with Rama, and, perhaps the story best known even to non-science fiction fans, 2001: A Space Odyssey.

Unlike Clarke's other novels, 2001 was written with the specific purpose of being adapted into a screenplay, starting from his short story, "The Sentinel". Director Stanley Kubrick had significant input into the story, but the novel was not completed before the screenplay, and differs in some details from the movie version. Clarke's account of collaboration was published in 1972 as The Lost Worlds of 2001. He describes the creative process that lead to the scene with the monolith teaching pre-human hominids how to use tools, which was inspired in part by the ideas of anthropologist (and screenwriter) Robert Ardrey. He didn't stop there, though, continuing to consult with both Kubrick and other anthropologists. From Clarke's diary:

October 2. Finished reading Robert Ardery's African Genesis. Came across a striking paragraph which might even provide a title for the movie: "Why did not the human line become extinct in the depths of the Pliocene? . . . we know that but for a gift from the stars, but for the accidental collision of ray and gene, intelligence would have perished on some forgotten African field" True, Ardrey is talking about cosmic-ray mutations, but the phrase "A gift from the stars" is strikingly applicable to our present plot line.
[snip]
November 20. Went to Natural History Museum to see Dr. Harry Shapiro, head of Anthropology, who took a poor view of Ardrey. Then had a session with Stan, arguing about early man's vegetarian versus carnivorous tendencies. Stan wants our visitors to turn Man into a carnivore; I argued that he always was. Back at the Chlesea, phoned Ike Asimov to discuss the biochemistry of turning vegetarians into carnivores.

November 21. Read Leakey's Adam's Ancestors*. Getting rather desperate now, but after six hours' discussion Stan had a rather amusing idea. Our E.T.'s arrive on Earth and teach commando tactics to our pacifistic ancestors so that they can survive and flourish. We had an entertaining time knocking this one around, but I don't think it's viable.

Ultimately, they went with tool use. Originally, the story had an alien named Clindar who came, observed that Earth's hominids had the potential for intelligence, and decided they were worth teaching. That chapter was cut, but was resurrected in The Lost Worlds of 2001:

It was a wonder they had survived, and their future did not look promising. [. . .] But Clindar, with the experience of many worlds behind him, knew that appearances could be deceptive. These unprepossessing near-apes had one great advantage over all he other creatures of their planet. They were still unspecialized; they had not yet become trapped in any evolutionary cul-de-sac. Almost every animal could beat them in some respect - in strength, or speed, or hearing or natural armament. There was no single skill in which the hominids excelled, but they could do everything after a fashion. Where the other animals had become virtuosos, they had specialized in a universal mediocrity - and therein, a million years hence, might lie their salvation. Having failed to adapt themselves to their environment, they might yet one day change it to suit their own desires.

Here's the dawning of tool use as depicted in the movie version of 2001:




The use of tools allowed our distant ancestors to more reliably obtain food and defend themselves, which in turn likely led to an increase in brain size and increased intelligence**. Several million years later, here we are. Clarke makes clear in 2001 that our current state is not the end of evolution. Astronaut David Bowman has an encounter with another monolith, which molds his mind anew. Bowman becomes the Star-Child, returning briefly to Earth to clear the skies of orbiting nuclear weapons before he explores the universe. I like to think that's the direction evolution will take the human race.

R.I.P Arthur C. Clarke

* There's an interesting article at Talk Origins about the inaccuracies in Leakey's human ancestral tree as published in Adam's Ancestors in 1934. The Smithsonian has a more up to date version.

** See, for example Flinn MV, Geary DC, and Ward CV. "Ecological dominance, social competition, and coalitionary arms races: Why humans evolved extraordinary intelligence." Evolution and Human Behavior 26: 10-46 (2005) (pdf)

Tags:Arthur C. Clarke, 2001, evolution, hominids, anthropology

Fairy Biology

This week's Lab Notes column at SciFi.com asks whether the "fair folk" in Guillermo del Toro's movie, Pan's Labyrinth, could actually exist.

Could a humanoid creature have wings? Certainly. Earthbound dinosaurs became pteranodons and birds. Tree squirrels became flying squirrels, and rodents became bats. Insects may have discovered the art of flying on two different evolutionary occasions, and even some species of fish have taken to the air. Biologically speaking, a flying primate is by no means out of the question. Clearly, under the right circumstances almost any animal can evolve the ability, if it's small enough to support its own weight by the flight muscles alone.

Read the whole column for discussion of other fairy traits, including shape shifting and teeny tiny brains.

Tags:fairies, biology

Living Neanderthals

The science blogosphere has been abuzz about the recent papers showing evidence of interbreeding between humans and neanderthals. First, Lahn and colleagues reported in Science that one human variant of microcephalin, thought to be involved in regulating brain growth, appeared to have evolved more than a million years ago, but only appeared in the human population 37,000 years ago (Evans et al. "Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage" Proc Natl Acad Sci (2006)).

The Lahn group concluded that the most likely scenario was interbreeding between prehistoric modern humans and a now extinct hominid that carried haplogroup D--most likely Neandertals. The haplogroup was probably beneficial enough to spread quickly in modern human populations, says Lahn. But he's not sure what advantage it offered. Because most researchers agree that Neandertals were not as cognitively advanced as modern humans, Lahn and his coauthors suggest that the haplogroup might have made Homo sapiens better able to adapt to the Eurasian environments that Neandertals had occupied long before modern newcomers arrived. (ScienceNOW article)

John Hawks has a nifty FAQ about the science. His colleague, Greg Cochran, speculates that Neanderthals may have given the human race a boost:

So when you think about the cultural explosion that occurred shortly after we overwhelmed the Neanderthals (cave paintings, sculptures, new tools and weapons, all that jazz) - well, you have to wonder if assimilating a passel of adaptive alleles in a few thousand years, way more than the typical number that would arise and become established over such a short time span, didn't give us a hell of a boost. There are signs of behavioral modernity a bit earlier in Africa - but those ostrich eggshells are dull as hell compared to Gravettian cave paintings. Expansion out of Africa must itself be a sign of new capabilities (I'd bet on sophisticated language) but you only see full-fledged behavioral modernity in the European Upper Paleolithic... Judging from neutral genes, it can't have happened often, but those few furtive human-Neanderthal couplings may well played a crucial role in the future development of the human race. I'm sure that this notion will suggest new pick-up lines to some readers.

Gene Expression rounds up the blogs discussing the results.

I have to confess, that when I read about interbreeding humans and Neanderthals, the first book that came to mind was Jean Auel's Clan of the Cave Bear. That doesn't really fall into the "science fiction" category, though, so I'll move on.

Neanderthals have made a number of appearances in the science fiction literature, most recently in Robert J. Sawyer's Neanderthal Parallax trilogy: Hominids (winner of the 2003 Hugo for best novel), Humans, and Hybrids. The novels are set on our earth and a parallel earth where Neanderthals became the dominant hominid. If you want more information about his take on Neanderthals, read Sawyer's essays Commiting Trilogy: The Origins of the Neanderthal Parallax and Neanderthals are a Separate Species, and his invented system of Neanderthal timekeeping.

There have also been numerous other science fiction stories with Neanderthal themes, such as:
• Greg Bear had a different take on the relationship between Neanderthals and humans in Darwin's Radio. One of his heroes, scientist Mitch Rafelson, find the frozen remains of a Neanderthal couple and their apparently human infant.
• In Paul Levinson's novel The Silk Code (winner of the 1999 Locus Award for best novel), forensic scientist Phil D'Amato investigates the possibility that a small group of Neanderthals have survived to the present day.
• Short story "Scout's Honor by Terry Bisson (read free online), stars scientist goes back in time to study Neanderthals
• Talk.origins also has a list of Paleoanthropology Fiction.

I'm sure there are others*.

It seems likely that we carry a little bit of the Neanderthal in us. I suspect that the sequencing of the Neanderthal genome will turn up even more "survivors".

* For example, there is a short story in which modern cloning and genetic techniques are used to bring Neanderthals back to life. They subsequently take over the world. Unfortunately, I can't remember the title or the author.

ETA 11/16: I should have waited a few days to post. Nature just published an article from the Pääbo lab analyzing 1 million bases of Neanderthal DNA (Green et al. "Analysis of one million base pairs of Neanderthal DNA" Nature 444:330-336 (2006)). Nature has collected text, video and audio links on the subject. An additional 65,000 bases were published in this week's Science (Noonan et al. Sequencing and Analysis of Neanderthal Genomic DNA Science 314:1113-1118 (2006)). ScienceNOW sums it up:

As expected, the Neandertal and human genomes proved more than 99.5% identical. Rubin's team calculated that the most recent common ancestor of the two human species lived about 700,000 years ago, whereas Green's analysis of 1 million bases found a more recent divergence time, about 465,000 to 569,000 years ago. As to the question of interbreeding, Rubin's group found no sign of it, but Pääbo's group did. "Taken at face value, our data can be explained by gene flow from modern humans into Neandertals," most likely from modern humans fathering children with Neandertal females, says Pääbo.

Afarensis and Gene Expression have more on models of human evolution.

Tags:science fiction, human evolution, Neanderthal