Wednesday, January 30, 2008

Talking Squids in Outer Space

This week's Sci Fi Weekly web site of the week is Talking Squids form Outer Space. The content is pretty what you'd expect from the title: science fiction featuring squids and other cephalopods. There is a squidliography, of course, and even free SF stories featuring squids.

This current featured story is "Sheena 5" by Stephen Baxter, which stars a squid with enhanced intelligence working for NASA.

It came after the kill.

The night was over. The sun, a fat ball of light, was already glimmering above the water surface.

The squid emerged from the grasses and corals where they had been feeding. Shoals formed in small groups and clusters, eventually combining into a community a hundred strong.

Court me. Court me.

See my weapons!

I am strong and fierce.

Stay away! Stay away! She is mine! ...

It was the ancient cephalopod language, a language of complex skin patterns, body posture, texture, words of sex and danger and food; and Sheena shoaled and sang with joy.

... But there was a shadow on the water.

Go read the whole story.

It's not obvious from it's face, but Talking Squids in Outer Space is a subsite of SF writer Vonda McIntyre's official web site. It looks like she has another cool hobby, in addition to creating bead creatures. Her Nebula-winning novel,The Moon and the Sun, features giant octopuses. From the epilogue:
The sea people stalked the ships. Soon they swam beneath the barnacled bottom of the pursuer. Sherzad sang at it, feeling it out with her voice, searching and questioning, finding nothing of interest and nothing worth saving. In the past, she would have swum away.

She gave her baby to her young brother to guard, and swam closer to the pursuer.

Sherzad and her companions plunged their spears of narwhal tusk into the bottom of the galleon. The ivory bit into the wood. Holding the tusks, they rode along with the ship.

Sherzad shouted at the planks. Her focused voice crashed into the wood. She shouted again. Her spear quivered in the quaking wood. Sherzad and her brothers and sisters shouted together. The wood cracked and split.

The bottom of the ship disintegrated. Men shrieked and dove into the water. Sherzad and the others made sure they never surfaced.

Waves washed over the deck. Singing their triumph, the sea people called their allies. A shadow rose, flickering all over with tiny sparks. The octopus stretched its tentacles into the moonlight and entwined them around the mainmast, and inexorably pulled the ship into the depths.
Cephalopods and sea people working together in harmony. Beautiful.

And if you love squids and science fiction, you'll definitely want to get the SFWA "Squid Happens" T-shirt for your wardrobe. Proceeds go to the Science Fiction and Fantasy Writers of America's Emergency Medical Fund.

Image source: Squid with eggs @ NOAA.gov
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Tuesday, January 29, 2008

Life After People

The History Channel has a web site to complement their special, Life After People. It asks a simple question: what would happen if all humans disappeared from the Earth?

You can watch video that explores whether a plague could kill us all, and what would happen to the (non-human) animals, our buildings, and the rest of the Earth, if it did. There's even a Survival Guide that should come in handy if you are the lone survivor. Even better, print it out now, in case the power fails . . .

Image: the documentary shows that Stephen Colbert's worst fears may come true.
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Monday, January 28, 2008

Bioscience News Roundup: 01-28-08

Here are some of the interesting biology stories from the past week:

First off, there are all kinds of interesting bioscience posts rounded up for the Tangled Bank blog carnival at The Innoculated Mind. Also, John Wilkins has rounded up basic science concept posts at ScienceBlogs.

The big news of the past week was a report from the Venter Institute that they had succeeded in assembling an entire microbial genome from synthesized DNA. As Technology Review reports:

Biologists creating genetically engineered organisms now routinely order pieces of DNA that are 10,000 to 20,000 base pairs long--big enough to incorporate the genes for a single metabolic pathway. That allows researchers to engineer microbes that can perform specific tasks, but the ability to synthesize entire genomes could grant a whole new level of control over biological design. [. . . ] In the new study, scientists ordered 101 DNA fragments, encompassing the entire Mycoplasma genome, from commercial DNA synthesis companies. These fragments were designed so that each overlapped its neighboring sequence by a small amount; these overlapping stretches stick together, thanks to the chemical properties of DNA. Researchers then bound the fragments piece by piece, eventually generating the full 582,970 base pair Mycoplasma sequence.

The next step is to show that the synthesized genome is functional. Venter Institutes's ultimate goal is to create a completely synthetic organism.
Wired has several related articles:
The Panda's Thumb reports on a couple of cool articles that show how unicellular organisms like the giant slime mould can learn and remember.

Greg Laden has video of a talk by UC Biologist Robert Full on analyzing the motions of cockroaches, crabs and geckos and applying the information to creating "the perfect robotic distributed foot."

New Scientist shares a report on space-bred cockroaches from the Russian News agency Novosti:
. . . baby cockroaches conceived aboard a satellite in September have apparently grown up to be faster and tougher than their terrestrial brethren.The first creatures ever conceived in space also grew more quickly than ordinary Earth-bred cockroaches.
A team of scientists from the University of Wisconsin, Madison and the University of Washington have analyzed the genome of the diatom Thalassiosira pseudonana and found a set of 75 genes involved in processing silica to form hard cell walls:
The new data will enable Sussman to start manipulating the genes responsible for silica production and potentially harness them to produce lines on computer chips. This could vastly increase chip speed, Sussman says, because diatoms are capable of producing lines much smaller than current technology allows.
Technology Review reports on studies of rural Ecuaorians who have a rare mutation making them resistant to grown hormone. The condition not only causes dwarfism and obesity, but also seems to protect from artherosclerosis and possibly cancer and type 2 diabetes. The hope is that it also increases longevity, as a similar mutation does in mice.
"In the mouse, the effect is major and striking," says Andrzej Bartke, a biologist at Southern Illinois University in Springfield, who is not involved in the project. "They seem protected from cancer and appear to have delayed aging by various measures. But there is almost no evidence that growth-hormone deficiency would extend life in humans."
Mind Hacks writes about a recent article by neuoscientist R. Douglas Fields that compares brain size and function across species.

It turns out that while whales have bigger brains, humans have more neurons. Nevertheless, whales have more glial cells.

Glial cells were traditionally thought to do nothing more than support and insulate the neurons, but it's becoming increasingly clear that they're actually part of the brain's processing system (although they're exact role is far from clear).

So maybe there's a lot more to the whale brain that it first appears.

Finally, ScientificMatch is a Boston-based dating service with a twist.
. . . personal chemistry matching is done via DNA analysis. The immune system is what has been found to affect sexual compatibility, with people tending to prefer those whose immune systems are different from their own. The benefits of well-matched immune systems, according to research cited by ScientificMatch, include a more satisfying sex life, increased faithfulness, higher fertility and healthier children. Members who sign up for the company's USD 1,995.95 service send a cheek swab to ScientificMatch, which analyses the portion of their DNA that relates to the immune system. Matches are then suggested with other members who have compatible chemistry. The matching process won't work for women on the pill or for people who weren't raised by their natural parents, ScientificMatch cautions. It will, however, work for those seeking same-sex relationships.
I'd be interested in knowing whether ScientificMatch has a higher success rate than eharmony or chemistry.com .

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Sunday, January 27, 2008

Biology in Science FIction Roundup: January 27 Edition

Here's my weekly roundup of biology in science fiction links:

io9 reports on a movie adaptation of Ray Bradbury's short story Chrysalis:
Bradbury himself has been involved in every step of the movie, which takes place in an Earth left barren after a third world war. Scientists in a research facility are struggling to find ways to revive plant life. One of the scientists apparently dies, but then a plant chrysalis grows around him and saves him. He starts changing into something new and scary.
Production Charts has the scoop on a movie adaptation of the comic book Y:The Last Man, to star Shia LeBoeuf:
A mysterious plague has killed every man on earth except Yorick Brown, who was somehow spared. That is the provocative premise of the comics series whose first five issues make up this book.

The sole Y-chromosomed survivor is an amiable, headstrong young man, the son of a U.S. congresswoman and, as it happens, an amateur escape artist. He spends most of the story on the run from a tribe of self-styled Amazons bent on eliminating the last vestige of patriarchy. He is also trying, with a bioengineer who may be responsible for the worldwide "gendercide," to figure out why he survived; hoping to reach his girlfriend in Australia; and, of course, contemplating the repopulation of the planet.

io9 also has some footage from the bad bad movie Repli-Kate:
Here's a great scene where one of the gene geeks uses his amazing high-throughput sequencer to create a clone of a hot chick from some blood drops on a CD-ROM. Even the genechip whiz kid Michael Eisen, whom I know for a fact has watched this movie, agrees that this is the most thrilling representation of genetic engineering ever captured on film.

SciFi Weekly reviews the midseason premiere of Kyle XY

Slice of SciFi reports on a campaign to save The 4400 from cancellation. You can participate by visiting Save The 4400.net.

David Ng writes about some lost cartoon episodes about science - I'd love to see "That's Biotechnology, Charlie Brown" myself.

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Friday, January 25, 2008

FREE FICTION: The Color of a Brontosaurus


If you are looking for some free fiction to listen to this weekend, check out Escape Pod's podcast of Paul Martens' The Color of a Brontosaurus.
There was no doubt that the femur was that of a modern human. Not a proto-human, or some previously unknown dinosaur. Joel and Renee had arrived at the same answer. It was demonstrable, provable. When they finally did release news of the discovery, people might argue about it, but they’d be unable to refute it.

But how did they answer the next question? How did the bone come to be embedded in solid rock millions and millions of years before such a bone could have existed?

It had to be a time traveler. There was no other answer. Or was that just what he wanted to believe?

Image: "Taking own the skeleton of a dinosaur" at what is now Dinosaur National Monument in Utah.
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Science Fiction Studies: Stanislaw Lem

Science Fiction Studies is a journal published three times a year by DePauw University that takes a scholarly look at science fiction, including reviews, interviews and literary analyses. They have posted a lot of interesting material online, so I've decided to start a series of posts on biology-related bits.

Two full issues of Science Fiction Studies (Vol. 13 (3) #40; Vol. 19 (2) #57)have been devoted to Polish science fiction writer Stanislaw Lem (1921-2006). Lem's works best-known novel is Solaris, first published in Polish in 1961, which features the futile attempts to communicate with a very alien alien - one that covers the entire surface of a distant planet. His novel His Master's Voice also focuses on the attempt to communicate with an alien in this case a transmission from space intercepted by scientists here on Earth. Fiasco is also about our inability to communicate with aliens. Needless to say, Lem doesn't believe the universe is populated by English-speaking humanoids.

In 1983, Raymond Federman interviewed Lem for Science Fiction Studies. Lem talks about the role of science in his fiction:
Federman. What about the role of science in your work?

Lem. What matters for me is what is called cognition. In other words, that which is the concern of the theory of cognition. And the question of whether or not it should be limited only to exact sciences, that is to say, natural sciences, remains open. I am interested primarily in the line of junction, the border between science and philosophy, and also in the fact that a certain species of "brained animals" on Earth, I mean Man, has made science one of its main preoccupations. I experiment in the sense that sometimes I examine real possibilities of science and philosophy, and sometimes I imagine how other thinking species would practice philosophy of science.

Federman. If I understand you correctly, you do not make any distinction between science and philosophy?

Lem. Right. After all, the same psychic processes underlie scientific thinking and imaginative thinking.
He also thought about the future of biology in his work.
Federman. Do you work on one book at a time, or do you work on several projects at the same time?

Lem. Usually I work on one novel at a time, but at the same time I write shorter things, essays and so on. Not long ago I was writing a forecast for the Polish Academy of Sciences about the progress of biology in the next 60 years. In this essay—this is funny but also very typical of the way I work—I used some material, some fantastic ideas from the novel [Wizja lokalna]
to include in the forecast. These ideas turned out to be very helpful in writing this essay. So you see, I take things out of my fiction to use in my essays, and vice versa.
Lem was interviewed again in 1986, by Istvan Csicsery-Ronay. He spoke about his concept of "literary realism" and the incorporation of science into his works

Lem: Literary realism, for me, is literature's way of dealing with the real problems of a dual (at least) type. The first kind is the sort of problem that already exists or is coming into existence. The second kind is the sort that appears to be lying on the path of humanity's future. Any attempt to differentiate "possible problems" from "fictional," or "probable situations (albeit seeming outrageous today)" from "unlikely," is probably too polarizing to be successful. In this field, it's every man for himself, as long as the particular reasons for claiming the status of expert on dichotomies like the ones cited above are more or less respectable. Thus, anyone can be a selfmade authority on this subject, and so I am one.

I must add, however, that only recently did I begin to believe that I must abide by this conception of literary realism I had formulated umpteen years ago. Nor did I apprehend it consciously at first. That is, I stuck to a sense of implied "realism," one implied through various hypotheses which only later became apparent to me.

This ought perhaps to be qualified by one more observation. The contemporary physicist would be surprised to learn that, in contrast to his or her 19th-century counterpart, he or she is not a "realist" but a "fantasist." After all, the physicist must in some sense continue to be a realist, still working within the empirical tradition shared with 19th-century science; he or she still converts guesses into testable hypotheses, to be crystallized into theories which are subject to falsification. Similarly—mutatis mutandis—my writing over the last 30 years has been subjected to tests imposed by the changing world. I dare claim that the thrust of the main changes (such as genetic engineering or computer science) would become apparent to me, roughly at the time when some very intelligent people simply laughed at my notions as fairy stories. Of course, I was quite a bit off when it came to details, but the strategic movements of civilizations I fathomed rather well. This sort of realism may be termed sound prognosticating. On the other hand, sheer fantasizing is characterized by its self_impossibility (for example, no one will ever manage to travel back into the past to beat up his or her grandfather; that, I think, is certain).

[. . . ] Readers with training in biological sciences may be the ones in the best position to enjoy my books like His Master's Voice, but I would shy away from drawing conclusions from this.

Both interviews are worth reading to get a sense of Lem's point of view. Lem is erudite and philosophical, and not at all coy about his disdain for most science fiction - and much of modern literature.



(I came across Science Fiction Studies via the latest People of Color in SF Carnival at Seeking Avalon)

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Wednesday, January 23, 2008

How alien should science fiction aliens be?

At the Science Fiction & Fantasy Novelists blog, Daryl Gregory* has a confession: he doesn't believe in aliens - at least not the typical aliens in science fiction.

My problem with most aliens is that they just aren’t alien enough-biologically, culturally, or psychologically. Especially psychologically, and that’s what I’ll focus on in this confession.

Most of the SF writers who take their alien-building projects seriously think like evolutionary psychologists. This is a good thing. The biology of the species and the evolutionary environment in which it developed inform what a typical individual’s needs and desires might be and how it perceives the world. For example, Niven’s paranoid puppeteers and predatory kzinti have species-wide character traits based on their evolution as prey and predator. You see similar determinism in Mary Doria Russell’s Sparrow and Children of God, between her two competing species of carnivores and herbivores-the eaters and the eaten.

I agree that when (or if) we meet another intelligent life form, it is unlikely to be bipedal, let alone humanoid. The problem is incorporating such an alien alien (for want of a better term) into an entertaining story.

Even Niven's Kzinti and Russell's Runa and Jana'ata aren't really that far from human, even if they are a giant step up from green Orion slave girls and floppy-eared creole-speaking Gungans. And there are indeed many science fiction stories in which the aliens are even stranger. Gregory mentions Peter Watts' Scramblers (Blindsight) and the Stanislaw Lem's nightmare-inducing alien in Solaris. To those I'd add Orson Scott Card's Pequeninos (Speaker for the Dead, Xenocide, Children of the Mind), Niven and Pournelle's Moties (The Mote in God's Eye), and Vernor Vinge's Skroderiders and Tines (A Fire Upon the Deep).

But at least a touch of humanness is necessary, I think, if you want your human characters to have meaningful interactions with the alien characters. Even Lem's alien ocean had to know that humans are another intelligent species and understand us enough to tap into our minds. I suspect that the greatest hurdle of our first first contact may actually be realizing that we should be trying to communicate at all. And even once we've settle on a physical means of communication, there is the difficulty in fining a common "universe view" - something that can even be a problem between different human cultures.

Another thing to consider is that almost all science fiction is told from the human point of view, and we are naturally inclined towards anthropomorphism - we ascribe human characteristics to objects and animals, and any aliens we meet will be perceived through this filter. While aliens might not really be human-like at all, we almost certainly will ascribe human motivations and emotions to them. Science fiction simply describes aliens through the eyes of unreliable narrators.

All that having been said, really I think Kelly McCullough has it right in her comment:
. . . doesn’t this kind of ignore that the main point of aliens in an awful lot of science fiction isn’t to portray aliens at all, but rather to isolate and examine some specific parts of the human condition? Sure, some aliens are really just supposed to be alien, but I think that a significant percentage–quite possibly the majority–are intended to help us look at some facet of human existence in a new way by pulling it out of our own melange of traits and making it more visible for what it is, or what the author believes it to be.
And that dovetails nicely with Clive Thompson's recent Wired column on "Why Sci-Fi is the Last Bastion of Philosophical Writing":

Alter reality — and see what new results you get. Which is precisely what sci-fi does. Its authors rewrite one or two basic rules about society and then examine how humanity responds — so we can learn more about ourselves. How would love change if we lived to be 500? If you could travel back in time and revise decisions, would you? What if you could confront, talk to, or kill God?

Most science fiction aliens aren't really meant to be alien at all - they are simply another way of looking at ourselves. (Of course that won't stop me from blogging about the bad biology . . . )

Image: Cheron natives from the Star Trek episode "Let That Be Your Last Battlefield"

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Read for yourself:

Monday, January 21, 2008

More on Aled Edwards and ReGenesis

It seems like ReGenesis is a hot topic - either that or I'm just primed to notice at the moment. Anyway, the latest edition of LabLit has an interview with ReGenesis' science adviser Aled Edwards. He talks about how he got involved as a science adviser and the kind of demands he makes:

Any conditions?

Well, I said I’d only do it if they stick to real science. No white coats. Show scientists who actually drink coffee in the lab, like we all do. They have to make the occasional mistake! And none of this doing an experiment that would take a month in real life being resolved in one day. For example, they wanted to have the guys solve a pandemic in three hours. I said, no, you can’t discover a new drug in one day. So we had them screening pre-existing compounds, which is actually more feasible.

The writers must hate this!

They do say it’s the hardest thing they’ve ever done, because they can’t just make it up – I won’t let them. It’s tiring for everybody. Plus they’re getting it from both ends. Management can veto entire stories, which happens about thirty per cent of the time: maybe there’s not enough tension, not enough human interest...or too much science. It must be a real pain in the ass to be a TV writer.
His lab members even get to help out with the consulting - very cool.

(In my previous ReGenesis post, I said that it was being shown on ABC at 1:30 AM Monday nights. I forgot to check last night (which I think of as Sunday, even after midnight.) I really wish some station would pick it up for an "earlier than the middle of the night" time slot.)

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Bioscience News Roundup: 01-21-08

Here are some interesting bioscience tidbits from the past week:

Valter Longo and colleagues have two upcoming papers that demonstrate the genetic control of aging (One of the articles will be in the January 25 issue of the open-access PLoS Genetics.). A combination of "genetic tinkering" - the inactivation of the RAS2 and SCH9 genes - and low-calorie diet allowed yeast to live 10 weeks instead of the usual one week. Longo and colleagues are studying a population in Ecuador that carry similar mutations.
“People with two copies of the mutations have very small stature and other defects,” he said. “We are now identifying the relatives with only one copy of the mutation, who are apparently normal. We hope that they will show a reduced incidence of diseases and an extended life span.”

Longo cautioned that, as in the Ecuador case, longevity mutations tend to come with severe growth deficits and other health problems. Finding drugs to extend the human life span without side effects will not be easy, he said.
Selva, The Scientific Indian, reports on a recent article in the New York Times about brain-machine interfaces. So far only monkeys, but can humans be far behind?

Nina Munteanu has an interesting post on synthetic bacteria and the possible dangers in "extreme genetic engineering."

Ed Yong writes about how and why temperature controls the gender of Jacky dragons.

io9 has a report on an experiment by Dr. Richard Behringer and colleagues that transplanted the DNA sequences that regulate the expression of the Prx1 gene from the bat to the mouse. The result was abnormally long forelimbs that were more bat-like than mouse-like.
Dr. Behringer describes the significance of his finding as such: "Darwin suggested that "successive slight modifications" would ultimately result in the evolution of diverse limb morphologies, like a hand, wing, or fin. The genetic change we engineered in mice may be one of those "slight modifications" to evolve a mammalian wing."
The news that hit the main stream media big this week was the announcement by the FA that cloned meat is considered safe to eat. The main public concern isn't that the cloned meat would be toxic, but that it's just "icky". Last October, Wired reported on cloned meat and milk that's already available, at least on a limited basis.

UK researchers have been given the go-ahead to make human-cow hybrids. Human DNA will be injected into "empty" cow eggs, resulting in embryos that are "99.9 per cent human in genetic terms", according to the article. There is more technical information on the proposal in Nature Cell Biology:
The proposals under consideration involve replacing the nucleus of an animal egg with the nucleus from a human somatic cell (Fig. 1), and allowing such an entity to develop in vitro for approximately 5 days until it forms a blastocyst (a sphere of 100 or so cells). This comprises an outer trophectoderm layer, destined to be part of the placenta, and the inner cell mass (ICM), which, if allowed to continue in the correct three-dimensional organisation, can give rise to the foetus and the remaining extraembryonic tissues. However, at this 5 day stage, the ICM cells would be used to establish hESC lines in vitro4. As there is no intention to implant any of these embryos to allow further development in the womb, which is already illegal in most countries (including the UK) whether using human or animal eggs as recipients, there is nothing in current legislation to prevent the experiments being conducted. The use of human oocytes to carry out similar procedures has already been licensed by the HFEA5, but the shortage of donated human oocytes6 has prompted the search for an alternative, hence the idea of using animal eggs.
It definitely won't result in critters that make LiveScience's Freakiest Lab Animal list.

Finally, the biotech company Stemagen has reported creating cloned human embryos using somatic cell nuclear transfer - the fusion of an adult skin cell with an egg. They didn't actuallly take the next step and demonstrate that the resulting embryos could be used as a source of stem cells. The reaction from the scientific community has ranged from skeptical to "what's the big deal?"

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Sunday, January 20, 2008

The Wasp Woman


OK, it's Sunday night and I'm feeling to lazy to blog about anything serious, so I offer to you a fabulously awful B-movie from 1960: The Wasp Woman. From its Wikipedia entry:
The founder and owner of a large cosmetics company, Janice Starlin (Susan Cabot), is disturbed when her firm's sales begin to drop after it becomes apparent to her customer base that she is aging. Scientist Eric Zinthrop (Michael Mark) has been able to extract enzymes from the royal jelly of the queen wasp that can reverse the aging process. Starlin agrees to fund further research, at great cost, provided she can serve as his human subject. Displeased with the slowness of the results she breaks into the scientist's laboratory after hours and injects herself with extra doses of the formula. Zinthrop becomes aware that some of the test creatures are becoming violent and goes to warn Janice but before he can reach anyone he gets into a car accident. He is thus temporarily missing and Janice goes through great trouble to find him, eventually managing and then transferring his care to herself. Janice continues her clandestine use of the serum and sheds twenty years' in a single weekend, but soon discovers that she is periodically transformed into a murderous queen wasp.
That's one serious royal jelly side effect!

The Wasp Woman is currently in the public domain, so you can watch it for free on Google video. B-Movie Central points out some of the most obvious flaws in its science (and basic logic), but if you aren't going to simply sit back and revel in it's badness, it's just not worth watching.

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Saturday, January 19, 2008

Biology in Science Fiction Roundup: January 19 Edition

A few Biology in Science Fiction bits from around the web:

Peter Mc at The Beagle Project Blog asks where are the fictional scientific heroes for our young people?
But where are the books for children and teenagers in which evolution does not cause mutated threats to the human race, where science and scientists save humanity and get the credit. Where scientists get the natty threads and the whip-crack one-liners. Where they don't just get to watch while their good work is taken by a cut lead man or woman and put to good use.
He's asking for some good science-based fiction for 2009.

Greg Burgas at Comics Should be Good blog lists his picks for the best comics of the year. Elephantmen by Richard Starkings and Moritat is one of his picks for best ongoing series.

Starkings’ science fiction tale, like all good sci-fi, illuminates issues that we grapple with in the present, such as war, bigotry, genetic engineering, and an unfair class system. [. . . ] Obadiah Horn and his consort, Sahara, are two other beautifully realized characters, giving us a view of what happens when a human-animal hybrid seizes power within Los Angeles and the prejudices he and the woman he loves faces. Like all good villains, Obadiah Horn isn’t completely villainous, and the tender moments he shares with Sahara make his dark side even more horrifice.

Slice of SciFi reports on the new internet-only series "IQ 145":
Shot almost entirely in front of green screen in hi-def, the series will follow Nate Palmer, the son of a renowned, inventor/futurist. Nate’s father, not known for fits of depression has mysteriously committed suicide. Nate is recruited by a secret organization to help search for his father’s last experiment but will soon discover that it is he that is the experiment.
IQ 145 starts next week.

J. Craig Venter isn't just about synthetic organisms. He recently announce that he had sequence his own genome and revealed his genetic traits to the public. The New Haven Advocate asked Yale professor Jim Noonan and Stanford professor Bill Hurlbut whether they thought that meant we are heading towards a real-life Gattaca. Noonan said:
"The problem with the movie Gattaca is that it's assumed that these are guaranteed diseases and conditions, whereas that's not the case." According to Noonan, the associated risks for these genetic indicators "aren't 50 percent—they're more like 5 percent." Still, he worries the information could be used irresponsibly, even discriminatorily.
io9 takes a look at the upcoming movie Sleep Dealer:
In Sleep Dealer, the U.S. has finally succeeded in stopping illegal immigrants crossing over from Mexico. But Mexicans can still work in American factories and farms for almost no money, thanks to the miracle of telecommuting. The people in Alex Rivera's film hook up their nervous systems to the Internet to control robots in the U.S., but it takes a toll on them, as you can see from the spooky clip and stills above. The film's title refers to workers who get so drained they collapse.
Greg L. Johnson lists his favorite science fiction books of 2007 for SF Site, including Thirteen by Richard Morgan:
Speaking of paranoia, Thirteen reeks of it. Set in a near-future Earth where concerns with genetically-influenced behavior has become a world-wide obsession, the 'thirteens' are humans whose genetic structure has been altered to remove most, if not all, of their inhibitions toward sudden, inter-personal violence. The main character is one of the thirteens, and it is a major achievement of Richard Morgan's novel that as the story goes on, the reader's sympathies align more and more with the actions of a character who scares the entire world.

Robert Sawyer writes about movie adaptations of Pierre Boulle's La Planète des singes (AKA Planet of the Apes).

Finally, Jay Garmon writes about "75 words every sci-fi fan should know" for TechRepublic. A few bioscience terms made his list, including (via ).
  1. mindfood (n.)
  2. posthuman (n.)
  3. sapient (n.)
  4. sentience (n.)
  5. wetware (n.)
  6. xenology (n.)

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Friday, January 18, 2008

Hard Science Fiction Ideas or How to Research Research

Science fiction writer James VanPelt* has written a helpful column for aspiring science fiction writers, "Generating Hard Fiction Ideas Painlessly":
So, do you need a degree in science or math to write hard science fiction? Nope. Numerous hard science fiction authors write their stories without that background. I’m one, for example. My college degrees are in English and history. Fred Pohl and Ray Bradbury didn’t attend college. Connie Willis was an elementary school teacher before her science fiction successes. Admittedly, though, the non-science or math authors will have to work a little harder to not write laughable hard science fiction. They need to cheat a bit. They may need help coming up with ideas, and they certainly will need help for the science that is not at their fingertips. Fortunately, the help is no farther away than the nearest bookstore.
He gives several suggestions for books, including one based on the excellent NPR program, Science Friday.

Jeremiah Tolbert responded with his own request:
Someone with access to the big primary biological sciences literature should post reviews/summaries in laymen's terms of each issue. Nature, Science, and more. People could volunteer and write in summaries for any primary literature they want. Group blog the literature. Get it out there in the web, in a format that science-interested people can understand. Because I think there's a barrier still between that level of academic knowledge and the web population. I'd like to see a gateway giving me a glimpse at what's going on. I don't know where the local unversity's science library is, and I can't afford to subscribe to those magazines (who can?).
Now my gut response to this is "Why aren't you reading what's already on the web?" Tolbert doesn't have comments on his blog, but I did comment on Futurismic, which quotes his request:
There are already people who blog about science breakthroughs - ScienceBlogs and Nature network being a good placed to start. Also, both Science and Nature have news sections that summarize the latest research in relatively non-technical terms.

Nature and Science are published every week, but the peer-reviewed science they publish is really just the tip of the iceberg, since they try to have articles in a wide range of fields and only publish relatively short reports. To really be up on the biological sciences, you have to keep tabs on the more specialized journals too - PNAS, Cell, Neuron, Genes & Development, EMBO Journal, Journal of Cell Biology, Journal of Biological Chemistry, Nucleic Acids Research, Journal of Molecular Biology , are a few of the big ones that come to mind. It would be a full time job to summarize every paper that came out in layman’s terms - and a bit of wasted effort, since most articles wouldn’t be of general interest anyway. The good news is that Science and Nature cover the hottest findings in their news sections, and the blogs usually pick up that info too. So the information is already out there for the reading if you are interested.

I suppose the issue is whether the news sections of Science and Nature are sufficiently non-technical for the layman. I'll confess that it's hard for me to judge, since I'm not a layman myself. However, the biggest science stories are distilled further yet by popular science magazines like Scientific American, Science Daily, Discover, Live Science, and Seed. If listening is your thing, there are lots of science podcasts to choose from, such as Science Friday, NASA Podcast, New York Times Science Times, not to mention the podcasts from Nature and Science Magazine, and many others. And if you like your science raw, you can always subscribe to the EurekAlert science press release service, which often combines science described in layman's terms with sensationalist prose.

Those sources are only the tip of the iceberg, of course. There are lots of other news sources and blogs that cover the latest science research daily. The problem is not that the information isn't out there, it's that there is so much that it's difficult for one person to take it all in. I subscribe to many science news sites and blogs and the best I can do is skim through the headlines, reading the articles that catch my eye. I'm not sure what more Tolbert wants, other than a distillation of the distillation that's already available.

The amazing thing is that all this information is out there for anyone who is interested enough to read it. A decade or two ago you would have had to go to the library or subscribe to the journals and decipher the technical language yourself (does anyone else remember using Current Contents?). Now, with so much information readily available at your fingertips, there is no reason not to be aware of the latest research.

One practical suggestion: don't try to visit every web site and every blog "in person" so to speak. The only way to really keep up is to subscribe to the feeds for the news sites and blogs so that you can easily browse through the headlines. Personally I use the Lite version of NetNewsWire, but there are many other options, including Google Reader, Bloglines and NewsGator. Most web sites have an orange-colored button to click to subscribe, like I do in the right sidebar. Anyone can keep up with the latest news in bioscience by putting a little effort into it.

ETA: I should have also mentioned ResearchBlogging.org, which aggregates blog posts on peer-reviewed research. That way you can get the best of science blogging without the politics, jokes or cat photos, if you are so inclined.

* You can read VanPelt's short story "A Flock of Birds" at SciFiction.

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Thursday, January 17, 2008

Fountain of Age

The process, what came to be called D-treatment, couldn’t make you younger. Nothing can reverse time.What D-treatment could do was “freeze” you at whatever age you had the operation done. Peter Cleary, among the first to be treated after FDA approval (the fastest FDA approval in history—mine wasn’t the only soul for sale) would stay fifty-four years old forever.

Supermodel Kezia Dostie would stay nineteen. Singer Mbamba would stay thirty. First came Hollywood, then society, then politicians, and then everybody with enough money, which wasn’t too many people because after all you don’t want hoi polloi permanently cluttering up the planet. When King James III of England was D-treated, the whole thing had arrived. Respectable as organ transplants, safe as a haircut. Unless the king was hit by a bus, Princess Monica would never succeed to the throne, but she didn’t seem to care.
The preliminary nominees for the 2007 Nebula Awards have been announced, and Nancy Kress's novella, "Fountain of Age" made the list. Elderly Max Feder lives in a not-too-distant future where treatments can rejuvenate your body and halt the aging process, neither of which is fully able to recapture the lost love of his youth. It's a great story, and you can read it for free at Asimov's Science Fiction.

If you'd like more free reads, SF Signal has collected links to most of the other nominated stories.

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Wednesday, January 16, 2008

Repressed Memories

On a hygenic bed Douglas Quail lay breathing slowly an regularly, eyes half-shut, dimly conscious of those around him.
"We started interrogating him," Lowe said, whit-face. "To find out exactly when to place the fantasy-memory of him single-handedly having saved Earth. And strangely enough --"
"They told me not to tell," Douglas Quail mumbled in a dull drug-saturated void. "That was the agreement. I wasn't even supposed to remember. But how could I forget an event like that?"
I guess it would be hard, McClane reflected. But you did -- until now.
-- "We Can Remember it For You Wholesale", by Phillip K. Dick
The plot is a familiar one. Our heroine always felt a little uncomfortable, like something was a bit "off" in her life. Then, out of the blue, a familiar face or a smell or a song triggers a rush of memory. Something terrible happened to our heroine, so terrible that that specific memory was completely suppressed. What happens next depends on the genre: she'll crumble, or investigate, or seek revenge. Of course, in science fiction it can be more complicated. Perhaps the repressed memory was physically erased, or may actually turn out to be a virus masquerading as a memory engram.*

It's used so often it's a cliché, but I've never considered whether it's something that happens in real life. Researchers at the Biological Psychiatry Laboratory argue that repressed memories, AKA dissociative amnesia, is actually a "romantic notion dating from the 1800s, rather than a scientifically valid phenomenon." Interestingly, they base their hypothesis on the absence of descriptions of repressed (and regained) memories in fiction and non-fiction prior to the 19th century (pdf). Most psychological phenomena - depression, anxiety, delusions, hallucinations, dementia, and regular amnesia - are documented in literature throughout the ages.

They turned to the wisdom of the masses, offering $1000 for any example of dissociative amnesia written before 1800. Their Repression Challenge was won by the person who submitted the libretto of the opera Nina (pdf), written by Marsollier in 1786, so just barely before the turn of the 19th century. Their conclusion is that
". . . dissociative amnesia may seem very real, and even commonplace, to contemporary clinicians an their patients, just a s pseuo-paralysis was commonplace at the Salpetriere of Charcot in the 1890s, or pseudo-seizures at the Salem witch trials in the 1690s's. But each of these syndromes appears to have represented a cultural product of its time, rather than an actual neurological disorder of the brain. Viewed in this light, dissociative amnesia is best characterize as a 'culture-bound' form of conversion disorder, a phenomenon pecular to our modern Wsestern culture.
I find it amazing that our psychological condition may be influenced by literature, just as literature is built on our psyches. I wonder what else we may take for granted that is just a figment of our collective imaginations.

* In addition to the stories I linked to – Dick's "We Can Remember it For You Wholesale" which inspired the movie Total Recall, Spider Robinson's Mindkiller, the Star Trek Voyager Episode "Flashback," and the Enterprise episode "The Seventh" – check out this discussion at Lexicon Harlot for lots of other science fictional examples.

(Information on the Repression Challenge via Mind Hacks)

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Learning bioscience from ReGenesis

The Canadian science fiction show ReGenesis has structural biologist (and head of the Structural Genomics Consortium) Aled Edwards to thank for it's scientific accuracy. He acknowledges that drama sometimes trumps reality.
"ReGenesis is the most accurate scientific drama out there, no holds barred, for sure," he claimed in a recent interview. He finds it difficult to watch those other popular programs [CSI and House], but isn't offended by their use and misuse of science either. "It's almost like watching a cartoon, where Batman or Superman or House is the same. When I watch Superman, I don't get upset: 'Hey, men can't fly!'" he laughed. "When I watch those shows, I turn off my scientific brain. I say I'm watching mindless entertainment here. Because if I put on my scientific brain, I'd get upset. So I just watch it and think this is not science, this is not medicine, this is television."

While he's proud of ReGenesis's devotion to basing its fictional stories on fact, he doesn't lay claim to documentary-like accuracy either. "None of these scientific programs are ultimately the truth because we have boring jobs. I sit on my ass all day in front of the computer. The action takes place in the head and you don't see anything. There's no shooting. But it's fun for people to start to realize what we do."

But educating the Canadian public about scientists and science has been taken a step further.

Part of his outreach efforts led to a couple of recent public forums, one in Vancouver and one in Hamilton, called "Revealing ReGenesis: Explore TV's Experiment with Gene Science Fact and Fiction."

Using clips from the series as conversation starters, the forums generated conversation among audience members and scientists sprinkled at tables throughout the room, as well as a panel discussion. Moderated by Jay Ingram, host of Discovery Channel's Daily Planet, the Vancouver panel was comprised of Edwards, fellow geneticist Dr. Elizabeth Simpson, ethicist Dr. Shane Green, and ReGenesis lead actor Peter Outerbridge.

"We used the draw of television and personalities to bring people there and then talk science and they realize man, that's kind of fun," explained Edwards. "That's why we were trying to link the art and the science together, because they're both about creativity and they're both about using your brain."

There is plenty of online information as well. The Ontario Genomics Institute has a companion "Facts behind the Fiction" web site, with episode guides and you can pay a virtual visit to the (fictional) North America Biotechnology Advisory Commission (NorBAC). There's even an "extended reality" game that is coordinated with each episode.

The IMDb indicates that it's appearing in the middle of the night on ABC (next episode, Monday, January 21, 1:35 AM). I'm hoping that if the writer's strike continues it gets a slot closer to prime time. Word to SciFi: I'd much rather watch ReGenesis than yet another episode of Ghost Hunters or a monstrous animal of the week movie.

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Monday, January 14, 2008

Hatchling

Israeli science fiction writer Guy Hasson dropped me a note to suggest that Biology in Science Fiction readers might enjoy his novella Hatchling. From his message:
I can't tell you what kind of biology it deals with, because that would spoil the surprises of the story. You'll see it two thirds of the way in.
I won't spoil it either - you'll just have to read it for yourself. I will say that it brings up some interesting issues in bioethics. If you like Hatchling, you should also check out Hasson's novella "Her Destiny "and the short story "The Dark Side".

Hasson has won two Geffen Awards. His novella "The Perfect Girl" won in 2005 and his short story "All-of-Me(TM)" won the short fiction award in 2003. Hasson blogs about culture and writing at The Storytellers.

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Bioscience News Roundup: 01-14-07

Some interesting bits of bioscience in the news (I apologize if some of them are old, I've been cleaning out my collected links):

Science News reports on making "life from scratch", with a focus on the work at the J. Craig Venter Institute (via BoingBoing) From the article:

"We eventually want to make an organism called Mycoplasma laboratorium," Smith says. The more familiar name for this hypothetical cell is Synthia.

Glass says that the team is on the verge of making such a cell within the next few months. In the Aug. 3, 2007 Science, the researchers announced that they had transplanted the entire genome of one species of Mycoplasma into a related species. The recipient cells began using the foreign genome as if it was their own, showing that the receiving cells can "boot up" the newly inserted DNA (SN: 6/30/07, p. 403). All that remains is to finish piecing together a minimal, synthetic genome and then to insert it into a Mycoplasma bacterium by the same technique.

Beyond serving as a hobby-kit cell for unraveling basic cell biology, Synthia might serve as a platform for developing novel biotechnologies.

"Learning how to rebuild something will give us control over a cell that we don't now have," Glass says. Craig Venter, the scientist-cum-biotech tycoon who led the private effort to map the human genome and now heads the Venter Institute, has said he hopes that a minimal genome will serve as a base upon which to add custom functions, such as genes for converting feedstock into hydrogen for fuel.

They should probably read io9's post about the "Dos and Don'ts of Biology Hacking"

Wired Science also looks at microbes reengineered "to do humanity's dirty work"

University of Minnesota researchers have created a beating heart in the laboratory. You can even watch a video of the process. (via Pharyngula).

Twisted Bacteria reports on the work of Chinese scientists to improve microbial strains by giving them a ride in space.

Wired Science has a report on cool new bioscience-related technology presented at the JPMorgan Healthcare Conference. Neo-Organs and anti-fat ray sound like something out of Futurama.

American Scientist has an interesting article about the possible origins of larvae that are very different from the adult forms.
Biologist Williamson has proposed that larvae are juvenile forms acquired through hybridization—the fusing of two genomes, one of which is now expressed early in an animal's life, the other late. This hypothesis, which goes against traditional thinking that branches on the evolutionary tree cannot fuse to form chimeric species, is one of several possible solutions to open questions about the evolution of larvae. Although an experiment did not yield convincing DNA evidence, the hypothesis is consistent with certain patterns seen in the distribution of genes across species. Along with other evidence of cross-species hybridization, it implies a pattern of evolution that looks more like a network than like Darwin's tree of life.
There is an interesting Ask MetaFilter discussion about whether you can use DNA analysis to determine the time of conception. I'm pretty sure I've seen that used as a plot device. On Enterprise maybe?

Ron at Beam Me Up writes about recent research on space agriculture. Does our future hold space bug entrées?

Did you know the first structure visible from space was made by wombats? Discover Magazine reviews the book Built by Animals: The Natural History of Animal Architecture, and links to images of some of the structures.

In legal news, Wired Science reports on the United Nation's report that recommends treating human clones as our equals.

Finally, in the category of "pseudoscience", The Mental Floss blog lists 5 creatures that probably don't exist, yet received government protection anyway.

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Saturday, January 12, 2008

The Gene Generation

In a futuristic world, Michelle lives everyday battling with DNA Hackers who use their skills to hack into people's bodies and kill them. She is an assassin, battling her past demons and trying to keep her younger and extroverted brother, Jackie, out of trouble. When Jackie gets involved in a petty crime of robbery, he propels himself into the world of DNA Hackers, Shylocks (Loan Sharks) and Gang Fights.
- Plot Summary of The Gene Generation
The Gene Generation stars Bai Ling as Michelle, with a supporting cast that includes Parry Shen and Faye Dunaway. According to the film's Myspace profile, it's based on the comic DNA Hacker Chronicles.

While the poster proclaims "coming soon", the official web site says "Summer 2006", and IMDb indicates the movie was released on October 31, 2007. The film's Myspace blog was updated on January 1st to say "We signed on Traction Media before the holidays and this year, we will be working on strategy for releasing this movie (FINALLY!)." I wouldn't be surprised if it never saw the the inside of a movie theater.

So, why post about it here (other than giving Bai Ling's fans a sexy crotch shot)? For some reason the companion "DNA Hacking" web site just makes me smile. It might be the image of multiple robots arms "hacking" a DNA strand, or perhaps it's the background rock music with the occasional binky sound thrown in for scienceness. It could be the poorly written explanation of DNA Hacking which caries the warning:
DNA Hacking has cause the results of many health hazards, most notably, death. But while the majority of DNA Hacks are mainly to instill a certain statement, many DNA Hackers have been known to use their skills as a tool for vengeance or revenge, usually for a legit cause.
But I think the thing I like best is the thinly disguised attempt to go viral (in the internet sense) with the option to "DNA Hack Your Enemies" via e-mail. As the site says, it's
"A total anoynamous way to get revenge. If you were a victim, why not send one to every suspect you can think of."
If only I could hack the genes of my enemies via e-mail in real life. I'd give the girl who was mean to me in 6th grade a pig's nose and a rat's tail. Vengeance would be mine! I would be as a god! Or, as the site says:
Some people call us gods for we utilize in our hands the very secret of life, death and the pain in between the senses.
And it's that pain that makes us human, natch.

(Thanks to Aardvarchaeology for posting the poster)

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Biology in Science Fiction Roundup: January 12 Edition

Biology in Science Fiction bits from around the web:
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Friday, January 11, 2008

B-Movie Biology: The Course

If you are going to be in the Northampton, MA area next week, Diane A. Kelly is going to be teaching a course in the Smith College Interterm Faculty Film Series called "B-Movie Biology". Each evening a single movie will serve as the basis for discussion an important biological concept. From her course outline:
Monday, January 14
To discuss: How does size affect the physiology of living organisms?
Them!
Nuclear tests in the American Southwest result in gigantic mutant ants that threaten cities as a team of investigators and the Army search for a way to control their spread in this Cold War-era monster film. (Gordon Douglas, director. 1954)

Tuesday, January 15

To discuss: What is a parasite, and how is its ecology different from a free-living organism?
Alien
A commercial space vehicle heading back to Earth picks up an SOS from a nearby planet. When the crew investigates, some of them leave the ship to explore the area when they come across an egg hatchery of some unknown creature. Unbeknownst to the exploring team, the ship's computer deciphers the message to be a warning, not a call for help. When a crew member disturbs one of the eggs, the parasite inside attacks him, and so begins the living nightmare. With Sigourney Weaver, John Hurt and Harry Dean Stanton. (Ridley Scott, director. 1979)

Wednesday, January 16

To discuss: How do genes control animal development?
The Fly
A brilliant scientist offers up his latest research on matter transportation to a journalist in an attempt to impress her. While his research has so far been successful, there is one last problem he discovers when attempting to teleport himself. Best line from the movie: “Be afraid. Be very afraid.” With Jeff Goldblum and Geena Davis. (David Cronenberg, director. 1986)

Thursday, January 17

To discuss: How does cloning work?
Jurassic Park
Huge advancements involving DNA extraction from ancient samples embedded in amber have enabled scientists to create an island theme park full of living dinosaurs. When the director of this island park invites a small group of scientists to visit, T. Rex and his Velociraptor friends get a little out of hand. With Laura Dern, Jeff Goldblum and Samuel L. Jackson. (Stephen Spielberg, director. 1993)

Friday, January 18

To discuss: Do genes matter when it comes to human behavior?
Gattaca (1997)
A genetically inferior man, one of the last “natural” babies born into a genetically-enhanced society that discriminates against imperfect genes, assumes the identity of a once-perfect specimen in order to remain a viable candidate for space travel with Gattaca Corp. Required to pass periodic gene tests, he must be diligent in his use of DNA samples from his assumed identity’s hair, skin and blood to remain undetected. How long and to what extremes must he go to continue the charade? With Ethan Hawke, Uma Thurman, Maya Rudolph and Gore Vidal. (Andrew Niccol, director. 1997)
It sounds like an interesting way to spend a cold winter evening!

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