Science In My Fiction

At least if you’re a mouse. Research published this month found that mice fed yogurt were slimmer, sleeker and shinier than those that didn’t.

The male yogurt-eating mice also had larger testicles. (The junk-food eating mice had smaller testicles.) Female mice weren’t left out: they were smooth and shiny too, and had larger healthier litters.

In other words, eating yogurt made mice more attractive and more fertile, and presumably healthier. The researchers don’t know why, but they suspect it might have to do with the live bacterial cultures in the yogurt.

By the numbers, the human body is mostly bacteria: about one trillion human cells, and about ten trillion bacteria. (I don’t know the numbers for mice, but they’re probably similar.) We don’t even know what most of them are, though scientists think there are around 500 different species.

Many of those bacteria live in the digestive system, having colonized the infant during birth or shortly after. They help to digest the things we eat, release vitamins, help to keep out disease-causing bacteria: all sorts of useful things. The humans studied so far fall into one of three enterotypes, each of which has similar distinctive gut assemblages (even though they eat similar diets).

Nobody knows exactly what that means yet, but one possibility is that different enterotypes are more efficient at digesting particular foods. They may also be more or less effective at providing vitamins to their host. The abundances of different species change in response to diet, but mostly within certain limits. Gut flora have been linked to obesity, suggesting that bacteria may affect metabolism or efficiency of digestion. Having (or eating) the right bacteria might also be related to longevity.

When gut bacterial assemblages decline or get unbalanced, often as a result of taking antibiotics to treat some other condition, all sorts of problems can occur. One particularly nasty invader is Clostridium difficile, a bacterium that can cause persistent diarrhea and may become debilitating or life-threatening. Even C. diff, as it’s not-so-fondly known, is vulnerable to a diverse and balanced set of gut bacterial: a fecal transplant from a healthy individual is an effective cure.

Gut bacteria could have global environmental implications too: scientists are looking for ways to modify ruminal bacteria in cattle so that they eliminate less methane, a powerful greenhouse gas.

This stuff has all kinds of science-fictional implications. What about modifying the gut flora of planetary colonists to help them digest new foods, or to produce vitamins that they no longer get from their diet? Or superfoods that promote health or shininess or fertility? Such superfoods could be proprietary, or addictive. What happens if people try to culture them at home? Making your own yogurt is easy, and using a commercial yogurt as the starter ensures that you have the same culture. For the probiotics to contribute to the gut flora, they have to be alive.

[Ed.: Today's post is by MJ Locke, but due to minor technical difficulties it appears under my name.]

Foreword: For several months during 2007, I collected data for a series of graphics-focused posts on space exploration. I wondered how far we humans have penetrated into space, in the years since our first vehicles rose above the layers of our world’s atmosphere.

Next Saturday, May 5, 2012, we will reach the fifty-first anniversary of the first U.S. launch of an astronaut into space. This is a revisit to a series of posts I put up then. I’ve updated the dates, but all of my analytical data is five years old.

Mercury Redstone 3

On May 5, 1961, 37-year-old Alan Shepard climbed into a tiny capsule atop a liquid-fueled rocket. He rode it up from Cape Canaveral, Florida to an altitude of 116 miles: about forty miles above the upper reaches of the atmosphere. He experienced six gees (six times Earth’s gravitational pull) during liftoff, stayed aloft about 15 and a half minutes, and then splashed down in the waters of the Gulf Stream.

I was very young then, a preschooler, but even so I remember my excitement, and also fear, as I watched the news footage. I recall watching the wind from the helicopter’s blades stirring up the waves that splashed against the capsule as it righted itself.

I can only imagine what it must have felt like, soaring up so high. Not to mention how it felt, coming down.

I remember seeking a glimpse of his face through the little portal, and the thrill I felt when the divers helped him emerge and climb into the sling.

President Kennedy was there, for that first launch.

Since that time, the US has launched over 170 piloted missions, and many, many robotic missions. Our astronauts have spent months at a time in the International Space Station, working in cooperation with people from a variety of other nations to do scientific and engineering research.

We have fifty-one years of human-piloted space exploration under our belt*. Alan Shepard and Mercury-Redstone 3 set the stage for everything that came after that.

Human Space Density, in Hours

What does that really mean, though? How far have we travelled in space, to date? How long have we lived there?

Here is a graph showing how many hours humans (only US astronauts, so far; see note below) have spent above the level of the atmosphere.

I’m counting the upper edge of the atmosphere as about 76 miles up, though you will find many different estimates–and in fact, it changes over time, with fluctuations in the solar wind and other factors, including global warming impacts. But 76 miles is a good average number for our purposes.

So how much time are we talking about, really? For comparison, the average American work-year is about 2,000 hours. A year has about 8,900 hours, all told.

As you can see in the chart above, after a promising start with Mercury, Gemini, and Apollo, the US manned space program languished, when SkyLab drew to a close. It wasn’t until 1981 that the space shuttle program re-energized space exploration. The hours really started racking up once the International Space Station was completed. You can also see the effect of the Challenger (1986) disaster. The Columbia re-entry breakup (2003) is not as easy to see, but it is the cause of the dip in 2003-2004. In fact, it slowed the pace of NASA shuttle missions through the remainder of its run.

If you were to add up all the hours every NASA astronaut has spent in space since our first manned mission, that’s almost 31 years. As of 2007, humans had spent nearly half a lifetime’s worth of time outside Earth’s atmosphere (A good deal more than that, in fact, if you include other nations’ efforts. I couldn’t find the data for them).

Granted, that’s a pittance, compared to how many people live beneath the atmosphere. (In fact, it surprised me. I thought it would be more.) But it’s a start.

As you can see from the chart above, the US has had seven major piloted space programs since we launched Alan Shepard into space.

Human Space Density, in Miles

You can think in terms of how many miles we have traveled overall, or in terms of how far away we have gotten away from the Earth, before we turned around and came back. At first glance, they might seem to be the same thing, but this is definitely not the case. An astronaut might travel many millions of miles in low Earth orbit, but never get any farther away than a handful of miles above the upper reaches of Earth’s atmosphere. Or an astronaut might take a trip to the moon and back, with very little in the way of orbiting either body—in which case their distance travel and maximum “altitude,” or distance they get from the Earth, would be very nearly the same.

Here is a chart that provides information on both kinds of travel.

The maroon tells you how many miles our astronauts traveled in all, by year, as if they had been traveling in a straight line away from Earth. The blue tells you how many miles away from the Earth’s surface they actually reached during their missions. In both cases, I used the annual miles traveled by US astronauts.

As you can see, the moon missions (that blue bump in the ’60s and early ’70s) stand out from the rest. The Apollo craft went much farther away from the Earth than any other space flights, before or since. For non-lunar missions, the average altitude was 179 miles, less than the distance from Houston to Dallas.

The maroon shows that 2001 was a banner year for space travel, when US space missions traveled a total of 233 million miles. That’s all the way to the sun and back, with enough left over to go to Mars. But our astronauts racked up all of those miles in low Earth orbit, never getting any farther from the Earth than about 250 miles.

The average distance missions travel, from the days of Mercury to the present day, is almost 10 million miles. For comparison, if you drive 10,000 miles per year on average, it would take you a thousand years to travel that far.

As you might guess, the International Space Station dragged the curve up all by itself, because astronauts spend months at a time on the ISS. The typical ISS mission lasts six months. An international team usually consists of three astronauts, who spend that half a year up there conducting experiments and maintaining the station. They’ve just added a new module to the ISS. The ISS has 15,000 cubic feet of living space. That’s about equivalent to a 2,100 square-foot home, down here.

By the way, some of my readers will note something odd about the above graph. The distances seem off. The 100-mile marker on the chart is the same distance from the 10-mile marker is the same length as the 10-mile marker is from zero. The thousand-mile marker is no farther from the 100-mile marker than the 100- is from the 10-. What gives?

It’s a logarithmic scale. A log scale scrunches the data together, to allow you to compare data that spans a very large range. In this case, I wanted to get the low-Earth-orbit data onto the same graph as the millions-of-miles traveled data. It’s useful to be able to look at them together, but it can be misleading. Here is a chart showing the actual distances, without the log scale.

The image above shows you about 250,000 miles’ distance, to scale (I couldn’t even begin to fit Mars and the sun on there, and still show you anything meaningful with regard to the NASA missions. The old space-is-really-big effect). Notice how most space missions barely leave the atmosphere, and notice how far it is, even just to our own moon.

The End of the US Space Era? Or a Pause?

Right now, our space exploration efforts seem becalmed. The fifty years between Shepard’s launch and the final voyage of the space shuttle Atlantis may have been our high-water mark, with regard to space travel. I’d be very sad if that were the case. I prefer to be optimistic, however. NASA’s rover, Curiosity, is nearing Mars. A variety of visionaries and entrepreneurs are seeking ways to commercialize space travel—everything from asteroid mining to space tourism, telecommunications, and spaceports in the New Mexican desert. New exoplanets are being discovered by the day now. Perhaps our robotic probes and astronomic surveys will reveal clues of life beyond our world, which might inspire us once again to reach upward again, and seek to escape the confines of Earth’s gravity. I hope so.

We have barely passed beyond the membrane of our atmosphere. Is there life on other worlds? What wonders lie in store out there? I hope that we will continue to find in us the spirit of our ancestors, and to continue to reach beyond our atmosphere, to explore and even someday perhaps settle on other worlds.

Notes: Let me haul out the usual caveats. I pulled the graphical data together primarily from NASA’s mission data pages, with Wikipedia as a secondary source (in particular for the International Space Station). About five percent of the data (in particular, maximum altitude and distance traveled) was not readily available online, in which case I SWAG’d^ it, based on data from other missions. In other words, there is slop in the data. Don’t use it for your doctoral thesis, or to calculate whether you have enough oxygen to survive till the rescue team arrives. Also, I only have information on US astronauts.

* Van Allen belt, that is.

^ Scientific Wild Assed Guess. It’s tethered to real numbers to some degree, but it definitely floats around in the ether to some degree, too.

I can’t find it online, but I read an introduction to Rose for Ecclesiastes in which Roger Zelazny was quoted as saying that he knew he had to hurry up and write the last of his Mars stories because he knew that new developments in science would make them impossible.

(Or possibly, he hesitated to publish that story because he already knew that science had outpaced him. Either way, it’s a fabulous story and you must read it.)

Rose was published in 1963, and Mariner 4 sent back the first close-up photos of the Martian surface in 1965.

Nope, no beautiful Martian dancers living there.

By now we know the surface of Mars better than we know the surface of Earth (those pesky oceans, you know.) But Zelazny’s fears aside, that hasn’t stopped the popular conception of Martians from appearing regularly in popular culture. (Yes, I enjoyed John Carter. Did you?)

The portrayal of Mars in more science-minded science fiction, though, has changed greatly as new information became available about the planet. Where Edgar Rice Burroughs and Roger Zelazny couldn’t have told their stories after 1965, Kim Stanley Robinson and Ben Bova couldn’t have written theirs earlier.

This leads me to two questions for you all: first, how much does it matter? Does science fiction have a place for both the most accurate possible science and for things we know aren’t true but love anyway? Is the answer different if the story used the best science of the time it was written, but knowledge has moved past that?

What kinds of stories are likely to become obsolete in the very near future? If you are a writer, are there ideas you love that you will never get to write because they are already past, or will you use them anyway? If a reader (and the two categories are by no means exclusive), are there topics you hate to see in SF because you know they’re already obsolete?

This is a true story, and it’s based on the research of Dr. Scott Nixon at the University of Rhode Island. I spent last week at a conference in Newport, and was entirely fascinated by his plenary talk. Besides being a neat juxtaposition of history and technology, it has some interesting implications for worldbuilding in science fiction.

Narragansett Bay within Rhode Island

First, let me orient you. This is Rhode Island, and Narragansett Bay is outlined in red. Providence, the largest city in Rhode Island, is at the north end of the bay, about where it touches the red box. Rhode Island itself is 48 miles (77 km) long and 37 miles (60 km) wide.

The Narragansetts and the Wampanoag tribes lived along the bay when Giovanni da Verrazzano found it in 1524, and the first European settlement was established in the 1630s. It’s really the Europeans we’re concerned with here.

Providence was founded in 1636 by religious dissenters. After the American Revolution it had 7,614 people. The economy depended mostly on the bay for fishing, with a bit of agriculture.

The Industrial Revolution made it to the new United States when textile machinery was built in Rhode Island in 1787, following English plans. Industrialization took off, and by 1831 the population of Providence had reached 17,000.

The city is right on the water, at the head of Narragansett Bay, so anything it does affects the water quality of the entire bay. But even as Providence became a thriving industrial city, its impact on water quality was surprisingly low. as its population increased enormously In 1865, when the population of Providence was 54,595, eelgrass beds were mapped all along the Providence River.

So what? Well, eelgrass (Zostera marina) is very sensitive to nitrogen levels in the water. All those people in Providence weren’t affecting the water quality much at all, or the eelgrass would be gone.

That’s a lot of people; how were they having such a small impact on the bay? Well, this is the age of outhouses. Most human waste was solid, or only small quantities of liquid. When you have to haul water from the town well, you don’t use very much of it. Most waste stayed where it was put, only leaching out slowly over time.

I’m certainly not claiming that outhouses are a good way to manage a city’s worth of human waste: Providence had at least two major cholera epidemics in the mid-nineteenth century. But that pollution wasn’t making it into the bay. Much of the human and animal solid waste was being hauled into the country and used as fertilizer.

The prospect of a public water supply was an exciting one, and after a couple decades of planning, the water was turned on in 1871. Public health and fire safety, not to mention simple convenience, were strong motivations.

People started using water at much, much higher rates: flush toilets! no more hauling buckets! (From 7-11 liters per person per day to 190-380.) The city planners expected that the existing street gutter system would be adequate to deal with the increased volume. They were wrong.

It didn’t take long at all for the cesspools and privy vaults to overflow and seep into the streets. Planning for a sewer system began almost immediately, but it didn’t begin service until 1878.

Providence wasn’t alone in this: many cities installed public waterworks in the nineteenth century, and none began planning for sewers until after the water was running.

The sewer system carried waste directly into the rivers. Where before the nutrients were being taken to inland farms, now they were swept right into the bay. The first Providence sewage treatment plant didn’t begin operation until 1901, and by then there were 175,597 people in Providence.

The eelgrass was long gone.

And it wasn’t just the people. Providence relied on horses for transport and hauling. The number of horses in the city peaked around 1900, and then fell off sharply when the automobile was introduced. During that peak, though, an estimated 90 g of horse manure per square meter coated the city streets.

Providence has gotten much better at managing its wastes over the past century, of course, although there’s still room for improvement.

I came away from this lecture with two thoughts about worldbuilding for fantasy and science fiction.

First, even though we often set stories in horse-dependent worlds and with primitive technologies, we don’t usually think about what comes in and what goes out. Scientists call this mass balance. Horses need to eat a lot, and they excrete a lot. So do people. How is this handled in fiction? (Usually by ignoring it!) Where do things come from, and where do they go? Thinking about this some can help to create a world that feels real. Energy too: where does it come from?

And then there’s the impact of new technologies. It seems so obvious in retrospect, but nobody considered how water use would increase when it became easy to use it. The city had to struggle to catch up, and the bay will never be the same. That kind of threshold event can make for a great story.

What are the human and environmental consequences of the next great thing?

I’ve written about 3D printers here before, but that was ten months ago and new things keep appearing. And they’re all so science-fictional.

How about building on the moon? Scientists at USC have come up with a plan to use lunar regolith to make concrete, and use that concrete in a giant 3D printer to build housing. Robots could do the building, so we could show up and move right in.

It’s only a tiny bit less science-fictional to use them to build structures here on Earth.

I mentioned previously that scientists were working on ways to build organs with 3D printers. How about a lower jaw? The Belgian and Dutch physicians and engineers built the jaw from fused titanium and implanted it. The elderly recipient did not have to undergo intensive reconstructive surgery, and could speak and swallow the day after receiving the implant.

My third new project isn’t as snazzy, perhaps, but I’m fascinated anyway. Using an Open Source 3D printer, Open Source modeling software, and public data from the UGSG, David Hirmes built a 3D map of the Hudson River valley. I think that’s dreadfully neat. How could the ability to readily create tangible 3D models of data be used in science? Education? Art? What else can we map, and what can be done with those maps?

(Photo by David Hirmes. Used by permission.)

3D printing has even found its way into fashion, something long-predicted by SF authors like Ian McDonald. Business is catching on too.

If you had a 3D printer, what would you make? Or do you already?

[Ed: I'm very pleased to be inaugurating Science in My Fiction's new irregular series of guest posts by noted scientists and authors today. Our first guest is Tobias Buckell, who blogs regularly about science and writing. Buckell's novel Arctic Rising, about the effects of global climate change on the Arctic, came out yesterday. I asked him to write about climate change and science fiction for us, and he was kind enough to oblige.]

Several years ago I was lamenting the fact that few science fiction writers seemed to be writing stories about climate change with Karl Schroeder, one of my favorite writers. He was also a bit gobsmacked. We were, after all, science fiction writers. Here was this vast area. We’d each admitted to holding off writing stories playing with any ideas there because we expected some of the field’s greats to be rushing in on it… any day. And after a year or two passed by, we decided to co-write a short story called Mitigation that explored the polar north after the ice had melted.

The idea wouldn’t let me go, though, even after finishing a story. I wrote a few more stories set in the near future, and enjoyed the debates and reactions they created. So somewhere in and around early 2008 I began sketching out the ideas for a novel called Arctic Rising.

I also picked up another friend who was doing just what Karl and I were hoping to see more of. Paolo Bacigalupi blew my mind every time I met him with more fascinating stuff that was going on. While Karl was a bit more of a techno-optimist than I am and Paolo a bit more worried about the negatives of what was around the corner, I began to think about my novel threading the difference between the two.

Basically because I find climate change fascinatingly complex. You get more access to oil after the ice goes away. Temperature rises, but as a result of melted ice caps, dumps more snow in areas. It looks like there’ll be more arable land in Canada and Siberia. These things will rearrange global power, patterns, focuses, and create land and resource rushes and booms.

And conflict. Which is of course something a writer enjoys. Conflict powers plot. So all that stuff makes for interesting stories. As I pulled all the pieces of research together from the US Navy, climate change reports, and basic newspaper and science articles that I’d been clipping for three or more years, the broad elements of Arctic Rising locked into place pretty easily.

Science in My Fiction is looking for writers, people interested in sharing neat science topics with the science fiction community. The ideal topic is of interest to both readers and writers in our genre, and presented at a not-too-technical level. While many of our writers have formal scientific training, that is not at all necessary.

We are not interested in reviews or non-science topics, nor are we currently soliciting fiction.

To apply, please email sarah.goslee at gmail dot com with a brief description of your qualifications and why you’re interested in SiMF, and either a link to relevant online articles you’ve written or a sample of your work that would be appropriate for SiMF.

In December 2010, NASA announced a momentous discovery: bacteria that could use arsenic instead of phosphorus in its genetic material, a direct substitution in the DNA. This would be a huge deal if true, rewriting much of what we know about basic biology. People were hoping for alien life forms, but this would be nearly as important, if much less glitzy.

We already knew that bacteria could use arsenic in their metabolism; the ability to use it in their DNA would mean that they didn’t need phosphorus at all. The most abundant elements in living organisms are: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. All are believed to be essential for life. Substituting arsenic for phosphorus would alter that basic principle.

Scientists were immediately skeptical of the claims of Dr. Wolfe-Simon and her colleagues. Many insightful critiques were published online, but the authors of the original paper stated that they would only answer peer-reviewed rebuttals. Our own Dr. Athena Andreatis discussed the arsenic findings on her blog, and for Science in My Fiction.

Such a tremendous claim requires immaculate science and immaculate reporting, and neither were apparent.

In June 2011, the original paper finally saw print in Science (it had been available online since December). The reason for the delay: eight additional peer-reviewed technical comments on the original paper, and a response to those comments by the original authors.

I read all of them carefully with the intent of writing a summary to accompany my earlier essays about the arsenic bacteria, but never did. The short version of what I would have said: The eight comments pointed out several errors in methods and analysis. Some of the most major problems were described by several of the comments. I’m not the right kind of biologist to appreciate the nuances of molecular technique, but these descriptions of failings in the research were convincing.

Dr. Wolfe-Simon’s response boiled down to, “We did so do it right.” There wasn’t a substantive response to any of the problems raised.

The story isn’t over, but perhaps close. Dr. Rosie Redfield, one of the most outspoken critics of the original study and author of one of the Science comments, has tried to replicate the arsenic study with stricter methods and failed. Dr. Redfield and her colleagues found no arsenic in any of the bacterial DNA.

The original study appears to be a case of how not to do science. Based on interviews, Dr. Wolfe-Simon and her collaborators set out to demonstrate that this particular bacterium could substitute arsenic for phosphorus, and did not consider alternative scenarios or design methods that might clearly disprove their hypothesis. Their results were rushed into public without adequate peer review, but with much fanfare from NASA.

But since then, science has proceeded exactly as it should. Other scientists have raised issues in clear, technical fashion, and have tried to replicate these controversial results with more appropriate methods.

Although the key bits are or will be peer reviewed, much of the discussion has occurred openly on the internet, at least among the critics. None of the authors on the original paper have spoken up publicly, to the best of my knowledge, and have only responded to the comments that appeared in Science.

This has been a fascinating story to follow, but for the way the research was presented and followed up on than for the findings themselves. I try to end these articles with some consideration of story ideas. Here, I think the story comes from the people involved, rather than the science itself. (As, arguably, all the best science fiction does.) The discovery could have been anything, but the misinterpretation, critique and defense are what make it so interesting.

Edit (1 Feb. 2012): Dr. Redfield has now posted her mansucript on Arxiv for public comment. I have not read it yet, but wanted to let you know.

Or to 2012, at least. Changing the numbers on the calendar often prompts me to think about calendars, and I’m not the only one. This year even more so than usual, what with all the Mayan calendar hype, and a proposed calendar reform in the news.

What’s wrong with what we’ve got, and why are calendars so complicated anyway?

Read the rest of this entry »

In the US, many of us are thinking about eating and digestion right now, after a holiday devoted to food. We usually think about digestion the way we do it, with food going in the mouth and into the gut, where the nutrients are extracted, and the waste products coming out the other end: a big tube, essentially. But we don’t have to resort to science fiction to come up with other ways to obtain nutrients: there are lots of options right here on Earth. Some of those methods might even inspire your next aliens.

Some very simple animals don’t have digestive systems at all. The single-celled Paramecium scoops in food particles and surrounds them with a membrane forming a vacuole, a space sealed off from the rest of the Paramecium cell. That separation is needed so the enzymes that break down the food particles don’t also digest the Paramecium.

Many sponges and other aquatic organisms do something similar, filtering food out of the water and getting the nutrients out without a distinct digestive system. This system doesn’t work if the animal doesn’t live in the water, or is big enough that all its cells aren’t directly immersed. Bigger, terrestrial, and faster animals (being active requires taking in more resources) had to come up with more efficient solutions.

Some of those solutions are pretty weird, at least from our perspective.

How about external digestion? Fungi do this, and spiders. Release digestive enzymes into the environment, let them do their thing, slurp up the predigested food. Fungi are unspecific about it, digesting all or most organic matter in the general area (decomposers, very important!). Spiders are more selective: they inject the enzymes into their prey and wait. That’s why a spider bite can be such a horrid experience: your flesh is being digested while you’re still using it.

Or how about coprophagy? Feces eating can be a normal part of the digestive process, not just a disgusting habit of your pet dog. Grasses are very hard to digest, since vertebrates can’t break down cellulose, so they need help from microbes that can break it down. Coprophagy is one method for making this system work. Rabbits partially digest their food, then excrete it. They eat the partially digested pellets and finish the digestive process. The feces after the second digestion is really a waste product, not an intermediate step, and isn’t eaten.

Ruminants such as cows took the opposite approach to having multiple digestions. They eat grass and start to digest it, then regurgitate the cud and chew on it for a while to further break it down. The second time it’s swallowed, it’s thoroughly digested and the nutrients extracted.

So which alien would you rather sit down to a diplomatic dinner with: a ruminant or a coprophage? And what would they find disgusting about our eating and digestion?

I don’t think a filter feeder is likely to evolve intelligence, but how about trying to design a system where that works. Nonsentient aliens with different digestions could be helpful or harmful to people trying to colonize a planet.