Science Tidbits: Sasquatch Genome, Human Evolution, and DNA Up Close

Some fantastic genetics news:

• Suspect Sasquatch Sequencing

Hoax? Viral marketing? or major scientific breakthrough? Texas company DNA Diagnostics,  headed by veterinarian Dr. Melba Ketchum, has announced that they have sequenced not one, but three different Sasquatch genomes. Dr. Ketchum has applied for a patent for a method of genetic analysis of wild and domestic animals, which suggests expertise in DNA analysis. Their claim is that not only that the Sasquatch is humanoid, but that they are hybrids between human females and "unknown" male hominins.

“Genetically, the Sasquatch are a human hybrid with unambiguously modern human maternal ancestry. Government at all levels must recognize them as an indigenous people and immediately protect their human and Constitutional rights against those who would see in their physical and cultural differences a ‘license’ to hunt, trap, or kill them."

So not only some amazing claims but a strong message about ethics to go with them. 

 Over at Teen Skepchick they have dug into the details that are available about Ketchum and Robin Lynne, who put out the press release. It turns out Lynne has made a number of claims about a large Sasquatch family that she has interacted with on her property.

But her evaluation of the evidence is beyond reproach. Apparently she went out one day to her feeding box to find it locked, and when she opened it, the food was gone but there was an opossum inside. She naturally concluded that the Bigfoot family had put the creature in there and locked the box as a joke.

Apparently the original manuscript also claimed that they found "angel DNA" in the samples. The more I read the more this sounds like the work of some serious deluded individuals who may have analyzed a sample of wild animal DNA contaminated with human DNA. Or maybe this is truly a history discovery (but I think not).

Image: Bigfoot statue in Silver Lake, Washington. by Plazak on Wikimedia Commons licensed under the Creative Commons Attribution 3.0 Unported license. May not be scientifically accurate.

Now some more realistic science:

• Human Evolution Enters an Exciting New Phase | Wired Science 

 I don't think it should be a surprise to anyone that humans are evolving. Evolution is not a ladder where humans have reached the top and will never change again.

But a recent detailed study of 6500 human genomes - Americans of European or African descent - did turn up something unexpected: the explosion of the human population over the past 5000-10000 years has resulted in a "vast abundance of rare genetic variants".

"... the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn’t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases arecaused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people." 

One limitation of this study is that it only compared the protein coding sequences of the genomes it analyzed. 98% of our genomes do not encode proteins, so it's possible that whole genome analysis might have told a different story. In fact, I think it would be interesting to compare mutation rates in protein coding and non-coding sequences (some of which is functional, but much of which is junk).

Original paper: Fu, W. et al. "Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants" Nature Advance online publication, http://dx.doi.org/10.1038/nature11690 (2012).

• Scientists snap a picture of DNA’s double helix for the very first time »

Despite what you might see in science fiction movies and CSI-like TV shows, the DNA double helix is not usually visible under a microscope. In fact Enzo di Fabrizio and his colleagues at the University of Genoa were able to take high resolution photographs of double stranded DNA using an electron microscope in which the DNA double helix is clearly visible.

The image is actually not a single molecule of DNA - it's six DNA molecules wrapped around a seventh, since the energy of the electron beam can break a single DNA molecule. It's hoped that in the future a single DNA molecule can be imaged.

Original paper: Gentile F et al. "Direct Imaging of DNA Fibers: The Visage of Double Helix" Nano Letters Article ASAP (2012)

Image: The famous twists of DNA's double helix have been seen with the aid of an electron microscope and a silicon bed of nails (Image: Enzo di Fabrizio, from Gentile F et al.)

• GATTACA Rises: building structures out of DNA

Last, but not least, a team of French physicists lead by Jean Michel Arbona have designed a new computer model that describes how DNA can fold and knot and weave together into 3-dimensional structures known as DNA origami. See the video here for more details.

Thanksgiving special: inbred turkeys and feasts in space

Happy Thanksgiving everyone!

While you are feasting, you might consider the humble origins of the turkey:

• Tracing the taming of the turkey

At Double X Science Emily Willingham looks at the origins of today's turkeys, whose wild ancestors were carried from Mexico, to Europe and back again to North America.

Image: Turkey by wattpublishing on Flickr (www.WATTAgNet.com), shared under a CC-By-2.0 license. 

• Turkey trouble: Genetics gone too far?

At KQED Quest Barry Starr takes a hard look at the turkeys on factory farms and it's not pretty. Turkeys bread for to have lots white breast meat are likely in constant pain and are prone to heart attacks. He notes:

All of this raises the obvious ethical question. Just because we can breed this turkey, should we? The turkey lives a short, miserable life but we get an affordable, healthy source of protein. It is obvious which choice we’ve made as a society, but is it the right one?

A bit sobering to think about.

Meanwhile, NASA engineers suggest some interesting cooking techniques, astronauts celebrate Thanksgiving in space:

• Four Crazy Ways to Cook Your Turkey Using NASA Equipment

Gizmodo asked NASA engineers and science writers how they would use NASA's high tech equipment to cook a turkey. If you have a spare satellite dish or an Antares-class sounding rocket you could try out their recipes yourself!

• Astronauts get Thanksgiving feast in space

The astronauts on the International Space Station will be celebrating Thanksgiving with a holiday meal that includes irradiated smoked turkey and themo-stabilized yams - yum!. Even though it comes freeze dried and in foil packets it's still a special treat.

You can even follow NASA's recipe for cornbread stuffing if you want to eat like the astronauts do.

Finally, a Thanksgiving message from Commander Kevin Ford on the International Space Station, who talks about the holiday meal he and crewmates Oleg Novitskiy and Evgeny Tarelkin will be eating:

Science & SF Tidbits: Speculative Genomics, Snot Whales, and Idiocracy (not)

Some fictional and speculative genetics and genomics for your reading pleasure:

Free Fiction:

• The Authors: Flash Fiction Fest - Four Weeks of Flash Fiction from December House »

Publisher December House is posting several new short fiction pieces every day of November. Many of the stories have a "science fiction feel". Sean Craven's stories feature Henry Cleary; the Colonel, who's a rooster genetically engineered to have teeth and a long muscular tail; and many other science fictional biological oddities.

Craven has also been posting some thoughts on the biological background of his stories on his blog. If you are interested in some real odd biology, give them a read here: Salamanders and Snot Whales, The Shade-Tree Biotechnician

Note that the stories are only available free through the end of November, so check them out soon.

Speculative genetics:

• Brazil To Clone Wild Animals In Danger Of Extinction » io9
EMBRAPA, the Brazilian government's agricultural research agency, successfully cloned a cow in 2001. Since then they've been refining their cloning program to the point where they have now announced they are going to try cloning endangered species. Their list includes eight animals on the threatened species list, such as the maned wolf (Chrysocyon brachyurus), the jaguar (Panthera onca) and the black lion tamarin (Leontopithecus chrysopygus).

EMBRAPA has stated that their goal is to keep the cloned animals in captivity and only use them for restocking zoo populations and study, rather than releasing them to the wild. But it makes me wonder: is cloning a good use of resources in situations where the wild populations are at risk?

• Cancer, Data and the Fallacy of the $1000 Genome » Forbes
Dr. Mark Boguski has a message: "The time of the $1000 genome meme is over. It served us well for years – driving advances in instrumentation, chemistry and biology. But now it is reducing clinical credibility. It’s time for it to leave the lexicon of healthcare; it has to go."

The fact is that genome sequencing for cancer patients is expensive (far more than $1000), not covered by insurance, available to a relatively limited number of people, and might not be that informative clinically. He argues that the focus should be on precision diagnostics, which involves "big data" and analytics. And because this article is in Forbes, that means that Boguski and colleagues have started a business - Genome Health Solutions - to do just that.

It seems to me that with potentially limited research funds it's not clear whether scientists should be striving to make genome available and affordable for everyone, or if it would be better if they instead focused on deeper analysis of the existing data - or, ideally, if both approaches are possible. Which would be better for the average cancer patient is still unclear.

Image: SNPs: Single Nucelotide Polymorphisms, Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science.science.energy.gov/ber/. Used with permission.

• Neuroskeptic: We're Probably Not Getting Dumber »
While it may be popular to argue that the human race is evolving to be dumber Idiocracy-style, the good news is that we're probably not actually getting less intelligent as a species. We won't even become beautiful-but-dim Eloi. In the linked article Neuroskeptic explains how two recent articles claiming that humans are getting dumber are based on faulty assumptions.

• Sci-Fi Political Thriller, Or Fact? - HuffPost Live »
Harvard geneticist George Church, SF author/futurist David Brin, and futurist Jamais Cascio, discuss the speculative possibility of "Hacking Obama's DNA". I'm glad the Huffington Post included a geneticist in the discussion!

The Gene in Pop Culture: Barbara Duden and Silja Samerski on How to Think About Science

What do you think of when you hear the word gene? Do you associate it with bad things like the risk of heart disease or cancer? or do you think about personalized medicine and the improvement of human health? or simply part of our nature and a determinant of heredity?

About a decade ago German historian Barbara Duden and geneticist and sociologist Silja Samerski collaborated on a project to try to understand what people mean when they use the term gene in everyday conversations. They found that people use the term frequently, even when they didn't have a good understanding or clear definition of what the term meant.

Duden and Samerski were interviewed on CBC's "How to Think About Science" radio show to talk about their work.

So what does the term gene signify in everyday speech? It turns out it means different things to different people. And even individuals may have contradictory feelings, associating the term not only with impersonal scientific experts and health risks, but also the potential for a utopian future where the failings the human body have been cured.

Understanding the term gene as a scientific construct requires a fair amount of background knowledge and education in genetics. Duden argues that for those without a scientific background, the term can be "mystifying and disorienting" when used in everyday speech, and that it has no place there.

Her colleague Samerski draws on her on experience as a geneticist to suggest that confusion in terminology can add to the stress and confusion pregnant women experience in genetic counseling sessions. Genetic counselors provide an analysis of the probability a developing fetus will have a genetic disorder such as Down Syndrome or cystic fibrosis. But they can only talk about what may happen, since they cannot know what will happen. That puts women in a difficult position of having to make decisions about their pregnancy based on a statistical risk analysis that can be difficult to understand.

Samerski argues that the "quasi mythic power" of genes in popular culture may make the statistical probabilities relating to genetic risk profiles more difficult for pregnant women to grasp.

So how can this situation be improved? If people are getting conflicting messages through popular culture regarding what genes represent, then perhaps popular culture is also the best way to generate better understanding of genetics.

"Genes" (along with "mutants" and "genetic engineering") are often used as a simplistic plot device in movies and TV shows to explain changes in human health and behavior and abilities ranging from childhood diseases to the sudden onset of super powers. But entertainment necessarily uses shorthand when it comes to science, and I think there is an assumption that viewers are at least passingly familiar with the scientific terminology they use. Certainly a genetics lecture would seem out of place in the middle of an X-Men movie.

I would argue that a better place to start would be the news media, which often seems to simply regurgitate exaggerated press releases when reporting new scientific developments. Breathless headlines and poor explanations of the latest genetic findings do make "genes" seem almost magical. It's not at all surprising that many people are confused.

And I'd like to think that better public understanding of genetics would lead to more realistic depictions of genes and mutations in popular culture as well. Imagine that!

-------
Listen to "How to Think About Science" Episode 15 with Barbara Duden and Silja Samerski.

Read the interviews with Duden and Samerski and other guests on "How to Think About Science" in the book Ideas on the Nature of Science.

(Just as a side note, my discussion is based on he CBC radio interview which only provides a limited picture Duden and Samerski's arguments. Unfortunately most of what they've written is in German, so I don't really have more information. Anyone who knows more about what solutions they have proposed is encouraged to discuss that in the comments.)

Top image: "DNA Strands" from the Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science (science.energy.gov/ber/), with credit to the U.S. Department of Energy Genomic Science program (http://genomicscience.energy.gov).Available through the Department of Energy's Office of Biological and Environmental Research Image Gallery Gateway.

William S. Burroughs: Body Modification and Biologic Courts

This continues the series on interviews with SF writers in the Paris Review. Yesterday, I posted about the 1960 interview with Aldous Huxley. Today, I'll take a look at the 1965 interview with William S. Burroughs

William S. Burroughs was interviewed by the Paris Review in 1965. His weird and controversial novel Naked Lunch had been published in the United States in 1959. At the time this interview was published, its sale was still banned in Boston.

Burroughs was interviewed the year after publication of his Nebula award-winning novel Nova Express. Nova Express was the third book in his Nova Trilogy, and was assembled using the cut-up method, in which "existing texts ... cut into various pieces and put back together in random order." Definitely not what most people would think of a standard science fiction novel.

The plot summary for Nova Express makes it sound hallucinogenic:

The Nova Mob—Sammy the Butcher, Izzy the Push, The Subliminal Kid, and others—are viruses, "defined as the three-dimensional coordinate point of a controller."[...] "which invade the human body and in the process produce language." These Nova Criminals represent society, culture, and government, and have taken control. Inspector Lee and the rest of the Nova Police are left fighting for the rest of humanity in the power struggle. "The Nova Police can be compared to apomorphine, a regulating instance that need not continue and has no intention of continuing after its work is done."

The novel also apparently involves biologic police agents and legal battles between competing life forms are fought "Biologic Courts".

As Mac Tonnies described it, it's "the literary equivalent of downing a few vials of choice LSD".

In the Paris Review interview, Burroughs expands on the idea of that the future of the human race will involve genetic engineering and require some sort of "biologic law" and courts to mediate the changes.

Science eventually will be forced to establish courts of biologic mediation, because life-forms are going to become more incompatible with the conditions of existence as man penetrates further into space. Mankind will have to undergo biologic alterations ultimately, if we are to survive at all. This will require biologic law to decide what changes to make. We will simply have to use our intelligence to plan mutations, rather than letting them occur at random. Because many such mutations—look at the saber-toothed tiger—are bound to be very poor engineering designs. The future, decidedly, yes. I think there are innumerable possibilities, literally innumerable. The hope lies in the development of nonbody experience and eventually getting away from the body itself, away from three-dimensional coordinates and concomitant animal reactions of fear and flight, which lead inevitably to tribal feuds and dissension.  

I'm struck by how much that last part  - about the future of the human race eventually "getting away from the body itself"  - sounds like some modern proponents of transhumanism who see the divorce of the mind from the limitations of the body as one of their ultimate goals. A man ahead of his time, perhaps? or is it a simply reworking of Buddhist ideas of mind-body separation within a scientific frame? I don't know enough about Burroughs' ideas to tell the difference.

In the interview, Burroughs also talks a bit about the inevitable cross-fertilization of science and art:

In the first place, I think there's going to be more and more merging of art and science. Scientists are already studying the creative process, and I think the whole line between art and science will break down and that scientists, I hope, will become more creative and writers more scientific.

Perhaps inspired by this notion is the "Mutate or Die" project, which involves isolating and manipulating DNA from a preserved sample of Burroughs' poop.  It definitely involves science, and it's meant to be art.

Read the whole interview for more from Burroughs about cut-ups, addiction, and how he created his fictional characters.


Tomorrow: Interview with Kurt Vonnegut.

@ SIMF: Perception, Neurology and Fiction

Check out my latest post for the "Science in My Fiction" blog:

Perception, Neurology, and Fiction.

My previous SIMF post: You Are What Your Grandad Ate

And there have been a number of other great biology in science fiction-related posts over there - go read!

Tags:science fiction, neuroscience

Holiday Free Fiction: The Christmas Count

The sky over the river is already light and I’m still six miles from his house -- ten more minutes. Provided I don’t get caught at the tracks by some goddamned, two-hundred-car freight train. Ron will have his audio equipment out, but it won’t do us any good. Not this late. Once the sun’s up, even a set-up as good as Ron’s is pretty much useless for calling in owls. Great-horned, screech, barred; usually Ron and I can call in at least two out of the three. Not this year. Maybe someone else in the McCarron count circle will have owls on their list, but it won’t be us. Two years ago the count had none at all, and Clover County beat us by two species. Two lousy species.

For over a century the Audubon society has sponsored a Christmas Bird Count, in which ordinary people help take a census of birds throughout the Americas. In the not so near future biotechnology may allow Christmas counters to spot birds that haven't been seen in decades . . .

Read "The Christmas Count" by David B. Coe.

Image: Passenger Pigeon, Ectopistes migratorius, from Orthogenetic Evolution in the Pigeons, 1920 (from Wikimedia Commons)

Tags:science fiction, biology

Genetics in Fiction @ Clarkesworld

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

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

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

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

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

The Unselfish Gene: Altruism and Zombies

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

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

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

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

Purchase The Unselfish Gene @ Amazon.com (affiliate link)

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




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







Richard Dawkins' The Selfish Gene



Tags:science fiction, zombies, genetics

The Human Genre Project

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

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

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

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

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

(via SF Signal)

Tags:science fiction, genomics, genetics

Biology in Science Fiction Mega Link Roundup: April 4 Edition

I've slowly - oh so slowly - been going through the links I collected for "future reading" over the past few months. I also had a link roundup post meant to be published in January that somehow never made it out of draft form. The result? A mega maxi link roundup!

General SF Rumination

Gerry Canavan presented a talk on "Science Fiction and Ecological Futurity" (via SF Signal)

Mike Brotherton: Why Science Fiction Rules the World (but not enough!!!)

More and more often these things are aspects of our modern reality that have no precendence in human history. Somehow history gets respect and people say it “repeats itself” even though that is not true. Science fiction isn’t exactly great at prediction, but the process is very useful for meeting the future with open eyes.

Jason Stoddard suggested that the burden of the modern science fiction writer is keeping up with scientific progress. In response, Jeremiah Tolbert explained why Stoddard is wrong. The central issue seems to be how important "realism" in science is to science fiction (via Futurismic).

Meanwhile, Megan at Teen Ink magazine is teaching teenagers how to research science before writing science fiction. (via io9)

BBC talked to Ken MacLeod, Paul Cornell, Iain Banks, and Ian Watson about whether science fiction needs to stay up to date with scientific breakthroughs to be relevant.

Arvind Mishra has a more detailed look at the First National Discussion on science fiction in India.

The Consumerist reports on a study showing people rate harder-to-pronounce words as "riskier". It's true for food additives and rolloer coasters - maybe it's true for alien names too?

Written Word

Vice Magazine interviewed Ursula Le Guin (via SF Signal):

Some sf writers decided a while ago that true sf can only be based on the so-called hard sciences—astronomy, physics, chemistry, engineering, computer science, and so on. The word “hard” brings some gender luggage along with it. And sure enough, these guys find stories based on the “soft,” or social, sciences to be a debased and squashy form of the genre. They see it as chick lit for geeks. So, OK. If anybody wants to build a ghetto inside the ghetto and live there, fine with me. But I wish this sectarianism hadn’t infected Wikipedia. If they want to call my stuff social science fiction, that’s fair enough. But so much of what I write isn’t sf at all.

Graham Sleight at Locus online: Yesterday's Tomorrows: Ursula K. Le Guin

[Left Hand of Darkness] traces a slow process of discovery — of Winter and its inhabitants. In that respect, in that it's about finding out, it's a perfectly science-fictional work. (The later Ace edition carries a provocative introduction by Le Guin, in which she administers a few well-judged kicks to the idea of sf as narrowly extrapolative or predictive.) We find out, for instance, via Chapter 7 how and why the Gethenian biology was created. This chapter is an ethnologist's report on the planet — what would, in other circumstances, be considered an "infodump." But Le Guin is so thoughtful a writer, the implications of her thought-experiments so thoroughly and deeply felt, that you find yourself wanting to hear this information, even if it is couched in as dry a form as this.

Mur Lafferty at Tor.com reviews Scott Sigler's Contagious.

Peter Watts reports that his novel Blindsight is "going to be a required text for a Biological Psychology course at the University of Miami"

Brian Switek at Laelaps rants about Monster, a creationist anthropology thriller:

Peretti also mentions that his favorite author (and chief writing influence) was Michael Crichton, and this makes sense. Not only does the book have an anti-science bent, but it reads as a sort of mash-up between Jurassic Park, Congo, and Icons of Evolution. Even though it is a monster story, the author makes it clear that the real monsters are the immoral evolutionists who will stop at almost nothing to uphold their crumbling intellectual doctrine.

Jeff Carlson writes about the background behind his novel Plague Year

Nancy Kress reviews Kazuo Ishiguro's Never Let Me Go and talks about "cloning-for-organ-donation" in SF in general.

Kress also looks at genetically modified mosquitos, as they appeared in her biothriller Stinger, and in real life.

Jo Walton writes at Tor.com about Octavia Butler's Survivor, a novel Butler repudiated and refused to be a allowed to be reprinted. Part of her problem is the simple interbreeding of humans and aliens, and the way the novel depicts race and color (literally).

Jo Walton also looks at aliens and sapience in H. Beam Piper's Fuzzy novels

Annalee Newitz at io9.com: The Rise of Science Among Insects in Greg Egan's Incandescence

NK Jemisin reviewed Naomi Novik's Temeraire novel Victory of Eagles last August for Fantasy Magazine and the discussion touched on alternative evolution.

Peter Watts posts a proposal for a new novel, Dumbspeech.

DamienBarret has a great Flickr set of his visit to Alan Dean Foster's house. He got to see Foster's awards and decorations including a "fossilized critter" that "might help ADF with his depictions of the Thranx or other insectile cratures in his books."


Television

The Oyster's Garter takes a look at what the Earth was really like 150,000 years ago, when the Battlestar Galactica folks landed in Africa.

James F. McGrath at Exploring Our Matrix writes about John the robot in Sarah Connor Chronicles who questions why God didn't make humans with more ball socket joints and uses to talk about evolutionand "the image of God" (via io9)

Science Not Fiction talks about the real science of Sanctuary's abnormals, gives the lowdown on Sanctuary's Bad Bad Prions, and looks at the series' gene therapy

Charlie Jane Anders at io9: Kyle XY: How Not To Do a TV Series Finale

Science Not Fiction: Battlestar Galactica, Self-Repairing Material and biofilms

Movies

ScienceOnline: Alexis Gambis brings science and film together to create a new genre of science fiction (ScienceOnline is a project of NYU's Science, Health and Environmental Reporting Program)

George Dvorsky posts about young filmmaker Jason Silva's short film "The Immortalists", which is "a love letter to science and philosophy that explores the idea of engineered radical life extension and biological immortality"

T. Ryan Gregory at Genomicron: Would you act as a consultant on a scifi movie? And more importantly, would you accept compensation if you did?

Jonathan Fahey at Forbes.com writes about The Science Behind 'Watchmen' and the teaming of Hollywood with scientists

John Scalzi @ SciFi Scanner on Video Game Movies:

In point of fact, the average gamer is nearly thirty, not dumb, and while he may enjoy bombs, blood and babes, I'm willing to bet he'd happily see a movie that doesn't assume he's stupid. When I watched Doom, the scene where a scientist explained that a certain percentage of the human genome has never been mapped (and the part that hasn't, well, that's your soul, you see) made me want to throw a rock through my TV -- which is ironic, as the film stars The Rock.

SciFi Scanner looks at directors that include some real science in their science fiction. Included are Andrew Niccol, director of Gattaca and Steven Spielberg, director of Jurassic Park (and lots of other movies, of course).

Matthe Nisbet at Framing Science: "What about the "Gattaca" Effect on Perceptions of Medical Cloning?"

James Sanford takes another look at GATTACA, plucked from Rotten Tomatoes' list of "Ten Sci-Fi Flicks for the Thinking Man... or Woman".

At Nature Jascha Hoffman reviews films about science at the Sundance Film Festival (subscription required). LabLit.com points out that "it seems a lot of this was more medical than scientific, with tales of mental breakdown, bipolar disorder, autism and psychopathology."

Scientific American 60-Second Science: Science at the Oscars

Ain't it Cool News reports that Ronald D. Moore's prequel to The Thing will be directed by Matthijs Van Heijningen, who is an experienced director of commercials. Hopefully he can make the transition from the 15 second to 90 minute storytelling. In any case, it's supposedly heavily based on John W. Campbell's 1938 novella "Who Goes There?", which I'd think makes it a remake of John Carpenter's 1982 The Thing, which itself was a remake of the 1951 move The Thing From Another World, rather than a prequel. Don't moviemakers realize there are SF stories out there that have never been made into movies? But what do I know.

Darren Naish at Tetrapod Zoology reports on the whereabouts of the Krayt dragon skeleton from Star Wars Episode IV: A New Hope.

BoingBoinger Xeni Jardin reviews her favorite B-Movie - The Food of the Goods - for Fancast.

Repo! The Genetic Opera is coming to DVD. Genevieve Valentine at Tor.com rounds up the special features. BloodyDisguisting.com has an exclusive peek at the DVD's "Sing-Along" feature.

io9 has a nice clip of Vegan Horror, Sheep Punching, and a Lot of Fart Jokes (with a clip from Black Sheep)

Miscellaneous

Torsten Reil gave a TED talk on how he studies biology to make realistic animation.

John Holbo at Crooked Timber points out that Jack Kirby's comic books are really bad on evolution and Norm Doering has more on creationist misconceptions about evolution that seem to be based on comic book science.

An article in the January 2009 issue of Scientific American looked at the depiction of evolution in the game Spore.

NotCot visited Alien Fresh Jerky in Baker - a small town out in the California desert between Barstow and Las Vegas. Despite the name, they don't sell jerky made from aliens, which might or might not be tasty. No, what they sell is beef jerky made from abducted cows and other alien-related products. Sounds awesome.

Correlation vs. causation: There are fewer babies and fewer storks - is it pollution? or space aliens?

Tags:science fiction, biology

Crossroads: Free Korean SF Stories in English

Crossroads is a science web site launched in 2005 by the Asia Pacific Center for Theoretical Physics with the theme "vision for Science, Future, and Humanity". It includes essays and articles in Korean and English about science and culture, as wells as a number of science fiction short stories. I'm not sure how the English translations were created, but I suspect that they don't do the original stories justice.

Here are a few with biological themes:

• "Good Morning, John Wayne" by MinGyu Park
• "Purfume" by Sunglae Nor
• "The Song of the Dreaming Genome" by Geoil Bok (unfortunately formatted without paragraph breaks)
  
• "A Case for Being Mortal" by Yunsu Sin - Part 1, Part 2, Part 3
• "An Old Story" by Kyungmun Oh - Part 1, Part 2 (the science is bad in this one!)
  

(via Gord Sellar and the World SF News Blog)
Tags:science fiction, Korea, biology

Beast Men and other Bio Horror SF at Apex Magazine

There is something about the nature of biology - growing things, squishy internal organs, monsters and mutants - that lends itself to the horror end of the science fiction spectrum. And they aren't always just chilling entertainment; such horrifying stories can be used to look at philosophical questions about what it means to be human. The March 3rd edition of Apex Magazine ("where science fiction and horror collide") has a couple of good examples of that this month. As Sarah Brandel writes in her introductory essay "Beast Men and the Human Animal":

Another facet of the question ‘What is human?’ addresses the differences between human beings and other members of the animal kingdom. If, in some respects, tiny variations in DNA are all that separate human beings physically from their closest primate relatives, where is the genetic line drawn between what is human and what is not? (There are easy answers from a species perspective—only members of the same species can produce viable offspring—but we’re not looking for easy answers here.)

I won't quote any more, because there are spoilers for the stories, but you can read them online yourself:

• "The Puma" by Theodora Goss
• "The Mind of a Pig" by Ekaterina Sedia
  

And for some more good creepiness, here are a couple of other biology-science fiction-horror stories from their archives:

• "Organ Nell" by Jennifer Pelland
  
• "The New Breed" by Michael A. Burstein
  

(And if you enjoy what you read at Apex, consider clicking on their "Donate" button and making a small contribution.)

Tags:science fiction, horror, genetic engineering, organ donation

The Mother of Us All

Friday night's two-hour-plus Battlestar Galactica finale was an excellent ending to the series, from its action-packed beginning to the more contemplative ending that allowed us to say goodbye to the characters and tied up most of the loose ends. I wasn't particularly keen on the final message: that humanity's "brains outrun our hearts", and our development and increasing reliance on technology will ultimately lead to our downfall - and, at least in the Galatica universe, has ended up destroying civilization again and again.

In the first part of the finale, Admiral Adama leads a small human and cylon crew (including all the show's principal characters, natch') on a mission aboard the failing Galactica to rescue Hera Agathon - the only known human-cylon hybrid - from her cylon captors. It is only through a series of highly improbable events that our heroes escape - ending up on our very own Earth.

It's not really "our" Earth though, it's the Earth of 150,000 years ago. The few tens of thousands of survivors from the defeat of the 12 colonies land in the grasslands of East Africa, just about the time that Homo sapiens emerged as a separate species. And there are indeed already inhabitants there. We don't learn much about them, except that they carry long spears, travel in groups, and likely have no language. And in what appears to be a coincidence of supernatural proportions, their DNA is similar enough to that of the humans (or perhaps "humans") from the fleet so that they are genetically compatible. The improbability of populations evolving so similarly on planets that are millions of light years apart is even commented upon by Doc Cottle, so it's no careless mistake by the writers. That the refugee and Earth populations will be able blend together seems to be part of the divine plan that is influencing the characters' fates¹.

That plan involves more than just humans, though. Young Hera Agathon's father Helo is human, and her mother Sharon is a humanoid cylon. The humanoid cylon models had tried unsuccessfully to reproduce for many years, and their experiments attempting to breed human-cylon hybrids also ended in failure. It's not clear to them - or us - why that is the case. They are anatomically identical to humans down to the "cellular level", and presumably pass standard fertility and genetic tests (otherwise why would they think reproduction was possible at all). With all of their resurrection ships destroyed the need to find a solution becomes urgent to the remaining humanoid cylons. They see Hera as the key to their own survival.

I always thought their hope in Hera holding the secret to cylon reproduction was probably unfounded. Would she be any more fertile than a mule? It turns out that I was totally wrong.

In the closing scenes to the finale we see the divine (or otherwise supernatural) versions of Baltar and Number Six in present-day New York City. They look at a magazine in a science article that claims that scientists had discovered the fossilized bones of "Mitochondrial Eve" and they note that she had a cylon mother and human father. Sounds like Hera!

But who exactly is Mitochondrial Eve? I always thought the name was a bit unfortunate, because the Biblican Adam and Eve story has so much cultural baggage. Just to be clear she was not the first female human, and she lived roughly 100,000 years before the similarly poorly-named "Y-Chromosome Adam". To understand what geneticists mean by the term, the first thing you have to know is how mitochondria are inherited. Mitochondria are energy generating organelles found inside our cells. Importantly, they carry their own DNA. Unlike the chromosomal DNA which we inherit equally from both parents, our mitochondria are inherited only from our mothers. That means that geneticists can use the sequence of our mitochondrial DNA to follow maternal inheritance². They followed this back for many many generations, until they arrived at the most recent woman who is the ancestor of all presently living humans. She is "Mitochondrial Eve" and she lived roughly 150,000 - 200,000 years ago.

If you are having trouble imagining how that works, Krishna Kunchithapadam has a pretty good explanation at Talk.Origins:

Consider all the humans alive today on Earth. Put them into a set S.
Next, consider the set of all those women who were the mothers of the people in the set S. Call this set S'. A few observations about this new set S'. It consists of only women (while set S consists of both men and women)---this is because we chose to follow only the mother-of relationship in going from set S to set S'. Also note that not every member of set S' needs to be in set S---set S consists of all people living today, while some of the mothers of living people could have died, they would be in set S' but not in set S. Third, the size of set S' is never larger than the size of set S. Why? This is because of the simple fact that each of us has only one mother. It is however overwhelmingly more likely that the size of set S' is much smaller than that of set S---this is because each woman usually has more than one child.

Repeat the process of following the mother-of relationship with set S' to generate a new set S''. This set will consist of only women, and will be no larger (and very likely smaller) than set S'.

Continue this process. There will come a point when the set will consist of smaller and smaller number of women, until we finally come to a single woman who is related to all members in our original set via the transitive-closure of the mother-of relation.

Well, it makes it clearer to me, anyway. She's not our most recent common ancestor or even our only common ancestor. She's not the only woman who was living at the time. She may not be the our common ancestor for chromosome 1 or 7 or 20.

And because the way mitochondrial inheritance works, in the Battlestar Galactica universe our mitochondria - passed down to us from Hera who inherited them from her number eight model mother - are entirely cylon.

That makes the series' suggestion that humanity is caught in an ever repeating cycle of technological development that ultimately leads to our destruction that much more circular because we are are inherently a part of that very technology.

We are them.

Related posts:

• Cylon killing virus
• Star Wars and the Midi-Chlorian Menace
• Farandolae
  

Read the original Mitochondrial Eve-related publication: Cann RL et al. "Mitochondrial DNA and human evolution" Nature 325, 31 - 36 (01 January 1987); doi:10.1038/325031a0 (free pdf or text version)

1. I think the scenario presented in the finale brings up a lot of issues of ethics and race that are beyond the scope of my post. One question that I have Racefail to thank: Is it problematic that the technologically advanced and mostly white members of the fleet are shown arriving on Earth and either breeding with or supplanting the native African population so that they became our ancestors? I think so, but I haven't been able to put my thoughts clearly into words. I'm hoping others will post on that subject.

2. In the 1980s, geneticist Mary-Claire King used mitochondrial genetics help identify children who had been taken away from their imprisoned mothers during Argentina's so-called "dirty-war". Since then she's worked with human rights organizations to help identify missing personas all over the world. It's not science fiction, but her work is an important demonstration of using science to support human rights.

Tags:Battlestar Galactica, genetics, evolution, mitochondria

How would you do as an alien geneticist?

Scientific American has a puzzle that tests your ability figure out the genetics on an alien planet:

On a certain planet, it takes a village to beget a child. Well, not an entire village in fact, but instead of a father offering sperm and a mother providing an egg, five parents must get together to produced a fertilized egg. The egg will produce 1,000 children, 200 of each of the five sexes. Your job is to figure out which sexes are genetically important in determining an offspring’s (non sex-related) traits.

The puzzle answers don't appear to require any knowledge beyond a basic understanding of Mendelian genetics. Give it a try!

The Planet of the Apes Movie that Never Was and the Movie that Will Be

Since the first Planet of the Apes movie was released in 1968, there have been four sequels and a short-lived television series. Tim Burton made a reimagined version of the original in 2001. In all of those versions, the intelligent apes that rule the planet turn out to be descendants of present-day Earthly apes.

According to Devin Faraci at Chud.com, there might have been a very different sequel, if Oliver Stone had had his way:

Talking to Entertainment Weekly in 1993, [Stone] said ''My concept is there's a code inscribed in the Bible that predicts all historical events. The apes were there at the beginning and figured it out. I don't want to (say) too much more, except the stars will be hairy.''

The idea was that a disease was wiping out the human race today. Arnold Schwarzenegger would play Will Robinson (I don't think this was meant as a Lost in Space tie-in, but who knows with this batty shit) as a genetic scientist who figures out the cause of the disease is in the distant past and, along with a pregnant colleague, travels back to the Stone Age to discover a world dominated by apes. To stop the plague they save a girl named Aiv. The time-traveling woman has a son named Adam.

That sounds pretty bad - from the Bible Code that's apparently hundreds of thousands of years old and created by apes, to the time traveler who becomes "Adam". It might have been amusing to see Schwarzenegger as a geneticist, but probably not worth sitting through a 3-hour-long Oliver Stone ape epic. We should all be grateful that the movie eventually fell into Tim Burton's creative hands.

It turns out there is Planet of the Apes prequel in the works, and writer/director Scott Frank plans to make it a hard science fiction movie. It will be set in the near future, and tell the story of Caesar, an "uplifted" chimpanzee with genetically enhanced intelligence who will become the ancestor of the apes who will eventually rule the world.

The science that creates a hyper-intelligent chimpanzee is based on current real world research - this film would just take that science one step further. He's also committed to telling a story based on character, not antic ape action. His plan for Caesar is one where you come to really feel for this ape, even as the final act sees him taking actions that may be hard for us to agree with.

[. . .] Since he doesn't want to have people running around in monkey suits, Frank is doing lots of research into the state of effects today - can he create a photoreal chimpanzee (one who is facially modified by the genetic engineering that grants him his intelligence) who will be the main character for this film? Can he create a character who is completely expressive through his face, eyes, and gestures (including sign language) without speaking a word of dialogue?

It sounds like an interesting idea. Lack of dialogue shouldn't be a problem, at least in principal - just look at how successful the robots in WALL-E conveyed emotion, despite their lack of facial features. However, I think a sort of chimp-human hybrid could be tricky to pull off, because it's almost-but-not-quite-human features might land the character deep in the uncanny valley. If Frank is successful, it might open the door to movies set in Brin's Uplift Universe, which I think would be awesome.

As for the science, we really are in the very early stages of understanding how genetics influence intelligence. Since both human and chimpanzee genomes have been sequenced, scientists have started to tease out what the differences in DNA sequence between our species mean at a functional level. Some intriguing possibilities have emerged, but I think we are a long way from being able to genetically engineer enhanced intelligence in either humans or chimps. That's not to say it won't be possible someday, but certainly not in the next couple of years.

Tags:science fiction, biology, Planet of the Apes, Caesar, genetic engineering, evolution

Evil Triplet Repeats and The Age of Magic

I'm not really much of a superhero comic book fan. Ask me whether I prefer the DC Universe or the Marvel Universe, and my answer is pretty much "who cares?" That isn't to say that I don't enjoy comics or other sequential art, though. For example, I love many of the titles in the Vertigo line of graphic novels¹.

I've been slowly working my way through the Books of Magic and related titles, which follow the adventures and trials of Timothy Hunter. Tim is a bit of a misfit teenager who learns that he is destined to be the most powerful magician of our age, and his story is about learning the ways of magic, while searching for the truth about his parents and learning to understand himself. While there are some superficial similarities to Harry Potter (which was published several years after the original Books of Magic series), I think the story of Timothy Hunter is much darker and much more wide-ranging, since Tim has to not only learn to navigate the good and evil of the magical world, but also the mundane world of his family and friends.

While the series is fantasy, it has occasionally included tropes that would be familiar to any science fiction fan, including time travel, alternate universes, and a steampunk cyborg. That's why it didn't surprise me that DNA sequencing, genomics and genetic engineering made it's way into the Timothy Hunter mythos.

In issues 8-11 of Hunter: The Age of Magic, genetics and magic become entwined. Tim meets a molecular biologist who has been studying the genomic sequence of evil individuals, including a young girl who became evil - and whose genome changes - when she was possessed by a demon. He discovers that sociopathic behavior is associated with an alteration of the "F5412 Gene".² In evil individuals the gene has the repeated insertion of three nucleotides in the sequence ACT.

While I wouldn't call triplet DNA repeats evil, they can cause serious problems in the human genome. A few examples of human genetic syndromes caused by trinucleotide repeat insertions:

• Fragile X syndrome is associated with CGG repeats in the FMR1 gene on the X chromosome. Proper FMR1 expression is required for normal neural development, and excess CGG repeats causes the DNA to be methylated, which silences FMR1 expression. The result is intellectual and physical disability.
  
• Huntington's chorea is caused by excess CAG repeats in the Huntingtin gene on chromosome 4. The symptoms include jerky, uncontrollable movements and impaired cognitive abilities, which usually appear when the person carrying the mutation is in her 30s or 40s.
• Myotonic dystrophy, a muscle wasting disease, can be caused by expansion of the sequence ACG in the DMPK gene on chromosome 19.
  

The trinucleotide repeats undergo dynamic mutation. Not so much over the course of a liftime, as in the case of a demon possessed little girl, but over the course of multiple generations. The severity of the symptoms can increase as the number of trinucleotide repeats increases from generation to generation. In adult-onset diseases like Huntington's, that means parents can pass a more detrimental form of the mutation on to their children even before they know they are affected themselves. That's a terrible situation, but certainly not evil.

Of course Age of Magic is fantasy, so DNA sequences have the same kind of transformative power as magical words. An analysis of Tim's DNA turns up a sequence with totally different properties that reflect the magic within him. And the DNA from an angel's feather is something else altogether . . .

If you'd like a glimpse of the series, you can download Issue #1 of the Books of Magic

Related reading: Sutherland GR and Richards RI. "Simple tandem DNA repeats and human genetic disease" Proc Natl Acad Sci U S A. 1995 April 25; 92(9): 3636–3641.

1. Yes, I know Vertigo is a DC imprint, but that doesn't mean the graphic novels they produce are exactly part of the DC universe the way the superhero comics are.

2. F5412 appears to be an entirely made up gene on human chromosome 2

Tags:Timothy Hunter, Age of Magic, genetics

Katherine MacLean and the cutting edge of biology

"Do you now anything about their home planet?" asked the man from the Herald.
[...]
"Their world must be earth-like to them," the weary-looking young man answered uncertainly. "The environment evolves the animal. But only in relative terms, of course."
~ "Pictures Don't Lie", Katherine MacLean (1951)

One of the things I love about the internet is how it had made it possible to see original historical documents from around in the world. Take, for example, the BBC Archive collection of documents related to "The Genesis of Doctor Who." We get to read the original in-house reports discussing bringing science fiction to the BBC. Of course we know that they ended up producing Doctor Who, but it's quite interesting to read about the other stories they considered.

This 1962 memo laid out the Beeb's requirements:

• No "Bug-Eyed Monsters"
• No "Tin Robots" as central characters
• No "large and elaborate science fiction type settings"
• "an opportunity for genuine characterization"
• "ask the audience to suspend disbelief scientifically and technologically on one fact only"

Stories with telepaths and time travelling were high on their list. Among the reports recommendations were Poul Anderson's Guardians of Time (time travel), Erik Frank Russell's Three to Conquer (telepath), Clifford Simak's Eternity Lost (immortal characters), C.L. Moore's No Woman Born (humanoid robot with a human brain), and Katherine MacLean's "Pictures Don't Lie" (alien contact).

"Pictures Don't Lie" was the most "biological" of the bunch. The plot is pretty straightforward: humans make contact with friendly aliens who are directed to land on Earth. The aliens follow the directions, but end up in a deadly swamp full of monsters. Even worse the humans can't figure out where they landed. Finally the humans figure out the problem: ** SPOILER ** the aliens are actually microscopic and have landed in a puddle on the tarmac in the airfield, which is rapidly drying out. ** END SPOILER **

The BBC's assesment? "The whole thing is absolutely possible and logical."

Well, that piqued my curiosity. BBC passed on the story, but it was produced for the NBC radio SF drama program X Minus One, which you can listen to at Internet Archive. It's an entertaining story, athough I'm not so sure about how plausible it is, but it does seem inspired by real science.

Author Katherine MacLean was well known for the use of "hard science" in her fiction. Born in 1925, she focused on math and science in high school, majored in economics in college, then, after graduation in 1950, began postgraduate studies in psychology. It was in 1947, while MacLean was working as a laboratory technician in penicillin research, that she began writing science fiction. One of her major influences was supposedly the General System Theory of biologist Ludwig von Bertalanffy, which was initially developed to explain the interrelatedness of organisms with their ecosystems.


Many of her short stories explore biological themes*, which sound remarkably modern considering they were written shortly before Watson and Crick published their model of the structure of DNA, and long before genetic engineering was a possibility. A few examples:

• "And Be Merry" or "The Pyramid in the Desert" (1950): A biologist tests an experimental longevity treatment on herself. The treatment, which regenerates the cells in her body, is initially successful, but mutations in some of the cells cause them to grow out of control, giving her cancer.
  
• "Syndrome Johnny" (1951): Engineered retroviral plagues genetically re-engineer the human race.
  
• "The Diploids" (1953): A young man "suspects he may be an alien because of certain physical and biochemical abnormalities but discovers that he is a commercial human embryonic cell line, sold for research and illegally grown to maturity"

In 2006 MacLean discussed the science behind her story "And Be Merry", which was far ahead of the molecular biology of 1950:

Finding she has no chance of evading eventual death, she immediately loses her obsession with safety, becomes interested in biochemistry again, and invents a new theory. (New at the time.) Mutation from background radiation does not just strike the sperm and egg making chromosome changes in the embryo and mutated progeny, it also strikes the chromosomes in each cell of any living creature, damages and mutates them also, and produces cancer. This cannot be prevented. She called it "somatic mutation" and used the new concept of body deterioration by slow radiation damage (age) to underpin her rediscovered recklessness, and be happy.

Even now most biotechs have not fully accepted the implication that every cell in the body can generate an entire copy of the person. But perhaps a copy will be changed and mutated for the worse by exposure to ambient radiation and other mutagens. Perhaps a cell needs to generate a placenta around it to develop into an entire body. Something like that is holding up the biochemists from successfully making copies of individuals from body or blood cells. Not for long! I wrote three more stories with novel genetic ideas before 1953. Some have not been followed up by scientists yet.

Her recollection is not entirely accurate. The idea of somatic mutation has been around since at least the 1920s, even if it was not known what "mutation" meant in the biochemical sense. However, the hypothesis that somatic mutations cause cancer was being debated in 1955 and probably later than that. And it's only in the last decade that DNA from adult somatic cells has been used to clone mammals - although no humans so far.

MacLean continued to publish short fiction through the 1990s. Her 1995 short story "The Kidnapping of Baroness 5", which blends biotechnology with fantasy tropes, was nominated for the Hugo. She was named Author Emeritus at the 2002 Nebula awards.

Unfortunately none of Katherine MacLean's early short stories are available online. However, they were collected in the 1962 anthology The Diploids and other Flights of Fancy, which was reissued in 2000.

Listen to MacLean's "Pictures Don't Lie" (14 MB MP3)

* as an interesting aside, the Katherine MacLean Wikipedia article was apparently edited by MacLean herself

Tags:science fiction, genetics, Katherine MacLean