Science In My Fiction

I recently read Ferrett Steinmetz‘s short story “Sourdough Station” that as the title suggests involves a sauerkraut-making operation on a space station. That’s not all the story is about, of course, but it did get me thinking about food and fermentation and what that might mean to folks living in space.

Sauerkraut is fermented cabbage and is high in vitamins, fiber, iron, folate and other nutrients.  Combine that with sauerkraut’s relatively long shelf life, and it seems like an ideal food for isolated outposts in space. Astronauts have already been experimenting with growing nappa cabbage and vegetables on the International Space Station, so it looks likely that growing leafy greens in space is within the realm of possibility. Assuming that the fermentation process works as well in space as it does on Earth, sauerkraut could become a space habitat staple as humans spread out among the stars. Or perhaps spacegoers would prefer something more like spicy Korean kimchi, since microgravity can dull the sense of taste.

Lactic acid bacteria  – primarily species of Lactobacillus – are not only involved in the process of fermenting sauerkraut and kimchi, but also the production of yogurt and cheese from milk, and making sourdough bread sour. But not any old microbe will do for optimal fermentation. Different species of bacteria are used in the production of different foods: Lactobacillus kimchii is a unique species found (naturally) in kimchi, Lactobacillus helveticus is used to ferment milk into swiss cheese, Lactobacillus delbrueckii subsp. bulgaricus (discovered in the course of researching the longevity of Bulgarians) and Lactobacillus acidophilus are used in yogurt production, and Lactobacillus sanfranciscensis gives sourdough bread its sourness.

The different species and strains of bacteria vary in their biochemistry and so can significantly affect the flavor of the sauerkraut or yogurt or bread being produced. Often there are several different species of bacteria that are involved in the fermentation process. DNA analysis during the sauerkraut production process has found a number of different bacterial species present during the fermentation process. There may be an entire ecosystem of microbes in every fermentation pot.

So why is this important to my hypothetical sauerkraut-eating spacefarers of the future?

Even assuming there are no technical issues with designing safe fermentation vessels or growing vegetables to ferment, culturing the necessary microbes might turn out to be a challenge.

Even under optimal conditions of temperature and humidity, space stations are unlikely to have gravity equal to that on Earth and that can affect bacterial growth. For example,  Lactobacillus acidophilus has been shown to grow more quickly in the microgravity environment of the International Space Station.

It’s not a stretch to wonder whether new strains of bacteria will have to be developed – or perhaps will arise naturally – for the production of deliciously fermented food in space. It wouldn’t be that far different from the development of new strains of yeast that revolutionized the brewing industry here on Earth.

But the fact that the background radiation levels on a space station or spaceship could be significantly higher than that on Earth could significantly raise the mutation rate in bacteria onboard, and there is always a risk that such mutations could render otherwise harmless bacteria dangerous. And even harmless bacteria could harbor mutations that modify their metabolism in such a way that it affects the fermentation process or the flavor of the fermented product.

At the turn of the 20th century Alaskan gold rush old-timers were known as Sourdoughs because they were reputed to protect their sourdough cultures during Arctic winters by keeping lumps of dough warm with their bodies. Spacefarers would similarly have to carefully protect and maintain any bacterial cultures used in food production.

I can imagine humans spread through our solar system and beyond, with different space colonies developing their own special fermentation cultures. Freeze-dried microbes would be easy to carry and trade, perhaps helping form the basis of a space culture barter system. They could be known for this, perhaps becoming the Sourdoughs of space*. They probably wouldn’t be so grizzled (or as nearly exclusively male) as the Yukon prospectors of a century ago, but like the original Sourdoughs would be living in an environment hostile to humans and they would known for the products of those precious microbes they maintained.

Since food plays such an important role in human culture, I like to think that’s how we’ll refer to ourselves.

Or maybe I’m just hungry …

Top image: Fermented foods made with lactic acid producing bacteria. From “Genomic comparison of lactic acid  bacterial published“, DOE Joint Genome Institute.

Bottom image: Lactobacillus casei uploaded by AJ Cann (AJC1) on Flickr and shared under a CC BY-SA 2.0 license.

I’ve spent a lot of time over the last few months trying to pare down a quarter century’s worth of files, photos and ephemera. Among the many boxes of paper, I’ve found photos from my high school years, notes from forgotten projects, and correspondence with friends and family and colleagues, some of whom I haven’t seen in years. It’s been a lovely trip down memory lane.

But I also discovered ancient floppy disks with college term papers, Zip disks full of archived emails, and CD photo albums. At least that’s how they were labeled. I no longer have a computer that can read floppies and even some of CDs have become unreadable. Fortunately over the years I’ve transferred many of my files to new media, but some of the files may be forever unrecoverable. While DVDs and hard drives can hold a lot more information – and weigh a lot less – than a box of paper printouts, the fact is that my old paper files are more likely to be readable 30 years from now than the digital files currently residing on my laptop.

This, of course, presents a difficult problem not only for people like me who want to be able to access their photos and letters and personal documents in the future, but also for archivists, historians,  governments and other organizations who want and need to ensure that today’s digital data will remain accessible decades or centuries from now.

It turns out that a biochemical approach to information storage may be part the solution. Naturally occurring DNA molecules encode information that directs the synthesis of the tens of thousands of proteins and other molecules that make up a living cell, along with the processes that allow the development of complex multicellular organisms (such as us humans). The development of ever faster and more accurate methods of both synthesizing and determining the sequence of DNA molecules has not only improved our understanding of normal DNA function, but also spurred the creation new nucleic-acid based technologies.

One such biotechnological innovation is the development of methods that use the information storage properties of DNA to encode digital data. Just a few months ago EMBL molecular biologists Nick Goldman and Ewan Birney published a paper demonstrating that one gram of DNA can hold more than 2 million gigabits of information, or “468,000 DVDs”. They were even able to build in error correction to be sure the encoded information would be stored and read accurately. And if kept in a cool dry environment, DNA can potentially remain stable for tens of thousands of years, making long term archival storage possible.

Naturally there are drawbacks to using DNA as a storage medium. Once the data is written by synthesizing the DNA sequence it cannot be changed. And there is no easy way to retrieve just a small portion of data without sequencing a big chunk of DNA. There is no equivalent to the list of files on your hard drive to find the data you are looking for. It’s not at all practical for information you would want to frequently retrieve or modify, and synthesizing DNA takes longer (and is more expensive) that saving a file on a thumb drive.  But unlike DVDs, which will eventually seem as archaic as papyrus as a storage medium, we humans should be able to sequence DNA molecules and decode the information stored therein – assuming, of course, that human society retains at least at the level of technology that exists today.

And to get a bit more speculative, the  biochemical properties of DNA leave open the intriguing possibility that the encoding methodology could be used to insert important files directly into human genomes creating living data repositories. The method could also be used to mark one’s self as part of a group or organization through genetic engineering.

Of course that idea isn’t new to science fiction. In Chris Lawson’s 1999 short story “Written in Blood”, a Muslim man has part of the Koran encoded as DNA inserted into his genome. That decision turns out to be fatal when the inserted DNA creates a mutation that causes leukemia. His biochemist daughter eventually develops a better method of encoding and she uses it to write what’s important to her into her own blood: photos of her wedding and her family, Martin Luther King’s “I Have a Dream” speech, Watson and Crick double-helix paper, Shakespeare’s Julius Caesar and a Muslim parable. And a paraphrase of Einstein’s words after the atomic bombing of Japan, expressing hope in humanity:

“The release of atom power has changed everything but our way of thinking,” then added, “The solution of this problem lies in the heart of humankind.”

Birney and Goldman selected similar data to test their real-world system: a digital version of Shakespeare’s sonnets, a photo of their offices, a pdf of Watson and Crick’s paper with the structure of DNA, and an audio clip from Martin Luther King Jr.’s “I Have a Dream” speech. If we were to use the technology to create a time capsule for our descendants to open millennia from now, Shakespeare and MLK are obvious selections of cultural significance.

What we choose to archive from our past to share with future generations says a lot about what we value today. I’d hope that ultimately we would include data representing a diverse range of cultures and voices. It’s up to science fiction to ask the question of what future humans might make of the information.

Reference:

Goldman et al. “Towards practical, high-capacity, low-maintenance storage in synthetic DNA” Nature (2013) doi:10.1038/nature11875

Imagine in the not-so-distant future an asteroid is on a direct course to hit the Earth. It’s large enough to destroy most life as we know it. NASA, the European Space Agency and China’s National Space Administration are scrambling to launch teams that will attempt to deflect the asteroid, but there is no guarantee that they will be successful.

Meanwhile a team of scrappy and resourceful aerospace engineers and biologists put into motion a plan meant to rescue at least a few species – including humans – from extinction. A spacecraft that will carry genetic material, along with live plants and animals, is readied for launch.

The hope is that after escaping the cataclysmic effects of the asteroid strike, the space ark would travel long enough for the Earth’s dust to settle (literally) so that the ship could return and restore life on our planet. Or perhaps the ship would continue on to a distant solar system, and the life it carries would be used to start a new settlement on a habitable planet.

This would obviously be a technically complex operation that would require substantial advance planning. One of the big tasks for the biologists on the team would be to decide how the genetic material and live travelers on the space ark would be selected and collected.

An obvious source of genetic material would be gene banks that collect and store samples of a wide range of genetic material. Such repositories exist today. The Millenium Seed Bank Partnership, for example, is an international project meant to save seeds from wild plants around the world. There are a number of other more agriculture-focused gene banks around the world that preserve seeds from a variety of crops.

Animal genetic material is a bit more difficult to archive than plant seeds. Projects like the US Department of Agriculture’s national Animal Germplasm Program primarily focuses on collecting and storing semen and eggs, not embryos.

There is also a current push to sequence the genomes of as many different species as possible. Perhaps in the future will have the technology to start from a raw DNA sequence to create a living breathing animal. There have been recent proposals to use DNA sequences along with reproductive cloning technology to restore wild animal populations on the verge of extinction.

But whether an “archived” animal is grown from germ plasm or from a synthesized DNA sequence, there still must be at least one female for the fetuses to grow in. Not a simple proposition.

But it would not be enough for our space ark to carry a male and female of each species. There must be a minimum number of genetically distinct individuals to allow a population to survive and thrive.  Conservation biologists estimate that such a “minimum viable population” would require anywhere from a hundred to several thousand members to survive at least a century. The lower estimates usually assume that there would be minimal environmental changes and human intervention to keep the population going.

Even with human intervention a lack of genetic diversity in a population puts it at serious risk for being completely destroyed by disease or unexpected environmental changes. That’s already a problem today. Disease outbreaks have put agricultural “monocultures” of some crops (like the Cavendish banana) at risk of extinction.

If samples from many individuals of a species are required for genetic diversity, our hypothetical space ark might not have enough space to carry every known species. So how would a biologist decide which critters are most important to save? That turns out to be a complicated question.

Restoring – or creating – a stable ecosystem needs to have a wide variety of different species from microbes to large vertebrates and algae to trees. The exact needs would depend on the local climate, soil and atmospheric conditions, among other factors. So far, we humans haven’t been very successful in creating an ecosystem from scratch. And the less that’s known about the environment where the ecosystem is going to be established, the longer the list of potentially necessary species.

So for the space ark scenario to work, it would not only need to carry a variety of species, but a variety of individuals in each species. And that is, of course, in addition to the humans – not just an Adam and Eve, but a large mixed group of people with enough genetic variation to start a healthy human colony. Throw in the complex social and political considerations in selecting who gets rescued and the population would probably have to number in the thousands.

Our hypothetical space ark would have to be huge to carry them all!

The space ark scenario is admittedly pretty implausible, at least with present-day technology. Even so, I think it’s worth seriously considering how it might be done. That’s not just because catastrophe is always a possibility, but because I’d like to think that some day self-sufficient extraterrestrial colonies will be a reality. We need to start thinking about how we might do that now so that the genetic material can be saved and reproductive technologies can be developed before they become a necessity.

But there are many questions that need to be considered:

If we are going to collect and archive seeds and animal germ plasm and genomic DNA sequences should the focus be on agricultural species? or should we cast our species net as far and wide as possible?

Should we seriously consider setting up a gene bank on the Moon, just in case something terrible happens to the Earth? or would it be better to have our archives closer at hand so that they can be more easily maintained and added to? How much redundancy should there be between different seed and germ plasm repositories?

Or should we focus more of our resources on developing synthetic biology techniques, in the hope that they will eventually become advanced enough so that collections of physical specimens will become unnecessary?

And if Earthly life is destroyed, would it be worth trying to restore Earth’s ecosystems or better to start over elsewhere among the stars?

What do you all think?

Technical Reading 

Blackburn HD “Genebank development for the conservation of livestock genetic resources in the United States of America” Livestock Science 120:196-203 (2009) (pdf)

Holt WV et al “Wildlife conservation and reproductive cloning” Reproduction 127:317-324 (2004) (text)

Traill LW et al “Minimum viable population size” a meta-analysis of 30 years of published estimates” Biological Conservation 139:159-166 (2007) (pdf)

Shaffer ML “Minimum Population Sizes for species Conservation” BioScience 31(2):131-134 (1981) (pdf)

Zhu et al “Genetic diversity and disease control in rice” Nature 406:718-722 (2000) doi:10.1038/35021046 (text)

The luxuries of our modern life are heavily dependent on having continuing access to a source of electricity. But power generation often requires consumption of limited resources like oil or coal, and generate high levels of pollution. Even “clean” energy sources like solar or hydroelectric power can significantly harm the environment.

Imagine a clean and green source of power that not only doesn’t harm the environment, but helps clean the air. Trees, for example, help reduce atmospheric carbon dioxide levels, and provide shade that makes use of electricity-hogging air conditioners less necessary. And trees and other plants, it turns out, can generate an electrical current that can be tapped.

The xylem tissue in vascular plants like trees transports water, ions and mineral nutrients as sap from the roots to the rest of the plant. There is a difference in voltage between xylem and the soil, which allows the potential for plants to generate an electrical current that could be tapped into.

Recently a team of Japanese scientists demonstrated that a battery could be created from 10 ordinary potted house plants connected in a circuit. They found their “green battery” could generate 3 volts and 3 microAmps of current. So far it has apparently only been used to power a blinking light.

Another research group lead by Brian Otis and Babak Parviz at the University of Washington has shown they can run a circuit entirely powered by Bigleaf maple trees. Their key to success seems to be the use of “nanocircuits”. These custom integrated circuits have lower power requirements than standard chips. Such low power circuits would have broad applications in wireless devices like smartphones and even biosensor contact lenses.

Current applications for tree-powered devices seem limited to monitoring of the environment and wildlife in remote areas where battery-powered devices would be impractical. Trees and other plants simply don’t generate enough power to run our appliances or smartphones.

But I think it’s possible that devices in the future using low-power chips might be able to run on plant power. And perhaps we could engineer trees to produce more tappable electricity. Perhaps we’ll end up living in real-life tree houses.

What do you think the future could bring?

More reading:

Ferris Jabr “The Shocking Truth: Trees are Electric“ ScienceLine (2010)

Love CJ, Zhang S, Mershin A (2008) “Source of Sustained Voltage Difference between the Xylem of a Potted Ficus benjamina Tree and Its Soil.” PLoS ONE 3(8): e2963. doi:10.1371/journal.pone.0002963 (free article)

Yamaguchi, T. and Hashimoto, S. (2012), “A green battery by pot-plant power.” IEEJ Trans Elec Electron Eng, 7: 441–442. doi: 10.1002/tee.21754 (subscription required)

Himes C. et al (2010) “Ultralow voltage nanoelectronics powered directly, and solely, from a tree” IEEE Transactions on Nanotechnology 9(1): 2-5 doi:10.1109/TNANO.2009.2032293 (free pdf)

Image: Violation by hapal, on Flickr, licensed under Creative Commons.

In the huge, crisp cocoon, extraordinary processes began.
The caterpillar’s swathed flesh began to break down. Legs and eyes and bristles and body-segments lost their integrity. The tubular body became fluid.
The thing drew on the stored energy it had drawn from the dreamshit and powered its transformation. It self-organized. Its mutating form bubbled and welled up into strange dimensional rifts oozing like oily sludge over the brim of the world into other planes and back again. It folded in on itself, shaping itself out of the protean sludge of its own base matter.
It was unstable.
It was alive, and then there was a time between forms when it was neither alive nor dead, but saturated with power.
And then it was alive again. But different.
~ Perdido Street Station, China Miéville

The metamorphosis of caterpillars into butterflies (either beautiful or terrifying) is an amazing process.

The larva encases itself in a chrysalis or cocoon and enzymes begin to break down its tissues. Eventually all that is left of the original larva are clusters of cells known as imaginal discs.  The digested tissue from the remainder of the caterpillar supplies nutrients to the imaginal discs which rapidly grow and differentiate into the wings, antennae, legs and other parts of the adult butterfly.  The adult emerges from the chrysalis fully formed.

Amazingly, a recent study has shown that behavior learned as a larva can be retained in the adult, suggesting that the neurons involved in memory also survive metamorphosis and are integrated into the adult nervous system.

There are a number of hypotheses to explain how such a complicated system might have evolved. But the oddest hypothesis comes from zoologist Donald Williamson , who suggests that the larval caterpillar and adult butterfly evolved from two completely different organisms, whose genomes somehow fused together. He proposes that the transformation of a caterpillar into a butterfly is more one creature turning into another, than a juvenile turning into an adult.

Williamson’s idea has been pretty thoroughly debunked in light of what’s known about butterfly and moth biology and evolution. It’s especially hard to explain in light of the experiments showing the persistence of memory through the process. But I think it’s a great science fictional idea.

In Orson Scott Card’s Speaker for the Dead the alien Pequininos (or piggies) go through metamorphosis from animal to plant, which never seemed very biologically plausible to me.

So are there good science fiction examples of hybrid lifeforms that shift from one to the other during their lifetime?  What do you guys think?

Related reading:

I find that there are few things that are more comforting than a tasty home-cooked meal. But cooking can take a fair amount of my time and energy, and requires that all the necessary ingredients on hand. Sometimes when I’m busy or tired or just feeling lazy, I wish there was a box of “people chow” in my cupboard that would make well-balanced and tasty meal, or perhaps a pill that could substitute for a satisfying dinner.

It’s not surprising that in the late 19th and early 20th century, when food preparation was much more labor intensive and time consuming than it is today, that writers who imagined scientifically advanced utopian societies of the future frequently described “instant” food that required no cooking.

The idea was common enough for writer Anna Bowman Dodd to satirize it in her 1887 novella The Republic of the Future, or, Socialism a reality:

The food is sent to us by electricity through the culinary conduits. Every thing is blown to us in a few minutes’ time, if it be necessary, if the food is to be eaten hot. If the food be cereals or condensed meats, it is sent by pneumatic express, done up in bottles or in pellets. All such food is carried about in one’s pocket. We take our food as we drink water, wherever we may happen to be, when it’s handy and when we need it.

Thus women were freed from the drudgery of the kitchen. Or as Dodd put it:

The perfecting of the woman movement was retarded for hundreds of years, as you know, doubtless, by the slavish desire of women to please their husbands by dressing and cooking to suit them. When the last pie was was made into the first pellet, woman’s true freedom began.

Dodd made it sound as if this would be a bad thing. But many thought that scientifically developed food substitutes would a positive development. At least in the first half of the 20th century, there were regular articles in the popular press about the “dream” of creating a meal in pill form.

And, of course, the pulp science fiction writers incorporated the idea into their stories.

By the way, have you folks eaten?”
“Not in a week,” said Karl.
“Von Sternberger’s food tablets,” informed the girl.
Carruthers nodded. His deep-set eyes regarded them appraisingly. “Any ill effects?”
“None whatever,” spoke Danzig. “Neither of us have the slightest craving for food.”
~ “Prisoners on the Electron” by Robert H. Leitfred (1930)

Sounds convenient, right? But here we are in the first part of the 21st century and most of us eat food that isn’t too far different from what people were eating a century ago.

So why don’t we have the equivalent of “Von Sternberger’s food tablets”? It turns out there are a number of reasons.

For one, we humans normally eat a wide variety of foods – a much wider variety than most other primates. A number of studies have shown that the diversity of foods we eat reflects the quality of our diet. Of course, that association is likely due at least in part to the link between poverty and a less diverse diet. Perhaps the lack of variety wouldn’t be a problem if scientists developed a food that met all human dietary requirements. It turns out not to be that simple.

We don’t actually yet know all the components that would make up an ideal human diet. For example, there are many compounds produced by plants – phytochemicals – that are thought to have anti-oxidant and other physiological properties. We are still learning what these compounds are and how they affect the human body, despite the bold claims of the dietary supplement sellers.

Another problem is humans have trouble eating the same food for every meal. Just imagine: there are 9 calories in one gram of fat, the most calorie-dense nutrient. That means you would need to eat a half pound of pure fat to get the 2000 calories burned daily by the average adult woman.  That’s a bare minimum, since balanced diets need to include less calorie-dense  components like proteins, carbohydrates and fiber.  While it’s not at all difficult to eat a pound (or more) of a tasty variety of foods per day, it’s harder to imagine happily swallowing a half pound of pills or eating a couple of pounds of not-particularly-tasty food pellets on a daily basis.

It’s not like people haven’t tried. A Canadian fellow named Adam Scott tried eating “monkey chow” for a week. At least in theory that diet should serve the nutritional requirements of most primates, including humans. The result? Scott lost weight, was tired and had serious cravings. While a diet of nutritious pellets might work as an alternative to Weight Watchers, it wouldn’t a very good replacement for human food. More seriously, even people who are malnourished have trouble eating enough food when the prescribed therapeutic diet is too monotonous.

And even if there is variety in our diet, food needs to taste good for humans to be healthy in both mind and body. For example, NASA has found that the “psychological well being” of astronauts depends at least in part on providing food that is tasty and has a “pleasant mouthfeel” . Because of that, NASA has moved away from the unappetizing food pastes and powders used to sustain astronauts on the Mercury missions, and worked on developing foods that the astronauts actually enjoy eating.

Naturally, science fiction has reflected many of those limitations.  In more recent SF stories, it’s more likely for mass-produced rations to be provided starving masses on resource-depleted and overpopulated Earth than to be eaten by the scientific or social elites.

All the TV shows have morale-builder commercials telling us how important our work is, how the whole world depends on us for food. It’s all true. They don’t have to keep reminding us. If we didn’t do what we do there would be hunger in Texas and kwashiorkor among the babies in Oregon. We all know that. We contribute five trillion calories a day to the world’s diet, half the protein ration for about a fifth of the global population. It all comes out of the yeasts and bacteria we grow off the Wyoming shale oil, along with parts of Utah and Colorado. The world needs that food.
~ Gateway by Frederik Pohl (1977)

Living on such food produced for basic sustenance, rather than for optimal health or pleasure, is a pretty bleak vision of the future.

Of course not all science fictional food is so unappetizing. In the resource-rich Star Trek universe, almost everyone can dine well on delicious synthetic food produced by replicators if they don’t want to cook for themselves.

Having access to a variety of food that tastes good, is nutritious and is available at the push of a button – that’s the future I’m hoping for.

Further reading:

• Paleo-Future’s “Meal in a pill” archives.

• Future Food section of David Szondy’s Tales of Future Past.

• NASA’s Space Food Fact Sheets and their Space Food and Nutrition site for students and educators.

• Cooper et al. “Developing the NASA Food System for Long-Duration Missions” J. Food Sci. 76(2):R40-R48 (2011) doi: 10.1111/j.1750-3841.2010.01982.x

Photo by epSos.de on Flickr

One of the staples of television and movie science fiction is the universal translator that allows humans and aliens to communicate fairly easily. But the reality is that we aren’t even currently able to automatically translate all human languages reliably. If we do someday run into an alien race, will we be able to communicate?

The difficulty of conversing with aliens isn’t limited to learning vocabulary, grammar, and body language. We humans all can (on average) produce and hear the same range of sounds. If the aliens we end up meeting use sounds or visual cues outside the human range of perception, we would be entirely dependent on computers to help us communicate.

Fortunately, scientists are currently studying the language of some of the aliens already among us. I’m not talking about extraterrestrials, but rather non-human animals like whales, elephants and birds. Parrots have been a popular focus of study, since it’s long been known by scientists and pirates alike that parrots can imitate human speech.

Are they talking about us?

But observing how parrots mimic human speech patterns doesn’t tell us how they normally communicate.

U.C. Berkeley ecologist Steve Beissinger and his colleagues have been studying a single population of Green-rumped Parrotlets (small parrots) in Venezuela for 26 years. In a project lead by Cornell ornithologists Jack Bradbury and Karl Berg, analysis of data collected from carefully placed video and audio recorders have allowed them to observe how wild parrotlets learn their “names” and socially interact with each other.

It turns out that young parrotlets learn their contact call – the sounds that serve as a personal identifier or “name” – from their parents. The call is modified a bit by individual chicks so that each has a “name” that is both unique and related to their parents’ own “names”.

But this isn’t a language that humans can imitate. The sounds are actually much too fast for us to follow. As Berg describes it, the fairly simple peeps we can hear are actually much more complex sounds :

“The parents can make 20 contact calls in the time it takes you to sneeze.” When slowed down for our ears, a parrotlet’s single peep sounds more like eh-ehhh-gehhhlll-grrr-whoeeeeee. [. . . ] “You can’t make sense of their vocalizations just by listening. You can’t imitate their calls like you can whistle a songbird’s tune,” Berg says. “The only way we can study them is by converting their calls to spectrograms, then running these through computer programs” that search for subtle similarities [. . . ]“

This video has the calls first in normal time, then slowed down so human ears can detect the difference between different contact calls so you can hear the difference for yourself:

Nestling Vocal Signatures from Karl Berg on Vimeo.

Berg and colleagues have suggested that their research may provide insight into human language acquisition during infancy. But it seems to me that their methodology could be used to help decipher the “talk” of non-terrestrial species as well. How could they neglect to mention that?

While their parrot communication research has taken years, I would think that it would go much faster with a species that is both more intelligent than a parrot and interested in helping us to learn to understand them.

And I’m wondering if there will come a time when we are able to use our translation devices to talk to Earthly non-humans in their own tongue, rather than “uplifting” them so that they speak in ours.

More information:

For more about the research on Venezuelan parrotlets, listen to the 22 July 2011 Science Podcast or read the podcast transcript.

There is also a video of cute parrotlet nestlings being fed by their father, who uses contact call “names” to greet them.

You can download software – Raven and XBAT – developed by the Cornell Lab of Ornithology Bioacoustics Research program for the analysis of acoustic signals.

Original articles:

Morell V. “Why Do Parrots Talk? Venezuelan Site Offers Clues.” Science 22 July 2011: 398-400. doi:10.1126/science.333.6041.398 (subscription required)

Berg KS et al. “Vertical transmission of learned signatures in a wild parrot, Proc. R. Soc. B. 13 Jul 2011 doi: 10.1098/rspb.2011.0932 (subscription required)

Top image: Three Birds on a Boardwalk by LancerE, on Flickr

Bottom image: Body parts I – What are you looking at? by Sami__, on Flickr

I am the Lorax. I speak for the trees. I speak for the trees, for the trees have no tongues. And I’m asking you sir, at the top of my lungs – that thing! That horrible thing that I see! What’s that thing you’ve made out of my truffula tree?

Find yourself a patch of forest. Sit among the trees and if you’re quiet (and a breeze is blowing) you’ll hear whispering and moaning. Folktales and legends say it’s the trees speaking to us. As Dr. Seuss’s Lorax points out, trees can’t really speak to us directly – at least not using words.

But even if they can’t speak, trees can indeed communicate. Back in 1982 Ian Baldwin, currently director of the Max Planck Institute for Chemical Ecology, published a paper showing that young trees that were damaged as if attacked by hungry insects increased production of tannins and several other chemical compounds. Those chemicals were known to inhibit growth and foraging of insect larvae and so presumably helped defend the trees from further attack.  They also discovered that undamaged trees in the same enclosure  started producing similar compounds. Baldwin and his colleagues concluded that the damaged trees were releasing volatile compounds into the air. Those chemicals served to warn the undamaged trees of potential danger, and induced them to begin to mount their own defenses.

Since then. advanced molecular analysis and genetics have been used to study the so-called “talking tree” phenomenon in more detail. Plant leaves release a number of different chemicals, from simple small molecules like ethylene to more complex compounds like methyl jasmonate. These compounds diffuse through the air, and if they come in contact with the leaves of responsive plants, those plants respond with changes in chemical synthesis and growth.

Plant roots also secrete a number of different communicating chemicals. These compounds aren’t able to travel as far through the soil as volatile compounds can drift through the air. Instead they locally fight of insect pests and battle nearby plants for growing room. Those chemical signals are also in the process of being deciphered, and that information is already being used to genetically engineer pest-fighting crops.

While the forms of chemical plant communication we currently are aware of are essentially  non-directed shouts of “Danger!” or “Stay away!” rather than conversations, a recent public Q&A session with Ian Baldwin touched on some more speculative possibilities.

So what about fiction?

SF has a number of examples of tree-like aliens (such as Orson Scott Card’s Pequeninos or the lonely female tree beings in Jack Skillingstead’s “Rescue Mission”) and fantasy creations like Tolkien’s Ents, but I couldn’t come up with any stories with scientifically plausible talking trees.

One big problem is intelligence – or more specifically the lack of it. To truly converse an entity must be able to think, and there is nothing that suggests that trees or other plants have any means of doing that. But once that hurdle is crossed (genetically engineered nervous systems, perhaps?), I think there’s a plausible leap to be made from the current simple modes of Earthly plant communication to full-fledged chemical conversation.

I wonder what they’d say?

More technical information:

• Baldwin IT and Schultz JC “Rapid Changes in Tree Leaf Chemistry Induced by Damage: Evidence for Communication Between Plants Science 221(4607):277-279 (1983) DOI: 10.1126/science.221.4607.277
• Baldwin IT et al. “Volatile Signaling in Plant-Plant Interactions: “Talking Trees” in the Genomics Era” Science 311(5762):812-815 (2006) doi: 10.1126/science.1118446 (free pdf)
• Bais HP et al. “How plants communicate using the underground information superhighway” Trends in Plant Science 9:26-32 (2004) (free pdf)
• Science Special Online Collection: Plant Volatiles — From chemistry to Communication (2006)
• Live@AAAS Ian Baldwin on Talking Trees (Transcript)

Top image: Oak trees in October. Perhaps they are discussing the cooling weather? Photo by me.

Middle image: Methyl jasmonate. According to Baldwin, “Heavier compounds with less volatility, such as terpene alcohols, methyl jasmonate (MeJA), aromatic compounds including methyl salicylate (MeSA), and green-leaf volatiles (GLVs), are more likely to function as signals over longer distances, because their comparatively slower dispersal allows development of plumes of higher concentrations that may be carried farther as intact parcels by turbulent flow.”

Bottom image: “A Criminal Lead By Three Watchmen”, an illustration from Baron Ludvig Holberg’s 1741 novel Niels Klim’s Journey Under the Ground,  involving a visit to the Planet Nazar, which is inhabited by walking and talking trees

Imagine that you are working on a home improvement project and, being a bit of a klutz, something goes horribly wrong: a slip of the saw and you’ve lost the tip of a finger. Is there any hope of regaining your lost digit?

While there young children reportedly have the ability to regrow amputated fingertips, in adults it’s possible with special medical treatments (or maybe not even that). Cut off your whole finger – or (stars forbid) an entire arm – and unless it can be reattached, it’s gone for good.

While lobsters can regenerate their claws, and many lizards can regrow their tails, humans and other mammals have notably poor limb regeneration abilities.

The notion  that such an “animal” ability could somehow be transferred to people has been a part of science fiction since its early years.  A good example of this is Romeo Poole’s 1926 short story “A Hand from the Deep”, which has a Doctor Whitby experimenting with crayfish extracts on an unsuspecting patient:

“The theory is nothing very new. As early as 1906 it was observed that when a limb is amputated at the middle of a bone, the bone starts to grow out again, but increases only about one-fiftieth of an inch in length before it is halted by some other influence. You know also, of course, about the little warts of so-called ‘proud flesh’ that apparently try to replace the original muscular tissue in case of injuries, but which are misshapen or misplaced. What Whitby was trying to get at, as I see it, was to so control these misdirected efforts of nature as to produce a new and perfect limb.
“The human body is already able to repair damaged bones by rebuilding small particles of the bony tissue; it is also able to replace muscle, nerve and even finger-nail tissue, although in somewhat imperfect forms. Whitby was trying to induce it to build a lost member in perfect form.
[...]
“It seems that Whitby has been experimenting for years with the ductless and other glands of shellfish in pursuance of this theory of regeneration, and we have upstairs the living proof that he was able to prepare a glandular extract that changes the bodily cell-structure as well as influencing the building-up processes of nature; but it appears that he near succeeded in isolating the one influence from the other, both being present in his preparation.

Of course there are terrible side effects to the treatment; quite improbably the patient starts turning into a crustacean himself.

Later science fiction tales usually assume as a matter of course that “autodocs” and other advanced medical treatment technology will make limb regeneration almost routine procedure, albeit often a slow and painful one.

But wouldn’t it be better for future humans to be able to do that on their own?

The only vertebrates able to regenerate entire arms and legs as adults are some species of salamanders.   After a limb is amputated, cells are mobilized to to start healing the wound.  In humans, scar tissue forms.  In newts, on the other hand, cells migrating to the wound site form a structure called the apical epidermal cap (AEC) . Cells under the AEC begin to proliferate and create a tumorlike mass called a blastema which eventually will grow into the newt’s new limb.

If humans could be given that ability,  you could create a superhero (or supervillain) or a super soldier. It’s no surprise that some research in limb regeneration is funded by the US Department of Defense.

But the exact molecular signals that direct salamanders limbs to regrow are still being sorted out.  And it’s not at all known whether similar mechanisms would function the same way in mammals (like humans) if they were somehow transplanted.

There was an interesting paper last year that suggested the removal of a single gene in mice can stimulate scarless wound healing. But despite the wildly speculative headlines, the study did not actually even try to look at whether the mutant mice could regenerate digits or limbs. Mouse limb regeneration – let alone human limb regeneration – is still firmly in the realm of science fiction.

Are there aspects of limb regeneration that haven’t been fully fictionally explored?  What would be the implications if all ordinary people had that kind of wound healing ability for society and medicine?

The wound healing ability in axolotls has also allowed scientists to surgically induce the formation of extra limbs.  What if humans had that ability as well?

Additional Reading and Watching

Video: Newt Limb Regeneration from the HHMI 2006 Holiday Lectures — Potent Biology: Stem Cells, Cloning, and Regeneration

Video: Superhero Science: Limb Regeneration

Gardiner David M and Bryant Susan V. Regeneration Basics. UC Irvine Limb Regeneration Lab.

Interview with Jon Mogford, Program Manager of the Defense Sciences Office at DARPA (2009) [Military projects on wound healing]

Whited Jessica L and Tabin Clifford J. “Limb Regeneration Revisited” Journal of Biology 8:5 (2009)

Bedelbaeva Khamilia et al. “Lack of p21 expression links cell cycle control and appendage regeneration in mice” Proc Natl Acad Sci 107(13): 5845–5850 (2010)
[note that the "appendage regeneration" refers to closure of a hole punched in the mouse's ear]

Illingworth, Cynthia M. Trapped fingers and amputated fingertips in children. J. Ped. Surgery 9:853-858. (1974)

Top Image: London Zoo – Adventure Animal – Donkeys – Danger Sign by ell brown on Flicker
Middle Image: California Tiger Salamander, Ambystoma californiense II by marlin harms on Flickr.
Bottom Image: “Red on Sale” by Artiii on Flickr

“You go to the Caves of Winter. That is the Plan.”

“Winter, yes. The cold. Mother told us. And after the cold winter comes the warm. I remember. The winter will pass, won’t it? Why did she say, the winters grow? Teach me, Old One. . . .

~ “Love is the Plan, The Plan is Death” by James Tiptree, Jr.

Here in the Northern Hemisphere we are moving through autumn towards winter. That means the days are becoming shorter and the weather is getting cooler. The seasonal changes become more dramatic the further North you go; for people living near the Arctic Circle, the shortest day of the year – December 21st – will have nearly 24 continuous hours of darkness.

The change in seasons is due to the axial tilt of the Earth relative to its orbital plane (see image). In the summer, the sun is more directly overhead, which not only makes the days longer but the intensity of the sun’s rays are greater. It also means that the Southern Hemisphere experiences summer while the Northern Hemisphere is experiencing winger.

Seasonal changes on other planets in our solar vary considerably. Mars , with a similar axial tilt to Earth, has seasons that last roughly 6 months. Uranus has a much greater tilt and longer orbit has 20-year-long seasons with extremely variable weather. On Venus, on the other hand, the seasonal differences are pretty insignificant, since the planet has little axial tilt.

Not surprisingly, the change in the amount of daylight over the course of the year has had evolutionary consequences.   There are many plants and animals on Earth that have evolved to use day length as a cue for physiological changes that affect growth, reproduction and migration.

Plant reproduction, for example, is often dependent on having the right amount of darkness in a 24-hour period.  “Long day” plants – like soybeans and ryegrass – require fewer than a certain number of hours of darkness to flower, while “short day” plants – like spinach and coffee – won’t flower if there are too few hours are darkness. There are even “long-short-day” plants – like aloe – that require long days followed by short days to reproduce, and so only flower in the fall and “short-long-day” plants – like white clover – that flower in late spring. Disruption of the light-dark cycle can prevent such picky plants from reproducing.

The shortening of days in the fall also triggers changes in deciduous trees that helps them prepare for the cold of winter. The green chlorophyll in their leaves breaks down – unmasking already present yellow pigments – and is used to provide nutrients to the trunk and roots. Some trees also start making red pigments in their leaves, likely to help maximize the nutrients it can store for the cold winter months. Not only do these changes produce lovely fall color, but they also help trees survive until spring.

Animals are also affected by changes in day length. An extreme example is the Siberian hamster, which in the summer grows quickly and reproduce. As days grow short in the winter, the male hamsters’ testosterone levels drop, their testes shrink, and they store fat. Female Siberian hamsters go through similar changes.  While it’s not quite so dramatic in humans, we also respond to seasonal changes in daylight,  particularly with regard to our moods.

So how can these changes be used in science fiction? I think seasonal changes in day length are an often-overlooked aspect of realistic world-building.

While some science fiction stories include planets with extreme cold and hot “seasons”, these are often due to the unusual orbits of the planets. Examples of this are Hal Clement’s Abyormen and Brian Aldiss’s Helliconia*. Imagine a fictional planet that has an axial tilt similar or greater than Earth’s. The length of day should change with the seasons, and there should be indigenous life forms that have adapted to those changes, such as the creatures in Tiptree’s  short story “Love is the Plan, The Plan is Death”.

Day length is also plays a role when a planet is terraformed for human settlement. The Earthly plants and animals brought by the colonists would have to be specially selected (or engineered) so they are not adversely affected if the nights are significantly longer or shorter than Earth’s, or if the day length doesn’t change over the course of a year.

And imagine what might happen to life if the tilt of Earth’s axis were altered. Assuming any life survived such a dramatic event, it would have to adapt to changes in the seasons.

The cold grows, it grows, and your Mother-eyes are growing, glowing. Soon you will be alone with our children and the warm will come again.
Will you remember, my heartmate? Will you remember and tell them?
Tell them of the cold Leelyloo. Tell them of our love.

~ “Love is the Plan, The Plan is Death” by James Tiptree, Jr.

More reading:

• James Tiptree Jr.s “Love is the Plan the Plan is Death” is about spider-like creatures that are intelligent in summer, but revert to instinct during the cold of winter (read the story at the archive.org copy of SciFiction)
• Gerald Weinberg’s short story “The Moon is a Harsh Pig” touches on the possible biological effects of moonlight.

• NASA Science: Interplanetary Seasons
• Phil Plait’s Bad Astronomy: Misconceptions about the Seasons
• Photoperiodism at terraformers.org.au (see also their list of species for colonisation)
• Clock Tutorial #16: Photoperiodism

Top Image: Diagram Earth and Sun from Wikipedia
Bottom Image: Four Seasons – Fenner Nature Center by Aunt Owwee, on Flickr

* Aldiss’s Helliconia may have has Earth-like seasons in on top of the centuries-long “seasons” due to its unusual orbit. It’s the latter changes that are the focus of the Helliconia novels.