Science and SF tidbits: middle-aged apes, fantastic cells, and SF genetics

Some recent reading about fictional biology:
• JIM: More Compelling Than GATTACA | DNA Science Blog »

If you are looking for a science fiction film with a scientifically plausible depiction of human genetic enhancement and cloning, you might want to check out JIM. Science writer/geneticist Ricki Lewis reviews the film and says:

"Although Jim, released in late 2010, shares with GATTACA the premise of widespread genetic enhancement, it’s much more subtle and nuanced. The film struck me with its stunning possibility, and the intentional gaps in the glimpse of future history still have me thinking a week later."

And watch a commercial for "Lorigen Engineering", which offers Better Kids, By Design®'

• Author Spotlight: Tom Crosshill 

Tom Crosshill's recent short story "A Well-Adjusted Man" takes a chilling look at the potential repercussions of erasing traumatic memories might have. In his interview with Lightspeed Magazine, talks about the psychology PTSD, the biochemistry of traumatic memories, and his inspiration for the story.

And some fantastic factual biology:

• Great apes go through mid-life crisis » Nature News

Psychologist Alexander Weiss and his colleagues wanted to find out if the human "midlife crisis" that hits somewhere between our mid-30s and 50s could have a biological basis. They decided to survey zookeepers about of the mood of the chimpanzees and orangutans in their charge. They found that our great ape cousins seem to have lower sense of well-being during their late 20s to mid-30s - the equivalent to human middle age.

It would have been nice if the study had included some quantifiable data, such as the level of stress hormones or other physiological measures. It's hard to know how much bias might be introduced by asking zookeepers to try to put themselves in the minds of their charges. But still, an interesting study.

Image: Orangutan Portrait by Chester Zoo on Flickr shared under a CC BY-ND 2.0 license.

• Introduction to Cells (Vimeo)

A dramatic video showing the beauty of cells. The video was created by science teacher Frank Gregorio who makes "introduction" science videos for middle and high school teachers to use in the classroom. I wonder how well it works to capture the imagination of fidgety teenagers?

• Paralyzed dogs walk again (video)

Jasper the dachshund regained some use of his formerly paralyzed hind legs after his spinal cord was injected with cells grown from the lining of his nose. Robin Franklin and his colleagues at the University of Cambridge, used nose cells (or more precisely olfactory ensheathing cells) because, unlike most nerve cells, the nasal nerve fibers continue to grow into adulthood. The injected cells grew new nerve connections restoring function to the dog's damaged spine.

While the treatment appears to have a lot of potential it will take a lot more research before it will be tested on humans. More about the study at the University of Cambridge.

• Chemical biology: DNA's new alphabet

Chemist Eric Kool is reengineering DNA with nucleotide bases not found in nature. He's one of a number of chemists and chemical biologists who are creating new types of DNA and RNA molecules that they hope can be used for studying the function of nucleic acids and that may have new biochemical properties. But Kool explains those aren't the only reasons:

".... researchers are still driven by what Kool calls the “science-fiction appeal” of designing or even improving on living systems. Earth's early life forms may have settled on their genetic alphabet simply because they were constrained by the chemicals available. [snip]
So if nucleic acids arose independently on another planet, would they have the same bases? Benner thinks not, unless the organisms were subjected to the same constraints. Some universal rules might apply, however."

And short of discovering extraterrestrial life, it's only by synthesizing and testing new molecules to see if they might be functional in living systems.

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!

Science & SF Tidbits: Presidential DNA Biohacking, Alien Jellies, Non-fruity Dragons

Recent links of interest:

• The Lovely Lobed Comb Jelly (YouTube)
This video from the Monterey Bay Aquarium is an artful display of beautiful and eerily alien-looking bioluminescent comb jellies.

Image: "Frolicking" comb jellies at the Monterey Bay Aquarium by Steve Jurvetson (jurvetson) on Flickr, shared under a CC-BY-2.0 (Creative Commons Attribution) license.

• Hacking the President’s DNA (The Atlantic)

"So, in November of 2016, when a first-time visitor with the handle Cap’n Capsid posted a challenge on the viral-design site 99Virions, no alarms sounded; his was just one of the 100 or so design requests submitted that day"

This article in The Atlantic begins with a detailed scenario describing the rise of amateur biohacking that spins out of control into outright terrorism. With today's technology that is pretty much just science fiction. But the potential current threat that that the relatively straightforward molecular manipulation of viruses and bacteria and the ease of genome sequencing represents is taken very seriously by the government.

There are claims that the DNA of the President of the United States is carefully being protected, while DNA from other world leaders is being collected. And reports of the creation of synthetic organisms has added to the fear that genetically manipulated bugs could cause unstoppable pandemics. With the spread of "biohacking" culture, there is fear that even amateurs could become bioterrorists. While all of that sounds alarmist, the article does take a more realistic look at what bioscience is capable of today.

• ‘The Hobbit’: Peter Jackson’s unexpected journey to three films (Hero Complex at the LA Times)
Peter Jackson was interviewed about his upcoming film version of Tolkien's The Hobbit. When asked about the design of Smaug the dragon, he explained why he wanted a traditional look:

"The trouble with redesigning dragons is that if you really get fruity with it, it suddenly starts to look like some sort of monster from another planet — you very quickly can go into science-fiction territory,” Jackson said. “I don’t want to do that. I mean, people expect a dragon. ‘The Hobbit’ is one of the most famous dragon stories in the world, really. So I’m not trying to step away from the dragon. I just want to present the most venal, scary, decrepit, nasty dragon that I possibly can.”

I'm looking forward to see what they come up with. The greatest adventure indeed!

Science and SF Tidbits: October 13, 2012: Nobel Prizes, Bringing Back Dinosaurs, Martian Biorhythms

Have you watched my live interview with artist Brian Kolm yet? We talk about his design of the Biology in Science Fiction logo, teaching art, and socializing with other artists. Be sure to check it out!

From around the web:

• G Protein-Coupled Receptors (GPCRs) win 2012 Nobel Prize in Chemistry | The Curious Wavefunction, Scientific American Blog Network
On Thursday the 2012 Nobel Prize in Chemistry went to two biochemists: Brian Kobilka (Stanford) and Robert Lefkowitz (Duke). Their work helped explain how a signal on the outside of the cell (such as a neurotransmitter, hormone or even light) is translated into physiological changes inside the cell and altered gene expression. Their research focused on a particular class of receptors in cell membranes that are associated with "G protein" signalling molecules inside the cell. The article linked above is a pretty good overview of how they function.

• An Interview with Sir John Gurdon winner of the 2012 Nobel Prize Winner in Physiology or Medicine
I recommend this Cambridge University video interview with John Gurdon. He talks about his original work on frog cloning in the early 60s, the relevance of his work today, and how his parents helped him pursue studies in science after his teacher made him out to be a failure in the subject.

• DNA has a 521-year half-life :: Nature News
After 6.8 million years nearly every bond in a DNA molecule would be broken. That means no Jurassic Part-style cloning of extinct dinosaurs will be possible. Sad news for those of us wishing for a cute cloned Sciurumimus as a pet. It also brings into question reports of extracting DNA from very ancient amber.

• Weird Things » Blog Archive » Who Needs DNA to Bring Back the T-Rex?
Perhaps dinosaurs could be reconstructed even without their DNA. The trick is to use what we know about T. rex anatomy and modern animal biology and fake the rest:

"The blueprint for this creature will be everything we know about the T-Rex. We can design bone structure, ligature and a thousand other tiny details we’ve learned from the fossil records. Although we may never find DNA, we have found cells inside T-Rex fossils, resembling the same kind in ovulating birds. Cells, protein and other kinds of information can help us build a replica that’s perhaps 95% accurate"

• Ridley Scott Explains Prometheus, Is Lovably Insane | Tor.com
Ryan Britt summarizes Ridley Scott's commentary from the DVD release of Prometheus. Sounds either quite brilliant or a bit unhinged, or maybe both.  I may have to watch the movie with commentary myself to see what he says about the dumbest biologist in the galaxy (ooh, the goo in this alien building full of dead bodies is unexpectedly turning into a snake-like creature - let me pet it!)

• Fossil of Ancient Spider Attack - only one of its type discovered
About 100 million years ago a young spider was about to start munching on a wasp caught in his web. But before he could commence munching, tree resin flowed over spider, wasp and web and they were trapped in amber.  Click here to see the fantastic large image.

• How Blue Light And Caffeine Will Help Humans Move To Mars
Mars days are 24.6 hours long, which means we humans with Earthly 24-hour internal clocks can find it hard to adjust. It turns out the key is carefully timed blue light, caffeine, and a comfortable sleeping environment. Tests on members of the Mars Phoenix mission suggests it works, even for folks here on Earth.

• Science In My Fiction » Mind-Control and Instant Skill
Optogenetics combines advanced genetic engineering of neural tissue in the brain and implanted fiber optics to allow external control of behavior and learning in mice. It has even been shown to work to some extent in monkeys. And simply stimulating the brain with electrical current and speed up learning in humans.  Not surprisingly, the military is at he forefront of this sort of research. But it's still in it's early stages - there won't be human "mind control" using this technology any time soon. But if it did work, would you allow your brain cells to be manipulated if it would give you instant skills?

• Report: Ukraine Trains Dolphins With Friggin' Pistols on Their Heads | Danger Room | Wired.com
Pistols attached to dolphins may be far fetched, but it's already the case that navies (including the United States) use dolphins for mine clearing and other underwater operations. The US also apparently uses sea lions "equipped with a spring-loaded clamp that can be attached to a diver’s legs. The sea lion then swims back to its handlers, who can reel the enemy diver in like a snagged fish."  But if you want to make dolphins really lethal, give them mechanical arms and hands. Not only will they be able to kill, before you know it they'll be piloting starships!

Image: Courtesy of Brian Kolm at Atomic Bear Press. Used with permission.

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.

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

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

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

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

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

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

He talks a bit about his inspiration:


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

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

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

I look forward to seeing the finished film!

(via io9)

John Carter versus the Clone Army

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

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

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

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

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

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

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

A gruesome sight.

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

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

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

You can read the rest of the story for yourself:

Project Gutenburg Australia has a copy of the Synthetic Men of Mars. If you are not in Australia, you can purchase an ebook: Kindle version (Amazon.com, affiliate link)
Further reading:

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

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

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

Controlling Our Creations Through Nutritional Requirements: Lessons from Science Fiction

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Background reading:

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

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

Uncommon Science Fiction Love for Valentine's Day

If you are looking for some science fiction romance (and lust) this Valentine's Day, be sure to check out the uncommon SF love stories highlighted over at the Free Science Fiction subsite of Biology in Science Fiction.


Read: Free Science Fiction February Highlights: Science Fictional Love


Image: from Galaxy Science Fiction, October 1955.  Published along with (but not illustrating) Cordwainer Smith's "Game of Rat and Dragon", in which a man loves his partner who just happens to be a cat.

The Science Effect: How Does Science Fiction Influence Public Perception of Science?

Public health and biodefense policy expert Laura Kahn has written an article in the Bulletin of Atomic Scientists that argues that science fiction influences public opinion of science and scientists and can ultimately lead to changes in science policy.  Her examples come from the life sciences in science fiction: neurophysiological experimentation in Mary Shelley's Frankenstein, vivisection in HG Wells' The Island of Doctor Moreau, and genetic engineering in Michael Crichton's Jurassic Park. 

She concludes that literature has affected the way that science is conducted, rather than the other way around:

And so, instead of science affecting culture (neurophysiology becomes the timelessFrankenstein), the culture (the potency of books about animals) affected the science: The scientific community has taken animal welfare to heart and has worked to minimize the number of animals involved in research as well as the animals' levels of suffering.  

That seems a bit too simple to me. It's not as if scientists (or science fiction writers) are completely isolated from the culture in which they live.  That suggests that there is an ongoing dialog between science, literary culture, and popular opinions about science.  

So how does Kahn suggest public opinion of the life sciences can be improved? Write stories with scientists as heroes, of course. 

But, if the scientific community wants to engage and inform the public, science fiction is an excellent strategy. Stories captivate people, they survive the test of time, and they become part of the popular culture. So, if any scientists with a creative-writing affinity want to captivate the public and inspire the next generation to pursue careers in science and technology, perhaps they should put pen to paper and start writing. The world needs more stories with scientist-heroes, not more scientist-villains.

I find it kind of tiresome when this suggestion is trotted out again and again. It's not that I think that positive depictions of science and scientists in science fiction aren't a good thing.  It's that heroic portrayals of science and scientists already exist.  

Of course when science and scientists are positively portrayed, it often just blends into the background. Take, for example, the Star Trek universe, which is so firmly entrenched in popular culture that even people who don't consider themselves science fiction fans are familiar with it.  The future according to Star Trek is a (mostly) happy place to live, in large part because of advanced technology available to the masses:  protein resequencers and genetic resequencers help provide food, tissue and organ regenerators are routine medical treatments and the medical lab on the Enterprise can whip up biomolecules on demand. 

Handsome genetically engineered villain

So Star Trek is chock-full of advanced biotechnology that's portrayed positively, and the medical staff . But what examples of biotech are people most likely to remember? Probably Khan Noonian Singh, sworn enemy of Captain Kirk and epitome of human genetic engineering gone wrong. Conflict is memorable. 

I do think that immoral or amoral scientific research is often unfairly portrayed as a source of evil in popular culture.  But I'm not sure that writing stories with the specific aim of positively portraying science is the answer. 

Fiction written with the purpose of advancing a particular point of view often isn't particularly entertaining.  I've put down more than one novel or turned the channel when a story seemed to be overly heavy-handed in promoting a particular cause.

So what's my solution? I'd suggest science fiction versions of shows like CSI or House where science is used to fight crime or treat rare medical conditions.  And considering that the science portrayed on both House and CSI is speculative enough that that they might already be considered to be dipping their toes in the pool of science fiction, I don't think that it would be too great a leap to create fully science fictional versions, where genetic engineering or cloning saves the day.   I'd watch a show like that!

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Original article:  "The science fiction effect" at the Bulletin of Atomic Scientists

Download Mary Shelley's Frankenstein for free: Project Gutenberg, Google eBooks, or for theKindle version from Amazon.com (affiliate link)
Download HG Well's The Island of Doctor Moreau for free: Project Gutenberg, Google eBooks, or the Kindle version from Amazon.com (affiliate link)

Top image: still from the documentary Experiments in the Revival of Organisms (1940). 
Bottom image: Khan Noonian Singh from Star Trek: TOS episode "Space Seed"

(Article via SF Signal)

Joseph Kulper: Brain viruses and strange equations to save the human race

Today I received a mysterious message:

My name is Joseph Kulper, I work as a geneticist at Celtran
Corporation, one of the world's leaders in bioengineering, and I'm
sending this message to you because I have discovered something very
important, something that has the potential to change everything we
know about human life. I'm not asking for anything from you, I don't
want you to reply or click anywhere, alI I'm asking of you is that you
watch the video I have posted on youtube. Search under my name 'joseph
kulper' and you will find it. It's for you that I'm posting this
video, for all of us, so please take just a moment to watch it.

It wasn't sent to me personally and has the appearance of hapless self-promotion or odd spam.

But I was curious, and I turned up "Kulper's" video, where he invites the viewer to "become part of something greater than yourself. You see the destructive effects of climate change are inevitable, and some sort of drastic action is required to save the human race. So what has Kulper done? Created the Elysium virus, designed to "speed up evolution" so that only the smartest will survive. Watch:


So what is this? This looks like a teaser promotional video, likely for Neill Blomkamp's new movie-in-progress, Elysium.

There are a bunch of images that flash for a fraction of a second during the video which presumably have clues in them. In particular, there are a series of equations at about 4:27. I don't recognize the equations, and they could just be a red herring. Take a look - any guesses?

I couldn't find out much about the movie itself, other than Sharlto Copley - who starred in Blomkamp's District 9 - is part of the cast, and that Matt Damon may join up as well.

Despite the buzz, there hasn't been much information regarding what the plot will actually be about. Another teaser video released in November shows mutant livestock:


So the movie involves global catastrophes and genetic engineering and a selective virus passed from mind to mind; it's apparently set in a dystopian near-future in which biotechnology has run amok.  So maybe it's an action-packed version of Oryx and Crake?

It could be interesting. I just hope there aren't any zombies.

Sneak Peek at The Bio:Fiction Film Festival

In May 2011 the Bio:Fiction Film Festival will be held at the Natural History Museum in Vienna. It's a competition for short films about synthetic biology.  It's meant to go beyond mere genetic engineering:

Synthetic biology is based on genetic engineering but goes much further. In genetic engineering the goal was to manipulate an organism’s genes, usually by transferring one gene from a donor to a host organisms. Synthetic biology, on the other hand, aims at creating whole new biological functions, systems and eventually organisms.

They are also clear on what it's not:

Synthetic Biology is NOT about cloning; stem cells per se; only reading DNA; random mutation through radiation or chemicals, old school genetic engineering (e.g. Monsanto GM crops)!

So what exactly do they have in mind?  You can check out the festival trailers to get a taste of what sort of entries they are looking for – unfortunately the deadline was today, so it's too late to submit your own.




The film festival will be accompanied by a BioArt exhibition, also at the Natural History Museum.

I'm hoping the finalist films will be shared online for those of us who can't make it to Vienna.

Lou Anders on Future Genetic Engineering

Lou Anders has posted a clip from an interview he did with John Blyer last fall:




That's a very science fictional view of our biotech future.

Tags:science fiction, genetic engineering

@ The Reef Tank: Mer-Women and Fish-Men: Humans Engineered for Ocean Living

I have a new guest post up at The Reef Tank blog about science fictional mer-people:

Mer-Women and Fish-Men: Humans Engineered for Ocean Living

Image: Mermaid by Brian Kolm, used with permission of the artist.

Tags:science fiction, genetic engineering

Christmas SF: The Rats

Are you tired of crowded shopping malls and all the stickily sweet holiday cheer? Then the 2002 sci-fi horror flick The Rats may be just the antidote you need. Here's the setup:

"A colony of rats—the result of a secret DNA research project—terrorizes the residents of New York City during the Christmas season."

Apparently the pesky rodents set up shop in a "posh Manhattan department store", spreading disease and terror.

Happy holidays indeed!

A few warnings:

- there is an entirely gratuitous dressing room T&A scene near the beginning of the movie, apparently because you can't have a horror movie without boobies

- according to IMDB the depiction of how rats spread disease is not scientifically accurate (which should come as a surprise to no one.)

- there are lots and lots of rats

Watch The Rats at Hulu.com (US only) or below.



Tags:science fiction, movies, rats

Holiday Free Fiction: Visions of Gingerbread

At this year's party, as usual, everyone from my executive VP to the mail clerk steered clear of me. An hour into the evening, as conversations buzzed in every other part of the room, I found myself standing alone, eggnog in hand, looking at the Christmas tree. It was as if I had never seen one before. There was something about the shape of the tree, about its deep green shadows and its smell, that spoke to me. It said, forest. It said, everything is alive. It said, this is the perfect moment. And at that perfect moment, I felt as if I were a key sliding into its lock. The universe and I, we fit.

Sometimes feelings of love, peace and joy need just a bit of chemical assistance.

Read "Visions of Gingerbread" by Bruce Holland Rogers.

Holiday Free Fiction: R3

Damn right we're Christmas—a holiday all about the foolish belief in the impossible. Flying reindeer are perfect for impossible. Doubters said you couldn't make flying reindeer, and they were right: We're not really reindeer; we're more like a whole new animal on a reindeer chassis.

R3 isn't really a reindeer, and he's had a rough life, but he brings Christmas all the same.

Read Read "R3", by Dennis Danvers.

And for a slightly different take on Reindeer physiology, see Robert Billing's Nature Futures short "Harnessing the brane-deer" (pdf).

Image: Image from the Bell Mobility animated reindeer commercial. 

Tags:science fiction, Christmas, genetic engineering

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

WiSF reading club: Woman on the Edge of Time - Equality Through Biotechnology?

Note: I've volunteered to host the WiSF reading club discussion about Marge Piercy's Woman on the Edge of Time. The post below is my take on one aspect of the novel - one that fits in with the "biology in science fiction" theme of my blog quite nicely - but I don't mean for it to limit the discussion. I think there are a number of other issues the novel touches on that would be interesting to explore, so please have at it in the comments.

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Marge Piercy's Woman on the Edge of Time is a disturbing novel. It's the story of Consuelo "Connie" Ramos, a poor Mexican-American woman who has been in and out of mental hospitals. She ends up committed once again after she physically defends her niece from her niece's pimp boyfriend and that's where the horror starts. In the "present day" (mid-1970s) mental hospital the patients are treated with both indifference and abuse by the staff, and Connie and several other patients are chosen to receive experimental neural control implants, not only without their consent, but in Connie's case explicitly against her wishes. The patients are considered little different than test animals by the physicians and doctors participating in the experiment:

[Connie] remembered something she had heard Dr. Redding say to Superintendent Hodges: that they had used up five thousand monkeys before they began doing these operations on patients. Used up. She had heard him say he had wanted to work with prisoners – he thought the results would be more impressive – but there had been such an uproar about three little psychosurgical procedures at Vacaville in California that his team decided to work with mental patients. "After all," he had said, smiling his best ironic smile, "they made a court case and a bleeding heart publicity brouhaha about three procedures, while San Francisco Children's Hospital does hundreds with sound and thermal probes – mostly on neurotic women and intractable children – and no one says boo."

This unfortunately wasn't just fiction. By the mid-1970s there had been a number of cases in which experimentation on human subjects without their informed consent had been revealed to the public.

But Connie has an escape of sorts*: she is visited by Luciente, a woman from 22nd century Massachusetts. She comes from a future in which time travelers leave can behind their unconscious bodies while appearing corporeally by forming a mental link with an individual at their destination. This allows Connie to leave the nightmarish hospital to visit Luciente's utopian future. What she finds is that Luciente lives in a small rustic-appearing village, a communal society in which everyone has their own space, works to their best ability, is free to pursue their interests and has their necessities are taken care of. However that appearance of rusticity is somewhat deceiving. Not only does everyone have a personal networked computer (a "kenner"), but the underpinning of their society is advanced biotechnology.

Luciente herself is a plant geneticist who develops new crops, in part by introducing new genes from the plants in carefully preserved wild areas. But the real difference that sets her society apart from Connie's is the elimination of discrimination due to gender or race. Their solution was two-fold: eliminate childbearing and child-rearing as female-only activities and separate genetics from parenthood. As Luciente explains to Connie:

"It was part of women's long revolution. When we were breaking all the old hierarchies. Finally there was that one thing we had to give up too, the only power we ever had, in return for no more power for anyone. The original production: the power to give birth. cause as long as we were biologically enchained, we'd never be equal. And males never would be humanized to be loving and tender. So we all became mothers. Every child has three. To break the nuclear bonding."

Their reproduction is based on vitro fertilization and fetuses grown in artificial wombs. After birth, each infant has three co-mothers, male and female, who are given hormonal treatments so that all can share in nursing. And because there are no genetic ties between parents and their children, they have eliminated discrimination by race. However, they have found a way to maintain cultural diversity by separating it from genetics:

"At grandcil – grand council – decisions were made forty years back to breed a high proportion of darker-skinned people and to mix the genes well through the population. At the same time, we decided to hold on to separate cultural identities. But we broke the bond between genes and culture, broke it forever. We want there to be no chance of racism again. But we don't want the melting pot where everybody ends up with thin gruel. We want diversity, for strangeness breeds richness."

As that quote hints at, people of Luciente's society can adopt any culture they chose, just as they select a name they feel suits them. Luciente's village is culturally "Wampanoag", while others are "Harlem-Black", "Cape Verde" and "Ashkenazi Jewish". I use quotes because only the elements of those cultures that fit their society are adopted - sexism, racism, and patriarchal religion are excluded.

But not everything is idyllic. Luciente and her people are at war with a neighboring society that is essentially their exact opposite. It's urban, uses genetic engineering to create super soldiers, and the common people eat bland food grown on factory farms. Connie accidentally travels to the future New York City where she meets a woman - Gildina 547-921-45-822-KBJ - from this society who has been "cosmetically fixed for sex use" and is sealed in her windowless apartment. Gildina's none to bright, and that's by design:

"She was born a dud. She's just a built-up contracty. All duds have brain deficiencies from protein scarcity in fetus and early childhood. Their IRP's are negative forty to negative fifteen. Her psych scan tests show negative twenty-five. She has no more mental capacity than a genetically improved ape."

Wealthy families and corporations in this version of the future use biotechnology to keep the lower classes oppressed. Gildina doesn't expect to live beyond her 40's while the "richies" live for centuries on involuntarily "donated" organs. It's a nasty place to be one of the masses.

Despite the novel's heavy handed (to my eyes) dichotomy between Luciente's idyllic pastoral Marxist society and the hellish capitalist urban society of New York, I thought it was interesting that both versions of the future are heavily dependent on technology - particularly biotechnology - for their existance. In one it's used to allow women to become independent equal members of society, in the other it creates women that are just sexual objects (among many other differences). If forced to chose I'd obviously prefer the former over the latter, but my perhaps naive hope is that we can achieve equality without reengineering our biology.

* There is some ambiguity as to whether Connie's trips to the future are real, or whether they are just manifestations of schizophrenia. It could be argued that she is a victim of being a poor non-white woman whose normal actions are interpreted with the assumption that she is mentally ill (something that has been shown to happen in psychiatric hospital).

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So that's my take on the biotechnology in WotEoT. I think there are a number of other aspects that would make for good discussion too.

If you are interested in an academic analysis, check out this essay by Clemson English professor Elisa Kay Sparks.

Tags:Woman on the Edge of Time, Marge Piercy, biotechnology

Rogue Farm

Now here's a strange tale by Charles Stross that you can listen to at Escape Pod: Rogue Farm. It's a good listen if you like surreal bioengineering, a pot-smoking dog, and, of course, a rogue farm. It also has a nice reference to the fantastic genetic engineering found in Niven's known space.

A taste:

“Buggerit, I don’t have time for this,” Joe muttered. The stable waiting for the small herd of cloned spidercows cluttering up the north paddock was still knee-deep in manure, and the tractor seat wasn’t getting any warmer while he shivered out here waiting for Maddie to come and sort this thing out. It wasn’t a big herd, but it was as big as his land and his labour could manage – the big biofabricator in the shed could assemble mammalian livestock faster than he could feed them up and sell them with an honest HAND-RAISED NOT VAT-GROWN label.

“What do you want with us?” he yelled up at the gently buzzing farm.

“Brains, fresh brains for baby Jesus,” crooned the farm in a warm contralto, startling Joe half out of his skin. “Buy my brains!” Half a dozen disturbing cauliflower shapes poked suggestively out of the farms’ back then retracted again, coyly.

“Don’t want no brains around here,” Joe said stubbornly, his fingers whitening on the stock of the shotgun. “Don’t want your kind round here, neither. Go away.”

Listen to "Rogue Farm".

Tags:science fiction, genetic engineering, free fiction