Friday, July 27, 2007

Light Blogging

Just a note to say that I'm not dead, I'm blogging lightly due to family obligations. All should be back to normal in a week.

Wednesday, July 25, 2007

Bioscience News Roundup: 7-25-07

Here's an overview of some of the interesting bioscience news from the past week.

The Search For Alien Life

The Register takes a look at the National Research Council's report, The Limits of Organic Life in Our Solar System (by which I think they mean The Limits of Organic Life in Planetary Systems) It may not require water, and it may not be carbon based, so how can we look for extraterrestrial life?

Add to this the new complexity of looking for life that is unfamiliar, and the already formidable challenge becomes truly daunting. Burchell puts his finger on the problem: it is too complicated to test for life remotely, but you can't send an astronaut to do it because you would, in the best tradition of a twisty CSI plot, contaminate the scene.

This is where the cameras come in.

"A better alternative is to send a camera and look for changes. If you see a change, you can try to assign a reason for it. Are the seasons changing and frost melting, or have you observed something else, maybe a biological process," he says.

Astrobiology Magazine's take on the report is that space missions will have to make their tests for life as inclusive as possible.
Planned Mars missions, for example, should include instruments that detect components of light elements -- especially carbon, hydrogen, oxygen, phosphorous, and sulfur -- as well as simple organic functional groups and organic carbon.
Astrobiology interviewed the European Space Agency's Jorge Vago about the ExoMars program, scheduled to land on Mars in 2013. The goal is to search "for past and present life."
The idea is that we want to pick up where Viking left off, in terms of looking for life signatures, and try to answer once and for all if indeed there are oxidants there, if the oxidants are destroying the organics, if we see a relationship - or actually, I should say an anti-correlation - between the presence of oxidants and organics as we move down in the subsurface. And of course we also have instrumentation that will be able to answer other questions, more classical ones, related to mineralogy. To understand the possible biomarkers and interpret whether indeed they are biomarkers or not, we also need to know a bit about the geological context. So we have these other instruments with us that, even if we don’t find any organics, will provide good science.
Earthly Science

Art of the future? At Eye on DNA Hsien-Hsein Lei reports on the combination of genetics and art. Dr. Peter N. Gray creates sculptures and paintings that "reflect concepts from genetics, microbiology, and physics." Adam Zaretsky is a bit more offbeat: he runs a workshop called Hybrid DNA Isolation: A Hobbyist Workshop and an Exploration of the Unnamable.

The Beam Me Up blog reports on scientists who have engineered nematodes so that their muscles respond to colored light.
One possibility is that the technology, coupled with a method of getting light into the human skull, could create a Brave New World of neuro-modification in which conditions such as depression or Parkinson's disease are treated not with sledgehammer drugs or electrodes, but with delicate pinpricks of light.
That getting light into the skull might be a major stumbling blog to this approach, unless trepanation makes a comeback. For an overview of the technology, see the Nature News and Views "Controlling neural circuits with light." (pdf)

The complete mitochondrial genome of a 50,o00-130,000 year old mastodon ago has been sequenced. While a significant achievement, mitochondrial DNA is only about 16,500 base pairs, a mere fraction of the roughly 4 billion base pairs in a typical elephant genome. We're still a long way from Jurassic Park. You can read the paper in the open-access journal PLoS Biology.

The New Scientist article "Why 'junk DNA' may be useful after all" was given a thumbs up by University of Toronto biochemist Larry Moran. Read his post for background about the current scientific thought on "junk DNA" (which is not the same as "non-coding DNA").

New Scientist reports that new software
has been developed that can recognize dolphin species by their whistles. It's a far cry from real communication, of course. Hopefully the first dolphin message we understand is not "so long, and thanks for all the fish."

Finally, Posthuman Blues points to a report that concludes "Deadly germs may be more likely to be spread due to a biodefence lab accident than a biological attack by terrorists." For some reason I find the idea of accidental plague more frightening than a planned attack.

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The Future of Augmented Cognition

Mo at Neurophilosophy looks at recent developments in attention-enhancing devices and memory that are part of the Defense Advanced Research Projects Agency (DARPA) program to develop augmented cognition. As part of that project, they commissioned a a short film The Future of Augmented Cognition:
[. . ] directed by Alexander Singer, who is probably best known for making episodes of television series such as The Fugitive, Hill Street Blues, Start Trek: The Next Generation and Deep Space Nine. This film is set in the year 2030, and takes place in a command centre which monitors cyberspace activity for threats to the global economy; it is a depiction of DARPA's vision of how augment cognition will in the future be used to integrate multiple sources of information.
Here's DARPA's vision of the future:


Monday, July 23, 2007

Biology in SF Bits 7-23-07

OK, I finally finished reading Harry Potter 7, so it's back to blogging! Here are some science fiction biology tidbits from the past week:

Washington Technology interviewed John Scalzi about Old Man's War and his other novels, some of which have biotech themes.

Q: Your books also touch on biotechnology. In your distant future, you imagine using the DNA of the dead to engineer supersoldiers. But if you look at the state of the science and its cultural barriers today, what do you foresee for the near future?

Scalzi: One of the things that has been very interesting about the biotech field is that a lot of it is going against roadblocks that have been put up politically. If embryonic stem cell research was not being blocked by the current administration, there would not be as much interest in [alternatives].

Q: Can you give an example?

Scalzi: [Scientists] recently took skin cells from mice and engineered them into [the equivalent of embryonic stem cells]. That’s a really interesting bioengineering achievement that would have been unnecessary had there not been ethical concerns about embryonic stem cells. We can argue whether that’s taking six steps sideways to take one step forward, but if they can take skin cells from me and make me a new liver, that’s a real advance.

Read the whole interview.

SciFi Weekly reviews Jeff Carlson's new novel, Plague Year. Rogue nanotech has destroyed most of the human (and other animal population). Carlson focuses on the survivors of this plague. While giving it a thumbs up for an interesting and believable science fiction premise, the review indicates that characterization is lacking.
This novel is so concerned with surface effects—cinematic effects, if you will, and I think this judgment about the book's movie models is sound—that the poetry, the emotions, the whole affect of the post-apocalypse novel goes missing. There's no true sense of desuetude or loss here, no Ozymandias Effect. Just compare this book to Wyndham's classic The Day of the Triffids (1951) to see what I mean

According to the Wired Underwire blog, ABC will be showing the Masters of Science Fiction series beginning Saturday, August 4th.
  • August 4: "A Clean Escape" based on John Kessel's short story by the same name.
    "In "A Clean Escape," set not too far in a post-Apocalyptic future, psychiatrist Dr. Deanna Evans (Judy Davis) interrogates a distinguished, if befuddled, man (Sam Waterston) who appears to be suffering from a lapse in memory. Why can't he remember - and why is it so important that she uncover the secret he holds deep inside?"
  • August 11: "The Awakening," based on a short story by Howard Fast.
    "[T]he episode opens outside Baghdad, where U.S. soldiers discover a mysterious casualty - one they can't even identify as human."
  • August 18: "Jerry Was a Man," based on the Robert Heinlein story.
    "Set in the future, the world's seventh richest couple, the van Vogels, find their lives changed forever when they acquire an anthropoid named Jerry."
  • August 25: "The Discarded," based on a story by Harlan Ellison.
    "John Hurt and James Denton star in this ultimate story of despised minorities sentenced to drift in the darkness of outer space forever. These men and women make a desperate pact in the hope of being offered refuge at home on Earth."
It certainly looks more interesting that the usual Saturday-night network fare.

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Is Science Fiction Obsolete?

Last week Discover posted an article that claims "sci-fi helped make the present; now it's obsolete." The author, Bruno Maddox, bases his argument on the assumption that the primary purpose of science fiction is to predict future technological development. I'm reluctant to take an article on science fiction too seriously when it uses notoriously anti-science author Michael Crichton as its primary example.*
But Jurassic Park, which came out in 1990, was pretty much it for Crichton as an effective, hard-SF prognosticator. When he returns to science fiction in 1999 with Timeline, something clearly has changed. The topic is time travel, and true to his career-long hard-SF principles, Crichton does at least sketch out for the reader how such a thing might actually be possible. Sort of. The key, he ventures, might be “quantum foam.” In the real world, quantum foam is a term used by hard-core physicists standing beside vast, cantilevered chalkboards full of squiggles to describe a theoretical state, or scale, or reality at which particles of time and space blink in and out of existence in a soup of their own mathematical justification. But in Crichton’s hands, it’s actual foam. His heroes step into their time machine, pass quickly through a metaphysical car wash of suds, and then spend the rest of the novel jousting with black-armored knights and rolling under descending portcullises. The science, in other words, is pure nonsense, and the science fiction is not so much “hard” or “soft” as what you might call, well, “bad.”
See, the thing is that Jurassic Park isn't very good prognostication either. Filling in the gaps in the recovered dinosaur DNA sequences with frog DNA is not a very likely scenario.

Of course Maddox's real point appears to be that fiction itself is dead.

As to the question of what happened, not just to Crichton but to all serious science fictionists, I reckon it boils down, like so many things, to a pair of factors.

For one, it was around that time, the mid-1990s, that fiction—all fiction—finally became obsolete as a delivery system for big ideas. Whatever the cause—dwindling attention spans, underfunded schools, something to do with the Internet—the fact is these days that if a Top Thinker wakes up one morning aghast at man’s inhumanity to man, he’s probably going to dash off a 300-word op-ed and e-mail it to The New York Times, or better still, just stick it up on his blog, typos and all, not cancel his appointments for the next seven years so he can bang out War and Peace in a shed.
The sense I get is that Maddox isn't much of a science fiction reader. If he was, he would realize that science fiction isn't just about predicting the future of technology. There's also social commentary - all the way back to H.G. Wells - and simply entertaining stories. And if you read science fiction by author's other than Crichton you would know that there is many a tale out there that is on the cutting edge of science. Certainly that's true in biology based sci fi - cloning, genetic engineering, uploading of memories to silicon and other biological wonders abound. We can only know in retrospect whether today's tales predict the future or are flights of fantasy.

* It also wastes a whole paragraph that on a slightly bizarre bean dip analogy.

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Friday, July 20, 2007

Biology of Harry Potter

It is now past midnight London time, and to great excitement the final Harry Potter book has gone on sale. Of course the Potter books are fantasy, not science fiction, but that doesn't mean they can't be a launching pad for a biology discussion.

Back in 2005 British geneticists Jeffrey M Craig, Renee Dow, and Mary Ann Aitken wrote a letter to Nature (reprinted by the Panda's Thumb) suggesting that the inheritance of wizarding abilities might be a good way to introduce kids to basic ideas in genetics.
Wizards or witches can be of any race, and may be the offspring of a wizard and a witch, the offspring of two muggles (‘muggle-born’), or of mixed ancestry (‘half-blood’).

This suggests that wizarding ability is inherited in a mendelian fashion, with the wizard allele (W) being recessive to the muggle allele (M). According to this hypothesis, all wizards and witches therefore have two copies of the wizard allele (WW). Harry’s friends Ron Weasley and Neville Longbottom and his arch-enemy Draco Malfoy are ‘pure-blood’ wizards: WW with WW ancestors for generations back. Harry’s friend Hermione is a powerful muggle-born witch (WW with WM parents). Their classmate Seamus is a half-blood wizard, the son of a witch and a muggle (WW with one WW and one WM parent). Harry (WW with WW parents) is not considered a pure-blood, as his mother was muggle-born.

The commenters get into the discussion with proposals for how genetics might explain squibs and the variability in magical powers, even though those issues were also mentioned in a rebuttal letter.
There may even be examples of incomplete penetrance (Neville has poor wizarding skills) and possible mutations or questionable paternity: Filch, the caretaker, is a ‘squib’, someone born into a wizarding family but with no wizarding powers of their own.
Now Anne-Marie of Pondering Pikaia has written a fun series of posts on the details of biology in the Harry Potter universe:
She promises a few more articles in the series, so keep an eye on her blog!

Eva Amsen (aka easternblot) also has a series of updates on Harry Potter biology.
I'm sure that book #7 will have more biological mysteries, just itching to be explained.

Do you know a lover of the Harry Potter books that you'd like to introduce to science fiction? The readers of SF Signal have compiled a list of titles you can suggest.

(thanks to Coturnix for pointing out both series!)

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Thursday, July 19, 2007

Promicin and Unlocking the Brain's Potential

Last Sunday night I watched The 4400 for the first time since the early episodes of the show. The last time I had seen an episode the source of the returnee's special powers was unknown. Now, apparently they've figured all that out. As the Wikipedia article* explains:
The human body produces four main neurotransmitters** that control and regulate bodily functions. In The 4400, every 4400 produces a fifth neurotransmitter called promicin that enables him or her to use parts of the cerebellum no human has previously used. This is the cause of the new abilities in each returnee.
While anyone can now have special powers equal to one of the 4400 by taking promicin, there is a great risk involved: half of the people who get a promicin shot die from a brain aneurysm. Is it worth the risk? There are several elaborate web sites that are taking part in the "debate."

Promicin Terror spreads the word about the dark side of promicin injections, including public service message videos and autopsy reports.

Promicin Power, on the other hand, is fighting to allow people to choose to take promicin. They are supported by the "personal" sites of people who have taken promicin and had a positive experience: Promicin Passion and Promicin Dance .

Meanwhile, Promicin Info is supposed to be a non-biased source of general information. You can't claim that the NBC promotional department hasn't been hard at work - it's even got a blog with fake comments.

But what about real brains? Could there really be another neurotransmitter that unlocks special abilities?

It's certainly possible that novel neurotransmitters are yet to be discovered. For example, it's only in the past 15 years or so that the endocannabinoid pathway (or as Scientific American calls it "The Brain's Own Marijuana") has been unraveled. It wouldn't surprise me at all if new neurotransmitter pathways were yet to be discovered.

There's a problem with promicin, though, at least the way I understand it. We humans are extremely unlikely to have receptors in the brain that could respond to promicin unless there is a promicin-like neurotransmitter already present. Sure, promicin could just do a better job of stimulating those pathways than the natural neurotransmitters (sort of in the way that morphine binds opioid receptors), but that wouldn't activate parts of the brain that aren't used under natural conditions.

And that leads to the second problem: the popular idea that we only use a fraction of our brain is just a myth. While we might not be using 100% of our brain at any particular moment, over time - a day or a week - we pretty much use it all. Use it or lose it, as they say. The idea that a part of our brains evolved to include a completely inactive region that won't function unless stimulated by a chemical that won't be synthesized until several centuries from now doesn't make a lot of sense.

Now if they claimed that our descendants boost their mental powers by grafting on an engineered extra bit of brain, that I might buy.

* I had to look stuff up during the commercials because I had no idea what was going on.

** There are definitely more than four neurotransmitters: acetylcholine, norepinephrine, dopamine, serotonin, glutamic acid, GABA, glycine, and others. I suppose that it might be right to say there are four "main types" in some specific regions of the nervous system.

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Wednesday, July 18, 2007

Bioscience News Roundup: 7-18-07

Some interesting bioscience stories from the last week:

What would happen to birds and the bees after a nuclear apocalypse? Studies of the wildlife around Chernobyl can give us a clue. An article in The Economist takes a look at a report on the bird life near the nuclear power plant that spread radioactive material around the countryside in a 1986 explosion.
When due allowance was made for habitat differences, they found that species which relied on a class of chemicals called carotenoids to tint their feathers fared worse when there was more radioactivity around. Intriguingly, that did not apply to birds that used melanin, another pigment, in their plumage, nor to those that employed iridescence—which is a result of the structure of feathers, rather than their chemistry.
Carotenoids serve at least two biological roles. They are pigments - the orange in carrots and oranges, the red in peppers and tomatoes, and the pink in flamingo feathers and salmon - and are antioxidants that protect DNA from damage. In this case it appears that birds that use their carotenoids to make pretty red and yellow feathers end up leaving their DNA vulnerable to radiation damage. While life survived the disaster, the variety of life has changed. There is more about the rebound of Chernobyl wildlife at Accidental Blogger. (via Gene Expression)

The Wired Science blog reports on
another science article in The Economist about modeling life on the computer. David Harel of the Weizmann Institute, for example, has been working on a computer simulation of the nematode C. elegans. But will it be a true representation of the original animal?
Indeed, he proposes to evaluate the result using an updated version of the Turing test. This was devised by Alan Turing, an early computer scientist, to identify whether a machine is capable of thought. The original test proposes that a person be presented with a suitable interface—say, a keyboard and a screen—through which to communicate. If the operator cannot tell the difference between talking to another person through this interface and talking to a computer, then the computer can be argued to be thinking. Dr Harel's version is a little more challenging. He wants to test whether scientists well versed in the ways of C. elegans could tell his computerised version from the real thing. So far, the distinction is obvious, but it may not always remain so.
That and more was discussed at a recent conference organized by Microsoft Research in Cambridge, England. Their website has more on their work on computational biology, computational ecology, and nature-inspired computation.

A post on Metafilter rounds up a bunch of links on the "double muscle" mutations in the protein myostatin. Humans, dogs, cattle, and mice that carry two mutated copies of the gene have hulk-like muscles.

Eye on DNA links to a Futures in Biotech podcast that interviews Dr. Svante Paabo about possible reconstruction of a complete Neanderthal genome.

Many women - perhaps more than half - have four different photopigments in their retinas rather than the standard three carried by most men. Cognitive Daily reprints a 2005 post on a study that shows women with four photopigments appear to perceive color differently from men and women with only three photopigments .

Mind Hacks links to a freely available article in Nature Clinical Practice Neurology about the potential for RNA interference (RNAi) technology to be used as therapy for neurodegenerative diseases. If you aren't sure what RNAi is, read the background information at Mind Hacks first.

The new podcast from the American Chemical Society, Science Elements, includes a regular report on the latest in biochemistry. The June 27/July 3 episode reports on extracting a novel mucin glycoprotein from the masses nuisance jellyfish that clog seawater intake pipes and contaminate beaches. The mucusy protein has potentially many uses - from cosmetics to new antibiotics. If you don't want to read the technical article in the Journal of Natural Products, the New York Times has an article about the report.

In other natural materials news, scientists have made a glue that combines portions of gecko and mussel adhesive. The result - called "geckel" - is a reversible adhesive (think sticky note) that still strongly binds under water. It has many potential uses, from water resistant bandages to consumer and military products. It will be the cover story on the July 19th issue of Nature.

The Beam Me Up blog links to a new MIT study that identifies the mechanism behind fear. The article in Nature Neuroscience reports that interfering with the appropriate enzyme in the hippocampus region of the brain actually results in the extinction of fear learned in a particular context. As Science Blog notes, this research might eventually be used to treat post traumatic stress disorder and panic attacks.

For even more biology-related posts, check out this weeks blog carnivals: Gene Genie at Med Journal Watch and Tangled Bank at The Voltage Gate.

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Free Fiction: Rhesus Factor

Some more free fiction for your summer reading list:

Australian science fiction writer Sonny Whitelaw has made an e-book of her 2005 eco-thriller Rhesus Factor free for download. From the description:
Marine engineer Kristin Baker advises the Pacific Island nation of Vanuatu on environmentally sustainable development projects. After meeting US Navy Commander Nicholas Page, she discovers her unwitting role in the Exodus Project, a scheme to protect the West's interests in the face of global warming. But what neither know is that a stealth virus has quietly become a global pandemic; one that health authorities cannot stop. For this virus hasn't emerged from an African jungle or a remote Chinese province, it's come from within our own DNA.

Rhesus Factor's claim to fame is that it's warning about the dangers of global warming inspired a politician to urge every member of the Queensland State Parliament to read a copy. Whitelaw is member of the "writing science fiction is more fun than doing science" club. From her biography:

Amidst the chaos and clutter of Sydney University life in the seventies I actually managed to acquire a degree - principally because most of my undergraduate life was spent on a beach. The best way to understand the mathematics of a breaking wave is to go surfing! Half way through writing the final draft of my thesis on sea level change and global warming, I decided that running a sail boat and dive operation in the South Pacific would be safer, and probably a whole lot more fun, than a career as an academic.
[snip . . .]
One evening in the late 1990s, sitting on the edge of an erupting volcano with a jug of slightly ashy margaritas in hand, I allowed a couple of my friends – a volcanologist and an epidemiologist – to talk me into finishing my thesis. With the philosophy that ‘the play’s the thing’, I chucked the thesis idea and instead began writing the factional eco-thriller,The Rhesus Factor.

You can download Rhesus Factor from Double Dragon Books or

(via DragonKat via the Australian Speculative Fiction Blog Carnival)

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Tuesday, July 17, 2007

Habitable Planets For Man

Robert J. Sawyer points out the classic 1964 study by the Rand Corporation, Habitable Planets for Man (or as Sawyer calls it "the world-building bible") by Stephen H. Dole, is now available as a free pdf.

The description from the download page:
An attempt to make an estimate of the probabilities of finding planets habitable to man, where they might be found, and the number there may be in our own galaxy. The characteristics of a planet that can provide an acceptable environment for man are presented in detail. The stars nearest the earth, most likely to possess habitable planets, are itemized. The author also discusses special and unusual planets that may be discovered, how new environments might affect people who migrate to them, how to search for habitable planets. He also gives an appraisal of the earth as a planet and describes how its habitability would be changed if some of its basic properties were altered. An attempt to make an estimate of the probabilities of finding planets habitable to man, where they might be found, and the number there may be in our own galaxy. The characteristics of a planet that can provide an acceptable environment for man are presented in detail. The stars nearest the earth, most likely to possess habitable planets, are itemized. The author also discusses special and unusual planets that may be discovered, how new environments might affect people who migrate to them, how to search for habitable planets. He also gives an appraisal of the earth as a planet and describes how its habitability would be changed if some of its basic properties were altered.
Sounds like a useful reference if you are building a world for humans or human-like aliens.


Monday, July 16, 2007

Biology in SF bits 7-16-07

Here's a roundup of interesting links from the past week:

Science in Science Fiction

Philip Ball's current Nature Muse column is about an article by CJ Efthimiou and R.A. Llewellyn about bad physics in the movies
But Hollywood's scientific absurdities do raise some interesting questions. Can we spot physics abuse? And when we see superheroic feats, do we sense that laws are being broken?

Our understanding of sporting prowess comes at the same questions from the opposite direction. No one supposes that baseball fielders or football players use newtonian mechanics to predict trajectories; rather, they seem to have a superior intuitive sense of its dynamical consequences.

The answers might imply interesting things about how much evolution has honed our senses to appreciate the laws of physics. British biologist Lewis Wolpert has argued persuasively that, on the contrary, much of science depends on subverting intuitive reasoning about the world4
Diane Kelly at Science Made Cool writes about becoming a cyborg.
The idea of melding people with machines has been a staple of science fiction for a very long time. Brian Stableford, writing in The Encyclopedia of Science Fiction, identifies its first major use in E. V. Odle’s 1923 novel The Clockwork Man. In that story, the eponomous man from the future has a clockwork mechanism built into his head that lets him move between dimensions. His machine is an enhancement; an add-on module that gives him abilities beyond what normal humans can do. It’s the great-great grandfather of the BrainPals in John Scalzi’s Old Man’s War series. And more often than not, when an author sticks a machine into a character it’s a means of examining whether your humanity is diminshed if there’s a machine attached to you that you can’t ever take off. Let me tell you one thing, it beats dying.

These stories are usually set hundreds of years in the future, but people are becoming cyborgs now. It’s not to become stronger, faster, or smarter. People become cyborgs because it’s a better option for living with a chronic condition, even when it isn’t life threatening.
Science Made Cool is the official blog of Zygote Games, which sells bio-fun board games Bone Wars: The Game of Ruthless Paleontology and Parasites Unleashed!

Blog Carnivals

First off there were two science fiction-related carnivals this week.

The first People of Color in Science Fiction and Fantasy Carnival has been posted: Painted With A Bitter Brush at Willow's Live Journal. As N.K. Jemison points out in "No more lily-white futures and monochrome myths" science fiction futures are usually depicted as much whiter than present-day America:
Star Trek, for example. The show is set several hundred years in the future. White men are in the severe minority now on this planet, destined to become far more so if current demographic trends continue. Yet the Enterprise has a crew overwhelmingly dominated by white men. Another example is the current longest-running SF show on TV, Stargate SG-1, which has pretty much relegated people of color to the role of superstitious space-primitives (carrying space-spears, no less). There’s a whole planet of ‘em, or two or three. But there still aren’t many in the show’s version of the American military.
If you haven't done so already, be sure to read Pam Noles' 2006 essay "shame" in Infinite Matrix written in response to the SciFi version of Ursula LeGuin's Earthsea starring a blond blue-eyed Ged. If you are interested in contributing the official PoC SF Carnival blog has submission information. They are especially interested in links to or about SF&F Illustrators of Color.

Also this week was the 15th Carnival of Feminist Science Fiction and Fantasy Fans at Feminist SF - The Blog! with a great roundup of posts about the panels at this year's Wiscon. The Feminist SF Carnival blog has submission information.

Book Bits and Free Fiction

John Scalzi has created an e-book version of his novel of genetically-engineered sheep interstellar diplomacy, The Android's Dream, that is free for overseas service people.

Robert J. Sawyer has made a number of his short stories available for free online. Colin Harvey at Suite 101 has reviewed his novel Hominids (Neanderthal Parallax trilogy) as part of the Essential SF Library series.

The June Issue of Hub Magazine has provides the story "More than a Butterfly"by January Mortimer for free (pdf version, Mobi Pocket version, MS Reader version). As SF UK Review sums it up: "It’s a story of genetic manipulation, fashion, butterflies and one woman’s passion for her work. There are some nice touches that help to flesh out the main character, showing her to be a complex person while hinting at the complexity of the subject without getting bogged down in technicalities." (via Andrew Wheeler)


Michael Crichton's Andromeda Strain is being developed as a miniseries for A&E.

SciFi Weekly reviews Kyle XY: The Complete First Season - Declassified DVD.

SciFi Chick has an update on the upcoming release of the Heroes Season 1 DVD set.

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"Science of Aliens" Lecture at the Science Fiction Museum in Seattle

If you happen to be in the Seattle area on August 8th, you might want to check out the Pop Culture Talk at Experience Music Project/Science Fiction Museum.

Topic: "The Science of Aliens"

Speaker: Dr. Tom Daniel, the Joan and Richard Komen Endowed Chair of Biology, University of Washington.
Daniel received his BS and MS at the University of Wisconsin, a PhD at Duke and was the Bantrell Postdoctoral Fellow in Engineering Sciences at Caltech until 1984 when he joined the University of Washington. He is the proud recipient of the University of Washington 1989 Distinguished Teaching Award and the 2001 Distinguished Graduate Mentor Award.
Time and Place: JBL Theater, 7pm
Cost: Free for EMP|SFM members, $5 for the public.
RSVP: 206-770-2702

Other upcoming live events:

July 17th (tomorrow!): Six Summer Evenings of Science Fiction 2007 Reading Series - Patrick Nielsen Hayden
Patrick Nielsen Hayden is a senior editor at Tor Books and the editor of the influential, award-winning Starlight anthology series. A witty, savvy observer of the business side of science fiction, he possesses an encyclopedic knowledge of the field's history. He will be interviewed by Nebula Award-winning writer Eileen Gunn, author of the short story collection Stable Strategies and Others.
July 24: Six Summer Evenings of Science Fiction 2007 Reading Series - Samuel R. Delany
Samuel R. Delany is arguably the most daring, wide-ranging, word-drunk, idea-besotted writer of science fiction and fantasy that the United States has ever produced. In his 45-year professional career, he has extensively explored issues of language, gender, race, sexuality, power and otherness. Author of Dhalgren, Babel-17, and numerous novels, stories, and critical and philosophical works including his new novel Dark Reflections, he never fails to deliver a dynamic evening. Delany has won numerous national and international awards including the Hugo and Nebula, and was inducted into the Science Fiction Hall of Fame in 2002. Delany is Clarion West's 2007 Susan C. Petrey Fellow.
The current exhibitions at the Science Fiction Museum and Experience Music Project are:

Out of this World: Extraordinary Costumes from Film and Television
June 16, 2007 – September 30, 2007

Sound and Vision: Artists Tell Their Stories
February 28, 2007 (permanent collection)

Disney: The Music Behind the Magic
November 4, 2006 – September 9, 2007

Alien Encounters
September 10, 2006 – November 4, 2007

Image: Detail from cover of Jack Vance's The Dragon Masters by artist Jack Gaughan, 1962. Image from the Science Fiction Museum's Alien Encounters exhibit.

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Sunday, July 15, 2007

Douglas Adams on Life

Back in 1998 Douglas Adams asked "Is there an Artificial God?" at Digital Biota 2 in Cambridge, UK. As I would expect his talk was both funny and smart. While his focus was on God and religion and the role it can play even in a modern scientific world, he had a bit to say about recognizing life.
The following strange thought went through my mind: that trying to figure out what is life and what isn't and where the boundary is has an interesting relationship with how you recognise handwriting. We all know, when presented with any particular entity, whether it's a bit of mould from the fridge or whatever; we instinctively know when something is an example of life and when it isn't. But it turns out to be tremendously hard exactly to define it. I remember once, a long time ago, needing a definition of life for a speech I was giving. Assuming there was a simple one and looking around the Internet, I was astonished at how diverse the definitions were and how very, very detailed each one had to be in order to include 'this' but not include 'that'. If you think about it, a collection that includes a fruit fly and Richard Dawkins and the Great Barrier Reef is an awkward set of objects to try and compare. When we try and figure out what the rules are that we are looking for, trying to find a rule that's self-evidently true, that turns out to be very, very hard.

It makes me wonder if we'll even recognize the first truly alien life form we stumble across. Adams also points out the danger of arrogantly believing that the universe was created just for us.

Now the real trap springs, because early man is thinking, 'This world fits me very well. Here are all these things that support me and feed me and look after me; yes, this world fits me nicely' and he reaches the inescapable conclusion that whoever made it, made it for him.

This is rather as if you imagine a puddle waking up one morning and thinking, 'This is an interesting world I find myself in - an interesting hole I find myself in - fits me rather neatly, doesn't it? In fact it fits me staggeringly well, must have been made to have me in it!' This is such a powerful idea that as the sun rises in the sky and the air heats up and as, gradually, the puddle gets smaller and smaller, it's still frantically hanging on to the notion that everything's going to be alright, because this world was meant to have him in it, was built to have him in it; so the moment he disappears catches him rather by surprise. I think this may be something we need to be on the watch out for. We all know that at some point in the future the Universe will come to an end and at some other point, considerably in advance from that but still not immediately pressing, the sun will explode. We feel there's plenty of time to worry about that, but on the other hand that's a very dangerous thing to say.

If there is another intelligent species in the universe it make think that it was created just for them. It seems like it's a recipe for a terrible culture clash.

It's well worth reading (or listening to) the whole talk. (via BoingBoing) While you're at, check out some of their interviews and projects developing virtual creatures and digital ecosystems.

Some days I think Adams was right about everything: we are indeed bugs in the greatest organic computer of all time, descended from a useless bunch of telephone sanitizers and marketing consultants. I'm sorry we lost Adams before he could tell us more.

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Friday, July 13, 2007

Julie Czerneda's Species Imperative Trilogy

Fantasy Book Spot reviews Canadian Science Fiction writer Julie E. Czerneda's 2005 novel, Survival, Book 1 of her Species Imperative trilogy (via Andrew Wheeler at ComicMix).
Our hero, Mackenzie Winifred Elizabeth Wright Connor, is a biologist studying the recovery of salmon in the Pacific Northwest. She has pledged devout loyalty to her salmon and pointedly ignores the goings-on of life on other planets, even when that life is being mysteriously wiped out. She is volunteered by the Ministry of Extra-Sol Human Affairs when an alien scientist, notable in his field of archeology, comes to beg her assistance in the search for the killers. Brymn is a Dhrin, a species that has ignored biology to the point of forbidding the study of all biological sciences. He hopes her experience in studying the survival of salmon will translate to knowing how to insure the survival of the Dhrin. One thing leads to another, of course, and she is soon embroiled in galactic politics as well as a fight for the survival of mankind.
Fantasy Book Spot rates it a "10". The other two books in the series are Migration and Regeneration.

Czerneda was formerly a researcher in animal communication and her fascination with biology on Earth has inspired her alien species. As she said in an interview with Strange Horizons:
JC: I use what I know about the mechanics and motivations of animal communication when building my aliens, definitely. For example, Esen, the main character of my Web Shifters books, typically finds herself either at an advantage or disadvantage due to a form's ability to communicate. I also like to put humans into situations where they have to communicate with the non-human, then show the potential for misunderstanding. Such fun. One of my favourites has been the Drapsk, from the Trade Pact books (A Thousand Words for Stranger, Ties of Power, To Trade the Stars). I loved finding ways to make communication technology for beings who smell meaning.
Czerneda has long been an advocate of using science fiction as a tool for science literacy (see her guide for teachers No Limits: Developing Scientific Literacy Using Science Fiction and the recently released science fiction short story collection Polaris: A Celebration of Polar Science), and that was part of the inspiration for the Species Imperative series.
LT: Tell us about Species Imperative: Survival, just out in May 2004. What sparked the idea for this novel?
JC: The idea echoes back to my interest in encouraging scientific literacy, particularly in biology. I mean, if we don't understand ourselves as living things, how can we hope to make informed choices? I wanted to write about a situation where there are many intelligent species, coexisting in space, all sure the big problems have been solved as long as everyone pays their bills, but. . .my "but" is that one of those species has an unsuspected biological drive, a "species imperative" that will come to threaten all the others. I chose migration, because staying on your side of the fence is part of being a polite neighbour. If you must migrate, rules of territory and property are lost. What happens then? Not to mention, I've made that migration a little more dangerous than most.
Czerneda's latest novel, Reap the Wild Wind will be available in September.

Find more books by Julie Czerneda at the Amazon Biology in Science Fiction store.

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Y: The Last Man and Blue Moon Butterflies

A paper in today's issue of Science by Sylvain Charlat and colleagues looks at the evolution of a population of Blue Moon butterflies that was infected with the Wolbachia bacterium, which selectively kills male embryos. The result was a population of butterflies with a female to male ratio of 100:1. When individuals in the population that were resistant to Wolbachia appeared, presumably due to a nuclear mutation, the resistance rapidly spread through the population and within 10 generations the sex ratio was back to 1:1.

PZ Myers compares the Wolbachia-infected Blue Moon butterfly population to the situation in the graphic novel Y: The Last Man, in which all male mammals are killed by a mysterious disease - except the hero Yorick and his monkey.
Substantial parts of it are biologically nearly impossible: the wide cross-species susceptibility, the near instantaneous lethality, and the simultaneity of its effect everywhere (there are also all kinds of weird correlations with other sort of magical putative causes, which may be red herrings).
A disease that infects only males is clearly plausible, but Yorick doesn't follow the example of his butterfly brethren, as PZ points out.
Now here's one thing that bugs me about Y: The Last Man. For this rapid dispersal of resistance to spread, resistant males should be procreating profligately. In the book, Yorick seems to be obstinately abstinent! (Some of the women, at least, understand the principle, and there are plots with attempts to capture the last man for breeding stock for their group.) I can understand how the author might want to resist turning the story into a boring male fantasy of having the only penis among teeming millions of fertile females, but come on, biological reality has to intrude at some point. The future of the human race demands it!
I suppose you have to read the series to find out if Yorick indeed does his part to save humanity.

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Wednesday, July 11, 2007

Bioscience News Roundup: 7-11-07

Some of the interesting biology and biotechnology news stories from the past couple of weeks:

Scientists at MIT were able to reverse mental retardation caused by fragile X syndrome by blocking an enzyme involved in cellular development. As Scientific American (and lots of others ) point out, this is reminiscent of Daniel Keys' Flowers for Algernon in which surgery is used to boost the intelligence of the mouse Algernon and janitor Charlie Gordon. Hopefully the long term results are better in real life than in fiction.

Technology Review talks to Ari Patrinos, president of Synthetic Genomics, about engineering microbes to harvest oil. Craig Venter, founder of Synthetic Genomics, reported a major step in that direction; transferring an entire genome from one microbe to another. As Technology Review reports:
For Venter's team, the genome transplant is a step toward engineering microbial machines to efficiently produce fuel. The researchers are currently trying to stitch together a synthetic version of the genome of Mycoplasma genitalium, a bacterium found in the human genital tract, which Venter's group has been studying for more than a decade. By rearranging or deleting specific chunks of the synthetic genome and inserting it into a bacterial host, scientists should be able to figure out which genes are critical for the organism to function--in essence, the minimal genome. This minimal genome could then be modified to carry fuel-producing genes, and the entire string of DNA could be transplanted into a bacterial carrier.
You can listen to an interview with Venter on the June 29 Science Friday.

According to Technology Review, the Rothberg Institute will be initiating what it calls the Methuselah Project: sequencing the DNA of 100 people who are 100 years old, or older. They will only be looking at the DNA sequences that encode proteins. They apparently believe any genetic changes that increase lifespan will most likely affect protein sequences rather than the stretches of DNA that regulate when and in which cells those proteins are expressed.

TED Talks has video of a lecture by professor of surgery and chemical engineering Alan Russell on Why can't we grow new body parts?

The New Scientist Short Sharp Science blog reports on the recent report of a test of a memory erasing drug, Propranolol, on people who had experienced traumatic events.

Margaret Talbot writes for the New Yorker about using brain scans to uncover lies. It sounds like the technology currently lies on the boundary of pseudoscience.

The June 22 issue of Slate looks at "recombination of man and beast" - animals carrying human DNA - based on a report from the British Academy of Medical Sciences (pdf).
Last month, ethicists from Stanford University and the University of Wisconsin detailed a proposal by a Stanford scientist to substitute human brain stem cells for dying neurons in fetal mice. "The result would be a mouse brain, the neurons of which were mainly human in origin," they reported. The payoff, if the fetuses survived, would be "a laboratory animal that could be used for experiments on living, in vivo, human neurons." Imagine that: a humanoid brain network you can treat like a lab animal, because it is a lab animal.
Meanwhile the Roman Catholic Church has opined that human-animal hybrids should be considered to be human. (via Womens Bioethics Blog)
"The bishops, who believe that life begins at conception, said that they opposed the creation of any embryo solely for research, but they were also anxious to limit the destruction of such life once it had been brought into existence. In their submission to the committee, they said: 'At the very least, embryos with a preponderance of human genes should be assumed to be embryonic human beings, and should be treated accordingly.'"
On June 26, the New York Times devoted the science section to stories about evolution. The stories (you'll need a free account or bugmenot):

Michelle Wirth takes at takes a look at human pheromones for Scientific American Observations. She points out some of the problems with a recent study by Claire Wyart and colleagues that tested whether women responded to a chemical - androstadienone - in male sweat.

The inhabitat blog reports on wall insulation grown from a culture of mushrooms (via Beyond the Beyond)

Neurofuture reports on a collaboration between University of Calgary researchers and artists Dr. Morley Hollenberg, Alan Dunning and Paul Woodrow called the Shapes of Thought.
Participants were monitored by EEG, and EKG sensors and asked to recall traumatic events from their past. Participants agreed to undergo hypnosis and aid in the recollection and reliving of events in which they were deeply afflected by anger, fear, joy or other primary emotions.
The EEG data was translated into three dimensional images in real time.

Finally, Mind Hacks reports that the text book Neuropsychopharmacology: The Fifth Generation is now available online for free. It ". . . covers the cutting edge of pretty much everything we know about how drugs affect the mind and brain."

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Kathie Huddleston has a review of the new kids' show Dinosapien on Lauren is a reluctant counselor at Dinosaur Explorer Camp in the Canadian Badlands, run by her paleontologist mother, Dr. Hilary Slayton. Meanwhile, after a small series of earthquakes three dinosaurs find themselves "on their own in a strange land."
The well-written pilot episode, "Dawn of the Dinosaurs," is an excellent introduction to the series. We get to know Lauren's world and begin to understand that these dinosaurs are intelligent beings in their own right. Both species of dinosaur have been developed in interesting ways, from the quick, birdlike Eno to the slow, armored and nasty Diggers. There's a sense that these dinosaurs have accidentally left behind societies of their own.

While Lauren is a terrific character as portrayed by Brittney Wilson, the animated Eno is just as well developed. The dinosaurs fit so naturally in the story that it's easy to forget that they aren't real. Without language, we come to sympathize with Eno, and it becomes easy to understand how these two lost souls, with Eno physically lost and Lauren emotionally lost, are destined to end up saving each other in one way or another.
The series was produced by BBC Worldwide, and premiered in the U.S. on Saturday, July 7 on Discovery Kids and in Canada on BBC Kids. The Discovery Kids Dinosapien site has more information about the cast and characters and has behind-the-scenes video. It seems to me that they missed the opportunity to give kids information on real dinosaurs and palenotologists. They could have at least linked to the Discovery Channel's own dinosaur guide!

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Genetic Engineering Tunes

It's not really science fiction, but it is fun: New Scientist Short Sharp Science Blog lists their top 10 science pop songs. Making the cut: Air's "Biological" (" XX XY, That's why it's you and me. Your blood is red, It's beautiful genetic love … I need your DNA") and "Genetic Engineering" by OMD, one of the faves of my youth (although not as catchy as "Tesla Girls" or "Electricity"). I love the bit in the video where the kids fight over the genetics text book.


Truly Alien Life On and Off the Earth

The National Academies has published a report from a panel of chemists, biologists, geologists, and astronomers on the "Limits of Organic Life in Planetary Systems". The press release sums it up: we shouldn't assume that life off the Earth will look like life on the earth.

The tacit assumption that alien life would utilize the same biochemical architecture as life on Earth does means that scientists have artificially limited the scope of their thinking as to where extraterrestrial life might be found, the report says.The assumption that life requires water, for example, has limited thinking about likely habitats on Mars to those places where liquid water is thought to be present or have once flowed, such as the deep subsurface.

However, according to the committee, liquids such as ammonia or formamide could also work as biosolvents -- liquids that dissolve substances within an organism -- albeit through a different biochemistry. The recent evidence that liquid water-ammonia mixtures may exist in the interior of Saturn's moon Titan suggests that increased priority be given to a follow-on mission to probe Titan, a locale the committee considers the solar system's most likely home for weird life.

"It is critical to know what to look for in the search for life in the solar system," said Baross. "The search so far has focused on Earth-like life because that's all we know, but life that may have originated elsewhere could be unrecognizable compared with life here. Advances throughout the last decade in biology and biochemistry show that the basic requirements for life might not be as concrete as we thought."

Besides the possibility of alternative biosolvents, studies show that variations on some of the other basic tenets for life also might be able to support weird life. DNA on Earth works through the pairing of four chemical compounds called nucleotides, but experiments in synthetic biology have created structures with six or more nucleotides that can also encode genetic information and, potentially, support Darwinian evolution. Additionally, studies in chemistry show that an organism could utilize energy from alternative sources, such as through a reaction of sodium hydroxide and hydrochloric acid, meaning that such an organism could have an entirely non-carbon-based metabolism.

The introduction to the report acknowledges that science fiction is a source of public information on the topic:
The natural tendency toward terracentricity requires that we make an effort to broaden our ideas of where life is possible and what forms it might take. Furthermore, basic principles of chemistry warn us against terraceentricity. It is easy to conceive of chemical reactions that might support life involving noncarbon compounds, occurring in solvents other than water, or involving oxidation-reduction reactions without dioxygen. [. . .] It is easy to conceive of alien life in environments quite different from the surface of a rocky planet. The public ahas become aware of those ideas through science fiction and nonfiction, such as Peter Ward's Life as We Do Not Know It.
Meanwhile, the report encourages astrobiologists to study the odd organisms that live under extreme conditions here on Earth (or Terra if you like). As ScienceNOW reports:
The report urges scientists to adopt a threefold approach to finding extraterrestrial life: research in the lab, in the field, and in space. Chemists need to create life in the lab with building blocks not used in Earthly organisms. Research already indicates that the four nucleotides that make up our DNA aren't the only possibility for genetics--a 12-letter alphabet makes a perfectly fine genetic code. Field studies of extreme environments, such as the martianlike Atacama Desert in Chile or the Arctic waters, might turn up organisms with a biochemistry vastly different from our own. Combining such lab and fieldwork, space missions should be better equipped to find strange life.
Read the full report (free online).

By coincidence (or design?) Discover published an article about the "Aliens Among Us" a couple of weeks ago:
The common assumption is that DNA triumphed because “our form of life is seemingly so superior that we would have eaten” all other life-forms, says Steven Benner of the Foundation for Applied Molecular Evolution in Gainesville, Florida. “That’s the sum total of the argument. But that’s just anthropocentric. These sorts of ‘we’re at the center of the universe’ arguments have always failed.” When Davies first started quizzing other scientists about alternative life a few years ago, he remembers their eyes widening as they asked, “Why hadn’t we thought of this?”

Benner believes there may be some organisms hiding on Earth today that are based not on DNA and proteins but on a more primitive type of biochemistry. A number of researchers now theorize that DNA-based life evolved from an RNA-based predecessor. RNA is an unusual molecule that can both store genetic information and act like an enzyme, cutting apart other molecules or putting them together. Benner is convinced that 4 billion years ago, Earth was home to simple RNA-based organisms that could find food, grow, reproduce, and even evolve. Over time, some of these developed the ability to build proteins and switched to double-stranded DNA to carry their genes.

The remnants of the RNA world - or even stranger organisms - may still survive today. We just have to figure out how and where to look for them.

Image: NASA Europa explorer.

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Tuesday, July 10, 2007

Endogenous Retroviruses and Smarts

Coturnix at Blog Around the Clock has a very interesting (re)post that muses about Greg Bear's Darwin's Radio and Darwin's Children and endogenous retroviruses.

After I read his last two novels, "Darwin's Radio" and "Darwin's Children" I decided to check on his science - it sounded very good, yet so fantastic at the same time. What I found was a surprise: the real science is really that fantastic! Greg only needed to add a very little twist in order to turn it from fiction into science-fiction. So, here is some of what I discovered (though I am a biologist, this is way out of my area of expertise, so assume this is a lay-person writing).

[great big snip . . . ]

What Greg Bear did in his novels is to allow one of the HERVs [human endogenouse retroviruses] to (re)evolve the capability to leave the cell and organism and infect another organism (or fetus). While doing so, it affects the patterns of transcription of many other genes in the human genome during embryonic development, leading to developmental changes in a number of subtle anatomical, physiological and behavioral traits - changes large enough for the "virus children" to be considered a new species. The novels are particularly good at describing how the new race is being treated by the xenophobic society. Of course, Bear is a novelist, so the new traits he picked are those that make for a really good story. Those traits are not any more or less probable than any others he could have picked (e.g., high sensitivity of the vomero-nasal organ).

Read the whole post for more information and speculation on the role of ERVs in evolution.


Monday, July 09, 2007

Weekly Biology in Science Fiction Bits

Bits about Bio in SF from the last week:

Janet Stemwedel at Adventures in Ethics and Science explains what she wants from science fiction.
What I find more interesting, frankly, is how relatively small technological advances from where we are right now could have big impacts on the way we live. Gattaca and Never Let Me Go both fall into this category for me. It makes it easier to get involved in the story if you can imagine yourself in that world -- or if you can see a trajectory by which your world could become that world.
Jeremy Bruno at The Voltage Gate chimes into the discussion with "stressing the fiction in science fiction."

SF should be entertaining above all, because, at its core, it is still fiction. It should be an escape, a place to hide when the real world becomes monotonous and frustrating. It should open minds and feed our imagination, give us an inkling of what could be and what we are, for better or worse.

Cotournix at A Blog Around the Clock starts out by reviewing Verne Vinge's Rainbows End, and ends up discussing the important elements of science fiction: SF as entertainment, SF as literature, SF as textbook (you know, when there are 3 pages about black holes including diagrams), SF as futurology, and SF as thought-provoker.

In Vinge's novel, science is backstage. There is not much he had to change or predict. The medical stuff is somewhat plausible. The molecular research (lightly described near the end) is almost plausible. The online technologies described are very plausible. All of that is just a backdrop for the story, should be understood as such and one need not ask for more (though, again, some of it may become more important in subsequent volumes set in this world). Just sit back and enjoy the story!

Interestingly, Vinge actually addresses an issue that is often ignored. How might the nature of scientific inquiry change in the future?
How does one get answers to scientific questions, or get new technologies developed? By using the hive-mind. There are online boards and forums. You go there, offer virtual money, and the collective effort of the people on there provides you the answer in a timely fashion. It is so powerful that you can rely on the people to design you a new technology according to your specifications, and do it in time for you to go ahead with your plans, certain that the technology will be available to you at the time when you need it.
Sounds interesting.

At the World's Fair, Benjamin Cohen reprints a piece by Joshua Tyree in McSweeney's about the implausibility of the Death Star's trash compactor. It's mostly about engineering of course, but there is the pesky question of where exactly the trash compactor creature lives.
5. And what of the creature that lives in the trash compactor? Presumably, the creature survives because the moving walls do not extend all the way to the floor of the room, where the liquid is. After all, if the walls reached the floor, the creature would be killed each time trash is compacted. The design employed on the Death Star must allow the organic trash to filter down to the bottom, where the parasitic worm-creature devours it. But what happens when heavier pieces of non-organic trash fall down there? Would such trash not get wedged under the doors, causing them to malfunction? Do stormtroopers have to confront the creature each time they retrieve pieces of un-compacted trash?
Commenter Jamie suggests the solution:

7- The worm has a chamber below the surface it can retreat to. The chamber isn't easy to find unless you're a processing worm. (or have the Death Star plans)

8- The Walls Move slowly to give the worm time to get out of the way.

Works for me!