Biology in Science Fiction

The Stonemaker Argument

2009-11-02T18:51:00.000-08:00

The latest episode of science-loving web comic The Stonemaker Argument features a little girl after my own heart.

Go read the whole comic!

(via Bad Astronomy)

Tags:science fiction, biology

Genetics in Fiction @ Clarkesworld

2009-11-02T18:49:00.000-08:00

Roger Moraga has a nice article in the current issue of Clarkesworld Magazine on "Modern Genetics in the World of Fiction":

Most of the time there is a certain amount of unrealistic superscience involved in the creation of speculative fiction, but as a geneticist I can't help but wonder if it is really necessary to trample all over what we do know about genetics to make it happen. Ultimately it is up to the creator to decide how much, and how soon, to depart from "real" Science, but before long it may not be necessary to depart much at all. A more in-depth look at what genetic engineering is doing today may be enough to make one's imagination run wild.

You should definitely go read the complete article for yourself, but I will note that I couldn't agree more with Moraga's conclusion:

If you are a writer considering genetic engineering for your next work, take a little time to invite a molecular biologist to a drink or two and pick his* brain. We don't bite, we love speculating about science fiction, and many of us even like free drinks.

* and don't forget that some molecular biologists are she rather than he (hint hint).
Tags:science fiction, genetics, genetic engineering

The Unselfish Gene: Altruism and Zombies

2009-10-31T12:55:00.000-07:00

The Unselfish Gene is the first published novel of science journalist Robert D. Burns, and it sounds like a lively mixture of pulpy science fiction-horror and genetics. The novel's blurb gives you a taste of that:

It's love and terrorism in the time of cholera. In the mid-21st century, a form of bird flu has killed billions and turned most of the rest into mindless, stumbling zombie-like invalids. The few humans who had immunity now face the threat of a comet on a collision course with Earth. Settlers from the Moon colony were spared the disease, but face their own threats to survival: radiation-induced mental illness, a limited gene pool and shrinking resources. The Moon settlers have launched a last-ditch mission to Earth to salvage human DNA and other crucial materials ... before the comet strikes. The salvage crew find the biggest threat to the mission is neither the zombies or the comet, but insanity within their own ranks.

Now if you are a biology geek like me, the first thing you think of when you hear the novel's title is Richard Dawkin's classic book on evolution The Selfish Gene. It turns out that that was indeed one of Burns's inspirations for the novel, as he told Irma Arkus in an interview on Hi-Sci-Fri (The interview begins at 22:17). They also discuss the evolution of altruism, the deleterious effects of radiation, and other sciency bits from the novel.

Read excerpts from The Unselfish Gene, and take a peek at the novel's illustrations.

Purchase The Unselfish Gene @ Amazon.com.

Bioscience books discussed on the Hi-Sci-Fi podcast:

David Sloan Wilson's Unto Others: The Evolution and Psychology of Unselfish Behavior.

Richard Dawkins' The Selfish Gene

Tags:science fiction, zombies, genetics

Creature Features

2009-10-30T18:25:00.000-07:00

If you plan to stay in this Halloween weekend, you might want to plug your laptop into your TV, dim the lights and watch one of the many free SF-horror movies featuring terrible (in more ways than one) creatures.

Here are a few to get you started:

Movie: The Killer Shrews (1959) (Google video)
The science fiction setup: A doctor performs experiments to make humans half-size which have the unintended side effect of creating giant, venomous shrews.

Sometimes called one of the worst sci-fi movies ever made, you can get a taste of Killer Shrews from the trailer:

Movie: Giant Spider Invasion (1975) (Hulu.com, US only)
The science fiction setup: "NASA scientists Dr. Langer and Dr. Vance try to save Wisconsin from 15-foot flesh-eating spiders from another dimension."

Movie: Empire of the Ants (1977) (Hulu.com, US only)
The science fiction setup: "An aggressive land developer takes a boatload of prospective buyers to a reclaimed swamp in the southeast. While there, the group is attacked by a swarm of huge ants, the result of genetic mutation after exposure to atomic wastes."

These movies may be more silly than scary, but they'll keep you entertained for a few hours while you are waiting for trick-or-treaters.

You can find more free horror movies at Classic Cinema Online, YouTube, and Hulu.com

Tags:science fiction, biology, horror

When it Changed - Science Into Fiction

2009-10-29T21:51:00.000-07:00

UK publisher Comma Press has just released When it Changed, a cool-sounding new anthology where writers and scientists have teamed up to produce something that incorporates both their specialities. From their book's web site:

When It Changed is an attempt to put authors and scientists back in touch with each other, to re-introduce research ideas with literary concerns, and to re-forge the alloy that once made SF great. Composed collaboratively – through a series of visits and conversations between leading authors and practicing scientists – it offers fictionalised glimpses into the far corners of current research fields, be they in nanotechnology, invertebrate physiology, particle physics, or software archaeology. From Planck's Length (the smallest indivisible distance) to Plankton (potential saviours of the Earth's ecosystem), from virtual encounters between Witgenstein and Turing, to future civilisations torn asunder by different readings of the Standard Model, together these stories represent a literary 'experiment' in the true sense of the word, and endeavour to isolate a whole new strain of the SF bug.

Edited by award-winning author Geoff Ryman, the scientists involved include two biologists and a bioethicist:

Dr. Jennifer Rowntree, post-doctoral researcher, Faculty of Life Science, University of Manchester. Rowntree is a plant evolutionary ecologist whose reseach includes "genetics of plant-plant and plant-animal interactions and the value of genetic diversity in plant communities."
Dr. Matthew Cobb, Programme Director Biology, the University of Manchester. Cobb and his laboratory study how genes and environment shape animal behavior and communication. Most of his research has focused on pheromones and olfaction in fruit flies. Cobb was paired with writer Simon Ings, who wrote the story "Zoology" for the anthology.
Professor Steve Williams, Williams develops and uses magnetic resonance imaging techniques to study appetite regulation and gut-brain interctions.
Professor John Harris, Lord Alliance Professor of Bioethics, and Director of the Institute for Science, Ethics and Innovation, University of Manchester. He has written a number of books, including Enhancing Evolution: The Ethical Case for Making Better People and On Cloning.

When it Changed had it's UK debut at an apparent joint event of the overlapping Manchester Literature Festival and Manchester Science Festival (which runs through the weekend -TThere's a lecture on "Exploring neuroscience through literature" on Sunday, Nov. 1, which is right up Bio in SF's alley). You can read all about the October 24th panel on the Manchester Literature Festival Blog.

When it Changed will be released in the US in April 2010.

(via io9)

Tags:science fiction, biology, When it Changed

Joan Slonczewski's Biology in Science Fiction Course

2009-10-27T22:41:00.000-07:00

The Columbus Dispatch published a nice article about Kenyon College biology professor and science fiction writer Joan Slonczewski's Biology in Science Fiction course:

"It's well-known as being amazing," said Kenyon student Ferrell Garramone, an 18-year-old studio-art major from Nashville, Tenn.

"I took (advanced-placement) biology in high school, and it was just a drone. This is much better than reading a textbook."

The offering has plenty of required reading: six novels, including two by Slonczewski. And it includes pop quizzes, class presentations and homework assignments known as "mutant challenges."
[snip]
Kenyon students -- most with backgrounds in literature, philosophy and the arts -- relate to the approach.

"I think it epitomizes liberal-arts education," said Rachel Rubenstein, a 21-year-old American studies major from San Francisco. "It's interesting, and it's exciting."

There has been a lot of discussion of late about how to make science interesting and engaging to non-scientists. This seems like a great approach - not only do students learn about biology without being put off by a dry textbook, but the course also probably introduces science fiction to students who wouldn't read it otherwise. It's a win-win!

Slonczewski has put the class syllabus, quizes, related links, and study guide online. The class has started a related wiki, and many of the students' projects are online.

This year the course focuses on "Mutants". Some of the science fiction references that were used:

Mutants in X-Men
Star Trek:TOS episodes "The Trouble with Tribbles" and "The Devil in the Dark"
Star Trek:TNG episode "The Measure of a Man"
X-Files episodes "The Host", "The Erlenmeyer Flask", "The Post-Modern Prometheus"
The Time Machine by HG Wells (full free text with audio, buy at Amazon.com)
Galapagos by Kurt Vonnegut (Wikipedia, Amazon.com)
Dune by Frank Herbert (Wikipedia, Amazon.com)
Jurassic Park by Michael Crichton (Wikipedia, Amazon.com)
Slonczewski's own Door into Ocean (Wikipedia, Amazon.com) and Brain Plague (Amazon.com)
Barlow's Guide to Extraterrestrials (Amazon.com)

See the course syllabus for the full list.

(I find it oddly comforting that her students are required to have a calculator that doesn't look much different than the one I used in my own college days, way back in the 80s. I suppose the difference is that my good old Casio was the fanciest bit of technology I carried around with me, while students today probably all have cell phones with more computing power.)

Related posts about Joan Slonczewski:

SF Pet Fish: Guest Post at the Reef Tank

2009-10-27T21:43:00.000-07:00

I have another guest post up at The Reef Tank blog, in which I talk about my favorite science fictional pet fish. Go check it out!

Image: Borg Hugh examines Livingston, Captain Picard's pet lionfish

Tags:science fiction, biology

ALL THESE WORLDS ARE YOURS, EXCEPT...

2009-10-12T21:21:00.000-07:00

" . . . relay this information to Earth. Tsien destroyed three hours ago. I'm only survivor. Using my suit radio – no idea if it has enough range, but it's the only chance. Please listen carefully. THERE IS LIFE ON EUROPA. I repeat: THERE IS LIFE ON EUROPA. . . "

~ 2010: Odyssey Two by Arthur C. Clarke

Europa, one of the Jupiter's large moons, holds a special place in the minds of science fiction writers and astrobiologists alike. What sets Europa apart from the other planets and moons in our solar system is that it is covered with a fairly smooth surface layer of frozen water, and its interior is much hotter than its surface, suggesting that there could be a zone of liquid water under that protective layer of ice where life might exist. That easily accessible source of water on its surface could also make Europa a handy refueling stop for space ships exploring the outer solar system – assuming there isn't the sort of life that destroyed the ill-fated spaceship Tsien in Clarke's 2010.

In the afterword to 2010, Arthur C. Clarke says his Europans were inspired in part by a 1980 article by Richard C. Hoagland – "The Europa Enigma" – which describes his "quite brilliant concept" that there might be life on Europa. Since then, NASA's Galileo exploration mission to Jupiter and its moons has provided more detailed information about the moon's surface:

Prior to the Galileo mission, scientists' knowledge of Europa was simply a small ice- covered moon with an exceptionally bright surface covered by faint curved and linear markings. Now, scientists see evidence of a young and thin, cracked and ruptured ice shell, probably moving slowly over the surface of a briny ocean that is 100 kilometers (62 miles) or more deep.

University of Arizona Professor of Planetary Sciences Richard J. Greenberg, a member of the Galileo Imaging Team, believes that Europa might even be able to support fairly complex life forms, as Discovery News reported last week:

Judging by how quickly Europa's surface ice is replenished, Richard Greenberg estimates that enough oxygen reaches the subterranean ocean to sustain "macrofauna" -- more complex, animal-like organisms. Assuming Europa life forms would need as much oxygen as Earth-like fish, Greenberg estimates the moon's ocean has enough oxygen to support 6.6 billion pounds of macrofauna.

Unconstrained by the limitations of biology, futurist/physicist Freeman Dyson has speculated a bit more wildly, suggesting that we should be looking for flowers on Europa's surface:

Life could be visible from orbiting spacecraft, however, if it made a home in cracks in Europa's shell that connect the surface to the interior, Dyson said.
Such life might take the form of flowers with a parabolic shape that focuses the dim sunlight falling on Europa on the interior of the plant. Flowers with such shapes [...] are found in Arctic climes on Earth, where the plants have evolved to maximise solar energy.

Europa flowers could be detectable through a phenomenon called retroreflection, in which light gets reflected back to its source, Dyson said. This optical effect is seen in light reflected from animals' eyes, and was used in the design of road signs and mirrors left behind on the moon by Apollo astronauts.

My first thought was that Dyson had wandered off into Larry Niven's Known Space, but on further consideration I think it's an interesting idea – assuming that Dyson was referring to life forms with a superficial resemblance to flowers, rather than actual Earth-type plants. Or as University of Washington astrobiologist John Baross explained:

As for Dyson's flower suggestion, he says it is "a very radical" idea. "On Earth, flowering plants evolved during the Cretaceous and became diverse by co-evolving with insects. . . . I would not include flowering plants to my list of life-forms to look for."
"Any photosynthetic system on Europa would have to live at a depth removed from the high radiation bombarding the ice surface and still get light," Baross says. "Having said this, it would be worthwhile to make more comprehensive observations and analysis of some of the surface features, including the deeply coloured ridges [...]," he says. "One might find evidence for biosignatures or very interesting chemistry."

More likely than surface flowers are organisms similar to those found around the deep sea hydrothermal vents on Earth. Frank Carsey and his colleagues at the Jet Propulsion Laboratory are designing robotic vehicles that will be able to cut through ice and explore the watery world beneath, initially in Antarctica, but with the hope of eventually exploring Europa's depths. Until we are able to send exploratory probes, the possibility of life on Europa is little more than educated speculation.

Free Short Fiction:

"A Spy in Europa" by Alastair Reynolds
"The Color of Sunfire" by Larry Niven (set in Know Space, with Slaver Sunflowers)

Further Background Reading:

Scans of Richard Hoagland's article "The Europa Enigma" (Star and Sky Magazine, Jan. 1980)
Discovery Channel Video: Top 5 Reasons Europa Rocks
Technical Presentation: "Checking up on Arthur C. Clarke: The next mission to Europa and the Jupiter System" by Dr. Bill Moore
University of Arizona's Richard Greenberg has written two popular science books about Europa. His most recent is Unmasking Europa: The Search for Life on Jupiter's Ocean Moon (link to Amazon.com)
2010: Odyssey Two (link to Amazon.com)

Top Image: The Conamara Chaos. "a view of a small region of the thin, disrupted ice crust in the Conamara region of Jupiter's moon Europa showing the interplay of surface colors with ice structures." From NASA's Galileo Image Gallery. More details.
Middle Image: Europa and the Thrace Region. This image shows an image of the cracked surface of Europa. From NASA's Galileo Image Gallery.
Middle Image:"Metal Flower" http://www.flickr.com/photos/quepollo/ / CC BY 2.0
Bottom Image: Artist's concept of a cryobot and hydrobot that can melt through ice and then explore the water beneath. From "The Search for A Planetary Ocean on Europa" at JPL.
Tags:science fiction, biology, Europa

Science Fictional Ribosomes

2009-10-07T21:10:00.000-07:00

"What you want is to add and subtract lengths of input DNA easily, and the feedback enzyme arrangement does this. When the feedback arrangement is in place, the molecule will open itself up for transcription much more easily, and more rapidly. Your program will be transcribed onto two strings of RNA. One of the RNA strings will go to a reader - a ribosome - for translation into a protein. Initially, the first RNA will carry a simple start-up code ––

~ Blood Music by Greg Bear, 1985

This year's Nobel Prize in Chemistry went to three scientists - Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath - for their study of the structure and function of the ribosome", the organelle assembles proteins from amino acids based on nucleic acid sequences. Since ribosomes are essential part of the cellular machinery, it's no surprise that writers who incorporate genetics and biotechnology into their fiction include it in their fiction. They even provided the name for the bioscience-based science fiction subgenre called "ribofunk".

This classic 1971 human reenactment of protein synthesis, made by the Department of Chemistry at Stanford, can give you a pretty good idea of how ribosomes work¹. (Click for bigger video)
The much abbreviated version:

DNA sequences that encode proteins are used as a template for the transcription of messenger RNA (mRNA)
a ribosome attaches to the mRNA
protein synthesis begins at a specific sequence of three nucleotides - the AUG start codon - within the mRNA
a transfer RNA (tRNA) that has a sequence complementary to the start codon sequence (the anticodon) carries the amino acid methonine to the ribosome.
a tRNA with an anticodon complementary to the next three nucleotides in the mRNA - the next codon - also binds the ribosome, and the amino acid it carries added to the initial methionine
this process continues along the length of the mRNA until a stop codon is reached and the newly synthesized protein is released from the ribosome

Greg Bear's mention of ribosomes in Blood Music gets the process right. Other science fiction writers have used ribosomes much more fancifully in their stories. Take, for example, the 2003 short story "Junk DNA" by Rudy Rucker and Bruce Sterling:

"You’re about to tell me that Alan Turing anticipated the notion of DNA as a program tape that’s read by ribosomes. And I’m not gonna be surprised."

"One step further," coaxed Veruschka. "Since the human body uses one kind of ribosome, why not replace that with another? The Universal Ribosome–it reads in its program as well as its data before it begins to act. All from that good junk DNA, yes Janna? And what is junk? Your bottom drawer? My garbage can? Your capitalist attic, and my start-up garage!"

"Normal ribosomes skip right over the junk DNA," said Janna. "It’s supposed to be meaningless to the modern genome. Junk DNA is just scribbled-over things. Like the crossed-out numbers in an address book. A palimpsest. Junk DNA is the half-erased traces of the original codes–from long before humanity."

While they use lots of sciency terminology, the description of ribosome function doesn't make much sense. Of course ribosomes skip over "junk DNA" - they don't interact with DNA at all. And while some "junk DNA" may be transcribed into "junk mRNA", it appears that those sequences are degraded before they can be used to encode protein. I'm just not grokking how "junk DNA" that is primarily made up degenerate coding sequences², could be translated into proteins that do anything more than muck up cells, even given an Universal Ribosome Turing-like machine.³

And I should say that "Junk DNA" is an entertaining story if you can gloss over the nonsensical biology details - read it for yourself for free at Asimov's Science Fiction.

I'm hoping that science fiction writers will embrace recent research exploring complex biochemistry of our cells to come up with some interesting variations on life as we know it. I just wish they would get their terms straight (of course, that's probably just me).

Oh, and if you know other SF that uses ribosomes as a plot device, mention them in the comments. I know there is an episode of Star Trek:TNG that does, but I couldn't come up with any other examples.

1. Note that the ribosomal components are not depicted to scale. They are also a bit more colorfully dressed than you find in your typical cell.

2. What most biologists call "junk DNA" is primarily made up of repetitive DNA sequences from transposable elements, not interesteringly "scribbled over" ancient genes.

3. While DNA-based Turing machines have been proposed (and even shown to work in rudimentary form), the "computations" are not performed by protein synthesis, which is the function of ribosomes I don't think that's the case, anyway. My understanding of Turing machines is a little fuzzy. Mark Chu-Carroll has posts about them here and here and here that I'm still thinking about.

My related posts:

Gregor Mendel Died for Your Sins! Biopunk and Ribofunk
Another Day, Another Woman Wins a Nobel Prize for Nucleic Acid Biochemistry (at Women in Science)

Animation: "Animation of the small subunit of the Thermus thermophilus ribosome. RNA shown in orange, protein in blue." Taken from PDB 1FKA and animated by David S. Goodsell
Tags:science fiction, ribosomes

Telomeres, Aging, and Science Fiction

2009-10-05T20:15:00.000-07:00

It was announced today that Elizabeth Blackburn, Carol Greider and Jack Szostack won the Nobel Prize in Physiology or Medicine for their "discovery of how chromosomes are protected by telomeres and the enzyme telomerase." While the winners' biochemical studies have been extremely important in our understanding of how cells divide, what has caught the attention of science fiction writers is the role that telomeres - or more precisely the loss of telomere sequences - plays in the process of aging.

A bit of biochemical background:

When Watson and Crick figured out the double-helix structure of deoxyribonucleic acid, or DNA, one of the cool aspects of their model was that the structure immediately suggested how identical copies could be produced when cells divide: the two strands of DNA could "unzip" and be used as templates to create a new double strand. Research into the actual biochemistry of DNA replication, however, discovered a problem. The enzymes that synthesize the duplicate strand of DNA - DNA polymerases - can only add nucleotides onto an existing nucleic acid sequence called a primer, which is made of RNA, rather than DNA.

When the DNA sequence that is being duplicated is a circle, like most bacterial chromosomes, the head of the growing DNA strand eventually meets up with its tail, completing the sequence. However, the DNA in the nuclei of eukaryotic cells - which includes fungi, plant and animal cells - is packaged into large linear chromosomes. Consider that every human starts out as a single cell but ends up with an estimated 10 trillion (10¹³) cells after many many cell divisions. If your chromosomes shrank every time a cell divided, they would be severely truncated by the time you were ready to pass on your DNA to your offspring and any functioning genes located near the ends of the chromosomes would be lost.

What chromosomes clearly needed is something to protect its ends during replication, and that "something" turns out to be a telomere. A telomere is a short DNA sequence on the end of the that is repeated many times and folds into a three-dimensional structure that protects the ends of chromosomes. Nobel winner Blackburn had compared telomeres to the plastic tips that prevent shoelaces from fraying.

Imagining biological aglets paints a pretty decent picture of what telomeres do, but doesn't really capture the dynamic nature of chromosome structure. An enzyme called telomerase can extend the repeating telomere sequence, but telomerase is absent from most adult cells, so a bit of the telomere sequence is lost every time a cell divides. Once its telomeres become too short, a cell loses its ability to divide and either ages or self-destructs.

If all that seems too complicated to visualize, check out this nice animated tutorial on "Solving the End-Replication Problem" or watch Elizabeth Blackburn's excellent recent lecture on telomeres and aging.

So how has telomere research been adopted into science fiction? I've looked at a couple of examples below.

Telomeres as Longevity Controls

"Look at me," said McGavin, spreading his arms again. "I'm sixty-two years old, according to my birth certificate. But my cells, my telomeres, my free-radical levels, and every other indicator say I'm twenty-five. And, if anything, I feel younger even than that."
Don's jaw must have been hanging open in surprise. "You thought I'd had a facelift, or something like that?" McGavin said, looking at him. "Plastic surgery is like a software patch. It's a quick, kludgy fix, and it often creates more problems than it solves. But rejuvenation, well, that's like a code rewrite — it's a real fix. You don't just look young again; you are young." His thin eyebrows climbed his wide forehead. "And that's what I'm offering you. The full-blown rejuvenation treatment."
~ Rollback by Robert J. Sawyer

A natural extrapolation from the correlation between the shortening of telomers and aging is that artifical means of keeping telomeres long would reverse - or at least halt - the aging process. That is one of the premises of Robert Sawyer's 2007 novel Rollback, in which the characters undergo anti-aging Rejuvination treatments that includes telomere lengthening. At least that's what the treatments are meant to do.

"We did succeed in lengthening your telomeres, Sarah, but for some reason the new endcap sequences are just being ignored when your chromosomes are being reproduced. Instead of continuing to transcribe all the way up to the end of your DNA, the replicator enzyme is stopping short, at where your chromosome arms used to end."
~ from Rollback by Robert J. Sawyer

I'm finding it hard to imagine how DNA replication would not occur in extended telomeres and be limited to the exact end of the original telomeres, since the extended telomeres should just be repeats of the same DNA sequence¹, at least the way I would do it.

The easiest way to extend telomere length is by increasing the activity of the enzyme telomerase. Scientists at the biotech company Geron, for example, have shown that expression of telomerase in adult human cells can signficantly increase the life span of those cells in culture. Extending that to "cure" human aging has been suggested by others, and is not surprisingly the claimed mechanism of action of overhyped so-called "neutraceuticals" currently on the market, as well as some anti-aging drugs that are apparently in development.

It's important to keep in mind, however, that there is a potential downside to allowing cells to divide indefinitely. The adult cells that do express telomerase are usually tumor cells. That's not particularly surprising, since one of the characteristics of cancer cells is that they keep dividing when they aren't supposed to be. While introduction of telomerase can immortalize human cells in culture without causing changes associated with cancer cells , transgenic mice with increased telomerase expression only show an increased lifespan if they don't die from tumors during their first year of life. I don't think that would be acceptable for a human therapeutic treatement.

So while telomeres are an obvious target to increase human longevity, I think we're a long way from safe and practical anti-aging treatments.

1. I haven't read Rollback beyond a few excerpts, so the speculation is all mine and not reflective of the what's in the novel. But to get all pedantic, that a particular passage seems to muddle the action of DNA polymerase enzymes, which replicate DNA, telomerase, which is a reverse transcriptase (a DNA polymerase that uses an RNA template), and "transcription" which is the synthesis of RNA using a DNA template (i.e., not DNA replication). I guess it all sounds good and sciency if you aren't familiar with the terminology. Or maybe there's a better explanation in the text. Clearly I need to put Rollback on my "to read" list.

Telomeres as the Human Equivalent of Tree Rings

While it it's been well established that telomeres get shorter as cells divide and an individual gets older, it wasn't until fairly recently that it was demonstrated that telomere shortening appears to occur at a predictable rate. In 2002 scientists at Kyushu University in Japan published a method of roughly estimating human age from DNA samples (see Tsuji et al. (2002) doi:10.1016/S0379-0738(02)00086-5). That's a nifty scientific device to determine an individual isn't the age he claims to be - say, for example if the character turns out to have been (dun, dun, dun) cloned from an adult cell.

The logic goes like this: as people age, their telomeres get shorter. When a clone is made by transferring the nucleus of an adult cell into an egg, the telomeres are presumably at their adult length, rather than the longer length found in embryos. As the clone ages, its telomeres would always be shorter than uncloned individuals of the same age. Not only would the shorter telomere length give away the fact that the individual was a clone, but the clone's life would be shortened because his cells would stop dividing at an earlier age.

Science fictionally, that was the scenario used on Stargate Atlantis. In the episode "The Kindred" the Stargate Atlantis team discovers an imprisoned Dr. Beckett. That wouldn't have been particularly remarkable if Beckett hadn't died heroically several years before. The man they found looked like Dr. Beckett, had the memories of Dr. Beckett and even was genetically identical to Dr. Beckett - except that his telomeres were 30% shorter than they should have been for a man his age. Sadly, his cells are also rapidly degenerating so that he needs to be kept in stasis until the ~~plot~~ team really needs his help.

Clone Beckett looks at the analysis of his DNA.

Now that we've been cloning mammals for more than a decade, we can ask if that scenario is plausible. The first mammal cloned from an adult somatic cell, Dolly the sheep, did indeed have shorter telomeres than expected for her age, and she died young. However, that doesn't seem to hold true for all other cloned animals. There is evidence from cloned pigs and cloned cattle, for example, that the presence of telomerase enzyme during embryonic development can rejuvinate the length of telomeres in clones. And it's still unclear whether Dolly's shorted telomeres played any role in her death.

And to complicate matters, telomere length isn't only dictated by age. For example, psychological stress has been shown to reduce telomere length to the equivalent of 10 years of aging, and men generally have shorter telomeres than women of the same age. While telomeres may be a good measure of an individuals physiological age, I suspect that they will never provide more than an approximation of chronological age.

----

So to sum it all up: telomere length can affect both the aging and health of cells, in ways that aren't entirely understood. Ideal science fiction fodder!

My related posts:

Are clones like cheap knockoffs?
Blackburn and Greider win the Nobel for Medicine: the first time two women share the prize (at Women in Science)

Top Image: Crystal structure of parallel quadruplexes from human telomeric DNA. The DNA strand (blue) circles the bases that stack together in the center around three co-ordinated metal ions (green). Produced from NDB ID: UD001 by Thomas Splettstoesser for Wikipedia.
Middle Image: Cartoon of a telomere forming a loop at the end of a chromosome. From Wikipedia.
Middle Image: Chromosomes with telomeres stained yellow. From the Human Genome Program, US Department of Energy, 1997.
Bottom Image: Clone Beckett looks at the analysis of his telomeres. Screen grab by Crystal @ Perspective.

Tags:science fiction, telomeres

And there were giants in those days . . .

2009-09-30T22:54:00.000-07:00

Imagine that at some point in the near future explorers on the moon discovered a dead space suit-clad body. Imagine further that examination of the body - nicknamed "Charlie" turned out to be 50,000 years old - and fully human. That's the premise of James P. Hogan's 1977 novel Inherit the Stars.

Now, Charlie's kind, Hunt told himself, must have evolved to their human form somewhere. That this "somewhere" was either Earth or not Earth was fairly obvious, the rules of basic logic admitting no other possibility. He traced back over what he could recall of the conventional account of the evolution of terrestrial life forms and wondered if, despite the generations of painstaking effort and research that had been devoted to the subject, there might after all be more to the story than had up until then been so confidently supposed. Several thousands of millions of years was a long time by anybody's standards; was it so totally inconceivable that somewhere in all those gulfs of uncertainty, there could be enough room to lose an advanced line of human descent which had flourished and died out long before modern man began his own ascent?

Now the novel itself isn't very good, as novels go. There is no character development and little plot beyond scientists lecturing about "Charlie's" origin. The only female character that appears in more than one paragraph is introduced via the "proud thrust of her behind under her thin skirt", provides a clue to translating Charlie's alien-language documents not through any particular expertise, but because she is familiar with the format of a diary, then spends the rest of the book pouting and winking. There is no conflict or personal relationships any of the other usual things that drive a story.

The novel provides the convenient discovery of additional artifacts to help the scientists with their analysis, including a 25 million year old spaceship with the skeleton of a non-human giant and preserved samples of Earthly flora and fauna. There's never really any question that the mystery of Charlie's life fully will be understood by the final chapter.

In the end, it's just a good old-fashioned "what if" story, and one that I found fairly interesting.(Yes I'm easy.) There aren't many science fiction novels that speculate about evolution, so that makes it fairly unique. Could technologically-advanced humans have existed on Earth 50,000 years ago? Could Charlie be the product of convergent evolution on another planet? If completely alien species were successfully introduced into a planet's ecosystem and survived (and evolved) for millions of years, how would that look to evolutionary biologists?

Now this being fiction, the scientists are able to extract a lot more information from poor Charlie's ancient freeze-dried body than you might expect, such as precise enough metabolic information to infer the composition of the atmosphere where he lived. But, very oddly from a modern perspective, there is no DNA sequence data or detailed molecular phylogenetics. That's not too surprising, since back when the novel was written DNA sequencing was in its infancy. since Sanger, Gilbert, and Berg didn't receive their Nobel Prize for their contributions towards recombinant DNA technology and sequencing until 1980, and the human genome project wasn't even a twinkle in Wally Gilbert's eye in the mid-1970s.
Professor Danchekker, the novel's chief biologist and paleontologist, is of the adaptationist school of evolutionary thought - he assumes that all of Charlie's apparent traits are due to adaptions to his environment. He also doesn't have that great a grasp on evolutionary theory, at least it seems that way when he is lecturing about it:

"The point you are overlooking here, I think, is that the evolutionary process is fundamentally made up of random events. Every living organism that exists today is the product of a chain of successive mutations that has continued over millions of years. The most important fact to grasp is that each discrete mutation is in itself a purely random event, brought about by aberrations in genetic coding and the mixing of the sex cells from different parents. The environment into which the mutant is born dictates whether it will survive to reproduce its kind or whether it will die out. Thus, some new characteristics are selected for further improvement, while others are promptly eradicated and still others are diluted away by interbreeding.

and later

"But this is typical of the way in which evolution works. The forces of natural selection will always operate in such a way as to bend and shape a new mutation, and to preserve a variation of it that offers the best prospects of survival for the species as a whole. [...]"

Evolution does not happen merely by random chance as he suggests, and he seems to be ignorant of the role that genetic drift plays alongside natural selection. And then there is his belief that humans are oh so very special:

"Have you ever stopped to think what it is that makes man so different from all the other animals on Earth? I know that we have larger brains, more versatile hands, and so forth; what I am referring to is something else. Most animals, when in a hopeless situation will resign themselves to fate and perish in ignominy. Man, on the other hand, does not know how to give in. He is capable of summoning up reserves of stubbornness and resilience that are without parallel on his planet. He is able to attack anything that threatens his survival, with an aggressiveness the like of which the Earth has never seen otherwise. It is this that has enabled him to sweep all before him, made him lord of all the beasts, helped him tame the winds, the rivers, the tides, and even the power of the Sun itself. [...]"

It seems he'd be a fan of the humanity test used by the Bene Gesserit in the Dune novels. As Reverend Mother Gaius Helen Mohiam tells Paul Atridies:

"You've heard of animals chewing off a leg to escape a trap? There's an animal kind of trick. A human would remain in the trap, endure he pain, feigning death that he might kill the trapper and remove a threat to his kind.

So it's a comforting notion that humanity's aggressiveness and ability to transcend suffering is both unique and an excellent survival trait, but I don't think there is any solid science to support that notion.

So the details of the evolutionary biology aren't at all perfect*. And yet, I still found myself entertained by the wild speculation and the final piecing-together of Charlie's life. Like I mentioned above, I'm easy. However, I probably won't be searching out the sequels - known as Hogan's "Giants Novels".

You can read Inherit the Stars for free at the Baen Free Library

If you do read it, you might be interested in some additional scientific background related to the story:

Becoming Human (an interactive web site about human evolution)
Human Population Bottleneck (Wikipedia), or more technically: Hawks J et al "Population Bottlenecks and Pleistocene Human Evolution" Mol Biol Evol 17:2-22 (2000)
On Fossil Coral Record Dates, or if you have access you can read the original paper: Wells JW "Coral Growth and Geochronometry" Nature 197:948-950 (1963)
Carbon dioxide toxicity (Wikipedia)

* Hogan is apparently a "skeptic" of the "I don't believe any modern science that touches a political issue" variety. His web site has positive links to books and sites about Intelligent Design, AIDS denialism and other pseudoscience. So his writing is likely not a good source for biology-based science fiction.

Tags:science fiction, evolution, paleontology

The Fiction of Now

2009-09-28T23:40:00.000-07:00

The September 19th issue of London-based popular science magazine New Scientist is a special section, "Sci-fi special: The fiction of now"*, guest edited by Kim Stanley Robinson.

I don't feel like I know enough to either agree or disagree with Robinson's assessment of British science fiction. I would agree with him, however, that the British SF writers who contributed flash fiction to the special issue are excellent.

Justina Robson's story "One Shot" is the only completely biological one of the bunch, but it's worth spending the short time it takes to read them all.

And if you think you could do better, enter New Scientist's Flash fiction competition with your story or 350 words or less.

* New Scientist unfortunately seem to have missed the memo that some consider SciFi a dirty word - perhaps the hyphen removes the sting?

Tags:science fiction, biology

Who knew cats had a high midi-chlorian count?

2009-09-27T19:16:00.000-07:00

Back to regular posting!

Image from Animals with Lightsabers (click for large version).

WiSF reading club: Woman on the Edge of Time - Equality Through Biotechnology?

2009-08-12T20:16:00.000-07:00

Note: I've volunteered to host the WiSF reading club discussion about Marge Piercy's Woman on the Edge of Time. The post below is my take on one aspect of the novel - one that fits in with the "biology in science fiction" theme of my blog quite nicely - but I don't mean for it to limit the discussion. I think there are a number of other issues the novel touches on that would be interesting to explore, so please have at it in the comments.

====

Marge Piercy's Woman on the Edge of Time is a disturbing novel. It's the story of Consuelo "Connie" Ramos, a poor Mexican-American woman who has been in and out of mental hospitals. She ends up committed once again after she physically defends her niece from her niece's pimp boyfriend and that's where the horror starts. In the "present day" (mid-1970s) mental hospital the patients are treated with both indifference and abuse by the staff, and Connie and several other patients are chosen to receive experimental neural control implants, not only without their consent, but in Connie's case explicitly against her wishes. The patients are considered little different than test animals by the physicians and doctors participating in the experiment:

[Connie] remembered something she had heard Dr. Redding say to Superintendent Hodges: that they had used up five thousand monkeys before they began doing these operations on patients. Used up. She had heard him say he had wanted to work with prisoners – he thought the results would be more impressive – but there had been such an uproar about three little psychosurgical procedures at Vacaville in California that his team decided to work with mental patients. "After all," he had said, smiling his best ironic smile, "they made a court case and a bleeding heart publicity brouhaha about three procedures, while San Francisco Children's Hospital does hundreds with sound and thermal probes – mostly on neurotic women and intractable children – and no one says boo."

This unfortunately wasn't just fiction. By the mid-1970s there had been a number of cases in which experimentation on human subjects without their informed consent had been revealed to the public.

But Connie has an escape of sorts*: she is visited by Luciente, a woman from 22nd century Massachusetts. She comes from a future in which time travelers leave can behind their unconscious bodies while appearing corporeally by forming a mental link with an individual at their destination. This allows Connie to leave the nightmarish hospital to visit Luciente's utopian future. What she finds is that Luciente lives in a small rustic-appearing village, a communal society in which everyone has their own space, works to their best ability, is free to pursue their interests and has their necessities are taken care of. However that appearance of rusticity is somewhat deceiving. Not only does everyone have a personal networked computer (a "kenner"), but the underpinning of their society is advanced biotechnology.

Luciente herself is a plant geneticist who develops new crops, in part by introducing new genes from the plants in carefully preserved wild areas. But the real difference that sets her society apart from Connie's is the elimination of discrimination due to gender or race. Their solution was two-fold: eliminate childbearing and child-rearing as female-only activities and separate genetics from parenthood. As Luciente explains to Connie:

"It was part of women's long revolution. When we were breaking all the old hierarchies. Finally there was that one thing we had to give up too, the only power we ever had, in return for no more power for anyone. The original production: the power to give birth. cause as long as we were biologically enchained, we'd never be equal. And males never would be humanized to be loving and tender. So we all became mothers. Every child has three. To break the nuclear bonding."

Their reproduction is based on vitro fertilization and fetuses grown in artificial wombs. After birth, each infant has three co-mothers, male and female, who are given hormonal treatments so that all can share in nursing. And because there are no genetic ties between parents and their children, they have eliminated discrimination by race. However, they have found a way to maintain cultural diversity by separating it from genetics:

"At grandcil – grand council – decisions were made forty years back to breed a high proportion of darker-skinned people and to mix the genes well through the population. At the same time, we decided to hold on to separate cultural identities. But we broke the bond between genes and culture, broke it forever. We want there to be no chance of racism again. But we don't want the melting pot where everybody ends up with thin gruel. We want diversity, for strangeness breeds richness."

As that quote hints at, people of Luciente's society can adopt any culture they chose, just as they select a name they feel suits them. Luciente's village is culturally "Wampanoag", while others are "Harlem-Black", "Cape Verde" and "Ashkenazi Jewish". I use quotes because only the elements of those cultures that fit their society are adopted - sexism, racism, and patriarchal religion are excluded.

But not everything is idyllic. Luciente and her people are at war with a neighboring society that is essentially their exact opposite. It's urban, uses genetic engineering to create super soldiers, and the common people eat bland food grown on factory farms. Connie accidentally travels to the future New York City where she meets a woman - Gildina 547-921-45-822-KBJ - from this society who has been "cosmetically fixed for sex use" and is sealed in her windowless apartment. Gildina's none to bright, and that's by design:

"She was born a dud. She's just a built-up contracty. All duds have brain deficiencies from protein scarcity in fetus and early childhood. Their IRP's are negative forty to negative fifteen. Her psych scan tests show negative twenty-five. She has no more mental capacity than a genetically improved ape."

Wealthy families and corporations in this version of the future use biotechnology to keep the lower classes oppressed. Gildina doesn't expect to live beyond her 40's while the "richies" live for centuries on involuntarily "donated" organs. It's a nasty place to be one of the masses.

Despite the novel's heavy handed (to my eyes) dichotomy between Luciente's idyllic pastoral Marxist society and the hellish capitalist urban society of New York, I thought it was interesting that both versions of the future are heavily dependent on technology - particularly biotechnology - for their existance. In one it's used to allow women to become independent equal members of society, in the other it creates women that are just sexual objects (among many other differences). If forced to chose I'd obviously prefer the former over the latter, but my perhaps naive hope is that we can achieve equality without reengineering our biology.

* There is some ambiguity as to whether Connie's trips to the future are real, or whether they are just manifestations of schizophrenia. It could be argued that she is a victim of being a poor non-white woman whose normal actions are interpreted with the assumption that she is mentally ill (something that has been shown to happen in psychiatric hospital).

======

So that's my take on the biotechnology in WotEoT. I think there are a number of other aspects that would make for good discussion too.

If you are interested in an academic analysis, check out this essay by Clemson English professor Elisa Kay Sparks.

Tags:Woman on the Edge of Time, Marge Piercy, biotechnology

Hugo Award Winner: Bear's Shoggoths in Bloom

2009-08-10T22:34:00.000-07:00

The sea-swept rocks of the remote Maine coast are habitat to a panoply of colorful creatures. It's an opportunity, a little-studied maritime ecosystem. This is in part due to difficulty of access and in part due to the perils inherent in close contact with its rarest and most spectacular denizen: Oracupoda horibilis, the common surf shoggoth.

This year's Hugo for best novelette went to Elizabeth Bear for her WWII-era alternate natural history tale "Shoggoths in Bloom". As the title suggests the story features shoggoths, creatures from HP Lovecraft's Cthulhu Mythos, but with a slightly different twist.

Read Shoggoths in Bloom

Image: Shoggoth by pahko @ wikimedia commons. Also see pahko at DeviantArt.
Tags:science fiction, biology, Elizabeth Bear, Hugo Award

Hugo Award Winner: Chiang's Exhalation

2009-08-10T20:54:00.000-07:00

It has long been said that air (which others call argon) is the source of life. This is not in fact the case, and I engrave these words to describe how I came to understand the true source of life and, as a corollary, the means by which life will one day end.

Ted Chiang's excellent short story "Exhalation" won a Hugo last night. The setting is an alien world where an argon-breathing metal scientist seeks to understand his world and himself. Admittedly, it technically isn't about biology - at least not carbon-based life - but if you read it for yourself I think you'll see the similarities.

Read Exhalation
Listen to a podcast of "Exhalation" @ Escape Pod or @ Starship Sofa

Image: http://www.flickr.com/photos/dmperez/ / CC BY-NC 2.0

Tags:science fiction, biology, Ted Chiang, Hugo Award

Hugo Award Winner: Kress's Erdmann Nexus

2009-08-10T02:53:00.001-07:00

Nancy Kress's novella "The Erdmann Nexus" won a Hugo yesterday. It's basis is a combination of the philosophical and scientific concept of emergence in complex systems along with a bit of neuroscience. In particular she uses the fact that activity in the brain changes when people go into deep meditative states as an indication that humanity could develop a group mind that goes beyond basic human consciousness. It's not a new science fictional idea, and not surprisingly the story has significant religious and mystical themes. I didn't find the story that interesting, other than Kress's inclusion of some recent science.

Read The Erdmann Nexus.

Image: fMRI data for expert meditators. From Brefczynski-Lewis JA et al. "Neural correlates of attentional expertise in long-term meditation practitioners". Proc Natl Acad Sci USA (2007) 104: 11483–8. doi: 10.1073/pnas.0606552104
Tags:science fiction, neuroscience, Nancy Kress, Hugo Award

Hugo Nominee: Pride and Prometheus

2009-08-05T22:53:00.000-07:00

Mary Shelly's 1831 classic, Frankenstein; or, the Modern Prometheus, is considered by many to have been one of the earliest science fiction novels. It is, of course, dear to me because of it's basis in biology, particularly the contemporary experiments on the effect of electricity on "reanimating" corpses.

Shelley's work is revisited in John Kessel's "Pride and Prometheus", a nominee for this year's best novelette Hugo Award. Kessel has Dr. Victor Frankenstein meeting a young Miss Mary Bennet, Elizabeth Bennet's bookish younger sister in Jane Austen's Pride and Prejudice. Mary is a Natural History enthusiast, and her meeting with Frankenstein changes her life . . .

Read "Pride and Prometheus" at Fantasy & Science Fiction

Download John Kessel's The Baum Plan For Financial Independence and Other Stories (including "Pride and Prometheus") at Small Beer Press

Image: Illustration from the 1831 Edition of Mary Shelley's Frankenstein
Tags:science fiction, biology, Frankenstein, John Kessel

Science in SF at the WorldCon

2009-08-03T20:58:00.000-07:00

The next big event on the summer convention schedule is the 67th World Science Fiction Convention - Anticipation - to be held in Montreal on August 6-10. Amidst the author readings, writing workshops, filk singing, costume crafting, there will be panels on many SF and fantasy topics, including science in SF.

The Master of Ceremonies is former biologist and SF author Julie E. Czerneda. Not surprisingly, Czerneda's novels have a strong bioscience basis. She is also the author of the non-fiction No Limits: Developing Scientific Literacy Using Science Fiction, which has suggestions for teaching science with SF, and runs the SciFiZone at ScienceNews for Kids, among other educational endeavors. Czerneda will be giving the keynote at the free Science Fiction in the Classroom workshop on Thursday August 6th.

I've listed below some of the panels I think sound interesting and have a strong "science in SF" component from the scheduled convention programming (pdf). If I was attending the con, I'd have a hard time deciding which panels to attend!

Thursday

12:30 1hr 30min: "Bio-Ethics"
Alison Sinclair, Judy T. Lazar, Laura Anne Gilman, Russell Blackford, Tomoko Masuda
Medical experiments, drug companies, cloning, insurance, bookies and you.

14:00 1hr 30min: "What is Consciousness?"
Pat Cadigan, Kim Binsted, Peter Watts
Studies of complex chemical systems, AI, neuroscience and MRI are beginning to find answers to this question. What are the results and what do they mean for our sense of self?

16:00 1hr "First Contact: Worldbuilding"
Julie E. Czerneda, Charles K. Bradley, Nina Munteanu, Eoin Colfer
Worldbuilding workshop: we'll discuss and create alien worlds and cultures.

Friday

10:00 1hr: "How to Effectively Talk about Science to Non-Scientists and Why it Matters"
Chad R. Orzel
Presenting one's ideas is ever more crucial for scientists. If we don't do it well, you can be certain someone else will do it badly.

10:00 1hr "In Space Everyone Can Hear"
Chris Becker, David Stephenson, Jeanne M. Mealy, John Douglass, Christopher D. Carson
No they can't, unless it's a really neat special effects explosion. Is it possible to do hard SF on screen (big or small), or is a certain amount of dumbing down inevitable?

10:00 1hr "Is Science Used Differently in French-language SF?"
Eric Picholle, Jean-Louis Trudel, Michele Laframboise, Laurent Genefort
SF in English often prefers technology to science, but how does SF in French handle science?

10:00 1hr "Just how does Creationist Science Work?"
Edward James, Jay Lake, Leigh Ann, Teresa Nielsen Hayden, Paul Chafe, Rev. Randy Smith
What stories are told in creationist science to explain things like fossils, dinosaurs, astronomy, geology and genetics?

10:00 1hr [Teen Programming] "First Contact: Extraterrestrial Life"
Charles K. Bradley, Geoff Hart
We'll discuss possible alien worlds, and the beings that might live there.

14:00 1hr 30min: "The Future of Gender"
Cheryl Morgan, Jason Bourget, Jeanne Cavelos, Veronica Hollinger
From contraceptives to computers, is technology undermining traditional gender roles andif so where is this taking us?

14:00 1hr 30min: "Getting it Right: Environmental Issues in Science Fiction or Fantasy"
Bob Sojka, Jason Tuell, Kristin Norwood, Nina Munteanu, Mike Gallaher
These panelists want to explain about using correct environmental details in science fiction (and fantasy): weather, green buildings; green processes and, yes, linoleum

15:00 1hr [Teen Programming]: "First Contact: Create and Design Aliens"
Carl Fink, Jane Carnall, Judy T. Lazar, Jean-Pierre Guillet, Dana MacDermott, Diane Kelly
A workshop conceptualizing other beings: What sort of biology are aliens likely to have? What might they look like? What personalities/behaviors? How will this affect our communications?

15:30 1hr 30min: "Are We Conscious and Does it Matter?"
Daryl Gregory, James Morrow, Kathryn Cramer, Peter Watts
What do we mean by consciousness? Has it become as much of a distraction as wondering whether there is a heaven? Would we act any differently if we didn’t think we were conscious? How important is the concept to fantasy and science fiction?

15:30 1hr 30min: "Anatomy for Writers, Heroes and Tavern Brawlers"
Darlene Marshall, Jetse de Vries, Sean McMullen, Kristen Britain
Author, karate instructor, fencer and first aid officer Sean McMullen provides a tour of how the human body can and cannot be damaged. Want to know where a hero can be punched without any effect? Worried about his vascular dilation? Curious about the real-life version of Mr Spock’s nerve pinch? Not sure whether a really long sword fight is three hours or seven seconds? Wondering why readers are laughing because your hero has microsecond reactions? Come along and find out in complete safety.

22:00 1hr: "Build a Better Astronaut"
David H. Brummel, Jeanne Cavelos, Nick Kanas, Steven Popkes, H.G. Stratmann
With rocket accidents, radiation, zero gravity, hard vacuum and long journey times is space travel just too dangerous for humans? And if so, how are we to reach the high frontier ourselves? What changes need to be made to the human body and mind to make it better suited for interplanetary and interstellar travel?

Saturday

9:00 1hr: "The Goldilocks Alien"
G. David Nordley, Judy T. Lazar, Geoff Hart
Many SFnal aliens come from worlds just like ours - not too hot, not too cold, not too radioactive. Is this realistic? Can't we do better than this? What if their evolutionary pattern was different?

10:00 1hr: "The Philosophy of Science"
Chad R. Orzel (blog post on the panel), Greer Gilman, James Morrow, Jeff Warner, Richard Crownover, DD Barant
To what extent does SF explore the meaning of science for scientists and create the ideas that our culture has of science?

19:00 1hr: "Panel in the Pool"
James Bryant (G4CLF), Kat Feete, Lindsay Barbieri, Seanan McGuire, Thomas A. Easton
What would dolphins do? What side of the road would cephalopods prefer? Do they make screwdrivers for right-handed octopuses? The panel, in the deep end with lead boots, discusses aquatic intelligences.

Sunday

9:00 1hr: "Cloning Dos and Don'ts"
Birgit Houston, Jeanne Cavelos, Judy T. Lazar, Kat Feete, Paolo Bacigalupi
Cloning frequently comes up in SF, but how does it work in real life? And what happens when it goes wrong?

10:00 1hr "Science for SF Writers"
Julie E. Czerneda, Alison Sinclair, David Clements, David D. Levine
Where can you get crash courses on science for science fiction writers? Is it actually useful?

10:00 1hr "Realism in Science Fiction"
Chris Howard, kyle cassidy, Pascale Raud, Joel Polowin, Tobias Buckell
A lot of near-future SF novels duck the problems we read about in the news – climate change or energy shortage – in favour of problems which look more solveable. We all know that SF shouldn’t be pure prediction, but how much of a duty does it have to be based on realistic assumptions?

21:00 1hr "Legitimizing the Woo"
Margaret Ronald, Eoin Colfer, Peter Watts
It is an ongoing tradition of science fiction to rehabilitate overtly fantasy tropes (vampires, zombies, fairies, god) by soaking them in SFnal rationales. What are the rules for hijacking a trope from one genre and reprogramming it for another? And why bother?

Monday

10:00 1hr "A Little Learning is a Dangerous Thing"
Amy Thomson, Carl Fink, Christopher Davis, Karl Schroeder
What happens when physicists try ot write biological SF; or when a writer's research goes badly wrong?

11:00 1hr "The Drake Equation and the Fermi Failure"
Ian Tregillis, Thomas Womack, Jordin Kare, Peter Watts
Recent discoveries have enhanced our estimates of the number of planetary systems in the galaxy; recent analysis suggest that the silence dominating the hydrogen band may be more an artifact of signal dissipation than evidence of an empty universe. Is there any real point in describing the frequency of technological civilizations using a 7-variable equation for which 5 of the parameters are completely unknown? Do we even know enough to *have* a reasonable debate?

12:30 1hr 30min; "Hard SF: Is it What You Do, or How You Do It?"
Amy H. Sturgis, Marc Schirmeister, Joël Champetier, Gabrielle Harbowy
Many critics – including David Hartwell – argue that hard SF is as much defined by an attitude (how you depict science in an SF story) rather than to do with detailed depiction of science. So a story, like Ted Chiang’s “Tower of Babylon” could be hard SF whilst being based in a completely imaginary scientific foundation. Is this a useful way to see things?

12:30 1hr: "Genetic Engineering Our Offspring"
Birgit Houston, John Wilson, Judy T. Lazar, Russell Blackford, Paolo Bacigalupi
Surgical modifications, perhaps with controlled re-growth. Cyborg technology. All standard SF tropes that are now just around the next corner but one. What will all these changes mean? To us as individuals? As a society? Will we try to postpone or control them? Will we succeed? Will we still be human and does it matter? And what reactions will there be from broader society?

14:00 1hr 30min: "Mundane SF vs Science"
Geoff Ryman, Henry Spencer, Karen Burnham, Mark Olson
Mundane SF aims to extrapolate from the science of today. But science doesn’t work like that. What’s happened to the paradigm shift?

And of course that's just the tip of the iceberg, programming-wise. I'm looking forward to seeing what people report back from the con. Maybe there will even be video (?)

If you are in the Montreal area, you should consider going, particularly since they are selling low-risk "taster" memberships at the door.

Tags:science fiction, biology, WorldCon, Anticipation

Summer Vaction-Style Random Thoughts

2009-07-28T18:52:00.000-07:00

So my brother is currently in town on his annual post-Comic-Con visit (we're going to Disneyland, yay!), so my posting will be even lighter than usual this week.

I've been reading some old SF novels over the past few weeks, and here are some of my random thoughts (spoilers, although I'm not sure the warning is necessary for novels over 20 years old):

• Stranger in a Strange Land would have been much much shorter if in Heinlein's future America effective birth control had been invented before a manned expedition was sent to Mars. Also, if Michael Valentine Smith had been raised by wizards instead of Martians you could place it squarely into the Fantasy genre without having to otherwise change the plot (sufficiently advanced technology looks like magic etc. etc. ).

• I think it's a bummer that Asimov decided to tie together his series of Foundation novels and Robot stories by making the humanity's expansion onto many worlds, the creation of the Galactic Empire and its replacement by the Foundation ultimately due to the meddling of a couple of mind-reading, mind-influencing robots. I'd like to think that we'll conquer the universe without the nudging of telepathic robot nannies. Maybe I just wasn't in the mood for more magic-with-a-thin-veneer-of-science after reading SiaSL.

(Also, I wonder about the Foundation movie in development - how will they successfully adapt the original trilogy which covers a lot of time and has a lot more talking than action? Also, why not film the robot novels, which have movie-friendly Earthman/robot sidekick solve-a-mystery plots?)

• I've also just read Marge Piercy's Woman on the Edge of Time. I'm putting together a post on it, since advanced biotechnology plays an important role, but I wanted to mention that there is going to be a discussion about it starting tomorrow on sajbrfem's journal as part of a "Women in Science Fiction" reading club.

• Every so often an article like this comes up on my newsreader:

". . . it’s what technology ethicist Paul Root Wolpe, director of the Center for Ethics at Emory University says during the piece that, for me, delivers an equally big (if not bigger) impact:

“It’s what I always tell my students that there is no science fiction anymore. All the science fiction I read in high school, we’re doing.“

And I wonder to myself what sort of mundane SF Wolpe read in high school. Do we have regular space travel or colonies off of the Earth? Nope. Have we found life on other planets (never mind sentient life)? Nope. What about human genetic engineering or cloning? We're approaching that ability, but it's still highly experimental. Can we upload our minds into a computer? Not yet. Time travel? Uh uh. Telepathic robots? Not even. Most of that fun stuff isn't going to happen in the near future if at all. We are living in the future, sure, but it's not the one of most science fiction novels.

• Also I've updated my posts about the Darwinism panel at Readercon and the science in SF-related panels at Comic-Con with attendee reports.

Anyway, that should hold you 'til I'm back.

Tags:science fiction, biology

Serialized Fiction: The Vector

2009-07-22T22:53:00.000-07:00

It’s the age of the home-made virus, and humanity is dying. It just doesn’t know it yet.

In Prague, a young woman named Eva returns home to escape the plagues, only to find her mother missing and the police blaming her for the worst outbreaks in recent memory. Events are complicated by the appearance of a Healer — a merciless Chinese agent — sent to neutralize a new strain that may bring Prague to its knees.

With only days until the launch of a super-virus, Eva must navigate a hostile city and escape to safety before she becomes another faceless victim in this global, slow apocalypse.

If you like dark end-of-the-world-due-to-genetic tampering stories you should check out MCM's serialized novel The Vector. There will be a new chapter every Monday and Wednesday through the end of December - or you can buy the complete story today for $5.

Read the beginning of The Vector.

(via io9)

Tags:science fiction, viruses, The Vector

Science in Science Fiction at Comic-Con

2009-07-22T19:56:00.000-07:00

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

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

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

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

Update 3: I've embedded video of the Mad Science panel below. There are more recaps linked here.
==========

For those of you willing to brave the crowds at Comic-Con (and lucky enough to have been able to purchase a ticket before they sold out) you might be interested in the Mad Science: Science of Science Fiction panel on Thursday, from 6pm-7pm:

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

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

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

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

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

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

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

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

Tags:science fiction, biology, Comic Con

Rogue Farm

2009-07-14T21:30:00.000-07:00

Now here's a strange tale by Charles Stross that you can listen to at Escape Pod: Rogue Farm. It's a good listen if you like surreal bioengineering, a pot-smoking dog, and, of course, a rogue farm. It also has a nice reference to the fantastic genetic engineering found in Niven's known space.

A taste:

“Buggerit, I don’t have time for this,” Joe muttered. The stable waiting for the small herd of cloned spidercows cluttering up the north paddock was still knee-deep in manure, and the tractor seat wasn’t getting any warmer while he shivered out here waiting for Maddie to come and sort this thing out. It wasn’t a big herd, but it was as big as his land and his labour could manage – the big biofabricator in the shed could assemble mammalian livestock faster than he could feed them up and sell them with an honest HAND-RAISED NOT VAT-GROWN label.

“What do you want with us?” he yelled up at the gently buzzing farm.

“Brains, fresh brains for baby Jesus,” crooned the farm in a warm contralto, startling Joe half out of his skin. “Buy my brains!” Half a dozen disturbing cauliflower shapes poked suggestively out of the farms’ back then retracted again, coyly.

“Don’t want no brains around here,” Joe said stubbornly, his fingers whitening on the stock of the shotgun. “Don’t want your kind round here, neither. Go away.”

Listen to "Rogue Farm".

Tags:science fiction, genetic engineering, free fiction

Hollywood, Science, and Unscientific America

2009-07-13T20:18:00.000-07:00

As those of you who are regular readers of The Intersection are aware, Chris Mooney and Sheril Kirshenbaum's recently published book, Unscientific America: How Scientific Illiteracy Threatens our Future, takes a look at how American culture influences science literacy (or the lack thereof). There has been a lot of controversy (at least in blogland) about some of the content, particularly in the authors' suggestions as to what scientists could and should do in promoting science to the public. Discussing the science in fiction is my whole reason for blogging here, so I was particularly interested in what Unscientific America had to say about science and Hollywood*.

As the chapter points out, the way that Hollywood portrays science is often egregiously bad and the way it portrays scientists is almost always negative. Because most of the public has little exposure to either quality discussions of science** or interaction with actual scientists, what people see on the big or little screen negatively influences their perception. I can't argue with any of that.

Mooney and Kirshenbaum point out that part of the problem is that many filmmakers consider scientific accuracy to get in the way of telling an entertaining story.

But throughout the industry, there is certainly a sense that science is inimical to storytelling, that it quashes creativity, which must be allowed to breathe. As screenwriter and ScienceDebate2008 founder Matthew Chapman explained about some of his fellow writers; "among the less talented, there's I think a kind of inherent prejudice against science, because science means being rational, and being rational is considered the opposite of being creative –– whereas fantasy, superstition, magic, all of these more child-like ways of looking at life, are somehow thought to be what the creative process is about."

I suspect that the large number of actors and Hollywood trend setters who embrace pseudoscience and New Age-style magical thinking adds to the problem. See, for example, quantum physics woo in What the (Bleep) Do We Know!, the quackery and pseudoscience promoted on the Hollywood-connected Huffington Post, stars drinking magical Kabbalah water, and so on. Of course not every screenwriter, actor, and director in the film and television industry is anti-science, but those who are make up at least a significant minority.

But Mooney and Kirschenbaum go a step further and claim that part of the problem is that science and storytelling that is based on the laws of nature is inherantly boring to most people.

The problem for science in this context is that the technical facts it furnishes can rarely hold the attention of non-scientists – and anyone who has watched presentations at a scientific conference knows why.

and

Such science-centrism simply won't work for the broader, non-scientist population. It ignores their compelling need not to be bored. Successes like March of the Penguins notwithstanding, most of the time people need to see and hear stories about other people, or about animals that are given human attributes, as in Disney-Pixar films.

Are scientists really all pushing for Hollywood to produce technical documentaries rather than fictional tales? I haven't heard or read such an arguments. Sure there is a lot of discussion of where the science in fiction goes wrong - right here among other places. But that's not a demand that Hollywood should stop making entertaining films - the vast majority of scientists that I know can both suspend disbelief and critique the silly science they've been watching. That's why the LSC movie series is such an institution at MIT: hard-core geeks and nerds enjoy watching summer blockbusters as much as they enjoy picking them apart (and shouting "LSC...sucks", of course). It's all part of the fun.

Personally, I don't get particularly annoyed at bad science unless it either does nothing to serve the plot – for example, the scientist in Red Planet naming the DNA bases A, G, T, and P (rather than C) – or if the writer or director has made a big fuss about how science-based their movie. A couple of recent examples of the latter are the TV series Eleventh Hour and M. Knight Shayamalan's The Happening. If you claim you are basing your show on science, I'm going to hold it to a higher standard. On the other hand, the outrageous science on Fringe doesn't bother me because that's the whole point of the series. And sure, I'm going to write about where they get it wrong, but that doesn't mean I think they should be doing things differently.

Anyway, the only example of a narrow minded entertainment-hating scientist that Unscientific America comes up is bioscience popularizer and unapologetic atheist Richard Dawkins:

And some scientists will also have to get over the idea that everyone ought to be as captivated by the intricacies of science as they are. "The natural world is fascinating in its own right," Oxford's Richard Dawkins has stated. "It really doesn't need human drama to be fascinating." He even reported told the New York Times that he wondered why Jurassic Park required a cast that included human beings –– after all, it already had dinosaurs.

Now, I looked up the 1998 New York Times story that that quote was pulled from, and from the way I read it, I would take what Dawkins is reported to have said with a big grain of salt. You see, the article is actually about a series of panel discussions hosted by the Sloan Foundation, which included Hollywood directors and producers and scientists. There was much disagreement and at one point the discussion "degenerated into a raucous name-calling exchange." It was at an interview after this meeting that Dawkins "wondered why ''Jurassic Park'' had to have any people in it at all when it had dinosaurs." I don't think it's far-fetched to think that he might have been speaking out of annoyance or less than completely seriously - something we can't judge because the article gives no context for Dawkins' paraphrased comment.

And no matter what Dawkins did say, he certainly isn't the spokesman for all scientists, or even all biologists. I'm disappointed that Unscientifc America indulges in the same sort of negative stereotyping of scientists that pop culture does. And maybe I'm misunderstanding, but the suggestion seems to be that scientists should not comment on or complain about "minor" scientific inaccuracies, because, well, just because:

Yet in marshaling scientific complaints against the entertainment industry, it's important to consider what really matters and what doesn't. Any specialist – a historian, say, or an anthropologist – is prone to get ticked off if a film or TV drama makes a mistake about his or her field. [ . . . ] So how worried should we really be if an inaccuracy or implausibility sips into a film to serve the plot or to satisfy audience expectations – if, say, Star Wars shows fiery explosions in space? Probably not very.

Again, I don't really get it. It's not as if scientists aren't filing formal complaints with the movie studios or organizing boycotts because of science bloopers. Talking or writing about where the movies go wrong harms no one (except maybe thin-skinned filmmakers) and actually can be an entertaining way to start a discussion about real science. And I'm not convinced that having more realistic space battles in Star Wars would have made it less entertaining.***

Anyway, they do have some suggestions that the "scientific community" can take to try to improve the depiction of science and scientists in films and television:

- First off, as noted above, scientists have to understand that people want to be entertained by the movies, which should include both drama and people. This is where scientists who are also science fiction writers can play a major role, since they are already familiar with the difficulties of balancing the science with the fiction to tell a compelling story. But as I noted above, there are many scientists who are great movie fans too, and who wouldn't have any trouble with the idea that telling a story requires some suspension of disbelief.

- Next, get to know the right people in Hollywood, and know them well:

Science consultants can have an impact on the scientific content in a film's script, on its set design, on its sound effects. In general, they are invited on board by those at the head of film projects –– directors, producers –– and their influence is proportionate to the closeness of their relationship to that leader.

The key is developing "relationships with important players and learn how to serve them to further shared goals, rather than merely issuing criticism and denunciation." There are, in fact, already number of scientists who already act as advisors for movies and TV shows, so that's clearly doable.

But I think criticism is important too, since bad science sometimes can't be helped – the superpowered "mutants" in X-Men, for example, aren't going to called anything different. The scientific community is not monolithic, and so it makes that some will be included to work with Hollywood from the inside, while others will be more comfortable critiquing Hollywood from the outside. There's no reason why there can't be doing scientists doing both, unless producers and directors are so sensitive to negative comments that any criticism will turn them away from attempting to accurately portray the functioning of the universe.

- Finally, scientists must realize, they may be called for advice on too late to make any substansive changes:

By the time a science consultant arrives on the scene to work on a project, many things such as plotline, cast, and budget are usually already agreed upon, and a script has likely been written, at least in draft form. Given all of this, any effective science consultant or adviser will be acutely aware of the realities and constraints of filmmaking and will work with them, rather than trying to overturn them.

And "factual accuracy" is the first thing to go when a movie is being made:

Dawkins and some other scientists fail to grasp that in Hollywood, the story is paramount –– that narrative, drama, and character development will trump mere factual accuracy every time, and by a very long shot. Either science will align itself with these overweening objectives or it will literally get flattened by the drive for profit.

I find it a bit disturbing that they are suggesting that scientists should ignore "mere factual accuracy" to get an "in" in Hollywood. Science consultants shouldn't be the ones worrying about profit - that's the job of the filmmakers. I don't think anyone should be surprised if their suggestions for scientific accuracy are sometimes ignored, but that doesn't mean that those suggestions shouldn't be made. If factual accuracy is completely off the table, what's the point in being a science advisor?

It all sounds a bit hopeless, at least from the perspective of an individual who doesn't have any Hollywood connections or much spare time to build personal relationships with filmmakers. That's where The Science and Entertainment Exchange comes in - it should be a useful mediator between scientists interested in Hollywood and filmmakers interested in science.

So overall, I think Unscientific America does make useful points about how science is portrayed by Hollywood. However, I don't think it's helpful that the book portrays most scientists as clueless joykillers who can't enjoy a less-than-documentarian movie, or that it suggests scientists should stop criticizing science in the movies. And yes, I took it a bit personally, because discussing bad science in science fiction is much of what this blog is about. I think it's worthwhile, not in small part because I've gotten comments from people who stumbled in here looking for information about whether the science in their favorite movie or TV show is "real". I'm glad I could give them the information they were looking for.

And if you are still reading, you might want to check out some of the other posts that have discussed the "Hollywood and the Mad Scientists" chapter of Unscientific America:

Stephanie Zvan @ Quiche Moraine has an excellent post: "Mere Factual Accuracy"

"Setting up story and accuracy as a dichotomy also ignores the richness that accuracy can add to a story. In fact, whole stories can be built from closely observed detail."
Janet Stemwedel @ Adventures in Ethics and Science: "Book review: Unscientific America"

"It struck me, while reading this book, that the root problem here is no fundamental flaw in the American character, but a capitalist system that squeezes out spaces for things that are not expected to sell widely for the lowest costs to produce. Science is brimming with complexities. Explaining it, understanding it, takes time and effort. But if the news media and Hollywood (and politics, too) are harbingers of doom for a scientific America, it makes it seem just as likely to me that a long term solution will involve replacing extreme capitalism with something different. Show me the alternative and the plan to implement it, and I'm ready to roll up my sleeves and help."

ETA: And definitely read Janet's excellent post "Are scientists all on the same team?"
PZ Myers @ Pharyngula has a scathing review: "Unscientific America: How Scientiric Illiteracy Threatens Our Future"
and
Chris Mooney @ The Intersection replies: "PZ Myers vs. Unscientific America"
(Note that PZ and Chris don't agree on anything, PZ was called out in the book, and there's a fair amount of animosity between them, so the comments reflect that.)

~~I think all the Scienceblogs.com bloggers got review copies~~, A number of Scienceblogs.com bloggers have also reviewed Unscientific America, so you can read more about the book as a whole over there.

--------

* The chapter titled "Hollywood and the Mad Scientists" is the only one I've read so far, so I can't comment on the rest of the book.

** It's unfortunately true that a lot of the reporting of science in the news media is really really really bad (click the links for examples just from this month).

*** But then I'm one of those freaks who thinks showing women having a conversation about something other than than boys, weddings or babies can be entertaining too, so what do I know?

Tags:science fiction, Unscientific America

The Human Genre Project

2009-07-08T22:27:00.000-07:00

One of the most unique offerings at SciFiction is Michael Swanwick's "Periodic Table of Science Fiction", which has a short short story linked to each element in the periodic table. It starts with "The Hindenburg" for Hydrogen (atomic number 1) and continues all the way through "Now You See It Now You" for Ununoctium (atomic number 118). I don't think it's surprising that some of the bits work better than others, but it's a clever concept.

Inspired by Swanwick, Scottish science fiction writer Ken MacLeod, writer in residence at The Genomics Forum, has has put together The Human Genre Project. It looks like each of the 22 autosomal and X and Y chromosomes can have more than one entry. That's appropriate, since each carries multiple genes, and can affect many different human characteristics.

It's a work in progress - only 7 of the chromosomes have an entry - and you can still submit a contribution inspired by genes and genomics. If you need inspiration, you can explore each chromosome using the Human Genome Project's Chromosome Viewer.

If you don't want to scroll over each chromosomal image to find the stories, you can just use the Index of Human Genre Project stories by author.

Also, you can read the winners of the Genomics Network's short story competition, which aren't so much science fiction as fiction with science.

(via SF Signal)

Tags:science fiction, genomics, genetics