Saturday, January 27, 2007

The Man Who Mutters at Movie Screens

Hugo award-wining author Mike Resnick explains on novelspot why his wife won't sit next to him at science fiction movies. The trouble is that Hollywood keeps churning out "intellectually insulting" science fiction movies.
Second, when I speak of stupidities, I'm not talking about the nit-picking that goes on in outraged letter columns. If the math or science are wrong only in areas that scientists, mathematicians, or obsessive science fiction fans would find fault with, I'll ignore it. If George Lucas doesn't know what a parsec is, or Gene Roddenbury and his successors think you can hear a ship whiz by in space, I'm willing to forgive and forget.
Even so, biology boners don't escape his notice.
Then there were Speilberg's mega-grossing dinosaur movies, Jurassic Park and The Lost World. The former hypothesizes that if you stand perfectly still six inches from a hungry Tyrannosaurus Rex he won't be able to tell you're there. I would like to see the screenwriter try that stunt with any hungry carnivore -- mammal or reptile -- that has ever lived on this planet. The latter film shows you in graphic detail (and with questionable intelligence) that a T. Rex can outrun an elevated train, but cannot catch a bunch of panicky Japanese tourists who are running away, on foot, in a straight line.
Read the whole rant. If you've ever watched a movie and thought "What the hell?" it'll make you smile and nod in recognition.

Here are a couple of Resnick's stories with biology-related themes:

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Tuesday, January 23, 2007

Diseases of the future

A recent issue of the Public Library of Medicine published an article speculating on what directions disease will take in the future. They compare three different scenarios: a baseline, and optimistic model and a pessimistic model. Their primary conclusion:
The three leading causes of burden of disease in 2030 are projected to include HIV/AIDS, unipolar depressive disorders, and ischaemic heart disease in the baseline and pessimistic scenarios. Road traffic accidents are the fourth leading cause in the baseline scenario, and the third leading cause ahead of ischaemic heart disease in the optimistic scenario. Under the baseline scenario, HIV/AIDS becomes the leading cause of burden of disease in middle- and low-income countries by 2015. [see the full comparison of causes of death 2002-2030]

Projected life expectancy at birth increases in all regions, but there are still huge discrepancies based on income and other factors - for example women in high-income countries may expect to live to age 85, while men in Sub-Saharan Africa will have a life expectancy of less than 55.

The details:

• "The proportion of deaths due to noncommunicable disease is projected to rise from 59% in 2002 to 69% in 2030."
That doesn't seem to be a very big change to me, so in 2030 we may have a similar rate of heart disease and cancer.
"Global HIV/AIDS deaths are projected to rise from 2.8 million in 2002 to 6.5 million in 2030 under the baseline scenario, which assumes coverage with antiretroviral drugs reaches 80% by 2012." This is a great increase, particularly in parts of the globe already hard-hit by the diesase.

"Total tobacco-attributable deaths are projected to rise from 5.4 million in 2005 to 6.4 million in 2015 and 8.3 million in 2030 under our baseline scenario. Tobacco is projected to kill 50% more people in 2015 than HIV/AIDS, and to be responsible for 10% of all deaths globally." So there is the big killer, unless human behavior changes appreciably (and future scenarios in which people don't take drugs of some sort seem implausible to me) or some way to counteract tobacco's effects.

Of course, unpredictable events are hard to factor into the projections. Will there be an infectious agent from space, alá The Andromeda Strain? Or perhaps an improvement as simple (yet with profound consequences) as sanitation*? That's where fiction comes in!

Paper Citation: Mathers CD, Loncar D (2006) Projections of Global Mortality and Burden of Disease from 2002 to 2030. PLoS Med 3(11): e442

* BBC article: Sanitation 'best medical advance', based on a survey by the British Medical Journal

(via Science to Life)

Saturday, January 20, 2007

Vampirism as Disease?

University of British Columbia chemistry professor David Dolphin has a hypothesis about the origin of vampire folklore. He is an expert on porphyrins, which are ring-shaped metal-binding molecules. The best-known porphyrin is heme, which binds iron and, when complexed with the protein hemoglobin, transports oxygen. Porphyria is a family of inherited disorders caused by faulty heme production. People with the cutaneous type of porphyria are acutely sensitive to sunlight, a trait often ascribed to vampires. And there are other possible connections to vampirism, as Dolphin explained in a recent presentation :
Dr. Dolphin admits it’s only a theory but drinking blood would have allowed them to absorb more heme, which feeds back to ease up on excess porphyrin production. In fact, porphyria patients today get heme injections. Porphyrin build-up in teeth can make them appear reddish, possibly like bloody fangs. The disease is even associated with excess hair growth, especially on the forehead, possibly leading to the vampire’s trademark widow’s peak. The aversion to garlic may be explained by the fact that some chemicals in the plant, such as diallyl sulfone, increase the production of porphyrins in the body. Of course, he points out, that a wooden stake through the heart would kill anyone. As for the lack of a mirror image, Dolphin joked, “I’m a chemist, so I’ll leave that to the physicists.”
While it's an interesting proposal, the Straight Dope takes a much more skeptical view:
(1) Porphyria comprises seven separate disorders. Skin problems are a fairly common symptom, but only the rarest form--congenital erythropoietic porphyria--causes severe disfigurement. Just 200 cases of this disease have been diagnosed, surely too few to account for the widespread belief in vampires. In any case, alleged vampires exhumed in the 18th century typically weren't disfigured but appeared as they had in life (except for being dead, of course).

(2) The idea that vampires abhor sunlight was an invention of fiction writers. In Europe during the 18th and 19th centuries, vampires were sometimes reported to have been sighted during the day. Bram Stoker's Dracula was deathly pale, but folkloric vampires, in the Balkans anyway, were said to be ruddy-faced due to blood consumption.

(3) Porphyria victims don't crave blood. Drinking blood will not alleviate their symptoms, nor has there ever been a general belief that it would. The blood chemicals porphyria victims need do not survive digestion.

(4) In light of the preceding, the scenario described in point #4 above [Porphyria symptoms can be brought on by stress - being bit by a sibling who also has the disease is stressful - the bite "causes" you to turn into a biter too] is unlikely.

(5) No one has proved that garlic worsens porphyria.
When the Straight Dope wrote the article in 1999, they asked Dolphin for comment:
When I phoned, he didn't wish to speak to me and would say only that "it was just speculation" and that "I haven't worked in this area for many years."
The response is a bit amusing in light of the fact that he lectured on the topic a just a few months ago. I guess the idea was just too interesting to give up.
Heme molecule via Dr. Karl Harrison's Chemistry, Structures and 3D Molecules site.
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Biologists as Mad Scientists

Emory University Physics Professor Sidney Perkowitz writes about physics (and physicists)in the movies ("Hollywood Physics"), and notes the stereotypical scientist-as-bad-guy may no longer be a physicist willing to blow up the world:
With new fears awakened in the public's mind by developments in biology - cloning, pandemic diseases, exotic viruses and biological weapons - the villains have become the bioscientists, in films like The Boys from Brazil (1978), Outbreak (1995) and The Island (2005). Meanwhile, some physicists are now even depicted as helping humanity. For example, in The Manhattan Project (1986), physicist John Mathewson (John Lithgow) abandons his method for making weapons-grade plutonium using laser separation after seeing how badly the government treats teenage scientific genius Paul Stephens (Christopher Collet). And in Chain Reaction (1996) and The Saint (1997), physicists and an electrochemist develop limitless, non-polluting fusion power and give the technology freely to the world.
I'm not sure if it's such a good thing that biologists are starting to get their props as mad scientists.

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Friday, January 19, 2007

Evolution Never Sleeps

"There's never been anything in the literature to indicate that chipmunks behave in groups."
"Well, maybe this is something new."
"What you saw was just normal duetting behavior. One animal barks, then the others join in. That's all."
If chipmunks began exhibiting cooperative behavior would we recognize it? Elisabeth Malartre's* short story Evolution Never Sleeps (pdf) asks that very question.

In the introduction to the story in the Year's Best SF 5 (1999), David Hartwell notes:
The hard science is evolutionary biology and the idea, while reminiscent of the riotously rubber-science B-movies of the 1950s, is rigorously executed and made serious. It teaches us something about the bedrock scientific theory of Evolution, upon which so much SF has been based since 1895.**
More recently, Malartre has written for the journal Nature's "Futures" short science fiction series (if you have a subscription to Nature, you can read "Words words words: Kissing a biotechnological blarney stone" and "Looking for Mr. Goodbug" online).

* Malartre is the pen name of a "biologist and writer living in Laguna Beach, California who teaches at the University of California, Irvine." She has collaborated on writing projects with her husband, UC Irvine physics professor/science fiction writer Gregory Benford.

** True, despite the claims of some naysayers.


Thursday, January 18, 2007

Biotechnology and the Frontiers of Science (Fiction)

Back in 2003, the PBS show "Closer to Truth" hosted a roundtable on the question: "Is Science Fiction Science?" The companion website has a transcript, video clips, and brief interviews with the participants: Michael Crichton, Octavia Butler, and David Brin. Interestingly, all three authors commented on biotechnology and the biological sciences.

David Brin, who is a physicist as well as an author, pointed to the rapid pace of biotechnology:
Q: Will technology outpace civil control?

A (Brin): The fact is that it seems likely that the biologists will do and the biochemists will do to their big, huge building-size laboratories what the cyberneticists did to the computer. And not only make them smaller, but cheaper. It's happening at a curve that's even faster than Moore's Law. Within 10, 15 years you will see the MolecuMac in which any teenager in America will -- on his desktop -- be able to fabricate any known or unknown organic compound. There are all sorts of possibilities, but science fiction is supposed to look ahead a little ways and see what they are, and I see the MolecuMac. Under circumstances like those, civilization cannot hold together if we remain stupid.
Not unexpectedly, Michael Crichton commented on the dangers of biotechnology, suggesting it is even worse than the nuclear threat at the height of the cold war:
Q: What do you think the biggest threat to life is today?

A (Crichton): I think that the greatest hazard now comes from biotechnology. In the heyday of the nuclear standoff, it was never conceived of really as wiping out the species. I think it is absolutely conceivable that somebody could do something in biotechnology that would wipe us out.
Octavia Butler noted that the only "hard" science she has used in her novels is from the biological sciences.
Q: Do your own science research?

A (Butler): I don't write hard science fiction for the most part. My Xenogenesis trilogy* is, I guess, as close as I've gotten to hard science fiction and that's biological science fiction. So far, I haven't been writing about the scientist busily doing science. I'm more likely to be writing about the people who are affected by the science. I always wondered when I watched movies or television what was going on with the ordinary people because so often you would see the leaders and the scientists and the generals, and I was much more interested in how all this was affecting Joe Blow, Jane Doe.
The discussion itself focused on the use of science in science fiction from the three authors' different perspectives, not to mention politics, science teaching, and cultural biases. It's definitely worth reading the transcript (pdf) if you are interested in science fiction writing.
It's also worth reading the full interviews, and looking at some of the suggested links for "further edification".

The take home message is that developments in the biosciences will necessarily have a role in our future, and science fiction should take that into account. Yes, I'm biased . . .

* Microbiologist and author Joan Slonczewski has written that Butler's Xenogenesis ". . . creates a stunningly vision of abduction and seduction by an alien species. This vision is presented in terms remarkably consistent with modern molecular biology, even predicting developments that have occurred since the novels were written." (from "Octavia Butler’s Xenogenesis Trilogy: A Biologist’s Response")


Tuesday, January 16, 2007

Cutting-Edge Astrobiology

Astrobiology Magazine is an online publication from NASA. In addition to news relating to possible life on other worlds, and Frequently Asked Questions about astrobiology, there are a number of interesting feature articles.

Some highlights:
Debating Life's Boundaries, Life as We Don't Know It, What is Life?, The Basic Rules of the Universe - panels from the Astrobiology Science Conference last March.

• "Great Debates" about terraforming , the possibility of life on other planets, and the threat of asteroids hitting earth. The "debaters" include both scientists and science fiction authors Kim Stanley Robinson and Greg Bear.

• An overview of Mars in Film

• Article about the possibility of alien infection ala Andromeda Strain.

• Film maker James Cameron on Mars and extreme life.

• "Table Talk" interviews with scientists and authors, including Bruce Runnegar, paleontologist and director of the Astrobiology Institute, Jack Farmer's testimony for the "Life in the Universe" hearings before the House Subcommiteee on Space and Aeronautics, and Philip Ball on "Water and Life"

• "
Perspectives" in essay form from a wide range of authors, from neurologist Dr. Oliver Sacks to Frank Drake (developer of the "Drake Equation")

• Special sections on the Extreme Life, possible Life on Mars, and more.

Here are the top 10 astrobiology stories of 2006:

January 2006: Stardust
As they clustered around the Stardust sample return capsule, Donald Brownlee, Stardust principal investigator from the University of Washington in Seattle, warned his team they might not be able to see any comet dust. The tiny particles may have made such small tracks in the aerogel collector that they would not be visible to the naked eye.
Wearing white bunny suits in a clean room at Johnson Space Center, the team anxiously examined the collector tray… and then broke into delighted celebration. Small black holes dotted the wispy aerogel tiles, and some were as large as half a centimeter wide.
January 2006: New Horizons Mission to Pluto Launched
After visiting Pluto, Charon, and the two newly discovered moons, an extended mission would allow the New Horizons spacecraft to encounter one or two Kuiper Belt Objects (KBOs). Because the Kuiper Belt is so vast, the closest KBO to Pluto is about 1 AU away, the same distance between the Earth and the sun.
March 2006: Water on Enceladus?
NASA's Cassini spacecraft may have found evidence of liquid water reservoirs that erupt in Yellowstone-like geysers on Saturn's moon Enceladus. The rare occurrence of liquid water so near the surface raises many new questions about the mysterious moon.
March 2006: MRO Test Snaps
The first test images of Mars from NASA's newest spacecraft provide a tantalizing preview of what the orbiter will reveal when its main science mission begins next fall.
March 2006: Icy Super Earth Found
An international collaboration of astronomers has discovered a "super-Earth" orbiting in the cold outer regions of a distant solar system about 9,000 light-years away. The planet weighs 13 times as much as Earth, and at minus 330 degrees Fahrenheit, it's one of the coldest planets ever discovered outside our solar system.
June 2006: Venus Seeing Double
ESA's Venus Express data undoubtedly confirm for the first time the presence of a huge 'double-eye' atmospheric vortex at the planet's south pole. This striking result comes from analysis of the data gathered by the spacecraft during the first orbit around the planet.
October 2006: Looking Down on Opportunity
While Opportunity spent its first week at the crater, NASA's newest eye in the Martian sky photographed the rover and its surroundings from above. The level of detail in the photo from the high-resolution camera on the Mars Reconnaissance Orbiter will help guide the rover's exploration of Victoria.
September 2006: Saturn's Methane Moon
Saturn's moon Titan seems to have little in common with Earth. At just 93 Kelvin, the giant moon is beyond ice cold, and its atmosphere is dominated by methane rather than nitrogen and oxygen. But in July, radar on NASA-ESA's Cassini-Huygens mission found a landscape with a striking resemblance to Earth.
A methane molecule contains a single carbon atom. The methane that formed these depressions was probably converted by solar-powered processes into the two-carbon hydrocarbon ethane, and eventually into other hydrocarbons and "a whole suite of nitrogen-bearing molecules," Lunine says. Under the right conditions, these simple molecules could become the building blocks of life.
November 2006: MGS Over and Out?
NASA's Mars Global Surveyor has likely finished its operating career. The spacecraft has served the longest and been the most productive of any mission ever sent to the red planet.
December 2006: Water Flows Today on Mars
NASA photographs have revealed bright new deposits seen in two gullies on Mars that suggest water carried sediment through them sometime during the past seven years.
Finally, if you can't find the information you are interested in, you can always Ask an Astrobiologist.

Monday, January 15, 2007

Imaginary Things and Science

A few weeks ago the physicist Sean Carroll* made an interesting post about using fiction (and video games) to teach science. He points to the books with the formula "The [field of academic inquiry] of [product of human imagination]" - think The Biology of Star Trek, The Physics of the Buffyverse, and their kin.
And as long as it’s been in circulation, the idea of subjecting TV shows or fantasy genres to scientific investigation has been the target of scoffing from curmudgeonly old folks who are taking a temporary break from chasing kids out of their yards. After all, they will tell you, how can you learn anything about science by studying fiction? Science is all about the real world! It has nothing to say about fake worlds that someone just made up.

Balderdash, of course. Neither physics, nor any other science, is some list of facts and theories to be committed to memory. There are a bunch of established pieces of knowledge that are worth remembering, no doubt about that, but much more important is the process by which that knowledge is acquired. And that process is just as applicable to imaginary worlds as it is to the real one. Any respectable universe, whether we find it out there or make it up ourselves, will be subject to certain internal rules of behavior. (When it comes to fiction, those rules are occasionally sacrificed for the sake of the plot, whereas in the real world they’re a bit more immutable.) Learning how to discover those rules, from the standpoint of an observer rather than one of the creators, is nothing more or less than learning how science is done.
I get the sense that a lot of people feel that science really is just the memorization of a bunch of boring facts. That attitude isn't too surprising, since many introductory science classes are taught in just that way. I'm hoping that more instructors will incorporate "fun science" (looking at science in fiction, playing video games that teach scientific principles, hands-on experiments, et cetera) into their curricula.

* Not to be confused with the biologist Sean Carroll.

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Zombie Evolution

It has been suggested that there could be no self-sustaining zombie population. The argument goes something like this: zombies "reproduce" by biting people, but not eating them. A fast zombie would be efficient at catching and eating people's brains, so no new zombies are made. A zombie that was so ineffective that he could bite, but not eat, his victims would be avoidable., so, again, no new zombies are made.

Anders Sandberg thinks that analysis is too simplistic.
First, there is of course always a slight chance of incompetence from efficient zombies and competence from inefficient zombies. This will lead to growth in any case.

Second, there might also be an evolutionary pressure on zombies. Assuming zombieness is in some sense heritable (why not? nothing about zombies makes sense anyway), there would be an evolution towards reduced virulence (i.e. biting, not killing as often). This is just as how many non-vector transmitted diseases evolve towards more benign forms where the host is not killed (diseases transmitted by vectors on the other hand have a weaker incentive to become less virulent). So the initial zombies would evolve towards an optimal speed to injure enough people to keep the spreading high, but not be too efficient. Maybe this is the "Hollywood optimum", since it provides with maximum uncertainty of the survival of the heroes.
Sandberg then runs a simulation of the evolution of a hypothetical zombie population. The results are frightening:
At first the very fast zombies expand, evolving towards ever more shuffling zombies while the humans are plentiful. Once the human population starts to decrease appreciably the zombies begins to evolve towards faster zombies again. But now there are so few humans left that the plentiful old zombies get them anyway and the evolution stops before it gets very far.
I'm convinced. We simply can't assume a zombie infestation will disappear on its own. Destroy them all! (via evolgen)



What could cause widespread infertility? In the movie version of The Handmaid's Tale, biotoxins are the culprit. In the recent Children of Men, the causes aren't spelled out, but "we're left with the impression of an ecology badly out of whack." Will McCarthy's latest Lab Notes column for takes a look at what we currently know about reproductive toxins. He concludes that the outlook of Children of Men is too bleak:
The harshest criticism I have for Cuarón's story, and James' before it, is that it's unremittingly, unreasonably, unrealistically grim. Where is the biotech industry in all this? Vague rumors of a secret project aren't enough; where are the millions of skilled workers, the trillions of dollars in R&D funding that would surely be directed at the problem? By injecting human DNA into the egg cells of pigs (or sheep, or some other mammal unaffected by the fertility apocalypse), we could clone large numbers of healthy children who would—after some respectable interval and an appropriate course of sex education—start reproducing the old-fashioned way. And while we're at it, why not improve their genomes a little, so this kind of thing never happens again? On the side, we could upload our consciousness into robot bodies, cross our DNA with that of the smartest apes, and of course create sterile dome cities where toxins and pathogens are ruthlessly scrubbed away.
Given enough time and resources the human race probably could at least come up with some sort of stop-gap solution. Whether it would work to save our species is harder to know. Could we clone forever? Could we remove the toxins from the environment that caused the infertility in the first place? If there was a breakdown in civil order, perhaps not.

For another take on the same issues - use of technology (particularly cloning) to overcome the near destruction of the human race due to environmental catastrophe - I recommend reading Kate Wilhelm's Where Late the Sweet Birds Sang.

Saturday, January 13, 2007


In San Diego, researchers are uploading lobsters into cyberspace, starting with the stomatogastric ganglion, one neuron at a time. ("Lobsters" - Charlie Stross)
The lobster nervous system is very simple compared to mammals. The neural circuits that control the lobster digestive system, including the stomatogastric ganglion, have been extensively mapped and studied, and those neurons have, in a sense, already been "uploaded" as a part of computer models of the stomatograstric neural network. Indeed, Stross was inspired by this research. Popular Science editor Gregory Mone investigated further for his article science fiction "posthumans":
A few days after I return to New York from the Plokta conference, I find the San Diego researchers* on the Web and check with Stross to make sure they’re the right ones. Then I forward a link to the first story in Accelerando, the aptly titled “Lobsters,” to the scientists. A few hours later, a physicist in the group, Henry Abarbanel, calls me. He’s excited but a little confused. Excited that his team’s work helped to inspire a massive SF novel, perplexed because he can’t find any specific reference to their research in the story, although there is lots of stuff about uploaded lobsters. We talk a bit about science fiction in general—he was an Asimov fan as a kid—and then Abarbanel explains what he and his colleagues are doing with those lobsters.

The research, led by biologist Allen Selverston, focused on the California spiny lobster because only 14 neurons govern a key part of its gastric tract. This number of neurons is unusually small, which makes the area easier to model. Still, understanding the neurobiology of those 14 neurons was not easy. It took Selverston 25 years. Then Abarbanel and his colleagues needed two more to figure out how to re-create the system electronically. This work, too, was difficult: Abarbanel likens the process to having all the parts of a 747 laid out on the floor of a hangar with no instruction manual on how to put them together to make an airplane.

All that work, and they’ve electronically simulated just 14 neurons. That’s a far cry from uploading the 1011 neurons that make up the human brain. Naturally, I assume Abarbanel will laugh at the idea that uploading a human mind could ever be possible. But it turns out that he approves of Stross’s leaps of imagination. “Frankly, I don’t consider it to be crazy,” Abarbanel says. “Whether it’s five years or 10 years or 500 years, I have no doubt that we’ll figure out how to do it.”
Read "Lobsters", for Stross's take on what happens when the nervous systems of many lobsters are uploaded into the same computer.

*Abarbanel and Selverston are faculty at the UCSD Institute for Nonlinear Science . Selverston is the author of the stomatogastric ganglion article linked above.
Image from the National Oceanic and Atmospheric Administration

Thursday, January 11, 2007

Not abandoned

Despite the look, this blog is not abandoned. I've switched to "New Blogger", and will be adding categories. In the mean time, I'll really really turn some of those draft posts into final versions. Honest!

Friday, January 05, 2007

The Genetics of Magic

The year-end edition of the British Medical Journal always covers topics that are typically overlooked in the biomedical literature during the rest of the year. This year Sreeram V Ramagopalan and colleagues have published a review of the literature* on the genetics of magic, "Origins of magic: review of genetic and epigenetic effects". Their conclusions:
Results Magic shows strong evidence of heritability, with familial aggregation and concordance in twins. Evidence suggests magical ability to be a quantitative trait. Specific magical skills, notably being able to speak to snakes, predict the future, and change hair colour, all seem heritable.

Conclusions A multilocus model with a dominant gene for magic might exist, controlled epistatically by one or more loci, possibly recessive in nature. Magical enhancers regulating gene expression may be involved, combined with mutations at specific genes implicated in speech and hair colour such as FOXP2 and MCR1.
They even propose a model of enhancer-driven gene regulation in individuals displaying the magical ability phenotype:

Now, like all good modern journals, BMJ allows comments on their articles (called "rapid responses" to make them sound less Live Journally, I suppose). One of the commenters has an excellent suggestion: a follow-up article on the heritability of Jedi powers. A tough research project since it would require sitting through Episodes I-III and reading the massive array related literature, but someone should definitely do it!

* The literature in this case being the Harry Potter series of books

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