Biology in Science Fiction

Science and SF Tidbits: May 31, 2012

2012-05-31T21:30:00.000-07:00

Some of the science and SF links originally posted on Google+, Twitter , and Facebook the past couple weeks:

A chart that reveals how science fiction futures changed over time @io9

The SF future is getting further away? In this analysis of how far in the future the the SF future SF stories are set it looks like there is a trend towards the future setting becoming more distant from the present day. But what I find interesting is that the "mid future" - 100-500 years in the future - seems to be the most popular. I don't think that's surprising. In 100 years technology will have developed in interesting and somewhat predictable ways, and culture isn't likely to have shifted so radically that it's unrecognizable.

Genetic Fiction: A Scholar's Faves

Duke genetic policy expert Misha Angrist lists his five favorite literary novels with genetics. Despite the Jurassic Park cover illustrating the story, the Crichton novel didn't make the cut. In fact no SF is included - maybe because it isn't "literary" enough?

(One of the recommendations was Allegra Goodman's Intuition, shown above)

Addiction in Science Fiction

Joan Slonczewski looks at drug addition in SF, including her own novel Brain Plague.

Reverse Terraforming? (For supervillains only)

How might a Martian supervillain remove all Earth's water to make our planet more Mars-like?

Life on Mars: Q&A with Pulitzer Prize winning poet Tracy K. Smith

Interview with poet Tracy K. Smith on her Pulitzer prize winning collection "Life on Mars". Smith's father was an engineer who worked on the Hubble space telescope, and the poems are in part inspired by - and a tribute to - him.

Shapeshifters among us

Watch this amazing time lapse metamorphosis of a tadpole into and the migration of a fish eye. It's not quite SF shapeshifting, but it's amazing to watch nonetheless.
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Berkeley lab scientists generate electricity from viruses

Scientists genetically engineered M13 virus to enhance its piezoelectric properties. A thin film of the modified virus can generate electricity when pressure is placed on it. Imagined uses include having a layer of the viral material in the bottom of your shoe so you could charge your phone as you walk. Very cool.

Superpower from cataract surgery?

Alek Komarnitsky that after he got Crystalens implants during cataract surgery he now seems to be able to see ultraviolet light. He's provided a fair amount of documentation to support his claim. So is tis another way to help create humans with "advanced" powers?

Scientists turn DNA into Hard Drives

Using synthetic biology techniques Stanford University scientists turn DNA into a rewritable memory module. While an impressive feat, the technology can't compete with a cheap thumb drive for storage:

"Now, while the team is exploring other enzymes to improve the efficiency of their method, their next big target is increase the storage capability of the module to 8 bits, or 1 byte."

5/24
Bionic eyes to be tested next year

Helping people with genetic eye conditions to see: Bionic Vision Australia is testing a special eyeglass camera that sends signals to an implanted chip that stimulates a patients retina. It's currently pretty low resolution, but higher res devices are also in development.

Uploaded to the Life Network

"Welcome to Life" is a short film by Tom Scott about what you might see when your mind is uploaded to an online storage cloud in 2052. The subtitle: “the Singularity, ruined by lawyers”.

Yogurt makes you .... shinier

At Science in My Fiction: By the numbers, we humans are mostly made of bacteria, and our gut flora can directly affect our physiology. What might that mean for space colonization? or science fiction?

5/25

We're all mutants now

Rare novel mutations in the expanding human population make it more difficult to determine the complex genetic basis of diseases.

"As far as research goes, the conclusion is pretty simple: even though we have more human genetic samples than ever before, most studies still haven't been able to survey a large enough population to see the influence of the rapidly expanding human population. That's beginning to change, so it's important that the researchers who are doing this work use the appropriate math, or they're going to have a hard time interpreting what they see."

(I'm ignoring the snark about biologists hating math. While some do, it's pretty clear that geneticists need to have a good grasp on statistics to be successful.)

Kim Stanley Robinson on gender and longevity in 2312

Kim Stanley Robinson talks to Space.com about his new novel and what 2312 might look like. He explains why he introduced characters that aren't purely female or male, but a little bit of both.

"I guess the novel is one way of throwing this all in people's faces, and saying, "Why do you link your character traits to your biology? Masculine and feminine, what does that mean compared to male and female? Can they be reversed, can they be confused?""

5/27

The Immortal: life support machines keeping each other alive.

In this art installation artist Revital Cohen linked together a Heart-Lung Machine, a Dialysis Machine, an Infant Incubator, a Mechanical Ventilator and an Intraoperative Cell Salvage Machine and had them 'breathe' in closed circuits. "The machines of The Immortal keep each other alive through circulation of electrical impulses, oxygen and artificial blood." So is it "life"? I'd say no, since we are more than the sum of our organs, but it certainly is "life-like".

5/28

Neil Degrasse Tyson: Science is in Our DNA

According to astrophysicist and science popularizer Neil Degrasse Tyson every child is born a scientist. "Universities may describe music, literature, and painting as "the humanities," but no activity is more fundamentally human than science, says Tyson.

Mental control of a robotic arm

Neurologist Steven Novella looks at the latest developments in brain-machine interfaces, including a recent report showing paralyzed patients able to control a robotic arm with just their minds.

5/29

Freedom from Fungus: Why don't humans have chestnut-style blights and white-nose style syndromes?

Fungi are responsible for 72% of the local extinctions of animals and 64% among plandts. Why don't humans seem to be affected? The clue is that bats suffering from white-nose syndrome are infected while they are hibernating. It seems that it's our body heat that protects us from a human version of Dutch elm disease.

5/30

New Jupiter Mission to Target Alien Oceans

Could the icy oceans of Jupiter's moons - Europa, Callisto, Ganymede - harbor life? A space probe to be launched in 2030 (JUICE) may be able to spot signs of biological activity.

When Gadgets Get Under Our Skin

Will we someday have our phone and other electronic gadgets implanted so we can interface with them directly? The technology is no longer solely in the realm of science fiction.

Science and SF tidbits: May 21, 2012

2012-05-21T20:02:00.000-07:00

Some of the science and SF links originally posted on Google+, Twitter , and Facebook the past couple weeks:
Free Fiction:

2011 Nebula Award Winners
Song of Bullfrogs, Cry of Geese »
It's a lovely and sad story, ultimately about living when those you love are dying. Be sure to read the interview with author Nicola Griffith as well.

Science, arts and SF:

April 17 Cover of Developmental Cell [see image above]
The journal Developmental Cell decided to illustrate it's April 17th issue with what looks like a clip from an action-packed science fiction movie. What it illustrates:
"On the cover: The image shows AP-1A adaptor proteins working in the trans-Golgi network to coordinate clathrin-dependent basolateral sorting of cargo proteins. For more information, see Gravotta et al., pp. 811–823. The illustration was produced by HyukJae Henry Yoo and TianXu Tim Guo of Pratt Institute."
Ridley Scott talks Prometheus with Geoff Boucher - Hero Complex
On +Nerdist's +YouTube channel's Hero Complex show: The Show Los Angeles Times reporter Geoff Boucher talks to Ridley Scott, the director of Blade Runner, Alien and the upcoming Prometheus. Ridley reveals the role storyboarding plays in his films, what it was like returning to the Alien franchise and how he may return to the Bladerunner franchise in the future.
Anthill: a six-legged adventure from science to fiction »
Biologist EO Wilson's novel Anthill lets you get inside the mind (or "mind") of ants:
"The central section is an extraordinary act of what you might call species empathy, of the biologist imagining exactly what it is like to be an ant. Wilson invokes the poet Homer in his introduction, suggesting that ant "histories are epics that unfold on picnic grounds", in which "ants are a metaphor for us, and we for them." By concentrating on the struggles of the ant colony in this way, he makes the ecosystem virtually a character in the book, to which the ants give body and life."
The Strange Creatures that Cronenberg's Total Recall Would Have Included »
Ganzi-bulls and sandsubs: what Total Recall could have looked like.
The ‘Hunger Games’ Mockingjay: Fiction, for Now »Could people currently engineer a Hunger Games-style mockingjay in real life?
Biologist and author Joan Slonczewski says: "The tools needed to modify organisms are already widely dispersed in industry and beyond. “Now anybody can do a start-up,” she said."
Auto-Tuned Opening Lines - The Day of the Triffids... »
Some Saturday music weirdness for you Day of the Triffids fans.

Cool Bioscience

Dinosaur Farts May Have Warmed Prehistoric Earth »
This conclusion may be a bit overstated, but I love the headline.
Science In My Fiction » Blog Archive » Our Epic Prehistory »
At Science in My Fiction +Ryan Anderson argues that setting stories in pseudo-medieval Europe with elves and orcs isn't necessarily as interesting as the real period when there really were several species of humans living together.
"In most fantasy settings, there are several intelligent species coexisting in the same world, each with a distinctive culture and appearance. In our modern world of course, there are humans of cultures and appearances that vary beyond anything seen in most fantasy, but there are no other similarly advanced intelligent species for us to interact with. This was not always the case. In the course of human evolution, we coexisted with several other species of human, including Neanderthals, Homo floresiensis, and the recently discovered Denisova hominin."
The Effects of Music on the Brain
Sounds like your brain - or at least Oliver Sack's brain - has a "mind" of its own.
More seriously, what this seems to show that what we mean when we say we "like" something is complicated and goes beyond whether what we believe to be our brain's emotion centers are active.
For more about music and the brain, I recommend Oliver Sack's book Musicophilia: Tales of Music and the Brain
Rudolph Thauer: Deep Chemistry
Aliens among us? Deep see microorganisms live off methane.
Robots that Reveal the Inner Workings of Brain Cells
The method is 30 years old, but apparently robots do it better: "The researchers have shown that a robotic arm guided by a cell-detecting computer algorithm can identify and record from neurons in the living mouse brain with better accuracy and speed than a human experimenter"
Meat-eating plant digests insects using ants | Not Exactly Rocket Science | Discover Magazine »
Ant poop gives insect-eating plants a boost
CultureLab: The biochemistry of love and empathy »
Oxytocin is the molecule that seems to be involved in empathy. I'm not sure it's fair to say it's involved in "morality", unless you define what is "moral" very specifically to mean "caring", and exclude religion-based "morality" that is based on rules rather than empathy.
What would life be like if pterosaurs were alive today? »
Could you ride a pterosaur to work? Looks like you could - much better than sitting in rush hour traffic!
Challenges for Future Generations: space, brain preservation and more! »
+David Brin has some suggestions for brain preservation that would be decorative, to say the least.
Touché: Enhancing Touch Interaction on Humans, Screens, Liquids, and Everyday Objects
This is very cool. One step towards the sort of hands-in-the-water interface the Cylons used on their ship.
Hidden Epidemic: Tapeworms Living Inside People's Brains | Infectious Diseases | DISCOVER Magazine »
Not for the squeamish! Tapeworms can take up residence in the human brain causing epilepsy, paralysis and other serious problems. The problem is when people ingest tapeworm eggs shed by an infected person. Not surprisingly this happens most frequently in parts of the world where people don't have access to source of clean water.
Measuring transient X-rays with lobster eyes
NASA scientists are developing X-ray monitor technology based on the structure of lobster eyes.
Paralysed woman moves robot with her mind - by Nature Video
This is amazing! A paralyzed woman was able to move a robot with her mind. In this case to hand her a drink. (It's hard to imagine not being able to do mundane things like feed yourself.)
Eureka! When a Blow to the Head Creates a Sudden Genius »
Recent studies have shown that after some brain injuries rewiring unlocks hidden skills. The cool thing is that the effect can be temporarily reproduced without the brain damage by using a device called the "Medtronic Mag Pro". Sounds like science fiction!

Extraterrestrials and Other Planets

Why Can't We See Evidence of Alien Life?
Why do we seem to be alone in the universe? An animated look at the Fermi Paradox.
We Must Explore
From the Young Scientists for Planetary Exploration and +Andrew Chaikin : A video showing our fantastic solar system and protesting the large cuts in funds for planetary exploration in NASA's budget.
More info:http://www.facebook.com/groups/232052633560745/

If aliens made first contact, which SF authors should be part of the welcoming committe?

2012-05-16T09:43:00.000-07:00

In the novel Footfall, by Larry Niven and Jerry Pournelle, unfriendly aliens attack the Earth, and science fiction writers are asked to join scientists to provide some insight into alien behavior and technology.

The latest Mind Meld over at SF Signal asks if that were a real situation, which science fiction folks should be included in an advisory or welcoming committee if aliens did make First Contact with Earth.

Ideally there would be a wide range of skills and philosophies represented on such a committee, since, let's face it, no one on Earth has direct experience in first contact with extraterrestrials. It's a common trope in science fiction that only SF authors (or avid SF readers) can fully understand what's happening when an extraterrestrial or time traveler arrives.

There is clearly wish fulfillment involved in that assertion, that I'm not immune to myself. I read and watch lots of SF, and I think I would do an excellent job advising the UN on how to treat with aliens. I would do at least as good a job as most politicians anyway.

That said, I do think there are some SF writers who would bring special skills to the table in the case of an alien arrival. Go read the whole Mind Meld to see who I and the other participants suggested.

Science and SF Tidbits: May 7, 2012

2012-05-07T22:03:00.000-07:00

Some of the science and SF links originally posted on Google+, Twitter , and Facebook this week:

Free SF and Science Books

May Highlighted Stories: Natural History on Alternate Earths « Biology in Science Fiction: Free Fiction »
Looking for some free fiction? Like alternate history and old-fashioned science? If so check out this month's free story highlights, with tales set on Earths with biology that's not quite like our own...
University of Chicago Press offers a free e-book every month. This month's offering is Carl Zimmer's A Planet of Viruses. The blurb:
"[it] presents the latest research on how viruses hold sway over our lives and our biosphere, how viruses helped give rise to the first life-forms, how viruses are producing new diseases, how we can harness viruses for our own ends, and how viruses will continue to control our fate for years to come. In this eye-opening tour of the frontiers of biology, where scientists are expanding our understanding of life as we know it, we learn that some treatments for the common cold do more harm than good; that the world’s oceans are home to an astonishing number of viruses; and that the evolution of HIV is now in overdrive, spawning more mutated strains than we care to imagine.

Science, SF and the Arts

The Art of the Brain: Turning Illness into Art
"Elizabeth Jameson developed a fascination with the brain after she was diagnosed with multiple sclerosis, and she turned her fascination into art. " A video about the artist: http://youtu.be/EUimgOr9D6s
Author Spotlight: Linda Nagata (Lightspeed Magazine)
An interview with Linda Nagata about her story "Nightside on Callisto". The tech in the story is partially inspired by biology. Nagata says:
I see the pressure suits and air skins as a kind of biotechnology that adapts and extends the tricks of living organisms. I find nanotechnology fascinating from the bio perspective, in that we—all living things—are built up from tiny components. I was a biology major in college, and took the usual classes covering physiology, cell structure, evolution, ecology, and it was fascinating stuff. Then in my last semester I took a lecture class on biochemistry and that was revelatory, because it pulled together everything that had gone before, providing a mechanism for the macro-scale effects. When nanotechnology became the buzzword, I looked at it mostly as a means toward designed life.
Get A Close Up Look At Rick Baker’s Creations For ‘Men In Black 3’ »
The aliens in MiB3 will have a retro 50s B-movie look to them.Cool Bioscience
David Brin on the Need to Restore Optimism to Science Fiction » io9
David Brin's new novel Existence is set in the near future and one of the issues it considers is the possible uplift of other species:
"One of the novel's sub-plots goes into how difficult — but not impossible — it would be to get started on a project to alter and "improve" the functional intelligence of dolphins and/or apes. It seems a worthy goal, if the end result might be other minds, treated as equal citizens, broadening our perspectives and adding wisdom to a wider Earth Civilization. It addresses a wider definition of personhood (as we'll surely do with AI)."
The Physics of The Hulk's Jump | Wired Science | Wired.com »
Physicist +Rhett Allain analyzes the Hulk's jump. Does the Hulk really have the density of cork?
Still unanswered: what fabric are the Hulk's pants made of that allow them to stretch so much without ripping?
Africa in SF – The Prequel | Cheryl's Mewsings »
Lots of SF mentioned I haven't read yet.
Neuroscience Fiction in the Newspapers (Guardian)
It seems the mainstream press is more interested in telling a story that will sell newspapers than providing accurate coverage of science. Not too surprising, I'm sorry to say.
" To summarise, it seems that when neuroscience findings are covered by the mainstream press, they're invariably interpreted in questionable ways in order to support political ideology or predetermined views and theories, up to and including discriminatory stereotypes - for example about homosexuals."

Cool Bioscience

Video: Avatar inspires scientists to plan brain transplants »
In the wake of the recent popular movie "Avatar", Russian scientists now have plans to transplant people's brains into robotsApparently Russian scientists have real plans to transplant a human brain into a robot. I am just a wee bit skeptical
Brainball - Cassils Vs. Choi (YouTube)
Brainball is a game where the ball moves away from you as you relax. Since the only way to win the game is to be relaxed, I would surely lose...
An Optical Illusion that Explains the Origins of Imaginary Monsters » io9
Monsters are all in your mind - and why chanting "Bloody Mary" while staring in the mirror will freak you out.
How will we build an artificial human brain? »io9
George Dvorsky has a pretty good overview of the state of research into building an artificial brain.
Dolphins that help humans to catch fish form tighter social networks | Not Exactly Rocket Science | Discover Magazine »
At least 3 generations of humans and bottlenose dolphins have helped each other fish in this Brazilian fishing village. It turns out the dolphins that spend more time helping humans seem to form closer social networks amongst themselves.
Glowing Pygmy Shark Lights Up to Fade Away (National Geographic)
Pygmy sharks glow as a form of camouflage.
Male water striders evolved antennae to grab females by the eyes | Not Exactly Rocket Science | Discover Magazine »"
The worst sex you have ever had pales in comparison with what female water striders have to put up with" Water strider mating sounds pretty unpleasant. Yikes!
Smart materials to aid camouflage »
Scientists at the University of Bristol have developed artificial muscles that mimic the color-changing ability of squid and zebrafish.
"These materials, and this approach, is ideal for making smart colour-changing skins or soft devices in which fluid is pumped from one place to another.
"This could help us create a whole host of new technologies, ranging from active-camouflage and clothes that change colour and pattern, to a smart second-skin that can cool you when you are hot and keep you warm when you are cold."
"Zombie Ant" Fungus Under Attack—By Another Fungus »
Even among the fungi, life is an ongoing battle.
Powering the Cell: Mitochondria (YouTube)
Imagine you were shrunk to the size of a molecule, Fantastic Voyage-style. This is what you would see if you explored the inside of a cell. Amazing.
Scientists switch mouse's genes off and on with radio waves »
This is very cool: Scientists have found a way to use radio waves to regulate insulin production in mice.
Ross Douthat: Aging Japan evokes science fiction future »
Is modern-day Japan like "Children of Men" come to life? Hopefully it's not that dire. The problem, it seems, isn't biological but sociological:
"Japan is facing such swift demographic collapse, Eberstadt's essay suggests, because its culture combines liberalism and traditionalism in particularly disastrous ways. On the one hand, the old sexual culture, oriented around arranged marriage and family obligation, has largely collapsed. [...]

Exploring Space

Our Reborn Future in Space (YouTube)
+David Brin gives an excellent overview of the recent proposal to mine asteroids and makes the case for why we should be doing that. Could this move us closer to permanent colonies in space?

Cinema and Synthetic Biology: The Bio:Fiction Film Festival

2012-05-03T22:14:00.000-07:00

The first Bio:Fiction film festival took place in May 2011 in Vienna, and since then has been touring the world. The festival was a celebration of synthetic biology, and includes short films, an art exhibition and science lectures and panels.

The film festival was part of the Cinema and Synthetic Biology (CISYNBIO) project. The CISYNBIO advisory board is an international team of scientists, artists and scholars interested in the intersection of bioscience and the arts.

While the festival is more focused on science than sci-fi, many of the short-listed films have a definite science fictional feel to them. Some of the entries I found particularly interesting:

Aphasia Mechanica by Danny Warner shows what the X-ray view of a mechanically enhanced human might look like. It's mesmerizing.

All American Hero (now retitled Need a Hero) is a first-person "documentary" about an ordinary man turned into a superhero (warning: possibly disturbing images) by artist and filmmaker Charlotte Jarvis.
Bruce is a slightly disturbing animation about the possible future of game play, by Tom Judd of the Royal College of Art in the UK.
Winged One by biologist, animator and composer Anna Lindemann starts with a lecture about the molecular mechanisms that guide the development of fly wings. That turns into an animated fantasy with lace proteins and yarn DNA.
Compound 74 by Christina Agapakis and Patrick Boyle is a fictional documentary set in a future where recreational drugs can be created easily and cheaply in a petri dish.

You can watch all the 2011 short-listed videos and see the lectures and panel discussion on Bio:Fiction's Vimeo channel.

Also check out the CISYNBIO resources page to learn more about synthetic biology.

Science and SF Tidbits: April 30, 2012

2012-04-30T21:37:00.000-07:00

Some of the science and SF links originally posted on Google+, Twitter , and Facebook this week:

Recommended free Kindle book (limited time only):

Amazon.com: Long Eyes eBook: Jeff Carlson: Kindle Store »
Free for the Kindle (or if you are running the Kindle App), at least at the moment:
"Long Eyes" by Jeff Carlson. This collection includes "sixteen stories about strange worlds, biotech, commandos, and the girl next door" along with Carlson's commentary about his inspiration for each story.
Kickstarter project plug:
Feminist Speculative Fiction Anthology »
Kickstarter plug: the Feminist Speculative Fiction Anthology will be edited by Ann VanderMeer and Jeff VanderMeer:

"The anthology will emphasize women's speculative fiction from the mid-1970s onward, looking to explore women's rights as well as gender/race/class/etc. from as many perspectives as possible. The contributors are not yet established so we hesitate to name names, but rights to reprint stories from Ursula K. Le Guin, Octavia E. Butler, Joanna Russ, and James Tiptree Jr. would be sought in addition to a wealth of newer voices in the field."

You can learn more about the project at http://blog.geekradical.org/

Geek Life:

What It Means To Be A Geek »
Are geeks the most enthusiastic people on the planet? And what does it mean to be both a girl and a geek?

Science and Science Fiction in the Arts

Harvard sociobiologist E.O. Wilson on the origins of the arts | Harvard Magazine May-Jun 2012 »
Could there be a Shakespeare of the ants? E.O. Wilson writes about the arts - painting, music, literature - and how they are influenced by neuroscience and human evolutionary history.
Strongest Female Protagonist in YA? | Strange Chemistry »
Who is your favorite female YA novel protagonist? For current novels, I'd have to go with Hermione from the Harry Potter series. From my youth, I'd vote for Mia in "Rite of Passage" by Alexei Panshin.
Scientist Spotlight: Aaron Blaisdell | The Science & Entertainment Exchange »
The Science & Entertainment Exchange interviews animal behavior expert Aaron Blaisdell, who has been a consultant to Disney Animation. He says:
"Practitioners of science and fiction are both in the business of exploring the question “what if?” For a scientist the question is a hypothesis to be tested, for the fiction storyteller the question is explored in the medium of film or writing. Personally, I find good fiction gets my creative juices flowing, which translates into better, by which I mean more creative and thoughtful, science."

How Movie Makers Use Science To Make Magic : NPR »
NPR talks to scientists from Pixar and ILM about creating digital characters:
"... capturing that emotion in a performance is very difficult, and that's what our animators bring to the table. Once the emotion is there, then other artists are responsible for making sure that, you know, the plastic looks like it should and that the lighting is going to reflect the desires of the director."
Untangling The Hairy Physics Of Rapunzel (YouTube)
Science Friday looks at the science behind CGI

Science of the Future?

14 extinct animals that could be resurrected »
If you could resurrect one extinct animal, which would it be? Saber toothed cats? Passenger pigeons? The dodo? Giant sloths? T-rex?
UK team develops Trek 'tricorder' »
This sounds very cool:
"At its heart are bacteriophages - viruses that attack bacteria. By attaching antibodies to the viruses, they can be made to "stick" to specific micro-organisms. [...] Like strands of pasta, the viruses "line up" when stirred in a solution. But just as meatballs disturb rows of perfectly aligned spaghetti, bacteria cause the viruses to separate and tangle.
Polarised light shone through the viruses makes it possible to show when the bugs are present. The light is blocked by aligned viruses, but passes through them when they become tangled. This generates an electrical signal displayed as a set of numbers on a computer screen. "
DVICE: Biophotovoltaic table harvests electricity from moss »

Cool Bioscience

The Virus that Destroyed the Dutch Economy »
A virus that infected tulips in 17th century Netherlands helped destroy the Dutch economy. Amazing how a simple virus could generate such unexpected consequences. Truth is stranger than fiction.
“Mythological Beast of a Virus” Found in Californian Hot Spring | 80beats | Discover Magazine »
A chimeric RNA-DNA virus would be a rare beast indeed. The results haven't been confirmed, but if they turn out to be accurate:
"... it suggests that viral evolution and the ability of different viruses to swap genes is more widespread and general than we had thought. "
Fish Glow Green After Genetic Engineering »
At +National Geographic: Zebrafish were genetically engineered so that their organs would glow green if affected by common freshwater pollutants, including endocrine disruptors.
Study reveals how ancient viruses became genomic 'superspreaders' »
Understanding the "dark matter" of our genomes - the ancient viruses incorporated in our DNA:
"We suspect that these viruses are forced to make a choice: either to keep their 'viral' essence and spread between animals and species, or to commit to one genome and then spread massively within it. This is the story of the epidemic within every animal's genome, a story which has been going on for 100 million years and which continues today."
Rare protozoan from sludge in Norwegian lake does not fit on main branches of tree of life »
From one of the scientists who made the discovery:
"We have found an unknown branch of the tree of life that lives in this lake. It is unique! So far we know of no other group of organisms that descend from closer to the roots of the tree of life than this species. It can be used as a telescope into the primordial micro-cosmos"

Other worlds

Giant lava coils seen for the first time on Mars
A beautiful pattern left by water and lava on ancient Mars.
(See the image at the top of the page)

Putting More Science into UK Fiction and Movies

2012-04-24T23:05:00.000-07:00

A group of UK SF writers, including Alastair Reynolds, Ken MacLeod, Geoff Ryman, Justina Robson, Simon Ings and Paul McAuley, are calling for a UK equivalent to the US Science & Entertainment Exchange, which connects scientists with the entertainment industry.

In their letter published in the Manchester Review they suggest that scientific credibility in entertainment is important to both scientists and the public:

In Britain, though, scientists, and people in arts, TV, movie and literary worlds do not work together as they should. This is a major problem: we all desperately need to understand each other’s constraints to create works that are entertaining, enlightening, and scientifically authentic. But worryingly, Britain is falling behind the United States, where organisations such as The National Academy of Sciences’ Science and Entertainment Exchange are forging these new and productive relationships between scientists and the entertainment industry.

The authors are participating in the "Putting Science in Fiction" symposium at the University of Manchester this week. The scientists participating in the conference include biologist Matthew Cobb, astrophysicist Tim O'Brien, and paleontologist Phil Manning. They are joined by David A. Kirby, author of Lab Coats in Hollywood (sample chapters), and Kirsten Shepherd-Barr, author of Science on Stage (sample chapter).

As Ryman told The Guardian, part of the problem is poor communication between scientists and science fiction writers:

"I work with a lot of scientists and one of the frustrating things they find is that all this fascinating stuff is being done which doesn't find its way into science fiction. They say look at the science fact pages – they're so much more imaginative than science fiction," said Ryman, winner for his novels of a British Science Fiction Association award, a World Fantasy award and an Arthur C Clarke award, and a creative writing lecturer at the University of Manchester. "It's my experience that scientists can find it difficult to understand the needs of scriptwriters or storytellers. [. . .]"

On this side of the Atlantic, the Science and Entertainment Exchange is a program of the US National Academy of Sciences. It will be interesting to see whether the UK group is successful in organizing a similar program with ties to the Royal Society or another scientific organization that can help with promotion within the scientific community.

And I wonder how interested the entertainment industry is in getting suggestions from scientists about "fascinating stuff" - from the interviews I've read on the Science and Entertainment Exchange site, it seems more common that scientists are asked to help with the implementation of scientific ideas that are already part of an existing screenplay. It seems to me that the more unusual scientific discoveries are more likely to appear in written science fiction than on TV or in the movies. But maybe that's a misperception influenced by my entertainment choices.

In any case, I strongly believe that popular culture influences the public perception of both science and scientists. Any improvement in the interaction between scientists, writers, and members of the entertainment industry is good thing.

Science and SF Tidbits: April 23, 2012

2012-04-23T16:15:00.000-07:00

Some of the science and SF links originally posted on Google+, Twitter , and Facebook this week:

Science and Science Fiction in the Arts

Mythical Creatures Infographic (Flickr)
I love this infographic that shows the components of Mythical Creatures. I never considered that a Mermaid = Human + Narwhal
Cats in Space | Tor.com »
Star Trek with cats. You've gotta say it in the right voice Cats...In...Space...!!!!
First Native Science Fiction Anthology Showcases Indigenous Imagination »
From the interview:
"Just as our science is not primitive, our storytelling has always contained the elements of science fiction that are considered forward-thinking, inventive and visionary today. Native intellectuals have begun pointing out that “our knowledge is not primitive,” as a recent book by Wendy Djinn Geniusz on the botanical scientific teachings of the Anishinaabe puts it."
The Innate Irresistibility of Film | Literally Psyched, Scientific American Blog Network »
Maria Konnikova explains how movies affect our brains:
"Films have tapped into something incredibly basic in the way our brains work. And there’s something remarkable about that. A tribute of sorts to the innate, deep-rooted nature of our predisposition for narrative, for a world of stories that we can all experience, share, and pass on."
CultureLab: Prickly personality of Rosalind Franklin »
A common SF trope is the lone scientist, working in an isolated lab who gets along with no one. In real life that doesn't always mean success.
Dinosaurs dressed like the Avengers
Artist Whitlatch studied zoology before becoming a creature designer, and her dinosaur superheroes are based on real dinos.
Star Wars: Identities premieres Thursday in Montreal »If you are a Canadian science and +Star Wars fan, you may want to check out the Star Wars: Identities exhibit.
"Experts in fields including psychology, neuropsychology and genetics were consulted during the crafting of the real-science portions of the exhibition. The real and the imagined complement each other throughout."
The exhibit opens at the Montreal Science Center starting April 19 and at the Telus World of Science in Edmonton in the fall. More information: http://www.starwarsidentities.com/
REVIEW: Never Let Me Go by Kazuo Ishiguro - SF Signal – A Speculative Fiction Blog »
From the review:
"... while it innocently depicts the lives of these three friends (strained as those relationships sometimes are), is really asking tough, thought-provoking questions about what it means to be human. These are the questions that resonate emotionally."
Science Fiction Killed the Dinosaurs | Tor.com »
at Tor.com: science fiction has killed the dinosaurs in so many ways...
Fight Fight Fight #1 (YouTube)
Chuck Norris vs. Darth Vader - who will win?

Science of the Future?

The 2080 Census: The World As We (Don't) Know It : NPR »
What will the Census of 2080 ask?
—Do you consider yourself to be a:
a) Homo sapiens (natural human being)?
b) Homo cyberneticus (mostly human with some external cybernetic enhancements)?
c) Homo hybridus (mostly human with some genetic enhancements)?
d) Homo machinus (slightly human but mostly machine)?
e) Other?
Alien encounters : Naturejobs »
Interested in becoming an astrobiologist? Nature Jobs has some tips.
DVICE: How eating bugs can help save the planet »
The problem with eating bugs is the "ew" factor. Maybe if they were battered and deep fried to disguise them it would help...
How to Make Your Own Evil Twin »
Just in case you need someone to do your dirty work.

Cool Bioscience

Divining Human History with DNA »
Our history is in our genes - and the genes of domesticated animals.
Memory Foraging: When the Brain Behaves Like a Bee: Scientific American »
Have our brains evolved to forage for memories?
Can a Brain Scan Tell You What Drugs to Take and Choices to Make? | Pharmaceuticals | DISCOVER Magazine »
Carl Zimmer looks at the Duke Neurogenetics Study, which looks for correlations between genetics, brain activity and behavior.
Researchers Show How Social Interaction and Teamwork Lead to Human Intelligence
Space Zucchini's Orbital Life and Times Blogged by Astronaut »
I'll bet space zucchini is delicious, especially with space garlic and space peppers.
Why we have blind spots - and how to see the blood vessels inside your own eye! (YouTube)
Sometimes fancy graphics aren't necessary to explain scientific concepts. This video is a good example of that. Find out why we have blind spots!
This microbe could become the "off" switch for biological machines »
DNA sequences from bacteria that thrive at either very high or very low temperatures can be used to design genes and proteins that are switched on or off when the environmental temperature changes. Very useful for bioengineering and synthetic biology applications!
The Brian Lehrer Show - Teaching Evolution with Biorobots »
Vassar Professor John Long talks about his lab's use of biorobots that mimic fish behavior to help understand both fish biology and evolution. More information.
How Eggs Shaped Dinosaur Evolution »
Eggs may have been the secret
Monkey see, monkey read (YouTube)
Can baboons read? Not exactly. What they can do is distinguish between different groups of letters and distinguish which ones correspond with "real" words, which is indeed one of the elements of reading. There is no evidence that they can understand what the groups of letters mean, though. More information
XNA is synthetic DNA that's stronger than the real thing »
As the article points out, "XNAs" - modified synthetic nucleic acids - aren't new. What is new is that MRC chemists Philipp Holliger and Vitor Pinheiro have shown that some XNAs can replicate and potentially "evolve".
The chemical bonds holding the XNAs together are stronger than native DNA. This may mean they are more suited to therapeutic applications than naturally occurring nucleic acids.
There are also implications for artificial life sometime in the future:
"... nothing would call the indispensability of DNA- or RNA-based life into question more than the generation of an entirely synthetic, alternative life form, built from the ground up entirely by XNA. Such an organism would require XNA capable of driving its own replication, without the aid of any biological molecules. Pinheiro says that's still a ways off. "Even in its simplest setup... it would be very challenging to develop an XNA system within a cell." Such a system would require XNA capable of self-replication, and capable of undergoing evolution in a self-sustained manner."

Eron Sheean's Errors of the Human Body: A New Genetic Thriller

2012-04-18T20:49:00.000-07:00

In 2007 Australian filmwriter and director Eron Sheean became an artist-in-residence at the Max Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany.

In his more than two years at the Institute, Sheean got a first hand look at real-life science. As he explains, the experience changed his outlook on genetics:

Like most of those unfamiliar with the mechanisms of science and scientists, I had a lot of naive assumptions about the reality of research and an overly active imagination as influenced by the mass media, with its undertones of modern Frankenstein and Promethean stories. Obviously, all technology can be exploited for both negative and positive purposes, and genetic research more than most evokes wondrous fear. I was struck by the knee-jerk reaction of artists to this form of research; artists who are supposed to enquire beyond the potential horror or destruction of our exploration into new frontiers, but to also celebrate the possible beauty and humanity.

Scientists at the Max Planck Institute study the development of the nervous system and heart, the genetics behind cancer, and flatworm regeneration, which I imagine provide plenty of science fodder for an active imagination.

Sheean's experience inspired his creation of a new film Errors of the Human Body. It's the story of a scientist (played by Geoffry Burton) whose son is born with severe and rare genetic disease. That drives his research into a "human regeneration gene" with the goal to "ensure a future line of people free from disease and deformity."

He talks a bit about his inspiration:

Set in Dresden, and filmed in part at MPI-CBG in early 2011, it looks like the bits of the film showing science taking place will be more realistic than depicted in most psychological thrillers. There are more images from the film on the official web site.

The first teaser-trailer has been posted at Twitch Film:

The release date has not yet been announced. If you are interested in contributing to the movie making process, donations are being accepted through Interactor.

I look forward to seeing the finished film!

(via io9)

Science and SF Tidbits: April 15, 2012

2012-04-15T23:47:00.004-07:00

Some of the science and SF links originally posted on Google+ , Twitter , and Facebook this week:

Good to know in an emergency:

Zombie Survival Maps Show Danger Zones, Armories and Food Sources for Entire U.S. | Gadget Lab | Wired.com »
"Red areas denote population centers where zombies might graze, while dark gray zones cover parks and wilderness areas, which are most likely to be walker-free."
But what about those of us who aren't in the cities? What will we do?

Science, Science Fiction and the Arts

Evil ... or the Victim of Framing? Bad Guys in Science Fiction Film »
Have some "bad guys" gotten a bad rap?
"Look, here's a simple fact: The alien didn't ask to be born. It didn't ask to have an evolutionary gestational strategy that relies partly on a third-party host. You can't in good conscience blame it for that. ..."
Rejecting Creationism: Building Better Monsters Through Evolution by James L. Sutter - SF Signal – A Speculative Fiction Blog »
I also prefer biologically plausible monsters. As James L. Sutter puts it:
"Taking the time to explain how your monster developed to be the way it is, how its strange traits actually make perfect sense as adaptations to its environment, makes your monster feel real and interesting even if, in a vacuum, it might seem absurd or poorly conceived."
Pop Culture's 100-year Obsession With Eugenics »
An excellent overview of eugenics and SF by Charlie Jane Anders and Gordon Jackson, from the eugenics movement of the early 20th century to the focus on "transhumanism" in the early 21st.
Eva Green’s ‘Womb’ Is Pregnant With Possibility That It Never Quite Delivers | Film School Rejects
A "lo-fi sci-fi" film that contemplates the ethics of cloning that ultimately disappoints:
"There’s no doubt that the ethical questions and ideas introduced in writer/director Benedek Fliegauf’s film are intriguing and thought provoking, but that introduction is where the film’s fascination starts and ends. He fills the movie with stark beauty and long moments of reflection, but he forgets to add anything of substance."
Scientist Spotlight: May Berenbaum | The Science & Entertainment Exchange »
May Berenbaum is the go-to expert for bugs in the movies and holds the annual Insect Fear Film Festival. She even had a character in X-Files named after her, which is wicked cool.
Read more about big bugs in the movies at the Science and Entertainment Exchange blog.
Rare Footage Of Steven Spielberg Directing Jurassic Park »
A blast from the past.
Digital butchery makes a monster of Frankenstein »
From the review of Dave Morris's interactive Frankenstein app:
" Frankenstein is lovely to look at: tastefully designed and illustrated with old anatomical drawings. It's when you start reading that things go downhill. What Morris has done is dismember Mary Shelley's novel and sew it into a digital version of a Choose Your Own Adventure story. In doing so, he has created a monster."

Interesting Bioscience

The Making of a Mutant: A Fruit Fly Love Story | Guest Blog, Scientific American Blog Network »
Some offspring only a mother can love...
10 Genes Named After Science Fiction and Fantasy Icons »
There is a long tradition of fun names for fruit fly (Drosophila) mutations and genes. It's no surprise that some of the names have geeky origins. The list left off vulcan and klingon!
There are more in this article at American Scientist
How Dark Matter Interacts with the Human Body - Technology Review »
The title of the article is a bit misleading: there is a new estimate of how often dark matter collides with atoms in the human body. What still isn't know is what the actual effect of such collisions might be. Maybe there isn't any noticeable impact on our bodies at all - or maybe it's turning us into mutant superheroes?
Could we create a perfect society by tweaking two areas of the human brain? »
It's all strictly hypothetical of course.
One Per Cent: Computers powered by swarms of crabs »
If your computer is powered by soldier crabs, does that mean you'd need to buy a special anti-bird protective case for it? And how would you keep the critters happy in your book bag?
"Strawberry" Leopard Discovered—A First »
A model for the genetic engineering of pink poodles?
Discovery: Bacteria From 4-Million-Year-Old Cave Resistant to Antibiotics | Healthland | TIME.com
I'm not sure why it's a total surprise that there are bacteria with antibiotic resistance even though they haven't previously been exposed to antibiotics. That's the way that selection for antibiotic resistance works: there is always a small population of bacteria that are resistant, and killing off all the non-resistant bacteria allows that resistant population to thrive.
The original paper is published at PLoS One
Why You Should Be Glad You're Not a Vulcan »
Of course Vulcans aren't actually emotionless. Instead they repress the emotions they do have - that's what sets them apart from those tempestuous Romulans.
Awake or Knocked Out? The Line Gets Blurrier (New York Times)
I find the idea of being awake during surgery disturbing. Even if we don't consciously remember it, might the experience lurk in our subconscious?
Animal Sex, As Illustrated by Humanoid Cartoons »
"Animals have weird sex, you guys. But if putting the weird, wild mating habits of the animal kingdom has always been hard for you to put into human context, then you are in luck this afternoon! Devian..."
Reverse Engineer the Brain (YouTube)
What can advanced brain imaging tell us about how the brain works?

Exploring Space and Extraterrestrial Life

Ancient Astronauts and Forgotten Dreams: End of Space Exploration — Features — Utne Reader »
Mark Dery remembers the time when dreams of space exploration looked like Disney's Tomorrowland and pulp science fiction.
"The Space Age is ancient history. Why not admit, then, that its greatest contribution to American culture is the rich fund of symbolism it has given us? The 20th century’s greatest myth, space exploration is the only true new religion since the Bronze Age. Christianity gave us the unforgettable fable of the alien messiah who touched down on planet Earth, assumed human form, sacrificed himself in order to save the species, then rose from the dead and returned to the stars."
Life discovered on Mars .... 36 Years Ago
"An international team of mathematicians and scientists have re-evaluated data from NASA's Viking mission to Mars over three decades ago, and have come to the conclusion that the data prove life exists on Mars. "
Short Sharp Science: How Earthly life could populate space by panspermia »
Could life have spread from Earth to the rest of the galaxy?
Dinosaurs From Space! »
Might there be advanced, hyper-intelligent dinosaurs on other planets? A recent paper published in the Journal of the American Chemical Society looked at "right handed" versus "left handed" chemical building blocks for life. All pretty straightforward biochemistry..
But for reasons that are unclear, the scientists (perhaps having just finished a+Syfy movie marathon) concluded the paper with a bit of bizarre speculation about dinosaurs on other planets (!!?):
Tardigrade Eggs Might Survive Interplanetary Trip | Wired Science | Wired.com »
Tardigrades and ticks may take over the galaxy...

Hand transplants, face transplants ... and brain transplants?

2012-04-11T23:45:00.000-07:00

If you can believe what you read in science fiction, in the future we'll be able to swap out any damaged or malfunctioning body parts for new and better functioning replacements. But not only are there serious ethical issues to be considered before that can become a reality - where or who do the replacement parts come from, exactly? - there are also many technical hurdles that need to be overcome. So what may the future bring?

There was a lot of buzz last month about a major surgical achievement: a man who had suffered severe facial disfigurement from a gunshot wound received a full face transplant. Using techniques less than a decade old, the transplant included facial tissue from his hairline to his neck, and included a replacement of his upper and lower jaw and teeth. The results were stunning.

Face transplants represent just the latest step in the development of transplantation technology over the past century. Experiments on dogs and other non-human animals beginning in the early 1900s demonstrated that limbs could indeed be transplanted successfully. But there were serious complications caused by infection and rejection of foreign grafted tissue. And even if the procedures could be successfully used to help human patients, there was a lack of donors.

It wasn't until 1944, in the midst of World War II, that Lieutenant Richard H. Hall, a member of the Navy medical corps, proposed a method for human arm transplants. The time was ripe: recently developed sulfa drugs, penicillin, and other antibiotics could prevent loss of the transplanted limbs to infection. And there was a need. With no end of the war in sight, Hall noted that "there is certainly a growing demand for this procedure." He proposed that "civil or military casualties" could be used as donors. It's terrible to consider, but wartime created a flood of both potential recipients and deceased donors.

It turns out that Hall was decades ahead of his time. In 1964 the first human hand transplantation was performed, but that failed after two weeks when the hand was rejected by the recipient. It wasn't until 1998 that a hand transplantation was performed successfully. And the first successful arm transplantation followed in 2008, more than 60 years after Hall's paper was published.

But even though Hall's proposed methods weren't immediately successful, that doesn't mean his paper went unnoticed. In 1959 Astounding Science Fiction published Anne Walker's short story "A Matter of Proportion" that explicitly cited Hall's 1944 paper. As one of her characters explains it:

By curiosity, I know a bit about such things. A big surgery journal, back in the '40s, had published a visionary article on grafting a whole limb, with colored plates as if for a real procedure [A]. Then they'd developed techniques for acclimating a graft to the host's serum, so it would not react as a foreign body. First, they'd transplanted hunks of ear and such; then, in the '60s, fingers, feet, and whole arms in fact.

But since this is science fiction, Walker takes the idea to it's logical extreme, from "simple" limb transplants to whole brain transplants:

"[...] When you cut your finger, it can heal in two ways. Usually it bleeds, scabs, and skin grows under the scab, taking a week or so. But if you align the edges exactly, at once, they may join almost immediately healing by First Intent. Likewise in the brain, if they line up cut nerve fibers before the cut-off bit degenerates, it'll join up with the stump. So, take a serum-conditioned brain and fit it to the stem of another brain so that the big fiber bundles are properly fitted together, fast enough, and you can get better than ninety per cent recovery."

"[...] There's a place in the brain stem called the isthmus, no cell masses, just bundles of fibers running up and down. Almost all the nerves come off below that point; and the few that don't can be spliced together, except the smell nerves and optic nerve. Ever notice I can't smell, Willie? And they transplanted my eyes with the brain—biggest trick of the whole job."

You'll have to read the whole story to learn about what sort of man is willing to risk being a brain donor.

Of course there's no real world brain transplantation, at least not yet. And maybe we're more likely to have our memories, thoughts and emotions uploaded to a computer than have our brains transferred to a new mortal body. Only time will tell.

On a side note, I am quite curious about the author Anne Walker. I've only found one other story attributed to her, published in 1961, and then she disappears. Was she a doctor or other medical professional? if not, how did she come across a Hall's article in a medical journal? If any of you readers have more information about Walker, I'd love to learn more about her.

References:

Hall RH "Whole Upper Extremity Transplant for Human Beings." Annals of Surgery 120:12-23 (1944)

"A Matter of Proportion" by Anne Walker at Project Gutenberg

Top image: Hall (1944) Figure 3 "Donor graft in place on recipient, medial aspect. Closure partially completed. (a) Details of vascular anastomosis."

Bottom image: Illustration from "A Matter of Proportion" by Bernklau

Science and SF Tidbits: April 9, 2012

2012-04-09T21:57:00.000-07:00

Some of the science and SF links originally posted on Google+ , Twitter , and Facebook this week:

Free for the Kindle (limited time):

Amazon.com: Daughter of Elysium - An Elysium Cycle Novel eBook: Joan Slonczewski: Kindle Store
It's excellent science fiction with a strong biological basis. Get your copy!
And if you've read it (or don't mind a few spoilers), see my related post about embryo visualization in the story.

Science and the Arts

Jonah Lehrer, science fiction writer | Gene Expression | Discover Magazine
Will increasing creativity mean mankind's demise?
The neuroscience of Bob Dylan's genius
But how is brain activity reflected in our brain's activity?
"Every creative journey begins with a problem. It starts with a feeling of frustration, the dull ache of not being able to find the answer. When we tell one another stories about creativity, we tend to leave out this phase of the creative process. We neglect to mention those days when we wanted to quit, when we believed that our problems were impossible to solve. Instead, we skip straight to the breakthroughs. The danger of telling this narrative is that the feeling of frustration – the act of being stumped – is an essential part of the creative process."
Cambridge Ideas - Bird Tango (YouTube)
A dance inspired by Darwin.
"By day Professor Nicky Clayton researches the social behaviour and intelligence of birds but by night she is an accomplished dancer. Recently, Professor Clayton has been encouraged by Rambert Dance Company to merge the two passions by becoming their Scientist in Residence....."
The music created by your brain waves could score a horror film
The video: http://youtu.be/XI4Mge8nLMw
"Brain waves are picked up from the parietal and frontal lobes, then sent by radio waves to the motherboard, which converts the radio waves into a wave pulse that is output as sound."
Do science fiction and fantasy cause recurring dreams?

Looking at the Future

TEDxBrussels - Rudy Rucker - Beyond Machines: The Year 3000 (YouTube)
Rudy Rucker's vision of the future:
"As in his novel "Software" where computers 'preserve' the human brain, a so-called 'life box' database remains which keeps our memories alive. These machines however cannot substitute humans as our minds perform more physical and biological processes, where artificial intelligence only relies on inferences."

Interesting Bioscience

How to Use Light to Control the Brain
"Over the last several years, optogenetics has provided powerful insights into the neural underpinnings of brain disorders like depression, Parkinson’s disease, anxiety, and schizophrenia. Now, in the context of memory research, this study shows that it is possible to artificially stimulate a few neurons to activate an old memory, controlling an animals’ behavior without any sensory input."
Contrary Brin: From Brain Imaging to Parasite Infestations
Short Sharp Science: World's toughest bugs survive electron beam and vacuum
Ticks may be the first invaders from Earth to take over other planet.
The Giant, Prehistoric Squid That Ate Common Sense
What happens when extraordinary scientific claims are made in a press release? As Brian Switek reports, in this case, the claim was made that super-intelligent giant prehistoric squids ate huge ichthyosaurs and artfully arranged their bones. Despite the fact that the claims were extraordinary and were primarily based on speculation, rather than evidence, most news outlet republished the original press release without any analysis of commentary from other scientists. Bad science, maybe, bad journalism, definitely. On the other hand, super-intelligent bone-arranging prehistoric squids would be a great subject for a novel, especially if they could travel through space!
The secret life of plankton | Video on TED.com
Some beautiful underwater photography.
Farm-fresh infringement: Can you violate a patent by planting some seeds?
This sounds like science fiction, but it's the present day reality for many US farmers: growing plants could be patent infringement. For a SF take on agribusiness-created plants as intellectual property, see Paolo Bacigalupi's "Calorie Man" (pdf)
The One-Ton Turkey: Further Adventures in Slow-Cooked Science | The Loom | Discover Magazine
Carl Zimmer reports on seeing feathered dinosaur fossils in China.The dinosaurs are cousins to Tyrannosaurus Rex, hinting that T. Rex could have been feathered too.
"The two fossils I saw, plus a third, all belong to a new species, which Xu has dubbed Yutyrannus huali (a mix of Latin and Mandarin, meaning beautiful feathered tyrannosaur). They had filament-like feathers, reaching several inches in length. Since they are preserved on widely separated parts of Yutyrannus’s body, Xu leans towards the dinosaurs being extensively covered with feathers."
Lighting up plant cells to engineer biology - Research - University of Cambridge
Common things under an electron microscope
The Mystery of the Glow-in-the-Dark Civil War Soldiers
Truth is stranger than fiction. (The answer to the mystery involves nematode vomit and hypothermia)

Other Planets and Extraterrestrials

What would your voice sound like on Venus?
I'd probably end up sounding like James Earl Jones.
Q&A: The Anthropology of Searching for Aliens | Wired Science | Wired.com
Anthropologist Kathryn Denning talks to Wired about how our cultural narratives affect the way we think about extraterrestrial intelligence and possible contact with alien cultures.
"From Star Trek to SETI, our modern world is constantly imagining possible futures where we dart around the galaxy engaging with bizarre alien races. Denning points out that when people talk about these futures, they often invoke the past. But they frequently seem to have a poor understanding of history."

Alien: The Easter Edition

2012-04-08T07:40:00.000-07:00

The crew of the USS Chocstromo discovers a suspicious (and delicious) giant egg. If you've seen Ridley Scott's 1979 classic Alien, you have an idea of how it all turns out. The movie features John Seaward (of the Inbetweeners). Also be sure to check out filmmaker Will Tribble's blog for a look at how the sets and various alien incarnations were created.

Whale Songs and Dolphin Chatter: Free Science Fiction

2012-04-02T19:44:00.000-07:00

The great mammals of the oceans, dolphins and whales are like intelligent aliens right here on Earth. They are intelligent and share their own language. Whales and dolphins may even be able to learn to speak to each other. It's been suggested that learning to better communicate with dolphins will help us better communicate with extraterrestrials, if and when we meet them.

It's no wonder that cetaceans frequently appear in science fiction. Often their intelligence has been given a boost - "uplifted" in SF terms - so that they can take their place beside humans.

This month the Biology in SF Free Fiction Directory highlights stories featuring dolphins and whales who communicate with humans in a variety of ways. Go check it out!

Photo: By IK's World Trip on Flickr

Science and Science Fiction Highlights: April 1, 2012

2012-04-01T18:39:00.000-07:00

Some of the science and SF links originally posted on Google+ , Twitter , and Facebook this week:

Science and the Arts

Ratha's Creature Graphic Novel Survey
Everyone who submits the survey by April 30, 2012 will be entered to win a $25 gift certificate to the bookstore of your choice, offline or online.
Chapter-By-Chapter Analysis – Daenerys I
For you Game of Thrones fans, here's an discussion of Targaryen inbreeding and genetics with reference to the deformities in the (real world) Hapsburg family lines. (via the Gene Expression blog)
Bring the love (Mindhacks)
The film The Love Competition is about a "love competition" held in a real MRI scanner. While it wasn't meant to be research or part of a scientific study, real MRIs were made.
"...when a group of participants were instructed to ruminate on the person or concept they associate with love, BOLD signal in the nucleus accumbens showed individual differences."
Link to the film: http://vimeo.com/33698394
Featured Entertainer: Maggie Malone | The Science & Entertainment Exchange
Maggie Malone, Director of Development at Walt Disney Animation Studios says:
"Science consultants have spent their lifetimes in the library, the lab, and the field. They have logged lots of boring hours and accrued some amazing tales of experiences you cannot find in books. When we speak with them, we get the benefit of all their years of study, with all the boring bits cut out."
gamrConnect Forums - How Evolution Defines Mass Effect's Aliens
This is some fun speculation about how the different alien races in Bioware's Mass Effect universe could have evolved. The author points out: "Evolutionary biology plays an important role in achieving immersion in the 'believable' ME galaxy"
Let There Be (Living) Light: Bioluminescence in Nature | Anthropology in Practice, Scientific American Blog Network
A look at bioluminescensce in folklore, plus a review of the new bioluminescensce exhibit at the American Museum of Natural History.
Anatomical Neon, Glowing Human Organ Sculptures
Fantastic glass sculptures of human organs filled with glowing neon "and other inert gasses"
So You Think About Dance? | The Scientist
Watching dance makes your brain activity similar to that of a dancer.
Should science fiction and fantasy do more than entertain?
Damien Walter argues that "fantastika" is more than just entertainment:
"If science fiction, fantasy, horror, and even relative new kids on the genre block such as steampunk are part of a centuries-long tradition of fantastika, then it's even more important that they are positive in their representation of issues like gender and race. "

Interesting Bioscience

How Pandemics Spread (YouTube)
Breaking: James Cameron Completes Record-Breaking Mariana Trench Dive
Scientists turn living cell into laser | SmartPlanet
It's a bit premature to talk about "attacking cells deep within the body", but it's pretty neat that putting together two mirrors, kidney cells expressing green fluorescent protein and a light source can stimulate living cells to generate a laser beam.
How do you buy organs on the black market?
From horror musicals like Repo! the Genetic Opera to the much more thoughtful novels like Never Let Me Go, science fiction often suggests that the real present-day problem of a lack of donor organs necessarily requires terrible decisions. While increasing the pool of voluntary donors is an obvious solution, I hope in the longer term we'll eventually be able to turn to more technological solutions like artificial organ replacements.
Butterfly wings' 'art of blackness' could boost production of green fuels
The tiny scales on butterfly wings are a natural solar energy collectors that the butterfly normally uses to keep itself warm. Now a research team at Shanghai Jiao Tong University in China is using the structure of the black butterfly scales as a template for titanium structures that catalyze the production of hydrogen gas from water. The hope is that could create a potential renewable energy source.
Living human gut-on-a-chip: Tiny device simulates structure, microenvironment, and mechanical behavior of human intestine
This new device looks like a pretty impressive simulation of the human gut, right down to the growth of common intestinal microbes. The secret is that the interior of the device is lined with living human intestinal cells. While it's designed as a model for human disease, could this also be a step towards artificial intestines?
Man Hugs Doctor after Seeing Face Transplant in Mirror
Amazing surgery gives a man a face.
Dolphin society 'is run by gangs'
Male dolphins form different kinds of alliances from "Buddiess" (groups of 2-3), "Gangs" (up to 14 males) and much larger "Armies". No word on whether female dolphins also form social alliances.("Buddies" is my own term. I figure it's no more anthropomorphizing that "Gangs")
New plastics 'bleed' when cut or scratched -- and then heal like human skin
When the plastic is damaged red splotches form. When the damaged area is exposed to visible light or a change in pH or temperature, the molecules that make up the plastic form "bridges" that heal the damage.
Life-changing experiments: The biological Higgs
I don't think it's really meaningful to compare the big questions in biology to the discovery of the Higg's boson in physics, since biology is more complicated than does-it-or-doesn't-it-exist type questions
The exception would be discovery of extraterrestrial life. But is that likely? I'm willing to bet that several more decades of meaningful-yet-messy research into how the brain works and how our lifespans could be extended is more likely to bear fruit than the search for life off Earth, even if there isn't a single "A ha!" moment.
How the Cost of Computation Restricts the Processes of Life - Technology Review
I don't feel like I have a good enough understanding of what is meant by "computation" in a biological context to decide if this sounds like it's a useful way of looking at biological processes like sporulation of yeast or not. Interesting idea, though.
Bart Weetjens: How I taught rats to sniff out land mines (YouTube)
Sometimes nature has invented tools that are as good as - or even better than - technology we humans create from scratch. In this case, Bart Weetjens and his organization APOPO has trained African giant pouched rats to efficiently sniff out land mines.
APOPO is also training the rats to detect Mycobacterium tuberculosis in human spit, which is faster than microscopy methods currently in use to diagnose tuberculosis.
MIT news: Conjuring Memories Artificially:
Simply activating a tiny number of neurons can conjure an entire memory.
Brain.mov (YouTube)
A dramatic 3D display of the connections in the brain of the owl monkey.
More information at Technology Review and American Scientist
CultureLab: The matter of your brain
Bridging the gap between the "physical" and the "mental": a review of "Brains" the new show at London's Wellcome Collection.
Slacker Rat, Worker Rat - Science News
Amphetamines make slacker rats work harder, but make worker rats slack off.
Scientists have proven that, up close, your brain is plaid
The brain is more organized that previously expected.
Foods in the Year 2000 | Oscillator, Scientific American Blog Network
Christina Agapakis looks at food synthesis in space, synthetic biology and what "future food" looked like from the perspective of the 1890s.
NYC Dept of Education wants to ban the word "dinosaur" from standardized tests
Apparently NYC standardized tests don't cover biology.
(It reminds me of Connie Willis's short story "Ado" where Shakespeare's Much Ado about Nothing is gutted as any bit that might offend someone is removed.)

Other Planets and Alien Life

Why black (or blue, or red) plants might be the key to finding life beyond Earth
Life on other planets may be colorful!
Science Fiction or Fact: ET Will Look Like Us
Seth Shostak, senior astronomer at SETI sums up the answer nicely:
"Why should they look like us? No other creatures look that much like us, except for other apes."
He also points out: "An alien will look like whatever its evolutionary niche is."
Despite that, the article gives a 3 out of 4 plausibility rating for the idea that extraterrestrial aliens will look like "us". What the heck?
If We Discover Aliens, What's Our Protocol for Making Contact?
It seems like the biggest mistake we could make is assuming that aliens will think and behave like humans and that they likewise understand our behavior. Do open gun ports signify an imminent attack or are they a sign of respect?
Science Fiction or Fact: Sentient Living Planets Exist
The article doesn't really focus on planets themselves that could be sentient, like the Gaia of Asimov's Foundation universe. Instead it asks whether a network of living beings on the surface of a planet could become sentient. In either case, the answer is "pretty darn unlikely".
“Snowing Microbes” On Saturn’s Moon?
It's all speculation at the moment, but Cassini imaging team leader Carolyn Porcini thinks there's the possibility of life in ice jets of Enceladus:
"In the end, it’s is the most promising place I know of for an astrobiology search. We don’t even need to go scratching around on the surface. We can fly through the plume and sample it. Or we can land on the surface, look up and stick our tongues out. And voilà…we have what we came for.”
Could Life Be Abundant In Our Galaxy?

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John Carter versus the Clone Army

2012-03-29T23:25:00.000-07:00

The Mars of Edgar Rice Burroughs is filled with technological marvels. Earthman John Carter discovers the Martians have anti-gravity "fliers", disintegrator ray weapons, and even a great factory that maintains the atmosphere of the planet.

The Martians also have advanced medicine and biological technology. Indeed the great Martian scientist Ras Thavas - known as The Master Mind of Mars - has perfected biotechnological techniques that are both fantastic and terrible.

Burrough's 1939 novel Synthetic Men of Mars reveals Ras Thavas's greatest achievement: a vast army of clones.

After Ras Thavas was driven from his great laboratories by Vobis Kan, Jeddak of Toonol," explained Gan Had, "he came to this island to perfect a discovery he had been working on for years. It was the creation of human beings from human tissue. He had perfected a culture in which tissue grew continuously. The growth from a tiny particle of living tissue filled an entire room in his laboratory, but it was formless. His problem was to direct this growth. He experimented with various reptiles which reproduce certain parts of their bodies, such as toes, tails, and limbs, when they are cut off; and eventually he discovered the principle. This he has applied to the control of the growth of human tissue in a highly specialized culture.

From a mass of cultured undifferentiated human cells, Ras Thavas was able to grow arms, legs and eventually whole bodies. The "synthetic men", known as hormads, would all be genetically identical to both the original human cells and to each other, making them clones even though that term is never used.

The technology isn't perfect. Most of the synthetic men aren't very smart or physically attractive. And left unsupervised, the process can fail horribly:

"In fact things seem to go all wrong without him," and when I reached the first vat room I realized that that was a crass understatement of fact. Things couldn't well have been much worse. The floor was covered with the remains of hideous monstrosities that the officers had had to have destroyed. The parts still lived. Legs were trying to walk, hands were clutching at whatever came within reach, heads were lying about screaming and moaning.

A gruesome sight.

So where did Burroughs find his inspiration for Ras Thavas's mad science? My guess is that he was influenced, at least in part, by the research of French biologist and surgeon Alexis Carrel. In 1912 Carrel took a piece of embryonic chicken heart and placed it in a flask with nutrients. He successfully cultured the cells for decades, a feat that caught the public's imagination. In the 1930s Carrel (along with aviator Charles Lindbergh) went on to develop techniques that allowed human organs to be kept alive outside the body during surgery. This achievement was also celebrated in popular culture, with Carrel appearing on the cover of Time Magazine in 1938.

Carrel's achievements inspired a number of writers during science fiction's "Golden Age", from Arch Oobler's 1937 radio play "Chicken Heart" in which cultured cells escape the lab and threaten to engulf the world, to the "Chicken Little" food source in Pohl and Kornbluth's The Space Merchants. The ever-growing human cells in Synthetic Men of Mars fits right in with these stories.

But science doesn't really play a central role in Burroughs' novels. Instead science and technology and unusual creatures are a backdrop for the real story, which usually involves a fight (or three) and romance. In Synthetic Men, it turns out that some of the hormads are quite intelligent, and they gather their brethren into an army in hopes of conquering the world. The hero - in this case the Martian Vor Daj - and John Carter work together to destroy the terrible mass of tissue and hormads run amok. And Vor Daj finds love, despite having his brain transplanted into an ugly hormad body.

You can read the rest of the story for yourself:

Project Gutenburg Australia has a copy of the Synthetic Men of Mars. If you are not in Australia, you can purchase an ebook: Kindle version (Amazon.com) or the Nook version (Barnes&Noble)

Further reading:

ERBzine has a detailed review, along with a great collection of covers from different editions of Synthetic Men of Mars.
Related Biology in Science Fiction post: Cultured Meat
Witkowski, JA "Dr. Carrel's Immortal Cells" Medical History 24:129-142 (1980) (note: pdf)

Top image: Cover of Synthetic Men of Mars, 1963 edition

Middle image: Colony of human embryonic stem cells by Ryddragyn at Wikimedia Commons. Bottom image: Fan cover of Synthetic Men of Mars by zimeta08 on DeviantArt

What do "humans" look like?

2012-03-26T23:35:00.000-07:00

Last year, Racebending took a look at Hollywood's tendency to use white actors to depict "human appearing" aliens. While that's not true in every movie - for example Mos Def played Ford Prefect in the Hitchhiker's Guide to the Galaxy - non-white aliens are the exception, rather than the rule. As the article concludes:

The overall fact remains that a balanced representation is hard to spot in “human alien” films, because when aliens are written to look like us, it’s the kind of “us” that racially dominates Hollywood and controls its creative processes. Despite the use of sci-fi premises that supposedly spur the imagination to the furthest reaches of space, the narrow focus of “white by default” is still pervasive enough to ground out-of-this-world concepts with business-as-usual biases.

But it's not just aliens who are "whitewashed". When science fiction stories are turned into movies, even characters originally depicted as non-white get portrayed by white actors. Some of the more egregious examples are the SciFi Channel's adaptation of Usula LeGuin's Earthsea novels and the live action movie version of Avatar: The Last Airbender.

So why does it matter? I think the representation of what is to be considered "normal" in popular entertainment can influence what we consider to be the norm in real life.

I think the recent tempest about the casting of the Hunger Games movie helps show why it's important to include human characters of different races. In the Hunger Games novels, the characters Rue and Thresh are described as having "dark brown skin and eyes". Given that description, it's not at all surprising that black actors (Amandla Stenberg and Dayo Okeniyi) were cast in the movie versoin those roles.

But it turns out a number of fans of the Hunger Games novels imagined the characters Rue and Thresh as white, despite their description. And those fans aren't just disappointed. They have been vocal on Twitter that depicting the characters as having dark skin made them less sympathetic and even ruined the movie for them.

And going beyond the explicit racism of many those tweets, some fans who had no problem with the casting in the movie originally imagined the characters as white, presumably because they unconsciously assume that the default human is white. That assumption is reinforced by the majority of movies and television shows.

To my mind, it only makes sense to imagine a future North America where the inhabitants have a range of skin colors and racial and ethnic backgrounds, simply because that is the case in present-day North America. Unless there is some action to eliminate or segregate humans by the color of their skin (such as the way black people were rounded up and resettled in the Handmaid's Tale), it makes no sense to depict an all white future.

And now that we have a black President, will Hollywood step up and show aliens looking who look like our leader when they say "take me to your leader!"?

(link to the Racebending post via My Sci Fi Online ; link to Hunger Games Tweets via Jezebel)

Science and SF highlights for March 25, 2012

2012-03-25T17:00:00.000-07:00

Some of the science and SF links originally posted on Google+ , Twitter , and Facebook this week:

Free ebooks through this weekend (so download your copy now!):

Science and SF:

The Four-Leaf Clover Gene? - Forbes
With some simple genetic engineering we could all have lucky four-leaf clovers.
The Neuroscience of Your Brain On Fiction (New York Times)
"The brain, it seems, does not make much of a distinction between reading about an experience and encountering it in real life; in each case, the same neurological regions are stimulated."
So science fiction lets you experience alien worlds without leaving your armchair!
Watching Harry Potter films enhances creativity in children
Science Daily reports on a study showing that children appear to be more creative after watching a Harry Potter film:
“Magical thinking enables children to create fantastic imaginary worlds, and in this way enhances children’s capacity to view the world and act upon it from multiple perspectives. The results suggested that books and videos about magic might serve to expand children’s imagination and help them to think more creatively.”
Neuroscience, Fantastika and Cliché: A Few Musings on the Effects of Reading Fiction - SF Signal – A Speculative Fiction Blog
Babylon 5: Watch Full Episodes on TheWB.com
This is awesome. My only hesitation to watching the old episodes is that I'm afraid they' won't be as entertaining as I remember them.
Cloning the mentat | Gene Expression | Discover Magazine
Should John von Neumann be the first human cloned?
Astronauts’ Eyeballs Are Deformed by Long Missions in Space
Perhaps a manned mission to Mars will have to include eyeglasses with it's gear.
How to grow a biological city of the future (io9)
From io9: A review of Rachel Armstrong's "Living Architecture". Imagine "a future where cities aren't built, but instead grown like plants or baked like bread."
Picturing Spring: An Equinox Celebration | Tor.com
A fantastic collection of spring paintings, from Botticelli to Miyazaki.
Spiderman May Not Be a Tarantula After All
From +WIRED: Arachnid specialists disagree on whether tarantulas climb using silk from their feet or another mechanism.
China Miéville and Monsters: “Unsatisfy me, frustrate me, I beg you.” | Jeff VanderMeer | Weird Fiction Review
An interview with China Mieville on monsters and meaning:
"I think, for example, that when Margaret Atwood invents the “pigoons” for Oryx & Crake, part of the problem with them for me is I think they are primarily a vehicle for considering genetic manipulation, and only distantly secondarily scary pig monsters. I think plenty of monsters get hobbled by their “meaning”."
Alien Civilizations, Asteroids, and the Fermi Paradox | EDWARD LU
Alien civilizations in our galaxy may have been destroyed by asteroids, argues +Edward Lu. Could Earth be next?
Prehistoric proteins: Raising the dead : Nature News & Comment
From the article:
"Thornton is a leader in a movement to do for proteins what the scientists in Jurassic Park did for dinosaurs: bring ancient forms back to life, so that they can be studied in the flesh. “Instead of passively observing things as most evolutionary biologists do, you actively go in and test the hypotheses experimentally,” says Antony Dean, a molecular biologist at the University of Minnesota in St Paul who heads another major group in the field. “His is one of the leading labs, no doubt.”"
SETI Wants Your Help to Find Aliens | IdeaFeed | Big Think
"New croudsourcing software can be downloaded at setilive.org and used by civilian-scientists who want to help SETI scientists fine-tune algorithms that search for patterns in noise recorded from space."
Time for a reality check on the technologies of 'The Hunger Games'
Is the genetic engineering and cross-species mashups depicted in the Hunger Games scientifically realistic?
Evolution Under a Temperamental Sun
The retinal pigments that give us night vision may be an "evolutionary fossil" of microbial life that thrived under the dimmer sun that warmed the Earth 4 billion years ago.
Do Zombies Poop? An Investigation
The most in-depth analysis I've seen of the zombie digestive system. Maybe more than you want to know.
Small Rewards: Tiny Frogs and Chameleons Find and Fill a Niche
What controls the evolution of body size?
Mars for the 'average person' (BBC)
Half a million dollars for a ticket and no amenities when you arrive..,
‘Bird Man’ Hoaxster Comes Clean on Dutch Television (Wired)
Floris Kaayk's birdman video was science fiction, rather than reality
Neuroskeptic: Brain Scanning - Just the Tip of the Iceberg?
You are probably using more of your brain than brain scans may indicate:
"So conventional fMRI experiments may just be showing us the tip of the iceberg of brain activity. In a small study, only the strongest activations pass the statistical threshold to show up as blobs, but that doesn't mean the rest of the brain is inactive. It just means it's less active. The idea that only small parts of the brain are 'involved' in any particular task may be a statistical artefact."
Meet The Global Winners & Watch Their ZERO-G Flight!
The teenaged winners of the YouTube Spacelab contest have a blast experiencing zero G
CultureLab: Joe Davis: The mad scientist of MIT? (New Scientist)
Are Joe Davis's biological creations art? science? or something else?
"Apart from art bordering on the perverse, Davis has invented a bacterially-grown radio and a frog-leg powered airplane. He developed supercode, a silent or bio-chemically inert genetic code to embed Greek poetry into the DNA of white-eyed flies and the image of the Milky Way into the ear of a mouse."
Dung fungus reveal that humans, not climate change, killed Australia’s giant beasts | Not Exactly Rocket Science | Discover Magazine
Aliens on Planet With Two Suns Need Rhythm : Discovery News
If live evolved under the light of two stars, how would it differ from life on Earth?"Given the awesome power of biological evolution, it's likely life would easily evolve to cope with living with a second star. There may be planet-wide migrations with anticipation of the approaching "super-summer." And there would be a variety of other novel coping mechanisms."

----

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Jellyfish and immortality: would you want to live forever?

2012-03-24T12:13:00.000-07:00

Last summer's Torchwood-goes-to-America series (more formally titled Torchwood: Miracle Day) had an interesting premise: what would happen if people stopped dying?

Plenty of science fiction stories involves humans who have become immortal or whose lifespans are so long that they seem immortal. But unlike fictional future societies like Ian Banks' "Culture", where genetic engineering and advances in medicine have allowed humans nearly unlimited lifespans, the living in Miracle Day live despite suffering unhealed grievous injuries and unchecked diseases. People suffer and yet they live on.

The crude global death rate is about 8.4 deaths per 1000 in the population in 2009. Given a total world population of 6.7 billion that is about 56 million deaths per year or 154 thousand deaths per day. Without death to intervene Earth's human population grows unchecked. And many of those who survive are sick and hurt and unable to care for themselves. The results are horrifying, as are the measures deemed necessary to stave off the possibility of overpopulation.

While Torchwood often seems closer to fantasy than SF, there is, in fact some science behind the fiction. As show writer Jane Esperson described it:

The amazing writer Bryan Fuller told the Torchwood writers room about the species of immortal jellyfish that Christina Colasanto talks about here [in Episode 8] — and we obsessed over it in the room. The idea that some creature here on Earth works in this way is amazing. That line, "Consider the jellyfish..." started echoing around the room, and here it is, in the episode. For a while, we joked that that should be the title of this episode.

The jellyfish Turritopsis nutricula is essentially immortal, as long as it doesn't get eaten or succumb to disease.

As the jellyfish matures it takes on several different physical forms. Fertilized eggs develop into planula larvae which settle on the sea floor. The larvae develop into colonies of polyps which bud off free-swimming medusa jellyfish. When those jellyfish reach sexual maturity after a few weeks they spawn to create a new generation of jellies.

All animals are able to reproduce and create new offspring, that's not what makes Turritopsis special. Turritopsis adults are actually able to revert back to the juvenile polyp form through a process known as transdifferentiation. This process renders the tiny jellyfish biologically immortal. See the video above for an overview.

But besides the concept of immortality that nifty bit of jellyfish biology isn't referenced in Miracle Day at all. I suppose having Gwen Cooper, Captain Jack, and Rex Matheson revert to their juvenile forms in a sort of Torchwood babies episode wouldn't work very well. At the least it would preclude having the usual sex scenes (at least I hope it would).

Miracle Day unfortunately doesn't completely live up to its original premise. The plot is slow to develop, the flashbacks to Jack's early 20th century relationships are long, and the world-wide conspiracy that sets the Miracle in motion I found more confusing than convincing. I think it could be much better if the 10 episodes were trimmed in half.

Torchwood: Miracle Day will be available on DVD in the US on April 3rd. You can preorder a copy at Amazon.com or at Barnes&Noble.

Controlling Our Creations Through Nutritional Requirements: Lessons from Science Fiction

2012-03-21T22:11:00.000-07:00

Last week a group of over 100 environmental and watchdog organizations released a report proposing increased government regulation of synthetic biology, which they consider "extreme genetic engineering". The report calls for a moratorium on the release and commercial use of synthetic organisms until such regulations are in place. Their position is a that drastic measures are necessary to protect both the public and the environment.

Not surprisingly, not everyone agrees with that assessment. Representatives of the biotechnology industry have pointed out that synthetic biology is part of the ongoing development of genetic engineering technology that is already covered by rules and regulations. And in 2010 a presidential bioethics commission concluded that no new regulations covering the use of synthetic biology were necessary.

One concern expressed by all parties is that "synthetic" organisms could escape into the environment.Where the disagreement lies is whether current technologies are sufficient for containment.

The presidential commission's report suggests that such organisms could be designed to have limited lifespans or to be dependent on nutrients only available in the laboratory. Such biological barriers to the spread of genetically engineered organisms have been part of the earliest recommendations for safe use of recombinant DNA technology.

The groups calling for a moratorium on the development of synthetic organisms claim that such measures are likely not sufficient and further study is required to ensure that such biological barriers work outside the laboratory.

So what is the lesson that can be learned from science fiction? If creatures are unable to synthesize all the compounds necessary for their growth and sustenance - auxotrophs - can indeed be contained if their nutritional requirements are alien enough.

"Look, we're not fools. We understand these are prehistoric animals. [...]They might have no predators in the contemporary world, no checks on their growth. We don't want them to survive in the wild. So I've made them lysine dependent. I inserted a gene that makes a single faulty enzyme in protein metabolism. As a result, the animals cannot manufacture the amino acid lysine. They must ingest it from the outside. Unless they get a rich dietary source of exogenous lysine - supplied by us, in tablet form - they'll go into a coma within twelve hours and expire. These animals are genetically engineered to be unable to survive in the real world. They can only live here in Jurassic Park...."

Take, for example, the dinosaurs in Jurassic Park. As noted in the quoted text, they were designed to only be able to live on a diet with high levels of the amino acid lysine. Since the local plants and animals in the Park wouldn't be able to supply the necessary nutrients, they could only survive on a diet provided by their handlers. That worked, at least for a while, but the setup had a fatal flaw.

Lysine is an amino acid, one of the twenty standard building blocks of protein. If an organism cannot synthesize one or more of those building blocks in its own cells, then it must eat foods that contain those amino acids to survive.

Humans normally require nine such essential amino acids in their diet, including lysine. That means that a balanced human diet must include foods rich in lysine, such as meat or beans. And that also meant that when a few dinosaurs were able to escape their island in Jurassic Park, they were able to survive on lysine-rich crops and meats on the farms managed by the local human population.

A dietary restriction that can be easily filled by eating the local produce is not a great way to contain your engineered critter. A better approach would use a nutritional requirement that cannot be so easily filled by Earthly plants or animals.

You can find that scenario in science fiction as well. In Michael Flynn's novel Eifelheim alien travelers - Krenk - were stranded in 14th century Germany where they eventually begin to starve. One of the alien scientists explains the problem to the local priest:

"There are certain . . . materials – acids is your alchemic word–which are essential for life. Perhaps four score of these acids befall in nature–and we Krenken need one-and-twenty of them to live. Our bodies produce naturally nine, so we must from our food and drink obtain the others. That food which you have shared with us holds eleven of those twelve. One is lacking, and our alchemist found it nowhere in all the foodstuffs he proofed. Without that particular acid, there is one . . . I must call it a 'firstling', as it is the first building block of the body, though I suppose it shoudl wear one of your Greekish terms."
"Proteios,"Dietrich craoked. "Proteioi."
"So. It puzzles me why you use different 'tongues' to speak of different matters. This Greekish for natural philosophy; the Latinish for matters touching your lord-from-the-sky."
Dietrich seized the Krenk by his forearm. The rough spines that ran its length pricked his hand, drawing blood. "That makes nothing!" he cried. "What of thisprotein?"
"Without this acid, the protein cannot be formed, and lacking it, our bodies slowly corrupt."

Earth foods, it seems, don't contain the full range of amino acids essential to the Krenk diet. They try to sustain themselves by extracting the essential nutrients from their dead companions. And even so they died, because their lives depended on a diet with truly alien components.

So the science fictional lesson is to engineer organisms that require amino acids or other nutritional building blocks that found nowhere in nature if you want to make sure that they are truly unable to live outside the confines of a laboratory. And that may eventually become a reality.

Scientists have successfully been able to engineer microorganisms, animal cells, and even nematode worms that are able to incorporate several different unnatural amino acids into their proteins. And, more recently, bacteria were engineered to incorporate a normally toxic modified nucleic acid base in their DNA. So the research looks promising.

But scientists are not yet able to create animals or plants that we can be reasonably certain would be unable to live in the wild. And life is so adaptable, there may always be the possibility that biological containment will ultimately fail.

So the question remains whether escaping organisms represent a high enough danger to the environment that current research should be more tightly regulated or put on hold. Or do the potential benefits of synthetic biology - novel sources of energy, more effective drugs, improved crops - outweigh the risks? I'm hoping for the latter.

Background reading:

"The Principals for the Oversight of Synthetic Biology" (2012) (pdf)
"New Directions: The Ethics of Synthetic Biology and Emerging Technologies", Presidential Commission for the Study of Bioethical Issues (2010)
Berg P. et al "Summary Statement of the Asilomar Conference on Recombinant DNA Molecules" PNAS 72;1981-1984 (1975) doi:10.1073/pnas.72.6.1981 (pdf)
Wang, Q; Parrish, AR; Wang, L. "Expanding the Genetic Code for Biological Studies". Chemistry & Biology 16 (3): 323–36. (2009) doi:10.1016/j.chembiol.2009.03.001.
Young TS and Schultz PG "Beyond the Canonical 20 Amino Acids: Expanding the Genetic Lexicon" J. Biol. Chem. 285: 11039-11044 doi:10.1074/jbc.R109.091306
Freie Universitaet Berlin. "Bacterium engineered with DNA in which thymine is replaced by synthetic building block." ScienceDaily, 28 Jun. 2011.

Top image: The bacteria Shewanella putrefaciens use chemical signals to coordinate biofilm formation and other community-level behaviors. [Credit: DOE Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory.]

Science and Science Fiction Link Roundup March 18, 2012

2012-03-18T16:25:00.002-07:00

Some of the science and SF links originally posted on Google+ , Twitter , and Facebook this week:

Guest Essay: ‘Machine’ Author Jennifer Pelland on Mechanical Immortality « Suvudu - Science Fiction and Fantasy Books, Movies, Comics, and Games
No Pulse: How Doctors Reinvented The Human Heart | Popular Science
Life without a pulse!
The Funny Thing About Research
CT Adams and Cathy Clamp explain how Mycobacterium leprae became a "magical" bacterium.
Cyborg snails power up : Nature News & Comment
"Cyborg snails! The dozen or so brown garden snails crawling around the plastic, moss-filled terrarium in Evgeny Katz’s laboratory look normal, but they have a hidden superpower: they produce electricity."
Nancy's Blog: Jane Austen and Gregor Mendel
Nancy Kress on genetics, families and science fiction
Shady scientists head up mission to clone woolly mammoths
If this were a SyFy movie of the week, the formerly disgraced scientist would use this opportunity to show every he was legit by making mammoths that take over the world.
CDC - Blogs - Public Health Matters Blog – Disaster Movies: Lessons Learned
The lesson from Contagion: "The chef should have been more careful about washing his hands so that he could have avoided spreading the animal virus to humans."
That wouldn't have been much of a movie, though.
Planarians and the New Battlestar Galactica
How Cylons in the new Battlestar Galactica are like planarian flatworms
Daniel Wolpert: The real reason for brains
Why do we have brains? It's all about movement
Precognition studies and the curse of the failed replications
Not too surprisingly, scientists had difficulty replicating an experiment that appeared to demonstrate precognitive abilities. A bit worrying, though, is the difficulty they had getting the replicated study published in a peer-reviewed journal.
DVICE: Should we re-engineer our species to save our planet?
If we humans can't learn to live sustainably as we are, should we genetically engineer humans to use less environmental resources? Some of the suggestions DVICE proposes are bit silly, but I can't argue with providing more general education to women, since that has been shown to correlate with lower birthrates.
Based on the suggestions in an article by philosopher S. Matthew Liao and colleagues:
http://www.smatthewliao.com/wp-content/uploads/2012/02/HEandClimateChange.htm
Stuffed in a vacuum and bombarded by electrons, a tick waves hello | Not Exactly Rocket Science | Discover Magazine
Ed Yong writes that ticks can endure "being dried and slathered in metal, starved of air, and bombarded with a high-energy electron beam". No wonder they are so hard to get rid of.
Neuron - brainawarenessweek
Brainbows, dancing parrots and sex differences: free content from Cell Press to celebrate Brain Awareness Week.
New Scientist TV: Fruit fly trapped in 'holodeck' fooled by the illusion
Alien Plants May Thrive on Many Wavelengths of Light
Alien plants may be able to use the light from red dwarf stars for photosynthesis. Another place to look for life!
Despite the Dark, Giant Squid Eyes See All : Discovery News
Giant squid eyes can be the size of basketballs - the better to spot predatory sperm whales..
'Luck' raises stakes on animals' use
Should live animals in films and television shows be replaced with CGI? Or will that only work on science fictional productions where the depicted creatures aren't expected to look "real" anyway.

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Vonda McIntyre on the inspiration for Dreamsnake

2012-03-17T01:43:00.000-07:00

I was doing a bit of YouTube surfing and stumbled onto this video clip of Vonda McIntyre winning the 1979 Hugo Award for her novel Dreamsnake. In her acceptance speech McIntyre acknowledges Avram Davidson, which made me curious what role he played in the story's genesis.

Dreamsnake, if you haven't read it (and you should), is set on a future Earth which has been laid to waste by nuclear war. Despite the widespread devastation, future humans have developed advanced biotechnology. The story follows the adventures of a healer named Snake, who travels from community to community using her genetically engineered snakes to treat the sick and hurt.

Fortunately for my curiosity, McIntyre has explained the story-behind-the-story in an afterword to Dreamsnake posted at the Book View Cafe. Avram Davidson was the writer in residence at the Clarion West writer's workshop. In a session he was leading, Davidson wrote words on slips of paper that the workshop participants drew from a cup. One of the words McIntyre drew was "snake" and one of her fellow students suggested that she create a main character named "Snake". The other elements of the story eventually fell into place:

Finally, during Terry Carr's week as writer in residence, I realized that a serpent named Grass should have hallucinogenic venom. The idea came from out in the ozone (or maybe the back 40 again), and my only excuse for not realizing it sooner is that during the 1960s I was a science geek.
[. . . ]
The next day the story got a pretty good reception, though the class snake expert and boa constrictor owner said that even genetic engineering would not excuse a venomous python. Never mind, I said, it's too heavy to carry, I'll make it a cobra.

The finished novellette "Of Mist, and Grass, and Sand" won a Nebula award in 1974. The story was later expanded into the novel Dreamsnake which won both Nebula and Hugo awards.

It's cool to see what can develop from a single word and some science geekiness!

You can read "Of Mist, and Grass, and Sand" for free at the Book View Cafe.

You can purchase the Dreamsnake ebook directly from the Book View Cafe. An audiobook version Dreamsnake is available from Amazon.com, from Barnes&Noble or from the iTunes store. .

(thanks to Cheryl Morgan posting the video clip on her YouTube channel!)

Photo:Snake 006 by cygnus921, on Flickr

Previously: Vonda McIntyre and "Of Mist and Grass and Sand"

Cloning? Genetic engineering? What should be the theme of the Sci-Fi London 48 hour filmmaking challenge?

2012-03-12T18:55:00.000-07:00

The Sci-Fi London 48-Hour Film Challenge gives competing teams only 48 hours to film a 5 minute movie. This year's competition has a twist: you can suggest a scientific theme for the filmmakers and possibly win two tickets to the Sci-Fi London film festival.

Last year's winner was the-intention-of-miles (Half Baked Films) about a man using extreme means to escape his past.

The-intention-of-miles by SFLTV

I think it would be neat if this year's competition had a biological theme: cloning, genetic engineering, brain enhancement, evolution - there are lots of great options.

If you are a UK resident, why not submit a suggestion!

Link roundup March 11, 2012

2012-03-11T12:48:00.000-07:00

Some of the science and SF links originally posted on Google+ , Twitter , and Facebook this week:

Living Plastic Eats Spilt Food: Scientific American Podcast
Center for PostNatural History: Sterile Male Screwworms
the original screwfly solution...
Spider silk violin strings made
An Absurdly Cool Behind-The-Scenes Look At The Jurassic Park Dinosaur Puppets
Scientists and tourists bring thousands of alien seeds into Antarctica | Not Exactly Rocket Science | Discover Magazine
Amateur Biologists Are New Fear in Making a Mutant Flu Virus
Bjork Explores The World Within For 'Hollow' : NPR
In the spirit of exploring the science of music, +Bjork turns the complex process of DNA replication and transcription into something as simple and beautiful as a pop song.
[GUEST POST] Jason Sanford Asks: Where Are All the Science Fiction Readers? - SF Signal

At +SF Signal Jason Sanford argues that there should be more "entry level" science fiction. I'm not familiar enough with current kid and YA fiction to know if this is really a problem or not.
ladybusiness: Coverage of Women on SF/F Blogs
Heisenberg Uncertainty Principle and Hummingbirds - Mad Art Lab

+Amy Roth illustrates the Heisenberg Uncertainty Principle with hummingbirds.
Kim Stanley Robinson: "Art is strongest when it is inspired by science"
"Art in our time is strongest when it is aware of science, includes science, is inspired by science, or is about science. [... ]. Then conceptually, science is creating new stories to tell, by deluging us with new information and potentialities."
A User's Guide to Hosting Beneficial Foreign Lifeforms (@io9)

What can probiotics do for you?
How the hunt for Mars life evolved
"an hourlong chat about the search for life on Mars, and why the Red Planet isn't exactly the way it looks in "John Carter."
Blastr: Are writing professors biased against sci-fi? Michael Chabon says yes
The Prozac Yogurt Effect: How Hype Can Affect the Future of Science | The Crux | Discover Magazine
Is overblown hype about synthetic biology affecting the future of science? +Christina Agapakisargues that it may be doing just that:
"The exuberant over-optimism about the possibilities of genetics, both sequencing and now synthesizing genes, has created outsized expectations of what DNA can do, blurring the lines between science fiction and science fact. [. . .] Cells are simply too complicated for the “gene for that” paradigm."
Could Humans Evolve into a Giant Hive Mind? (@io9)

Are we too individualistic and xenophobic for our minds to come together as one?
MIND MELD: The Secrets Behind Speculative Fiction’s Love Affair With Mars - SF Signal
The Fact and Fiction of Fantastic Hybrids
Artistic "mutants" created by artist Sandra Yagi and writer Julie Benbow.
The cell biology of regeneration (@JCB)
Earthly animals that regenerate better than +Doctor Who
"The Doctor’s slightly defective regenerative power is not only a boon for the show’s fans (and producers), but it is also a rare example of science fiction being outdone by the real world. On Earth, a wide range of actual organisms can regenerate missing parts after injury. Unlike the fictional Doctor, these animals can rebuild new structures that are indistinguishable from those they are replacing"
Jane Goodall on the Lazarus Effect | New Species | DISCOVER Magazine
Rediscovery of a long-lost species sends a message of hope about second chances for all of us"
DIY Kit Overclocks Your Brain With Direct Current - Technology Review
Welcome to the Brain Bank (YouTube)
Visit the Harvard Brain Bank, where there are never enough normal brains to go around.

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Link Roundup March 4, 2012

2012-03-04T10:00:00.000-08:00

Some of the science and SF links originally posted on Google+ , Twitter , and now Facebook this week:

Curiosities of fly genes
The origins of scientific cinematography
Rise Of The Robotic Bees : NPR
Brain Cells Know Which Way You'll Bet - Science News
Strange Horizons Articles: Writing Climate Change: A Round Table Discussion, by Niall Harrison
Making of Creatures of Light - American Museum of Natural History
Should people be allowed to erase traumatic memories by taking a pill a la "Eternal Sunshine of the Spotless Mind"? - Pandagon.net
The Forgetting Pill Erases Painful Memories Forever- Wired.com
Science Fiction: A Mirror From the Future
John DeNardo suggests SF is like a mirror that forces you to compare what you are reading to your own world view.
The Genetics of Luck - Wired
Could Teela Brown exist?
Computer modelling: Brain in a box : Nature News & Comment
Is neurobiologist Henry Markram a visionary for his pursuit of developing a detailed model of the mammalian brain? Or is he understating the complexity of the project?The latter, according to his critics.
In 1994, the Air Force proposed a magic bomb designed to turn foes into gay vampires with bad breath - io9
Alien Planets Would Likely Have Leap Years, Too
Teller Reveals His Secrets
The smaller, quieter half of the magician duo Penn & Teller writes about how magicians manipulate the human mind.
How Dolphins Say Hello
If you want to talk with dolphins, you'll have to learn how to whistle.
How you or anyone can help find ET
Crowd-sourcing the search for extra-terrestrial intelligence.
The biological science behind Martian gardening game 'Waking Mars' (Wired UK)
DVICE: Japanese build gun that jams your brain and shuts you up
NOVA: Extract your DNA
NOVA teaches you how to extract your own DNA with common household supplies. Using it to create your clone may be more complicated.
An Evolution Animation Unlike Any You’ve Seen Before… | PsiVid, Scientific American Blog Network
Possibly the best evolution primer ever -- in a silent animation made by primary school children.
The pros of science fiction outweigh cons | The Albert Lea Tribune
"Good sci-fi stories are all really about people .... The best sci-fi stories — like all great literature — become mirrors that frame questions for us: Who am I? What am I afraid of? What is a family?"
3D crystals camouflage the Diamond Weevil with their super shine - io9
Beautifully bejeweled up close, a blurry mass from a distance. Lovely camouflage!
Immortal worms defy aging | KurzweilAI
Planarians defy aging by rebuilding their telomeres. It's unlikely to be applicable to humans in the near future since we haven't learned how to reproduce asexually - yet.

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