Posts Tagged ‘alien life’

“Arsenic” Life, or: There Is TOO a Dragon in My Garage!

Note: This article was originally posted at Starship Reckless.

GFAJ-1 is an arsenate-resistant, phosphate-dependent organism — title of the paper by Erb et al, Science, July 2012

Everyone will recall the hype and theatrical gyrations which accompanied NASA’s announcement in December 2010 that scientists funded by NASA astrobiology grants had “discovered alien life” – later modified to “alternative terrestrial biochemistry” which somehow seemed tailor-made to prove the hypothesis of honorary co-author Paul Davies about life originating from a “shadow biosphere”.

As I discussed in The Agency that Cried “Awesome!, the major problem was not the claim per se but the manner in which it was presented by Science and NASA and the behavior of its originators. It was an astonishing case of serial failure at every single level of the process: the primary researcher, the senior supervisor, the reviewers, the journal, the agency. The putative and since disproved FTL neutrinos stand as an interesting contrast: in that case, the OPERA team announced it to the community as a puzzle, and asked everyone who was willing and able to pick their results apart and find whatever error might be lurking in their methods of observation or analysis.

Those of us who are familiar with bacteria and molecular/cellular biology techniques knew instantly upon reading the original “arsenic life” paper that it was so shoddy that it should never have been published, let alone in a top-ranking journal like Science: controls were lacking or sloppy, experiments crucial for buttressing the paper’s conclusions were missing, while other results contradicted the conclusions stated by the authors. It was plain that what the group had discovered and cultivated were extremophilic archaea that were able to tolerate high arsenic concentrations but still needed phosphorus to grow and divide.

The paper’s authors declined to respond to any but “peer-reviewed” rebuttals. A first round of eight such rebuttals, covering the multiple deficiencies of the work, accompanied its appearance in the print version of Science (a very unusual step for a journal). Still not good enough for the original group: now only replication of the entire work would do. Of course, nobody wants to spend time and precious funds replicating what they consider worthless. Nevertheless, two groups finally got exasperated enough to do exactly that, except they also performed the crucial experiments missing in the original paper: for example, spectrometry to discover if arsenic is covalently bound to any of the bacterium’s biomolecules and rigorous quantification of the amount of phosphorus present in the feeding media. The salient results from both studies, briefly:

— The bacteria do not grow if phosphorus is rigorously excluded;
— There is no covalently bound arsenic in their DNA;
— There is a tiny amount of arsenic in their sugars, but this happens abiotically.

The totality of the results suggests that GFAJ-1 bacteria have found a way to sequester toxic arsenic (already indicated by their appearance) and to preferentially ingest and utilize the scant available phosphorus. I suspect that future work on them will show that they have specialized repair enzymes and ion pumps. This makes the strain as interesting as other exotic extremophiles – no less, but certainly no more.

What has been the response of the people directly involved? Here’s a sample:

Felisa Wolfe-Simon, first author of the “arsenic-life” paper: “There is nothing in the data of these new papers that contradicts our published data.”

Ronald Oremland, Felisa Wolfe-Simon’s supervisor for the GFAJ-1 work: “… at this point I would say it [the door of “arsenic based” life] is still just a tad ajar, with points worthy of further study before either slamming it shut or opening it further and allowing more knowledge to pass through.”

John Tainer, Felisa Wolfe-Simon’s current supervisor: “There are many reasons not to find things — I don’t find my keys some mornings. That doesn’t mean they don’t exist.”

Michael New, astrobiologist, NASA headquarters: “Though these new papers challenge some of the conclusions of the original paper, neither paper invalidates the 2010 observations of a remarkable micro-organism.”

At least Science made a cautious stab at reality in its editorial, although it should have spared everyone — the original researchers included — by retracting the paper and marking it as retracted for future reference. The responses are so contrary to fact and correct scientific practice (though familiar to politician-watchers) that I am forced to conclude that perhaps the OPERA neutrino results were true after all, and I live in a universe in which it is possible to change the past via time travel.

Science is an asymptotic approach to truth; but to reach that truth, we must let go of hypotheses in which we may have become emotionally vested. That is probably the hardest internal obstacle to doing good science. The attachment to a hypothesis, coupled with the relentless pressure to be first, original, paradigm-shifting can lead to all kinds of dangerous practices – from cutting corners and omitting results that “don’t fit” to outright fraud. This is particularly dangerous when it happens to senior scientists with clout and reputations, who can flatten rivals and who often have direct access to pop media. The result is shoddy science and a disproportionate decrease of scientists’ credibility with the lay public.

The two latest papers have done far more than “challenge” the original findings. Sagan may have said that “Absence of evidence is not evidence of absence,” but he also explained how persistent lack of evidence after attempts from all angles must eventually lead to the acceptance that there is no dragon in that garage, no unicorn in that secret glade, no extant alternative terrestrial biochemistry, only infinite variations at its various scales. It’s time to put “arsenic-based life” in the same attic box that holds ether, Aristotle’s homunculi, cold fusion, FTL neutrinos, tumors dissolved by prayer. The case is obviously still open for alternative biochemistry beyond our planet and for alternative early forms on earth that went extinct without leaving traces.

We scientists have a ton of real work to do without wasting our pitifully small and constantly dwindling resources and without muddying the waters with refuse. Being human, we cannot help but occasionally fall in love with our hypotheses. But we have to take that bitter reality medicine and keep on exploring; the universe doesn’t care what we like but still has wonders waiting to be discovered. I hope that Felisa Wolfe-Simon remains one of the astrogators, as long as she realizes that following a star is not the same as following a will-o’-the-wisp — and that knowingly and willfully following the latter endangers the starship and its crew.

Relevant links:

The Agency that Cried “Awesome!”

The earlier rebuttals in Science

The Erb et al paper (Julia Vorholt, senior author)

The Reaves et al paper (Rosemary Rosefield, senior author)

Images: 2nd, Denial by Bill Watterson; 3rd, The Fool (Rider-Waite tarot deck, by Pamela Cole Smith)

Life, Death, and Water Mythology

I’ve been anxiously awaiting the release of Disney’s Pirates of the Caribbean: On Stranger Tides for some time. The movie is loosely based on Tim Power’s  novel by the same name. In anticipation of this event, I talked my fearless editor into letting me celebrate with a post or two.

While chatting about potential topics related to the movie centering around water and the fountain of youth, she mentioned water myths in the context of space travel. I was surprised at first. I so seldom think about such things when I consider space exploration. Sure on alien lands, encountering alien cultures I can absolutely see it. I just don’t think of any kind of belief system in relation to spaceships and travel. The one exception might be John Scalzi’s  The God Engines.

Ok so let’s try an experiment. I am going to share with you locations, creatures, and ideas both real and fantastic that belong to our collective human mythology involving water. They will be direct quotes from various sources.  As you read over them, try and think how they might fit into stories involving space travel. Are you with me? Good. Read the rest of this entry »

(W)hole Hearted

In preparation for this month’s post, I’ve been reading up on the heart. The post was inspired by my friend, Francesca Forrest’s, recommendation that I read The Sublime Engine: A Biography of the HUMAN HEART by Stephen Amidon and Thomas Amidon, MD. NPR had done a piece on the book discussing the man that toured Europe with a hole in his chest that allowed folks to see his heart hard at work deep within his chest. I was intrigued. Read the rest of this entry »

Non-Conformist Aliens Wanted

It occurred to me the other day that many fictional alien species conform to a small number of body plans: humanoid, insectoid, feline, robot, and reptilian. There’s a huge amount of creativity in appearances and cultures, admittedly, but most races out there fit one of those body plans. The Wikipedia list of fictional aliens is a good overview, for the above and other body plans, though it’s definitely not complete.

I realize there are reasons why most aliens are humanoid or nearly so. It’s easier to sympathize with something that looks human. It’s easier to conceive of aliens based on familiar Earth species. It’s easier to put make-up on an actor than to deal with CGI, or it was until recently. Still, why doesn’t more science fiction push the envelope? Why don’t we see more unusual body plans? It’s not as though we’d have to create entirely new physiologies, though we need those too. Earth has a whole host of creatures that have been underutilized in science fiction, including a few with proven intelligence.

Sharks, for instance, are ancient. They have cartilage instead of bone. They sense electricity and have an excellent sense of smell. They have problem-solving and social skills. There are documented cases of parthenogenesis. They’re built for predation and we’re already conditioned to cast them as villains.

Octopuses, corvids, parrots, and dolphins also have intelligence, or at least use tools and solve problems. Ravens can mimic sounds and have a wide range of calls, often for social purposes. Parrots are capable of communicating with humans. Dolphins have proto-language as well and are highly social. When was the last time you saw them (or parrots, or octopuses, or sharks) cast as aliens? Well, except for Hitchhiker’s Guide to the Galaxy…. Other possible species include: horseshoe crabs, trilobites, rabbits, elephants, slime molds, moss, bacterial hive-minds, and marsupials, including monotremes.

And as I mentioned above, we need more entirely new physiologies too. Species that don’t match up with the Earth life we’re familiar with, or even with our extremeophiles. If we make the environment first, the species second…

One possible environment, close to home: the diamond oceans of Uranus and Neptune. This would be a hot, high pressure place to live. There probably wouldn’t be a lot of gas mixed into the diamond, let alone oxygen, so either the aliens wouldn’t breathe, they’d use a system like photosynthesis where they’d break down carbon for energy, or they’d be like whales, surfacing to breathe hydrogen, helium, or methane (those being the abundant gases). The aliens would almost certainly be carbon-based, and would consume other carbon-based life for energy. They’d likely evolve something like fins or flagella to propel themselves. Maybe they’d use jet propulsion.

There’s no reason why these aliens couldn’t evolve intelligence or even civilization, though I doubt they’d achieve buildings as we know them, because short of building on the solid-diamond floes, there’d be nothing solid, and the caps probably wouldn’t be all that stable. I can see floating structures tethered together, however, provided the aliens had something to build with. Perhaps after millennia of them using these structures, they’d adapt to them, becoming more amphibious than aquatic or losing the flippers and gaining something more like hands. Or perhaps not.

I have no idea what first contact will look like when we make it. The realistic version, of us finding microbes on Mars or one of Jupiter’s moons, lacks a certain something, though I’ll be pleased when it happens. But wouldn’t it be great if we ran into alien blue jays or giant platypuses or sentient hammerhead sharks?

An earlier, rougher version of this essay was posted on my blog, Specnology.

Once Again with Feeling: The Planets of Gliese 581

Gliese 581 may be small as stars go, but it looms huge in the vision field of planetfinders.  As of late last week, measurements indicate the system has six planets of which three are Earth-size and -type, within the star’s habitable zone, with stable, near-circular orbits.

The Gliese 581 system has a persistent will-o-the-wisp quality.  Almost each of its planets (c, d, e and now g) has been pronounced in turn to pass the Goldilocks test, only to have expectations shrink when the data get analyzed further.  The first frisson of excitement arose when 581c was determined to be Earth-type, which quickened the usual speculations: atmosphere? water? life?  We don’t know yet and our current instruments cannot detect biosignatures at that distance (short of an unencrypted request for more Chuck Berry).  But there are some things we do know.

Gliese 581 is a red dwarf, a BY Draconis variable.  This makes it long-lived; on the minus side, it may produce flares and is known to emit X-rays.  Planets in its habitable zone are so close to it that they are tidally locked, always presenting the same face to their star.  The temperature differentials resulting from the lock imply hurricane-force winds and tsunami-like tides.  Gliese 581g, like 581c, is large enough to retain an atmosphere; the hope is that, unlike 581c or Venus, its specific circumstances have not resulted in a runaway greenhouse effect.

The real paradigm shift is the discovery that this solar system has many earth-size rocky planets, in contrast to the hot-Jupiter/hot-Neptune preponderance in most others.  The second enticing attribute of Gliese 581 is its relative closeness — a distance of merely 20 light years.  It is still millennia away by our present propulsion systems.  But I nurse the dream that if we see anything remotely resembling a biosignature, we will strive to reach it.  In the meantime, I suggest we give it a name that fires the imagination.  Perhaps Yemanjá, the Yoruba great orisha of the waters, in the hope that the sympathetic magic of the name will work.  Perhaps Kokopelli, the trickster piper of the American Southwest cultures, who may entice us thither.  I will conclude with the final words of my first article on Gliese 581:

“Whether Gliese 581c [g] is so hospitable that we could live there or so hostile that we could only visit it vicariously through robotic orbiters and rovers, if it harbors life — even bacterial life, often mistakenly labeled “simple” — the impact of such a discovery will exceed that of most other discoveries combined. Unless supremely advanced Kardashev III level aliens seeded the galaxy like the Hainish in Ursula Le Guin’s Ekumen, this life will be an independent genesis, enabling biologists to define which requirements for life are universal and which are parochial.

At this point, we cannot determine if Gliese 581c [g] has an atmosphere, let alone life. If it has non-technological life, without a doubt it will be so different that we may not recognize it. Nor is it a given, despite our fond dreaming in science fiction, that we will be able to communicate with it if it is sentient. In practical terms, a second life sample may exist much closer to home — on Mars, Europa, Titan or Enceladus. But those who are enthusiastic about this discovery articulate something beyond its potential seismic impact on biology and culture: the desire of humanity for companions among the sea of stars, a potent myth and an equally potent engine for exploration.”

Images: Top, comparison of the Sun and Gliese 581 habitable zones (the diagram is by Franck Selsis, Univ. of Bordeaux; the image of 581g was originally created for 581c by Ginny Keller); bottom, Kokopelli playing his flute.

The color of alien pants

On June 4, Peggy Kolm posted her article Red hills of distant planets. Prior to that date, one title proposed for the article was “The color of alien plants”. During a discussion about the article, the proposed title was misheard as “The color of alien pants“. And the idea for this article was born.

Really, what color would alien pants be? And for that matter, would they wear them at all? This isn’t to suggest that all aliens are exhibitionists: maybe they just don’t need clothing.

Human use of clothing dates back (most likely) between 100,000 and 500,000 years. Its main purpose (initially) was protection against environmental threats; as humans evolved and lost natural physical protections like body hair, we needed extra help surviving harsh weather and difficult terrain. Clothing has evolved along with us, growing more sophisticated as we have: sewing needles date back as far as 30,000 years; flax fibers are known to have existed 30,000 years ago; and there’s strong evidence that humans have been weaving for a good 10,000 years or more.

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Red hills of distant planets

Imagine you are standing in a jungle. You are surrounded by lush healthy foliage;  a sea of green, perhaps punctuated by the occasional flower in a contrasting hue.

Now imagine yourself on a distant planet with similarly abundant plant life. What would it look like?  It might well be scarlet or vermilion, rather than verdant.

Most Earthly plants are green because contain the pigment chlorophyll, which reflects green light and absorbs red and blue light. The energy from the light absorbed by chlorophyll is used for photosynthesis – the conversion of carbon dioxide into sugars and other organic compounds.

Along with green light, chlorophyll also reflects near-infrared light – called the “red edge” – which is invisible to the human eye, but can be detected remotely using near-infrared sensitive cameras. Currently satellites use such systems to remotely monitor the health of vegetation on Earth. That ability makes chlorophyll detection a reasonable potential molecular signature of extraterrestrial life.

But it may wrong to assume that plant life (or the equivalent) on other planets will necessarily be green.

Once the light from our Sun is filtered through the ultraviolet light-absorbing ozone layer, more photons at the red end of the spectrum reach the Earth’s surface than at other wavelengths. It makes sense, then, that Earthly plants primarily use red light.

A planet that orbits a star hotter than our own sun or that has an atmosphere that absorbs a different range of wavelengths than Earth’s, might have a greater abundance of blue photons than red photons on its surface. Orange or red plants might dominate there.

And Washington University chemist Robert Blankenship has suggested that alien plants might use black pigments that absorb all visible wavelengths of light. That might be necessary for plants on planets orbiting cool red dwarf stars.

The only plant color that is considered to be unlikely is bright blue, since that would mean that high energy blue light is being reflected from the leaves, rather than utilized.  But I consider that to mean  that blue plants are unlikely, not impossible.

So how are plants portrayed in science fiction?

H.G. Wells’ invaders in the War of the Worlds carried invasive red-colored weeds to Earth. That fits nicely with the notion of Mars as the “red planet”, but isn’t really based on biology – not too surprising, since photosynthesis was not well understood in the early 20th century.

Other SF novels do include strange and alien plants, but to the best of my recollection they generally have green foliage.  It seems like a missed opportunity to increase the strangeness of alien worlds.

I’d love suggestions for SF stories that do include alien non-green plants in the comments.

Additional Reading

Image (top): “Jungle Green” by Flickr user JoetheLion, recolored
Image (bottom): “Jungle Green” by Flickr user CaptPiper, recolored

Alien Languages: Not Human

Contrary to Hollywood and the majority of fictional languages, alien languages are almost certainly not going to look like human ones. They’re not going to have the same sounds, the same word orders, or the same way of solving problems like time, direction, and ownership. Why? Because human DNA and culture help determine what human languages look like, and aliens will, by definition, not share that background.

That’s not to say there won’t be similarities, though. Because language is a communication system and therefore has to convey information efficiently, there are some facts that won’t change.

On Neurobiology

The ability to use language will be coded in the aliens’ genes. Either the aliens evolved language and have basic linguistic structures in their brains at birth, or every individual has to independently invent the language from scratch. With humans, we call this nativism and it applies to a whole range of mental traits, not just language.

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You Only Find What You’re Looking For

Author’s Note: This is the first SiMF post picked up for reprinting by io9 — I know it will be the first of many!

Extraterrestrial life is a staple of SF and the focus of astrobiology and SETI.  Yet whereas SF has populated countless worlds with varying success, from Tiptree’s haunting Flenni (Your Haploid Heart) to Lucas’ annoying Ewoks, real ETs remain stubbornly elusive: nobody has received a transmission demanding more Chuck Berry, and the data from the planetary probes are maddeningly inconclusive.  Equally controversial are the shadowy forms on Martian asteroid ALH84001, although the pendulum has swung toward cautious favoring of the biological possibility after scientists discovered nanobacteria on earth and water on Mars.

In part, we’re hobbled by the limits of our technology, including the problems of sample contamination and method-specific artifacts.  But we’re also severely limited by having a single life sample.  Despite its dizzying variations in form and function, extant terrestrial life arose from one source.  We know this because our genetic blueprint and its associated molecular machinery are identical across the three domains (archaea, eubacteria, eukarya).  So to be able to determine if something is alive, we need to decide what is universal and what is parochial.  We stumble through redefinitions each time our paradigms shift or our techniques achieve higher resolution.  Worse yet, our practices lag considerably behind our theories.

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