Friday, November 24, 2006

Friday Free Fiction: Old MacDonald Had a Farm

As an appropriate post-Thanksgiving tale, I offer to you Mike Resnick's Old MacDonald Had a Farm, which was nominated for a best short story Hugo in 2002.
According to the glowing little computer cube they handed out, MacDonald and his crew spent close to three decades manipulating DNA molecules in ways no one had ever thought of before. He did a lot of trial and error work with embryos, until he finally came up with the prototype he sought. Then he spent a few more years making certain that it would breed true. And finally he announced his triumph to the world.

Caesar MacDonald’s masterpiece was the Butterball, a meat animal that matured at six months of age and could reproduce at eight months, with a four-week gestation period. It weighed four hundred pounds at maturity, and every portion of its body could be consumed by Earth’s starving masses, even the bones.
Do you know where your dinner came from?

Edit 03/07: The Beam Me Up podcast now has an audio version of Old MacDonald.

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Wednesday, November 22, 2006

Personalized Skin-Hardware Interfaces are Still in the Realm of Fiction

Technovelgy reports on the "Dattoo", a DNA-based "tattoo" proposed by German industrial designer Hartmut Esslinger. According to the description, the Dattoo would actually be a hardware interface printed on the skin. The DNA doesn't seem to do anything except "personalize" the design:
To achieve absolute personal identification, the hardware would capture DNA from the user’s body, enabling direct participation in the political and cultural landscape. The technology would link remote users through engagement with their areas of interest. The system would be personalized not only by this DNA inclusion, but by a more standard procedure in which users choose the applications they carry. Content I/O - including tools like cameras, microphones and laser-loudspeakers - would be connected to “interface pods”, then function as generic hardware.

[. . . ] Once users are satisfied with their specific configurations, they have this fully-functioning circuitry - including all UI-interactive and display functions - “printed” onto recommended areas of their skin. Energy would be pulled from the human body to run the programs. At the end of the day, users would simply wash the Dattoos off, beginning anew the following day.
Technovelgy points out that such "skinprint" interfaces have been proposed in science fiction, such as John Varley's novel Steel Beach. Read the whole Technovelgy post form more details.
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Tuesday, November 21, 2006

The Fake "Ethics in Genetics" Blog

As an update to my post on Michael Crichton's soon-to-be-released novel, Next, I'd like to point out that HarperCollins has also created a fake blog called Ethics in Genetics. The posts are all about "weird transgenics" and such, and written as if a real person is behind the posts*. The blogger says that the idea of genetically-modified animals or foodstuffs "scares" him. That is definitely a running theme. I think it's pretty safe bet that the novel will be about genetic engineering run amok.

It looks like the comments are open, so I'm going to leave a couple. We'll see if they get through moderation.

(via AdJab, which points out that there are fake ads on YouTube as well.

* Yes, I know there is a real person (or people) behind the blog, but what I meant is that it's written in a folksy first person style.

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Saturday, November 18, 2006

Glossolalia and Programming the Brain

University of Pennsylvania psychiatrist Andrew Newberg has published a study showing that "speaking in tongues" (also called glossolalia) is associated with changes in brain activity. From the ScienceNOW article:
Glossolalia produced a significantly different pattern of brain activity than singing, the team reports in the November issue of Psychiatry Research: Neuroimaging. Perhaps the most important difference was a decrease in frontal lobe function, Newberg says. "The part of the brain that normally makes them feel in control has been essentially shut down." Another notable change was increased activity in the parietal region--the part of the brain that "takes sensory information and tries to create a sense of self and how you relate to the rest of the world," Newberg says. The findings make sense, says Newberg, because speaking in tongues involves relinquishing control while gaining a "very intense experience of how the self relates to God." Interestingly, he notes, the glossolalia responses were the opposite of those seen in subjects in a meditative state. When people meditate on a particular sacred object, Newberg has found that their frontal lobe activity increases, while their parietal activity goes down. This conforms with the notion that in meditation one has a controlled focus while losing a sense of self.
In the novel Snow Crash, Neal Stephenson proposes that glossolalia is essentially the programming language of the brain.
"We've got two kinds of language in our heads. The kind we're using now is acquired. It patterns our brains as we're learning it. But there's also a tongue that's based in the deep structures of the brain, that everyone shares. These structures consist of basic neural circuits that have to exist in order to allow our brains to acquire higher languages."
"Linguistic infrastructure," Uncle Enzo says.
"Yeah. I guess 'deep structure' and 'infrastructure' mean the same thing. Anyway, we can access those parts of the brain under the right conditions. Glossolalia -- speaking in tongues -- is the output side of it, where the deep linguistic structures hook into our tongues and speak, bypassing all the higher, acquired languages. Everyone's known that for some time."
"You're saying there's an input side, too?" Ng says.
"Exactly,. It works in reverse. Under the right conditions, your ears -- or eyes -- can tie into the deep structures, bypassing the higher language functions. Which is to say, someone who knows the right words can speak words, or show you visual symbols, that go past all your defenses and sink right into your brainstem. Like a cracker who breaks into a computer system, bypasses all the security precautions, and plugs himself into the core, enabling him to exert absolute control over the machine."
"In that situation, the people who own the computer are helpless," Ng says.
"Right. Because the access the machine at a higher level, which has now been overridden. In the same sense, once a neurolinguistic hacker plugs into the deep structures of our brain, we can't get him out -- because we can't even control our own brain at such a basic level."
In ancient Babylon civilization the language was used for verbal "programs", or me, to allow people to perform basic tasks - making bread, planting grain, etc. In Snow Crash the bad guys have rediscovered this language, and are using it for their own purposes. Their tongue-speaking victims have very much "relinquished control".

Related Links: Brain Imaging and Religion
• Newberg also answers questions about what his research might mean about religion and God
Mind Hacks reports on an earlier study that also found changes in temporal lobe function during glossolalia.
PZ Myers was unimpressed by the study, and is highly critical of the way it has been reported in the popular press.

Related Links: Snow Crash
Snow Crash at Aleph Null
Snow Crash annotations from the Quicksilver Metaweb
Commenary on Stephenson's Snow Crash ( from members of English 65, The Cyborg Self (Spring 2005), and English 111, Cyberspace, VR, and Critical Theory (Spring 1998), Brown University.
• Amazon.com: Snow CrashSnow Crash

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Friday, November 17, 2006

Friday Free Fiction: The Ugly Chickens

The selection for this week's link to free science fiction with a biological theme is The Ugly Chickens by Howard Waldrop. It received the Nebula for Best Novelette 1980.
I spent last summer crawling through The Big Thicket with cameras and tape recorder, photographing and taping two of the last ivory-billed woodpeckers on the earth. You can see the films at your local Audubon Society showroom.

This year I wanted something just as flashy but a little less taxing. Perhaps a population study on the Bermuda cahow, or the New Zealand takahe. A month or so in the warm (not hot) sun would do me a world of good. To say nothing of the advance of science.
The birds our hero ultimately finds are rare indeed. Read the whole story at SciFiction.

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Thursday, November 16, 2006

The Next 50 Years of Scientific Advancement

New Scientist asked a number of prominent scients what they thought the biggest breakthroughs would be over the next 50 years. Here is a sampling of what the biological scientists had to say:

Sydney Brenner (winner of the Nobel Prize in Physiology/Medicine for studies on organ development and cell death):
I think the most important advances will come in the understanding of the biology of the most interesting species - Homo sapiens. [. . .] However, if things do go on in the same way I predict that by about 2020 - the year of good vision - consciousness will have disappeared as a scientific problem much as embryonic determination has vanished today.
Lewis Wolpert (developmental biologist, member of the Royal Society and science popularizer):
In the next 50 years, as systems biology and computer models take over, the embryo will become fully "computable": given a fertilised egg, with the details of its genome and contents of its cytoplasm, it will be possible to predict the embryo's entire development.
Francis Collins (Director of the Human Genome Research Institute)
Genomic research will prove key to discovering how to reprogram the mechanisms that control the balance between the cell growth that causes cancer and the cell death that leads to ageing. It is possible that a half-century from now, the most urgent question facing our society will not be "How long can humans live?" but "How long do we want to live?"
Bruce Lahn (studies human brain evolution and stem cell biology.):
I anticipate that one exciting breakthrough in biomedicine will be the ability to produce unlimited supplies of transplantable human organs without the need for human donors.
Richard Miller (studies the mechanisms of aging)
In aging research, the key breakthrough will be the elucidation of the molecular pathways that render cells from long-lived animals - whales, people, bats, porcupines - resistant to many forms of injury.
Ellen Heber-Katz (studies the molecular basis of autoimmunity, wound healing and regeneration):
I believe that the day is not far off when we will be able to prescribe drugs that cause severed spinal cords to heal, hearts to regenerate and lost limbs to regrow.
Daniel Pauly (Director of the Fisheries Centre at UBC)
[. . .]I think the most important development for the oceans would be a device that could detect, amplify and transmit to us the emotions and fleeting, inarticulate "thoughts" of animals in such a form as to evoke analogous emotions and thoughts in human brains.
Elizabeth Loftus (expert on false memory syndrome)
Psychological scientists have learned so much about planting false memories that some say we almost have recipes for doing so. But we haven't seen anything yet. Over the next 50 years we will further master the ability to create false memories.
Carl Djerassi (helped developed the oral contraceptive pill, currently does policy research on human fertility control and writes "science-in-fiction")
The biggest breakthrough in my field will be the development of an efficient and convenient means of storing a young woman's ovarian tissue or eggs to be used years later.
See the comments of some of the other biological scientists (below) for predicted developments in understanding the brain, consciousness, evolution, cell biology, life on earth and (potentially) other planets and more.

This is what science fiction authors should be incorporating into their work today!

Commenting scientists with a biological bent:
Edward O. Wilson, Paul Nurse , Frans de Waal, Niles Eldredge , Igor Aleksander, Bernard Wood, Michael Benton, Andrew Knoll, Geoffrey Miller, Stephen Pinker, Simon Baron-Cohen, Antonio Damasio, Dan Dennett, Jane Goodall, Monica Grady, Susan Greenfield, Piet Hut, Carolyn Porco, Charles Nemeroff, Alan Walker, Beverly Whipple

Check out the whole list.

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Next: Michael Crichton and Genetics

Back in September, HarperCollins announced the new Michael Crichton thriller, Next, would be released on November 28. As reported by galley cat:
"Prepare to enter a world where nothing is as it seems and a new set of possibilities is opening up at every turn," the publicity department warns us. "Next challenges your sense of what is happening, what is true and what is ethical." Along the way, they ask a couple goofy questions—"Are blondes becoming extinct? Is everyone at your dinner table of the same species?"—but, personally, I think this one'll turn out to be the kicker: "Could you and your family be pursued cross country just because you happen to have certain genes in your body?"
In preparation for the book launch, HarperCollins has put up a web site for the fictional biotech company, NEXTgencode, with the slogan: "Your Destiny Is No Longer in Question". The site links to sensationalistic genetics news articles, such as the much derided news report on the potential for "Blonds Becoming Extinct" and "Human and Chimps Interbred Until Recently" (with "recent" meaning 4 million years ago).

At the Women's Bioethics Blog ALong points out that, if nothing else, the new novel should spur discussion:
Given Crichton’s ability to quickly put his finger on the pulse of hot topics in popular science -The Andromeda Strain (about a scary virus), Jurassic Park (genetically engineered dinos) Prey (nanotech gone amuck) State of Fear (global warming = scientific conspiracy) etc, I think this book is likely to generate a great deal of interest in genetic engineering and questions of ethics.
"Science run amok" and amoral scientists are common themes in Crichton's novels, and I'm sure Next won't be any different. It would be nice if Crichton gets more of the actual science right than in his most recent bestseller, State of Fear, but I'm not holding my breath.

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Tuesday, November 14, 2006

Living Neanderthals

The science blogosphere has been abuzz about the recent papers showing evidence of interbreeding between humans and neanderthals. First, Lahn and colleagues reported in Science that one human variant of microcephalin, thought to be involved in regulating brain growth, appeared to have evolved more than a million years ago, but only appeared in the human population 37,000 years ago (Evans et al. "Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage" Proc Natl Acad Sci (2006)).
The Lahn group concluded that the most likely scenario was interbreeding between prehistoric modern humans and a now extinct hominid that carried haplogroup D--most likely Neandertals. The haplogroup was probably beneficial enough to spread quickly in modern human populations, says Lahn. But he's not sure what advantage it offered. Because most researchers agree that Neandertals were not as cognitively advanced as modern humans, Lahn and his coauthors suggest that the haplogroup might have made Homo sapiens better able to adapt to the Eurasian environments that Neandertals had occupied long before modern newcomers arrived. (ScienceNOW article)
John Hawks has a nifty FAQ about the science. His colleague, Greg Cochran, speculates that Neanderthals may have given the human race a boost:
So when you think about the cultural explosion that occurred shortly after we overwhelmed the Neanderthals (cave paintings, sculptures, new tools and weapons, all that jazz) - well, you have to wonder if assimilating a passel of adaptive alleles in a few thousand years, way more than the typical number that would arise and become established over such a short time span, didn't give us a hell of a boost. There are signs of behavioral modernity a bit earlier in Africa - but those ostrich eggshells are dull as hell compared to Gravettian cave paintings. Expansion out of Africa must itself be a sign of new capabilities (I'd bet on sophisticated language) but you only see full-fledged behavioral modernity in the European Upper Paleolithic... Judging from neutral genes, it can't have happened often, but those few furtive human-Neanderthal couplings may well played a crucial role in the future development of the human race. I'm sure that this notion will suggest new pick-up lines to some readers.
Gene Expression rounds up the blogs discussing the results.

I have to confess, that when I read about interbreeding humans and Neanderthals, the first book that came to mind was Jean Auel's Clan of the Cave Bear. That doesn't really fall into the "science fiction" category, though, so I'll move on.

Neanderthals have made a number of appearances in the science fiction literature, most recently in Robert J. Sawyer's Neanderthal Parallax trilogy: Hominids (winner of the 2003 Hugo for best novel), Humans, and Hybrids. The novels are set on our earth and a parallel earth where Neanderthals became the dominant hominid. If you want more information about his take on Neanderthals, read Sawyer's essays Commiting Trilogy: The Origins of the Neanderthal Parallax and Neanderthals are a Separate Species, and his invented system of Neanderthal timekeeping.

There have also been numerous other science fiction stories with Neanderthal themes, such as:
• Greg Bear had a different take on the relationship between Neanderthals and humans in Darwin's Radio. One of his heroes, scientist Mitch Rafelson, find the frozen remains of a Neanderthal couple and their apparently human infant.
• In Paul Levinson's novel The Silk Code (winner of the 1999 Locus Award for best novel), forensic scientist Phil D'Amato investigates the possibility that a small group of Neanderthals have survived to the present day.
• Short story "Scout's Honor by Terry Bisson (read free online), stars scientist goes back in time to study Neanderthals
• Talk.origins also has a list of Paleoanthropology Fiction.

I'm sure there are others*.

It seems likely that we carry a little bit of the Neanderthal in us. I suspect that the sequencing of the Neanderthal genome will turn up even more "survivors".

* For example, there is a short story in which modern cloning and genetic techniques are used to bring Neanderthals back to life. They subsequently take over the world. Unfortunately, I can't remember the title or the author.

ETA 11/16: I should have waited a few days to post. Nature just published an article from the Pääbo lab analyzing 1 million bases of Neanderthal DNA (Green et al. "Analysis of one million base pairs of Neanderthal DNA" Nature 444:330-336 (2006)). Nature has collected text, video and audio links on the subject. An additional 65,000 bases were published in this week's Science (Noonan et al. Sequencing and Analysis of Neanderthal Genomic DNA Science 314:1113-1118 (2006)). ScienceNOW sums it up:
As expected, the Neandertal and human genomes proved more than 99.5% identical. Rubin's team calculated that the most recent common ancestor of the two human species lived about 700,000 years ago, whereas Green's analysis of 1 million bases found a more recent divergence time, about 465,000 to 569,000 years ago. As to the question of interbreeding, Rubin's group found no sign of it, but Pääbo's group did. "Taken at face value, our data can be explained by gene flow from modern humans into Neandertals," most likely from modern humans fathering children with Neandertal females, says Pääbo.
Afarensis and Gene Expression have more on models of human evolution.

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Friday, November 10, 2006

The Dragons of Summer Gulch

If you enjoy fantastic paleontology, you will probably enjoy Robert Reed's short story "The Dragons of Summer Gulch" ( ETA: current story link), published in SciFiction in 2004. It takes place in an alternate Wild West. Like our own world, terrible lizards once roamed the plains; the difference is that the prehistoric lizards were mighty dragons rather than dragons rather than dinosaurs. The tale starts with Barrow, a prospector for dragon fossils, which are rather valuable.
Back in town, an educated fellow had explained to Barrow what science knew today and what it was guessing. Sometimes the dragons had been buried in mud, on land or underwater, and the mud protected the corpse from its hungry cousins and gnawing rats. If there were no oxygen, then there couldn't be any rot. And that was the best of circumstances. Without rot, and buried inside a stable deep grave, an entire dragon could be kept intact, waiting for the blessed man to ride by on his happy camel.
Barrow turns up more than he expected at his digs, with major consequences. Read the story online at SciFiction on Robert Reed's web site.

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Cylon Killing Virus

*** BATTLESTAR GALACTICA SPOILERS BELOW ***
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If you are following Battlestar Galactica, you know that a Cylon ship searching for Earth found an ancient space beacon, possibly left behind by the 13th tribe from Kobol. The probe carried a plague that killed almost all the Cylons that came into contact with it, and apparently has the potential to survive the process of "resurrection", in which the consciousness of a dying Cylon is transferred to a new body. In tonight's episode, Doc Cottle analyzes the disease and finds it is caused by a virus:
I identified the virus. We know it as lymphocytic encephalitis*. The disease is carried by rodents, rats mostly. But a couple of hundred years ago, humans developed an immunity.
* I'm sure Doc Cottle really mean lymphocytic encephalitis virus, since encephalitis is the disease. Of course the doctor's description leaves a few questions.

What's an encephalitis virus?

Encephalitis refers to brain inflammation that is usually caused by viral infection. There are several types of viruses that cause encephalitis in humans. The arenavirus Lymphocytic Choriomeningitis Virus (LCMV) is carried by rodents, can be transmitted to humans and causes both meningitis and encephalitis. So far, so good.

The biological basis of the humanoid Cylons hasn't been explained. According to an infected Simon Cylon, the infection affects their electrical systems.
They told us . . . that there was a bio-electric feedback compoent to the pathogen. It corrupts how our brains manage our immune systems.
While that may be plausible, I still can't figure out how the virus might be sent along with the Cylon consciousness to the "Resurrection Ship".

Could a virus remain infectious for thousands of years?

While some viruses can only live a few hours or days outside of an animal host, in 1999 tomato mosaic virus was found in 500-140,000 year old ice in Antarctica with its RNA intact. If the virus has a tough protein coat, it might survive in the frozen wastes of space for just as long.

Could humans become immune to a particular virus over the course of a few hundred or thousand years?

That the entire human population could evolve immunity over such a short period seems unlikely to me. For example, here on Earth evolutionary pressure by malaria is strong, but immunity is not universal, even in exposed populations. Now imagine a population spread over 12 separate planets, with the technology for both effective rodent population control and the development of antiviral agents. Such rapid evolution seems even less likely under those circumstances.

Perhaps the 12 Colonies used some sort of anti-viral gene therapy?

Verdict?
Battlestar Galactica is really about the interactions of the characters, and science is secondary. You have to suspend disbelief and accept things like consciousness-transmission (not to mention virus transmission) through space. I don't let scientific inaccuracy get in the way of my enjoyment of the show.

At the end of the episode, it's revealed that the virus was an exact match to one reported "over 3,000 years ago", about the time the 13th tribe left Kobol. It looks like the colonists are on the right track for Earth!

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Tuesday, November 07, 2006

Neurology and Victorian Horror

Dr. Jekyll and Mr. HydeMind Hacks has an interesting post on a recent paper by English Professor Anne Stiles about the influence of 19th century neurological research on Bram Stoker's depiction of Dracula. The post points to a transcript of Stiles' appearance on Australian Broadcasting Company Radio's All in the Mind. In that interview she discusses both Dracula and The Strange Case of Dr. Jekyll and Mr. Hyde. What I find particularly interesting is the evidence that both Stevenson and Stoker were familiar with the current scientific literature and incorporated that knowledge into their works.
Natasha Mitchell: What do you know - because you went searching for evidence to see if Robert Louis Stevenson has actually been reading some of the scientific literature around the double brain of the time -how do you know that all these debates he actually informed his character?

Anne Stiles: I suspect they did because his wife was writing in an introduction to one of his later works that he was inspired to write Jekyll and Hyde by an article in Revue Scientifique which was a French psychological journal and then I found those same studies described again in Cornhill Magazine which was a publication that Stevenson himself was contributing to during the same time periods so the late 1870s. And so I think these articles on two particular case studies could not possibly have escaped Stevenson's notice since they were writing in the same periodical.
Stiles' recent paper in the Journal of the History of the Neurosciences expands on Stoker's contemporary neuroscience knowledge:
Stoker came from a family of distinguished Irish physicians and obtained an M.A. in mathematics from Trinity College, Dublin. His personal library contained volumes on physiology, and his composition notes for Dracula include typewritten pages on somnambulism, trance states, and cranial injuries. Stoker used his knowledge of neurology extensively in Dracula.
Both authors used their knowledge to comment on the human condition. As Stiles concludes:
I suggest that Stoker's vampire protagonist dramatizes the pervasive late-nineteenth-century fear that human beings are soulless machines motivated solely by physiological factors.
I believe that same fear is held by many people today, which is why these stories resonate with contemporary audiences more than a century after their original publication.

Download pdf of Strange Case of Dr. Jekyll and Mr. Hyde
Download pdf of Dracula

Photo: Part of ~1895 portrait of Henry Van der Weyde, star of the London stage version of Dr. Jekyll and Mr. Hyde. From the American Museum of Photography.

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NLB on Bio-technology Fiction

The National Library Board of Singapore (NLB) has an online brochure on SCIENCE FICTION - SubGenre: Bio-Technology (pdf). It's pretty generic, simply listing a bunch of authors without citing any particular works. However, I thought their view of the genre was interesting:
What is unique about this sub-genre of Science Fiction is that it explores the possibilites of technology that challenges the limits of morality. It is, in simple terms, stories of how we, as homo sapiens, can reflect on what it means to be human.
There is more about science fiction on the NLB ASK! blog. (via SF Signal).

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Monday, November 06, 2006

Biology in Peter Watts' Universe: Vampires, Madonnas and more

Commenters to my Vampire and Zombie post have recommended Peter Watts' Blindsight. It's on my "to read" list, but I thought I would point out a couple of interesting blog posts and web sites about Blindsight and the biology of Watts' universe. Because Watts has used his background in biology to construct plausible species in his novels, it's especially fun to read about.

Blogger Jeremy Byrne links to Watt's PowerPoint presentation (large swf file) on the creation of cryptogenic vampires by "FizerPharm". It's a humorous version of real pharmaceutical company presentations, including a bullet point list of the restrictions on their funding from "Texans for a Wholesome America", the mandatory fluorescently-stained neuron photos, company slogans on every page ("Flexible ethics for a complex world", "Trust Profit Deniability", "Taming the Nightmares of Yesterday for a Better Tomorrow"), and slides titled "Why eat humans anyway?", "Survival of the least inadequate", "Vampires: Myths and Realities" (Myth: Can't enter a house uninvited, Reality: Can't enter a house with open eyes), "Future Promise: Vampires in the Workplace" and much more. It's very funny if you've ever sat through such a presentation (or, I suspect, even if you haven't).

The slide show is part of the official Rifters web site, which has extensive background on the biology of Watts' universe, including the Rifters in Starfish, the ßehemouths in Maelstrom, the Madonnas in Behemoth, and, of course, the Vampires in Blindsight. You can even read Starfish and Maelstrom free online or as downloadable pdf files. Cool stuff!

Watts' described his vision for the vampire species in a 2004 interview. It was the rise of civilization that originally caused the vampires to originally go extinct:
Unfortunately, their pattern-matching wetware is inextricably linked to a defect in the retinal receptors that detect right angles. Euclidean geometries trigger a form of incapacitating epilepsy in vampires, which must be controlled with seizure-suppressants. Sarasti has a serious drug habit.

(Just to add to the above: It was this very linkage that led to their extinction. It developed in a natural fractal environment without Euclidean geometry, and hence wasn't weeded out before it got fixed in the population via genetic drift. When baseline Homo figured out how to build huts, it was the beginning of the end. With the development of straight-line architecture--specifically, intersecting right angles-- vampires found themselves unable to approach the domiciles of their prey without spazzing out. You can be damn sure the prey figured out how to use *that* to their advantage.)
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Technovelgy has entries for several biology-related items in Starfish: cultured brains called "head cheese or smart gel, the medical mantis and the "almost alive" diveskin.
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The blog Pinnochio Theory discusses the sociobiological aspects of Watts' book.
Watts is a hardcore sociobiologist, in outlook. Which is often something that drives me up a wall. But he has enough conceptual audacity that he makes it work, chillingly and powerfully, in Blindsight.
On Watts' zombie characters:
I will skip over their biophysiology, though Watts is amazingly inventive in this respect (he is helped by his background as a marine biologist, who is therefore with all sorts of weird invertebrates). What really distinguishes the aliens is that they are zombies: not in the George Romero, living dead sense, but in the sense that the term has been used by cognitive science and the philosophy of mind. A zombie is a being who acts just as you or I do, who shows clear signs of language, intelligence, and so on; but who is inwardly devoid of sentience or consciousness.
Read the whole post for a fascinating discussion.
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Finally, the Vector editorial blog, Torque Control, discusses Blindsight in the context of hard science fiction.

I am looking forward to delving into the Watts' universe.

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Sunday, November 05, 2006

Panspermia in Star Trek

Last week, Nick Matzke, public information project director for the National Center for Science Education, was interviewed on the SciPhi Show, a podcast about science and philosophy. The focus of the interview was evolution and intelligent design, but it touched on science fiction as well. According to Matzke's post on the Panda's Thumb:
In addition to pointing out all the usual ID mistakes, there was an interesting discussion about Star Trek: Remember that Star Trek episode where they discover that the suspiciously coincidental bipedal, humanlike form of all of the Star Trek aliens was (somehow) encoded into bacteria seeded across the galaxy billions of years ago, by an ancient bipedal race, a fact revealed when a 3-D holograph recording is deciphered out of the ancestral DNA genome (somehow!). The only thing the episode left out was an explanation for human-klingon-vulcan interfertility. Great episode, typically ludicrous science, but does it help the ID guys make their case?
The Star Trek: The Next Generation episode, "The Chase " reveals that, in the Star Trek universe, the galaxy's humanoid races have a common ancestor that was seeded on many planets by a technologically advanced race. As an ancient humanoid explains to Captain Picard:
You're wondering who we are; why we have done this; how it has come that I stand before you - the image of a being from so long ago. Life evolved on my planet before all others in this part of the galaxy. We left our world, explored the stars and found none like ourselves. Our civilization thrived for ages, but what is the life of one race, compared to the vast stretches of cosmic time?

We knew that one day we would be gone, and nothing of us would survive - so we left you. Our scientists seeded the primordial oceans of many worlds, where life was in its infancy. The seed codes directed your evolution toward a physical form resembling ours: this body you see before you, which is of course shaped as yours is shaped, for you are the end result. The seed codes also contain this message, which is scattered in fragments on many different worlds.

It was our hope that you would have to come together in fellowship and companionship to hear this message, and if you can see and hear me, our hope has been fulfilled. You are a monument, not to our greatness, but to our existence. That was our wish - that you too would know life and would keep alive our memory. There is something of us in each of you, and so, something of you in each other. Remember us.
This is a variant of the panspermia hypothesis, which proposes that "that the seeds of life are ubiquitous in the Universe, that they may have delivered life to Earth, and that they may deliver or have delivered life to other habitable bodies; also the process of such delivery". It shows up in a number of different science fiction stories.

Is it possible in real life? Not in the version presented in Star Trek*. Based on the ancient humanoid's description, the alien "seeds" co-opted the primitive organisms that were already evolving on many planets, and "directed" their evolution. The implication is that the "seed codes" took over the evolutionary process, allowing the life forms to bypass the forces of natural selection and develop into humanoids in the image of the "seeders". I would think that this would often result in species that were poorly adapted to their local environments and ultimately cause extinction of the proto-humanoid species on some planets. Of course for the special "code" hidden in the genomes of many worlds to be readable after millions of years that sequence must be essentially impervious to mutation.

Even if we assume that a "seed code" could direct evolution into humanoids, the basic genetic starting material of the original primitive life would have presumably been different on each planet. After millions of years of evolution, there should be remnants of that original genetic code in the genomes of modern species. The more likely alternative would be that the "seed" was the real progenitor of life in our galaxy, simply out-competing the indigenous primitive species. Even so, it's hard to imagine how the resulting humanoids, after millions of years of evolution, would be genetically similar enough to allow human-vulcan, human-klingon, and other interspecies hybrids. It's not even clear that humans can form hybrids with our closest cousins, the chimpanzees, so it's incredibly unlikely that humans could hybridize with species that have a different number of ribs, hearts, lungs and other organs.

What about more scientifically plausible versions of panspermia? At one time, no less a scientist than Francis Crick suggested that it was indeed possible:
It now seems unlikely that extraterrestrial living organisms could have reached the earth either as spores driven by the radiation pressure from another star or as living organisms embedded in a meteorite. As an alternative to these nineteenth-century mechanisms, we have considered Directed Panspermia, the theory that organisms were deliberately transmitted to the earth by intelligent beings on another planet. We conclude that it is possible that life reached the earth in this way, but that the scientific evidence is inadequate at the present time to say anything about the probability." (from Crick & Orgel, "Directed Panspermia", Icarus 19: 341-346 (1973) (pdf))**
It turns out that spores from other planets are actually a possibility. There is an interesting article in last November's Scientific American that describes recent research suggesting that microorganisms could indeed survive the trip from Mars to Earth. Of course, "possible" is not equivalent to "probable". The authors point to the issues needed to be resolved before science can even project whether that's a likely scenario or not.
Because it is not possible at this time to quantify all the steps of the panspermia scenario, investigators cannot estimate how much biological material or how many living cells most likely arrived at Earth's surface in a given period. Moreover, the transfer of viable organisms does not automatically imply the successful seeding of the planet that receives them, particularly if the planet already has life. If, for example, Martian microbes arrived on Earth after life independently arose on our planet, the extraterrestrial organisms may not have been able to replace or coexist with the homegrown species. It is also conceivable that Martian life did find a suitable niche on Earth but that scientists have simply not identified it yet. Researchers have inventoried no more than a few percent of the total number of bacterial species on this planet. Groups of organisms that are genetically unrelated to the known life on Earth might exist unrecognized right under our noses. (Warmflash & Weiss "Did Life Come from Another World?", Scientific American (2005)).
The question of whether life on earth (and other planets) originated elsewhere in the universe is still unanswered. Listen to the SciPhi interview to find out Nick Matzke's take.

NOTES:
* Star Trek often resorts to scientifically ridiculous versions of "evolution" as a plot device. For example, see Star Trek: The Next Generation "Genesis" ("Barclay's Protomorphosis Syndrome" causes activation of "dormant" genes and introns (!), resulting in "de-evolution" of the crew: humans Riker and Barclay turn into a Neanderthal and spider (!), respectively, Klingon Worf becomes a lizard-like humanoid, and Betazoid Troi turns amphibian-like) and Star Trek: Voyager "Threshold" ("Transwarp Evolutionary Syndrome" causes "hyperevolution" of humans into amphibian form). There is too much bad biology in these episodes to go into in this post.

** Orgel and Crick revisited the issue of the origin of life in 1993 and conceded that development of life on earth was more likely than they had originally concluded, based on research pointing to an initial "RNA World", rather than a "protein world" (Orgel & Crick "Anticipating an RNA world. Some past speculations on the origin of life: where are they today?", FASEB J. 7:238-9 (1993) (pdf)).

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Wednesday, November 01, 2006

A Gift From Earth: Artificial Liver

Technovelgy is reporting on a new report that University of Newcastle scientists Colin McGuckin and Nicolas Forraz were able to grow an artificial liver from stem cells isolated form umbilical cords. While previous work had shown that liver cells could be grown in culture, this work actually replicates the structure of the organ.

Artificially grown organs are proposed in Larry Niven's A Gift from Earth.
"We need to discuss three types of medical care," said Millard Parlette. "Organ transplants, the ramrobot gifts, and minor medical treatment. You already have some access to standard drugs at the medcheck stations. We can expand those. I'm sure we can offer free access to the heartbeasts and liverbeasts and so forth. For a while your colonists will have to come up to the Hospital to get treatment with the ramrobot symbiots, but eventually we can build culture tanks in Gamma and Delta and Eta."
Of course a "real" artificially grown liver is still in the realm of fiction. The original article in the Daily Mail reports that actual transplantable livers are more than a decade in the future:
As it stands, the mini organ can be used to test new drugs, preventing disasters such as the recent 'Elephant Man' drug trial. Using lab-grown liver tissue would also reduce the number of animal experiments.

Within five years, pieces of artificial tissue could be used to repair livers damaged by injury, disease, alcohol abuse and paracetamol overdose.

And then, in just 15 years' time, entire liver transplants could take place using organs grown in a lab.
For the time being, we'll have to rely on the extracorporeal liver-assist device (ELAD), an external artificial liver that uses hepatocytes (cultured liver cells).

NOTE: I haven't figured out where this research has been (or will be) published, other than the Daily Mail (obviously NOT a scientific journal). If I find the citation, I'll update the post.

ETA: Here is the article in Seed Magazine, which cites the Daily Mail.

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