Friday, October 31, 2008

Plants Take Manhattan

The final scene of the 1986 Frank Oz musical version of Little Shop of Horrors ends on a positive note: Audrey survives being chewed by the menacing man-eating plant and Seymour defeats it in a fight. Audrey and Seymour live happily ever after. But that was not the original version.

In the original ending, Audrey is eaten, Seymour loses the battle and the plant takes Manhattan.
A miniature effects team led by Richard Conway went to great lengths to create this dramatic finale during which Audrey II takes over New York City, attacks the Brooklyn Bridge, fights the U.S. Army, climbs the Statue of Liberty and, in homage to the 1933 classic monster movie King Kong, scales the Empire State Building. There are also various nods to the 1953 film The War of the Worlds. Finally, in the last shot after the title "THE END?!?" has appeared, the plant crashes through the screen of the film and laughs as the camera (the audience) comes closer and closer to its gaping maw. The sequence cost $5 million to produce.
Audiences apparently found that too disturbing. But now, thanks to the magic of YouTube, you can watch the ending as it was meant to be:




Happy Halloween!

(via Slice of SciFi)

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Thursday, October 30, 2008

Scary Stories for Halloween

All Hallow's Eve is almost upon us, and so it's the perfect time to snuggle up with your iPod (or computer) and listen to a scary story.

The Pseudopod horror podcast is a great place to start. They've had several recent episodes that feature horror with a biological bent:
You can listen to all of Scot Sigler's novel Infected. The premise via Amazon.com:
In Sigler's riveting horror thriller, alien seeds from outer space infect a number of unlucky humans, who develop some unusual symptoms—itchy, blue triangular growths on their skin—that eventually result in the carriers becoming screaming, homicidal maniacs.
Head to Scott Siglers site for more podcasts, including Nocternal and The Crypt.

Slice of SciFi points out that today is the 70th anniversary of the radio broadcast of "War of the Worlds". You can listen (or download the MP3) to the original show at The Mercury Theatre on the Air.

And if you want a bit more science, Nate at AboutSF was on the Walt Bodine show at KCUR radio this morning talking about supernatural fiction and the psychology of fear. Listen to the Walt Bodine show podcast.

Top Image: Find out how to make your own biohazard suit costume at Instructables.
Bottom Image:

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Tuesday, October 28, 2008

Gene Genies Worldwide

I was doing some sorting of old files, and I ran across a brochure for "Gene Genies Worldwide" my husband picked up about seven years ago on a trip to Pasadena. From what he remembers, there was a storefront with a large window. Inside there was a clean lab-like setup with Erlenmeyer flasks filled with colored liquid on the shelves*. It was late evening, so it was closed, but there were brochures outside the door. The text has an odd description of the Gene Genie Worldwide business, and he wasn't sure if it was strange, but serious, new-age woo or an art installation. You can see for yourself if you click the images below:



The founders, "internationally renown biodesigners" Karl Mihail and Tran T. Kim-Trang, offer a special service for people who want to change their personality:
Gene Geneies Worldwide's Dream Tools are the new genetic reality and, for our clients, the greatest shopping experience of all time. Finally, the best Personality that medical science can produce!

Our most prized line of Dream Tools are the Transgenic traits. For the first time in history we are no longer bound at the organism or species level. Now at the genetic level, manipulations can extend to cross-fertilization of species which are incapable of mating in the natural world. Imagine acquiring the personality traits of your favorite creatures in the animal kingdom (i.e. the cunning of a fox or feline intuition). Human to human and animal to human transgenic augmentations are our specialty. Gene Genes Worldwide has secured sole patents for our gene pool and hybrid genetic codes to ensure against biopiracy.
Who wouldn't want badger fierceness, canine loyalty, reptilian cool, otter playfulness, or internal firefly glow? Unfortunately, all but the firefly glow aren't likely to be easily transferred genetic traits. Most of the behaviors they list are pretty vague - are reptiles really "cool", or just lethargic when the temperature drops? That's not to say that our genes don't influence our behavior. There is, in fact, an ongoing project that uses purebred dogs to understand the behavioral genetics of behavioral issues such anxiety disorders and aggression. I suspect that "loyalty" is a bit harder to quantitate.

So what exactly is Gene Genies Worldwide? There's the old Gene Genies website, but it doesn't say much more than the brochure. A little Googling on the names of the "biodesigners", however, turns up page from the November 2002 LA Freewaves festival that provides the background for the project, which is indeed an art installation:
Gene Genies Worldwide?? is a collaboration between Tran, T. Kim-Trang and Karl Mihail. We are artists posing as scientists who aspire to be artists. As Gene Genies Worldwide?? we create work that addresses the conjunction of genetic engineering and consumer culture to provide a critical evaluation of biotechnology while serving to raise consciousness, foster civic dialogue on accountability, and ownership concerns. The project is a catalyst for action by imagining a possible future and challenging viewers to question that future.
The project made Tran and Mihail runners-up for the 2001 Leonardo New Horizons Awards. The award site gives a bit more background about the installation:
Tran T. Kim-Trang and Karl Mihail's public art installation Gene Genies Worldwide (1998) [...] created a seductive retail space for a fictitious company offering to custom design clients' genetic codes. Behind an immaculate red brick facade, Plexiglas display cases presented the various bio-related components of the installation with formality and great attention to aesthetics. One pristine display case contained a row of literary classics updated by the artists ("Eugenic America"; "Genetic Scarlet Letter"); a single text lay open to reveal grinning images of artists/providers peering into microscopes. [... ] Elsewhere, human and animal skulls were grouped against a satin backdrop --- and a mini DNA strand, a model of molecules, and a row of pristine test tubes completed the depiction of science as art and retail. The presentation, presided over by life-size images of the two scientist/artists, was an ironic evocation of a viable future scenario that raises provocative ethical, economic, and social issues.
They also claim to have been technical consultants for a number of movies featuring genetics and genetic engineering, including Race for the Double Helix, The Boys From Brazil, Jurassic Park, Gattaca, and The X-Files. Given the often silly ways that genetic engineering is portrayed by Hollywood, it wouldn't surprise me if that bit were true.

ETA: Gene Genies Worldwide doesn't have anything to do with the Gene Genie genetics blog carnival, despite the similar logos.

* He's actually not sure if he's accurately remembering the way it looked, but colored liquid in flasks sounds plausible.

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Saturday, October 25, 2008

Biology in Science Fiction Roundup: October 25 Edition

A few collected links from the past couple of weeks:

On Biology as "Hard" Science

Fantasy & Science Fiction interviewed women science fiction writers, and Nancy Kress commented:
From a personal standpoint, the only time I have felt gender discrimination in SF has been in sometimes not being taken seriously as a "hard SF writer," partly because I write about biology rather than astronomy or physics, but also perhaps because I'm female. However, I think even that prejudice has lessened over the years.
Henry Gee writes about the "hardness" of biology:
I can’t help thinking that there is an implied value judgement here, stemming from the invasion of traditional biology by physicists that resulted in the birth of molecular biology in the 1950s. The result was a kind of replacement theology in which molecular biology was seen as an exact science (in other words, ‘hard’) whereas traditional biological pastimes were seen as so much vague stamp collecting (that is, ‘soft’).

Such prejudice carries on to the present day. It is the ‘hard’ biology, big on expensive laboratories and machines that go ping, that gets the funding and the grants, whereas ‘soft’ biology is usually seen as dispensible, and because it is much cheaper, it is thought that it can probably survive on nothing at all, and even then, it wouldn’t matter if it disappeared entirely — except, of course, when some big anniversary comes around, and biologists, hard or soft, come out and celebrate the legacy of Mr Darwin. But he’s a historical figure, and poses no threat.
Written Word

Mike Brotherton has a simple formula for putting more science in your science fiction: scan the science news to find a report that piques your interest, consider what the new technology or findings might mean in terms of unintended consequences or who might get hurt or marginalized, and remember:
SCIENCE IS FREAKING AWESOME! We figure out the coolest shit with science. If you’ve picked an article or topic that fascinates you, get that fascination into your story! If it’s about the methodology, focus there. Or the technology, or the potential, or the insight, or the dedication. Whatever you think is the coolest thing, that should be your focus.
Jennifer Rohn describes concerns about including technical details when writing "science in fiction" novels:
Interestingly, non-scientists are not as concerned as you might expect about “understanding” the science. For them, the experience of hearing about science – including the lingo – is part of the atmosphere, and is absolutely fine as long as they can follow the human story. Think of Scotty on the original Star Trek, babbling on about “plasma reflux in the warp core interfering with the delta configuration of the dilithium crystals”: we never needed to know what that meant: all we needed to know was that the ship was in danger and that Kirk had only ten hours to fix it. It is part of the setting, the scene, the milieu. Provided it’s made clear that this detailed content is not required for understanding the characters’ motivations and actions, it’s actually irrelevant whether they get it completely.
The Harry Potter's World: Renaissance Science, Magic and Medicine exhibit at the National Library of Medicine that explores the Renaissance science and medicine that inspired the magic in the novels. They also have an older online exhibition "Do Mandrakes Really Scream: Magic and Medicine in Harry Potter" (via bioephemera)

Television

LiveScience talks to to Rob Chiappetta and Glen Whitman the "science guys" behind Fringe. As JP at SF Signal put it:
I guess it shouldn't come as a shock that the science consultants don't have backgrounds in science. In fact, they're doing what anyone with a computer, a reasonable internet connection and a healthy sense of curiosity could do. But they get paid for doing it. The bastages!
Not coincidentally, there's a mini-industry in writing articles about how awful the science on Fringe is.

At Popular Mechanics: Scientists Debunk Personal Electromagnetic Fields on Fringe: Sci-Fi Fact vs. Fiction.

At SF Scope: Stupid Science - a review of Fringe's "The Cure"

At Popular Mechanics: On Fringe, Radioactivity is Real, But Cures are Junk Science

At the Discover Science Not Fiction blog: Eleventh Hour: Advanced Pest control and the troble with GMOs

Movies

Phil For Humanity has a bit of a rant about "How Science Fiction Misrepresents Cloning" (via SF Signal)

io9 has some cool artwork of alien parasites that are apparently part of an as-yet-unnamed independent horror film.

At io9 Charlie Jane Anders gave a mixed review of the movie version of Blindness: "Blindness' Dystopian Fable Becomes An Overwrought Movie"

Cool Bioscience

The Imagine Science Film Festival in New York included the short "A Fruit Fly in New York":
... a 12-minute flight over New York City, the laboratory and the history of fruit fly research. Beyond the informational content, the film also explores the personal rapport that a scientist may have with his model organism as a painter may have with his canvas. Through the microscope lens, the fruit fly appears human-like – a monstrously beautiful animal that has sacrificed itself in the pursuit of science.
National Geographic reports on a "bio-computer" created from "snippets of engineered RNA assembled inside a yeast cell." There's a slightly more technical post on the research at io9.

Scientists directly wired single neurons in the brain of monkeys to wrist muscles. The monkeys were able to teach themselves to use those new connections to move those muscles. The Knight Science Journalism Tracker rounds up the news reports.

Discover Magazine looks at the latest experiments "melding humans and machines" to create real-life cyborgs.

A study published last year compared the sequence of FOXP2, the so-called "language gene", in modern humans (us!) and Neanderthals, and found that we carry the same version. Greg Laden dug behind the hyperbole in the media to explain what that may actually mean for the possibility of Neandertal language.

It's 19th-century meets 21st-century in Second Life, where the University of Cincinnati is recreating the Galapagos islands and making it possible to retrace Darwin's voyage aboardthe Beagle.

In 1953 Stanley Miller showed that zapping a flask filled with simple chemicals thought to represent Earth's atomosphere billions of years ago- water, methane, hydrogen, ammonia - created amino acids, crucial components of life as we know it. Recently original samples from Miller's experiments were discovered and reanalyzed using more sensitive equipment than Miller had access to. It turns out that Miller ran the experiment using different conditions that are now thought to be closer to the conditions on early Earth, but condered the results "a dud". The new analysis turned up 22 amino acids, 10 of which had never been found before in similar experiments. Read the details in Wired and at NASA.gov. And for some background on the subject, check out this talk by Professor Jeffrey Bada on "Prebiotic Synthesis in Planetary Atmospheres."

Finally, it turns out that clever data diggers can figure out censored DNA sequences in publically posted human genomes.

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Friday, October 24, 2008

Is the Evolution in Spore at all Realistic? Biologists Say 'No'

Imagine you could design your own primitive creature, then watch it change as it produces generation after generation of offspring. Eventually your creation becomes a spacefaring race and heads for the stars. That's pretty much the premise of the game Spore: you create a creature that "evolves" and interact with other players' creations. It's a pretty nifty-sounding idea, but does the game play have any resemblance to actual evolution? Spore creator Will Wright - and National Geographic - would certainly like you to think so.

But what do actual biologists think? John Bohannon "The Gonzo Scientist" played Spore with a team of scientists and reported on their experience in Science. Two evolutionary biologists - T. Ryan Gregory of the University of Guelph and Niles Eldredge of the American Museum of Natural History - rated the "Cell" and "Creature" stages of the game. The "Cell" stage fared OK science-wise, but the "Creature" stage got a poor review:
"The problem is that the game features virtually none of the key ingredients of evolution as we understand it," says Gregory. "There's no shared common descent between species, since every single creature in Spore can trace its lineage back to a different single-celled organism that arrives from space." Spore also lacks biological variation. "When you run into other members of your species, they are always identical clones of you." Nor does it have natural selection. "There are no consequences for dying, since you just reappear at your nest." Your organism does evolve, says Gregory, "in the sense that it changes over time, but it really has no bearing on how things evolve in the real world."
[. . . ]
You might think that Spore's fatal flaw would be that it supports intelligent design rather than Darwinian evolution. (That's what I initially thought.) But it turns out to be not even that interesting. "Spore is essentially a very impressive, entertaining, and elaborate Mr. Potato Head that uses the language of evolution but none of the major principles," conclude Gregory and Eldredge.
Bohannon has created a page at the Spaceguild Wiki that gives a more detailed report card of Spore's science. If it were a college student, it would have flunked out long ago:
Organismic biology: D-
  • Cell biology: D
  • Genetics: F
  • Development and reproduction: D
Evolutionary processes: F
  • Evolution as fact: B
  • Mutation and variation: F
  • Natural selection: F
  • Sexual selection: F
  • Genetic drift: F
  • Historical contingency: D
  • Constraints: D
  • Evolutionary history: D
So overall pretty awful. Gregory and Eldredge also contributed a detailed explanation of why they gave Spore such poor grades for its depiction of evolution.

You may be asking yourself, why does this matter? It's only a game, right? I actually don't think it would matter much at all, if it weren't being marketed as educational.
The game's makers are clearly aiming for the highly lucrative family and education markets. "Since the game's release we've received a lot of interest from various schools and universities around the world," a Spore spokesperson wrote me in an e-mail. "So that's a good sign that there's a lot of interest in [the] academic/education community."
I would hope that any adult that bought Spore with an eye to education would use it as a way to initiate discussion of the actual science of evolution, but I suspect that that doesn't happen very often. Instead parents will buy the game and just hand it to their kids, assuming it has some educational value. And while it may keep kids entertained, they won't end up knowing any more about biology than they did before they started. Hopefully the inaccurate use of biology terms and concepts within the game won't end up confusing them when they do learn about real science.

(via The Loom)

Image: Punky Quillibra, the creature created by evolutionary biologists T. Ryan Gregory and Niles Eldredge. They were able to change every component of Punky's body in a single generation, a game feature that is totally unlike evolution.

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Thursday, October 23, 2008

Erasing Memory

"What is your name?"

[...] Norman Kent's name leaped into his mind, in response to the question - and vanished.

It was not simply the name itself tha t vanished. with it went eh associations and mnemonics keyed to it in his memory. Jokes from childhood about Superman, jokes from adolescence about the Norman Conquest, jokes from he jungle about the Norman DeINvastion. An old Simon Templar novel he had read many eyars ago, and remembered all his life because it featured a hero named Nroaml Kent, who laid down his life for his friends. Certain times when the speaking of his name had been a memorable event. The sight of his dogtags. The nameplate on the desk in his office at the University. His face in the mirror.

If you take a hologram of the word "love" and try to read a page of print through it, you will see only a blur. But if the word "love" is printed anywhere on that page, in any typeface, you will see a very bright light at that spot on the page. In much the same way, one of the finest computers in the world riffled through the "pages" of Norman Kent's memory, scanning holographs with a reference standard consisting of the sound of his name. Each one that responded strongly was taken from him.

All this took place at computer speed. Without perceptible hesitation the man on the table answered honestly and happily, a puppy fetching a stick. "I don't know."
~ Mindkiller, Spider Robinson
The ability to erase specific memories is an old one in science fiction. While not the first to use it as a plot device, Robinson's 1982 novel Mindkiller goes into detail about how the erasure of something as simple as a name from the mind requires the removal of many different associated memories. And unlike the characters in Eternal Sunshine Of The Spotless Mind, the man who is given the treatment is well-aware of the holes in his memory.

In this week's issue of Neuron, scientists at the Shanghai Institute of Brain Functional Genomics and the Brain and Behavior Discovery Institute at the Medical College of Georgia in Augusta reported the first step in developing such technology: they successfully erased specific fearful memories in mice while those memories were being retreived. The specific method the neuroscientists used won't be easily transferred to humans because it involved specially constructed transgenic mice that allow induction ofexpression of high levels of an enzyme involved in the memory process (CaMKII) while the memory to be erased was being recalled. Even so, the study's principal investigator, Joe Z. Tsien, has speculated about the method's usefulness to treat people suffering from traumatic memories:
"While memories are great teachers and obviously crucial for survival and adaptation, selectively removing incapacitating memories, such as traumatic war memories or an unwanted fear, could help many people live better lives," Tsien said.
It's not clear, however, whether even selective removal of such memories would leave the patient with the feeling that some important part of them was missing.

Original article: Cao X, et al. "Inducible and Selective Erasure of memories in the Mouse Brain via Chemical-Genetic Manipulation" Neuron 60(2): 353-366 (2008) doi:10.1016/j.neuron.2008.08.027

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Tuesday, October 21, 2008

The Global Genome and Biotech in Pop Culture

Eugene Thacker is a Associate Professor in the School of Literature at Georgia Tech whose studies touch on philosophy, science fiction, and horror, with an emphasis on the expanding role of biotechnology. In 2006 Thacker was interviewed by Roy Christopher about his book The Global Genome: Biotechnology, Politics, and Culture, which looks at biotechnology as a global phenomenon. Thacker expanded a bit on biotechology in pop culture:
It’s pretty obvious, if one looks around, that the life sciences and biotechnology have pervaded popular culture. A great way of demonstrating this is to look at all of the re-makes of Cold War-era science fiction and comics: Spider-Man, Hulk, X-Men, Fantastic Four, etc. It seems to now be a requirement to somehow put genetics in the stories, even if it really doesn’t make any sense (which is often). I’m less interested in what the director ‘intended’ to mean by this than what it means culturally that genetics, biotech, and even nanotech are always found in SF. One thing it means is that these sciences and technologies are normalized in a way that the general public going to a film will ‘accept’ their inclusion as a matter of course. Certainly there are always SF-geeks who dispute the technical accuracy of how the genetic mutation actually creates the superhero or villain, but on a general level these technosciences have become a part of a certain cultural imaginary. So the question is ‘what conditions had to be in place such that these particular technosciences could become normalized as a part of a certain world-view?’ Perhaps this process is somewhat parallel to the normalization of medicine and public health practices themselves.

So I think that popular culture is relevant, not because I believe that films should educate and moralize, but because there is actually a great deal of ambivalence in pop culture’s treatment of technoscience. We can’t live without it, and yet it seems to be our downfall. The movies that moralize about the ineradicable human spirit do so using the most advanced computer graphics and special effects. There’s also a sense in many of these films, books, and comics, that we as a culture are not quite sure what to do with all of this information and all these gadgets. It’s almost as if the greatest challenge posed to SF now is finding something interesting to do with all the technology that exists.
I think Thacker makes an interesting point that genetics has been "normalized" in pop culture, even though the science isn't usually accurately portrayed. I wonder if that (inaccurate) familiarity with biological concepts is actually a detriment to the public understanding of science. Is learning about real biology like unlearning a bad habit to the general public? I hope not.

Other publications by Eugene Thacker:
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Monday, October 20, 2008

Jules Verne Adventures Film Festival

This coming weekend is the Jules Verne Festival at The Edison and ImaginAsian in downtown Los Angeles, with a full program of adventure and science fiction movies. They will also be presenting two awards: the Jules Verne Nature Award to Roy E. Disney, with a special screening of Steamboat Willie, Fantasia 2000, and the new movie Morning Light; and the Jules Verne Achievement Award to Ron Moore with a tribute to Battlestar Galactica featuring special guest Edward James Olmos.

The biology connection? The closing event on Sunday, October 26, is "Planet of the Apes, 40-year Evolution". The movie will be introduced by Linda Harrison, who played Nova in the 1968 version of the movie.

At $10 for an all-day movie pass, it's a steal.

(via Hero Complex)

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Friday, October 17, 2008

Big Giant Heads

talosians
She studied him for a long moment. He was twice her size, with an enormous head. Yet his ears were small and his nose was stubby, like an afterthought. "Yes, they were more our size. Their heads were human and –"
"Ur-human," the man corrected absently, as though he was distracted.
"What?"
"Oh, I am sorry, We term your kind Ur-human, since you are the earliest form available."
Her mouth whitened. "And what do you call yourselves?"
"Ah, humans," he said uncomfortably.
~ Beyond the Fall of Night, Arthur C. Clarke and Gregory Benford.
Before transhumanism became all the fashion, science fictional depictions of far future often gave our human descendants fantastic mental powers along with giant brains. But there is a serious problem with that idea: human brain size at birth is limited by the size of the opening in the pelvis, and those far future women never seem to have extra-wide hips to go along with their giant heads. A solution, of course, is assume that human birth will ultimately require medical technology. And it appears possible that even technology we use today might allow humans to start heading down that evolutionary path.

At The Panda's Thumb PZ Myers looks at the suggestion that the wide availability of relatively safe Cesarean sections in developed countries allows the evolution of bigger-headed humans.
Babies have very big heads that squeeze with only great difficulty through a relatively narrow pelvis, so the relationship in size between head diameter and the diameter of the pelvic opening has been a limitation on human evolution. We know this had to be a factor in our evolution: the average newborn mammal has a cranial capacity that is roughly 50% of the adult size, chimpanzee babies have heads about 40% of the adult size, but human babies have crania that are only 23% of what they will be in adults. While our brains have gotten larger over evolutionary time, they have not gotten proportionally larger in utero, because large-headed babies increase the difficulty of labor and cause increased mortality in childbirth. If childbirth could bypass the pelvic bottleneck, that would allow for fetal heads to grow larger without increasing the risk of killing mother and/or child.
There is some circumstantial evidence that bigger babies are being born in the US, and that the increased size has a genetic component. That's certainly not proof that humans are evolving along those lines, but it does make the idea plausible.

But is bigger necessarily smarter? Given a similar genetic background larger brain size doesn't seem to improve cognitive abilities. It's the connections between neurons that have the greatest effect on brain function. A recent review of human brain evolution described some of the other potential problems of increasing brain size.
For one thing, a big brain is a metabolic drain on our bodies. Indeed, some people argue that, because the brain is one of the most metabolically expensive tissues in our body, our brains could only have expanded in response to an improved diet. Another cost that goes along with a big brain is the need to reorganise its wiring. “As brain size increases, several problems are created”, explains systems neurobiologist Jon Kaas (Vanderbilt University, Nashville, Tennessee, United States). “The most serious is the increased time it takes to get information from one place to another.” One solution is to make the axons of the neurons bigger but this increases brain size again and the problem escalates. Another solution is to do things locally: only connect those parts of the brain that have to be connected, and avoid the need for communication between hemispheres by making different sides of the brain do different things. A big brain can also be made more efficient by organising it into more subdivisions, “rather like splitting a company into departments”, says Kaas. Overall, he concludes, because a bigger brain per se would not work, brain reorganisation and size increase probably occurred in parallel during human brain evolution. The end result is that the human brain is not just a scaled-up version of a mammal brain or even of an ape brain.
So our brains may get bigger, but they won't necessarily get better. And while both brain size and intelligence are both influenced by genetics, we haven't yet found any genes that affect both characteristics. For example, two genes that affect brain size, ASPM and Microcephalin, appear to have been evolving adaptively in modern human populations, there is no consistent correlation between the different genetic variants and IQ. But there is a correlation between specific variants of those genes and populations that use tonal languages, so perhaps their effect on brain function is more subtle than development of intelligence.

So will humans evolve Talosian-like giant brains? There is no way for us to know. What we can say is that elimination of the requirement for that babies' heads pass through the pelvis makes that development more plausible. And even if humanity does become big-headed, we may not end up any smarter - and almost certainly not psychic.

There is more discussion at Pharyngula.

Related Articles:
Bradbury J. "Molecular Insights into Human Brain Evolution" PLoS Biol 3(3):350 (2005)
doi:10.1371/journal.pbio.0030050

Mekel-Bobrov N. et al. "The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence." Hum. Mol. Genet. 16(6): 600-608 (2007)
doi:10.1093/hmg/ddl487

Schoenemann PT et al. "Brain size does not predict general cognitive ability within families." PNAS 97(9):4932-4937 (2000)

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Thursday, October 16, 2008

Eleventh Hour Facts


I should start out by saying that I haven't actually seen an episode of the new CBS version of the Eleventh Hour yet. Our household has been watching Life on Mars, and I haven't felt compelled to watch a second hour of (recorded) drama. Fortunately, they are available for viewing online if I do feel the urge to watch.

The premise of the show isn't too different from Fox's Fringe, at least superficially. An attractive blond female FBI agent, Rachel Young, is the handler for "brilliant biophysicist" Dr. Jacob Hood. The two of them investigate science-related crimes across the country. The primary difference, as far as I can tell, is that instead of Fringe's almost-paranormal fringe science, Eleventh Hour plays the science straight. See, for example, this SciFi.com interview with the series' stars where they emphasize the "reality" of the science on the show.

But do they really use good science? It seems not so much. In Annalee Newitz's review of the first episode, she goes into great detail how Eleventh Hour actually goes out of it's way to make the scientists seem sleazy and evil. That episode apparently involves a rogue gang of human-cloning scientists that impregnate down-on-their-luck women and throw away malformed fetuses by chucking them out of a moving car. Dr. Hood then potificates and solves the crime. Now this just sounds bad:
5. The main thing scientists bring to the table are poignant aphorisms.
We never see Hood actually geek out about anything, or go into a lab. Instead, he just says sciencey things like "In science a negative result is just as valuable as a positive one," or "DNA is like a personal barcode."
He also explains cloning - badly - with a bunch of grapes. Maybe episode 2 was better, but I suspect that "all scientists except our tame one are evil" is one of the major themes of the show.

For completely different view of episode 1, see Stephen Cass's review at Science not Fiction. He thought the show "stuck close to today's science". And he thought the grape-cloning bit was a "lucid and accurate explanation of the cloning process". I'm not sure he and Annalee were actually watching the same program.

The Biotechnology Industry Organization (BIO) clearly believes the science was bad - or at least poorly explained - and has decided to fight the misinformation with its own web site, Eleventh Hour Facts. Actually, to be fair, they don't say that they are trying to correct the record. Instead they frame the site as simply providing additional information.
Like the intriguing characters on Eleventh Hour, biotechnology works to solve crises. Our researchers work to unlock the power of nature to produce breakthrough solutions to some of the world’s most persistent challenges. However, because this show is a dramatic interpretation of the power of biotechnology, we encourage you to return here to see how the actual science works. Eleventh Hour can take creative license with these intriguing processes to ensure that the dilemma is solved in 60 minutes, but our scientists are working every day to improve quality of life for all of us.
It looks like it's going to be used to explain the positive side of biotechnology as it relates to each episode. For the first episode they have posts about reproductive cloning, and this video interview with Michael Werner of the Coalition for the Advancement of Medical Research.


The Eleventh Hour web site has it's own meager science section with links to news articles and YouTube videos (scroll down for the links).

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Tuesday, October 14, 2008

Visualizing the Embryo

The elephantine embryo loomed before him above the holostage, its triangular head folder over with two round bulging eyes. "This is the first month, a critical stage for Eyeless," Onyx explained. "As you can see, the eyes are normal with this allele."

She stepped onto the holostage. The "skin" of the embryonic form puckered as her arms entered, and she stepped inside. Her hand rested lightly beneath he pulsating bulge of the heart tube, which had yet to develop separate chambers. She reached up into the head between the eyeballs, cupping them in her hands. "You can see the lens and cornea tissues are shaping up. Come on in," she urged.

~ Daughter of Elysium, Joan Slonczewski
For me, one of the most difficult aspects of embryology is envisioning the complex movement of cells in three dimensions. Sure, you can watch an embryo develop under the microscope - at least those that can fully develop in a petri dish like frog and fish embryos - but it is nearly impossible to follow the paths of individual cells. Now scientists at the European Molecular Biology Laboratory (EMBL) have created a tool that does just that.

New microscope technology has been used to track every cell of a zebrafish embryo for the first 24 hours of life, from one cell to 20,000 cells. You can download movies constructed from their image data (I used MPlayer to view them). The videos are gorgeous, but they are more than simply pretty to look at. According to the article published in Science, the images have provided new insights into the embryonic development of the heart and other organs.

Is this the interactive 3D model of science fiction? The press release claims that they have created the equivalent of "Google Earth" for embryonic development. That may be true if you have the Matlab software to visualize the original data, but the videos don't even meet that level of interactivity. I would love for the data to be integrated into a real Google Earth-like tool, which could be used to easily zoom in on and rotate the embryo, and which could run on any personal computer. I don't see why that couldn't be available in the near future. For the time being, though, I'm happy watching the movies.

(If you are having trouble seeing the movies, or find they are too large to download, PZ Myers has created a lower-resolution YouTube version.)

Article: P.J.Keller, A.D. Schmidt, J.Wittbrodt, E.H.K. Stelzer. Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy, ScienceExpress, 9 October 2008

Image: Still images from the digital zebrafish embryo [left halves, colors encode movement directions of cells] compared to microscopy data [right halves] at different time points in development.

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Saturday, October 11, 2008

Biology in Science Fiction Roundup: October 11 Edition

Once again it's time to clean out my accumulated links:

Written Word

Suvudu takes a look at another frequently banned book: Flowers for Algernon.

The Guardian Books blog asks whether science fiction really needs to be so glooomy:
The world needs warnings from its future, and science fiction has been there to provide them. But there are no end of reasons to have hope for tomorrow. Biotechnology and genetic research offer fantastic advances in medicine, yet their portrayal in science fiction is typified by the gloom of Margaret Atwood's Oryx and Crake. [...] To look at the infinite possibilities of the future and see only darkness is a failure of imagination.
Rudy Rucker talks about sex and science fiction.

Movies

Warner Bros. plans a prequel to I Am Legend. Will Smith will reprise his role as a virologist who is one of the few survivors of a plague caused by a mutant engineered virus.

Jeff Carlson's thriller Plague Year will be made into a feature film

io9 reports that there will be a significant difference between the comic book version of Y The Last Man and the movie adaptation of the story.
First of all, we are going to lose all the interesting subplots about how the political regimes of the world reconstitute themselves in the wake of losing every single creature with a Y chromosome. We'll get very few chances to learn about the Israeli military, the Amazonian terrorists, the Japanese all-girl Yakuza, the women's prison-turned-farm-coop, and the female scientists working to make it possible to rebuild the world out of the DNA they've got left. In other words: A comic book about a world entirely filled with women is going to turn into a movie about a dude.
Is it possible that a movie with a single male character will end up failing the Bechdel Test?

Television

Jennifer Oullette at Cocktail Party Physics took a look at the science-based shows appearing on prime time

At The Bones Blog Vanessa Uy looks at the Anthropology of Star Trek (via SF Signal)

AMC has announced that it will be adapting Kim Stanley Robinson's Red Mars. It's not clear if it will be a movie or mini-series. I hope the latter.

Web Series

io9 has an interview with Joshua Fialkov about his web series LG15:The Resistance, an unlikely spin-off to lonelygirl15.

io9: LG15: The Resistance is, oh, roughly a million miles away from what people think of when they think of lonelygirl15, in part because the mainstream hype for that really peaked before the series' revelation of a wider, more SF and fantasy-based mythology. Is it a problem when you explain to people that this series isn't really just a girl sitting in front of her webcam at home, talking about her life, but instead all about secret societies and genetically superior beings?

Joshua Fialkov: Yeah, I definitely think there's a huge audience out there that would love the show if they just knew what it really was.

Theatre

Watch video of The Fly:The Opera at io9

Cool Science

The Times reports that geneticist Steve Jones says that "human evolution is over". His claims have been refuted in so many places that there is nothing for me to add. Read more: John Hawks, Gene Expression, Evolving Thoughts, discussion at Sandwalk.

io9's biogeek looks at whether human evolution will result in beings of pure energy (sadly, no)

Carl Zimmer writes about the latest research on genes and intelligence (so far not much progress). He also has an an article in Conservation Magazine about "The Most Popular Life Style on Earth" - parasitism!

Kevin Kelly discusses why he doesn't think the singularity will happen, at least not in the way Kurzweil has described it: thinking, even really fast thinking by an AI, isn't sufficient to solve our problems. The assumption that it is sufficient he terms "thinkism". (via Futurismic)
Let's take curing cancer or prolonging longevity. These are problems that thinking along cannot solve. No amount of thinkism will discover how the cell ages, or how telomeres fall off. No intelligence, no matter how super duper, can figure out how human body works simply by reading all the known scientific literature in the world and then contemplating it. No super AI can simply think about all the current and past nuclear fission experiments and then come up with working nuclear fusion in a day. Between not knowing how things work and knowing how they work is a lot more than thinkism. There are tons of experiments in the real world which yields tons and tons of data that will be required to form the correct working hypothesis. Thinking about the potential data will not yield the correct data. Thinking is only part of science; maybe even a small part. We don't have enough proper data to come close to solving the death problem. And in the case of living organisms, most of these experiments take calendar time. They take years, or months, or at least days, to get results. Thinkism may be instant for a super AI, but experimental results are not instant.
We are still finding alien creatures that exist right here on Earth. An example of this is the newly characterized Desuforudis audaxviator, which lives deep in a gold mine nearly 3 kilometers beneath the surface of the Earth. There is no light, little air and an ambient temperature of 160°C (140°F). It lives on the hydrogen and sulfate produced by the radioactive decay of uranium.
"One question that has arisen when considering the capacity of other planets to support life is whether organisms can exist independently, without access even to the sun," says Chivian. "The answer is yes, and here's the proof. It's sort of philosophically exciting to know that everything necessary for life can be packed into a single genome."
Nina Munteanu looks at growing fuel from algae.

Genetic Future reports that a new company, Complete Genomics, has promised to provide whole-genome sequencing for only $5000 by the middle of next year. The perfect Christmas gift?

In what is a grossly misleadingly-headlined post, SciFi Scanner says "Scientists say our eyes evolved to see through objects". Um, no, our binocular vision allows us to integrate information from both eyes, so if our right eye can see behind the right side of an object and our left eye can see behind the left side of an object, our brain can piece together that information into an image of what is "behind" the object.

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Friday, October 10, 2008

Voyage of the Space Beagle

Macmillan has reissued A.E. van Vogt's 1950 space opera, The Voyage of the Space Beagle. Now readers of this blog almost certainly understand the reference in the title. Apparently, that's not common knowledge, however, since in a review of the book for the August 2008 issue of Interzone David Mathew commented:
“The very title…is falsely cute, especially if it brings to mind a scampering puppy…”
Obviously Mathew isn't up on his biology history!

It's particularly surprising given that Interzone is a British publication. I thought the HMS Beagle Project had been given a fair amount of publicity there.

(via Making Light)

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The Creatures We Don't See

This week Vandana Singh has been guest posting some fantastic essays about India and fiction over at Jeff Vandermeer's Ecstatic Days. Today she writes about growing up surrounded by animals. Not pets, but urban wildlife: birds and insects and snakes and pariah dogs.
So it was surprising and disappointing to me, as I grew up (and still is) that these 99.9999…% of Earthlings didn’t figure much in our modern-day consciousness, from economic policy and city-planning to literature. As far as literature was concerned, if I wanted to read about non-human living things, I would have to look for them in a special section of the bookstore.[...]

I have come across this oddly blinkered view in other circumstances. For instance in almost every TV science fiction show I’ve seen, the ship that travels across space is a sterile, hospital-like environment where you rarely see a plant or animal. Even the living ship Moya in the show Farscape is strangely devoid (as far as I can tell) of other denizens living symbiotically within her. Yet we know that each living organism is an ecosystem — as attested by anyone who’s suffered a disturbance in the balance of their intestinal flora due to sickness or antibiotics. (Part of it is that we have this modern icky attitude toward germs, as though all germs are “the enemy” and health is a state of being germ-free — tell that to the mitochondrion). For a ship that goes on long, interstellar journeys, it makes sense to create an ecosystem inside it, to assure oxygen and a fresh food supply, among other things. The one book I’ve read where this is beautifully worked out is Molly Gloss’s stunning generation ship story, “The Dazzle of Day.”

[...]

So what I’m suggesting is this: just as there are and were “The Women Men Don’t See” as immortalized by James Tiptree Jr. and others, there are also the “Other living things humans don’t see.”
She speculates that this attitude, this blindness to nature, is one of the causes of our current environmental crisis.
A paradigm shift in our attitude toward other species is a prerequisite for change. Speculative fiction writers are practitioners of the art of imagining alternative scenarios — what would be the consequences of imagining a different relationship with other species? Which works of fiction have done that? (One that comes to mind is Ursula K. Le Guin’s extraordinary Always Coming Home). How would such works contribute to the shift in world-view that we need?
She imagines living in a Zoopolis, where humans lives are more integrated with rather than divorced from nature. The way she describes her vision is very appealing.

Go read her entire essay.

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Wednesday, October 08, 2008

How Dangerous is Biohacking?


The Boston Globe recently had an article about DIYbio and amateur biohackers. The article quotes Tom Knight as concerned about the potential dangers:
Tom Knight, a senior research scientist at MIT who is cofounding a synthetic biology company called Ginkgo BioWorks, sees the transformative value of biohacking - the phrase used to describe doing to living organisms what computer hackers have long done with electronics. But he has reservations about putting such power into the hands of amateurs."I think if the safety issues can be addressed, there is a big opportunity," Knight said. "It's a huge issue; how do you regulate so [people] don't cause havoc.
And that is what is potentially scary: while computer viruses can significantly interfere with business or goverment operations, a badly - or malevolently - engineered bacterium or virus can kill. In a recent article in Systems and Synthetic Biology, Markus Schmidt of the Biosafety Working Group in Vienna points out that an informal hacker "code of ethics" isn't much protection:
It is true that there is a kind of informal code of ethics for the hacker community6be safe, do not damage anything, do not damage anyone, either physically, mentally or emotionally, be funny, at least to most of the people who experience it”. This hacker ethics, however, did not and could not prevent the tons of malware programmes out there in the worldwideweb. The more successful the attempts to program DNA as a 2 bit language for engineering biology become (Endy 2007) the more likely will be the appearance of “bio-spam, bio-spyware, bio-adware” and other bio-nuisances. An unrestricted biohackery scenario could put the health of a biohacker, the community around him or her and the environment under unprecedented risk. This scenario has not gone totally unnoticed in the biohacker community and some have started to show at least some interest in safety issues, asking e.g. “how to use a pressure-cooker as an autoclave” or thinking to obtain some lab safety videos.7
I have mixed feelings about regulation. While I'd prefer my next-door-neighbor not be developing potentially virulent new strains of E. coli, the regulation of at-home labs here in the US has been, IMHO, rather excessive. A case in point is that of artist Steven Kurtz, who was arrested in 2004 by the FBI as a possible bioterrorist because he was preparing an art installation in his home that involved nonpathogenic bacteria. He was finally cleared of charges in April of this year.

While it may sound like science fiction, biohacking is here and we should start thinking about if and how it should be regulated. I'm hoping that we figure out some kind of medium between assuming any non-scientist with a vial of bacteria is a terrorist, and letting anyone who can afford to purchase a few enzymes free reign. Maybe the solution is education. If more people understood biohacking techniques - and the possible risks - I think the risk of potentially dangerous mishaps could be minimized. Malicious hacking, on the other hand, I'm not sure we can do anything about.

Find out more about synthetic biology:
(The Globe article is via blog.bioethics.net)

Image: Bacterial art of Eshel Ben-Jacob, Professor of Physics at Tel Aviv University. Ben-Jacob is working on the development of a "living, learning memory chip", in which neurons in culture can be imprinted with memories. (Looks like the beginnings of another post ...)


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Tuesday, October 07, 2008

Science Online '09: Science Fiction on Science Blogs

Blogging can be a lonely thing. I get a few comments and some feedback, of course, and I comment on other people's blogs too, but it's not really the same as having a face-to-face conversation. That's why I'm excited I'm going to be attending ScienceOnline09, an annual science blogging conference that meets in January at Research Triangle Park, North Carolina.

Speculative fiction writer Stephanie Zvan and I will be co-moderating a session on "Science Fiction on Science Blogs". We are in the early stages of hammering out what exactly we'll be talking about, and suggestions are welcome. If you are interested, you can add to the discussion of our session on the ScienceOnline'09 wiki.

I hope I get to meet some of you there! (See who else is attending)

You can read some of Stephanie's fiction here.

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Monday, October 06, 2008

Brain Power

Our brains are marvelously intricate computing machines. It is estimated that the 100 billion neurons in the human brain average 7000 synaptic connections to other neurons. While rat brains are much smaller, rat brain neurons have a similar connectivity. It seems only natural to try to utilize the brain's natural computing power in place of silicon-based microchips.

Along those lines Steven Potter - a professor at Georgia Tech's Neuroengineering Laboratory - has developed a so-called "hybrot", which uses cultured rat neurons to control a robot. A 2002 article in Technology Review described the machine as "a thinker, not a fighter":
And while the hybrot's movements may appear less than graceful, the knowledge gained could lead to computer chips modeled on biological systems-and perhaps even to computers that incorporate biological components. Such computers might one day learn, repair themselves, and perform certain tasks-such as dictation-at which binary-based systems are miserable. "I'm banking my whole career on the fact that there is a world of emergent properties in these neural networks that we don't know anything about," says Potter, who is a professor of biomedical engineering at the Georgia Institute of Technology.
(Watch a video featuring Potter's work from BBC Horizon)

More recently, Missouri University of Science electrical engineering professor Ganesh Kumar Venayagamoorthy has been collaborating with the Georgia Tech scientists to create a living neural network that is able to control a simulated power grid.
"We want to develop a totally new architecture than what exists today," says Venayagamoorthy, who also directs the Real-Time Power and Intelligent Systems Laboratory at Missouri S&T. "Power systems control is very complex, and the brain is a very flexible, very adaptable network. The brain is really good at handling uncertainties."
Venayagamoorthy's goal is to develop what he calls "biologically inspired artificial neural networks" or BIANNs, which would ultimately be able to control not only power grids, but also "other complex systems, such as traffic-control systems or global financial networks." While those applications are only at the planning stage, the Missouri S&T lab is currently able to simulate a power grid the size of Nigeria's or part of the New England-New York power grid here in the US. Presumably their next step is to try to control a real power grid.

I'd hate to think what would happen if the neural networks controling the traffic control systems was infected by a virus or contaminated with bacteria. Would the systems be as easy to replace or repair as non-organic computers?

Some free science fiction featuring neuron powered machinery:
  • In Peter Watts' Rifter's trilogy -Starfish, Maelstrom, Behemoth - cultured brain cells are used as "smart gels" (AKA "head cheese") to manage complex tasks like flying airplanes
  • Anne McCaffrey's short story "The Ship Who Sang" features a ship run by a very real human brain
(via Peter Watts)

Top Image: Golgi-stained neurons in the somatosensory cortex of the primate, Macaca fascicularis from BrainMaps.org
Bottom Image: B'Elanna Torres, chief engineer of the USS Voyager, inspects a bioneural gel pack for infection

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Friday, October 03, 2008

Sanctuary Premieres Tonight


The new television series Sanctuary premieres tonight at 9pm. It stars (and is produced by) Amanda Tapping as the 157-year-old Dr. Helen Magnus, a brilliant scientist who studies monsterous human "abnormals". The series is unusual in that it started life last year as eight online-only webisodes. The original episodes were shot in front of a green screen, with the sets and special effects added during production. The television version does that as well, using fancy virtual sets and effects. It does promise to have at least as many monsters as the original, but it remains to be seen whether the series is closer to fantasy than science fiction.

Tapping is joined by Robin Dunne as forensic psychiatrist Dr. Will Zimmerman, Emilie Ullerup as Helen's daughter Ashley Magnus, Ryan Robbins as Magnus's tech geek Henry Foss, and Christopher Heyerdahl as sinister "abnormal" John Druitt. All but Dunne have appeared in other Vancouver-based science fiction series such as Stargate, Stargate:Atlantis, and Battlestar Galactia.

Unfortunately most of the content has been taken down from the original Sanctuary web site, so if you want to see the webisodes, you'll have to do some creative searching on YouTube. But why not go for the current version? Watch the extended sneak peek, or just tune into SciFi in the US or the Movie Channel in Canada tonight. Its UK premier is next week on ITV.

Related post:
Sanctuary and Secrets of Evolution

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