Abiogenesis, chirality and narrowing down the alternatives

In the great “mythmaking” that is the scientific process, discovering things about events long lost to history is done a little bit differently than the method might suggest in more mundane circumstances. We develop plausible hypotheses regarding events like the abiogenesis event that occurred here on Earth, and then test them rigorously attempting to falsify each one in turn. Like Sherlock Holmes, or Dr. House, we’ll get to the kernel of the matter by eliminating all the alternatives until we are left with but one plausible truth. We know we’re on the right track when predictions about certain aspects of the theory are demonstrable in laboratories.

We may never learn the exact nature of the exact abiogenesis event that led to us (among multiple possible such events) any more than we’ll know the exact daily routine, shape, facial features, birthday or date of death of the single individual last common ancestor (among multiple possible last common ancestors of that ancestor’s species) between us and chimpanzees, but we know (by genetic and fossil evidence) that we are not that far removed. This should not matter in the investigation of how it could have happened — despite the fact that there are many theories about the event of abiogenesis. We know the first chemicals breached that fuzzy boundary between “mere chemical reaction” and “self-perpetuating chemical reaction” — in other words, between non-life and life — so we know abiogenesis had to happen somewhere. If it didn’t happen here, and we got here by panspermia, then it happened elsewhere in the universe first, but it happened once at the very least.

New research has been very promising as of late with regard to the greatest mystery our planet yet holds, potentially unlocking each of the sub-mysteries one at a time with plausible answers. One of these sub-mysteries involves the chirality of all life on Earth — every amino acid this planet uses as its biological Lego can exist in a right-handed or a left-handed form and would spontaneously form either one at identical odds, but every speck of life on this planet uses only the left-handed version. With our ever-improving knowledge of the early environment of the planet, we’ve discovered that aspartic acid trends sinistral, creating left-handed versions in large quantities in a crystalline structure under those conditions. This certainly does not confirm the theory, but it provides a good hypothetical “seed” that explains how the amino acids that form us all tended to be left-handed.

There’s also the question of why those simple building blocks like aspartic acid might have influenced the other amino acids that self-generated in the environment to follow suit in their chirality. So, scientists built on the earlier result and introduced the left-handed acids into an environment with equal proportion left- and right-handed amino acids, and found the left ones crystallized much like the aspartic acid crystal in the earlier experiment.

“These amino acids changed how the reactions work and allowed only the naturally occurring RNA precursors to be generated in a stable form,” said Hein. “In the end, we showed that an amazingly simple result emerged from some very complex and interconnected chemistry.”
The natural enantiomer of the RNA precursor molecules formed a crystal structure visible to the naked eye. The crystals are stable and avoid normal chemical breakdown. They can exist until the conditions are right for them to change into RNA.

This experiment had every possibility of falsifying the earlier hypothesis but it did not. More research will either disprove both these hypotheses, or confirm them repeatedly over many iterations until our confidence level has increased so that they’re the best plausible explanations. Or, who knows? Perhaps we’ll one day unearth some new evidence, and we’ll need a better explanation to incorporate that new knowledge.

That’s how science works.

How we know things in science, and how we can know things about abiogenesis

Nicked from astrobio.net on the Miller-Urey experiments. That's the actual equipment used

On this blog post over at Greg Laden’s, I’ve made a damn fine effort (if I do say so myself) at explaining the process of scientific inquiry to a pair of commenters who’ve taken issue with the idea that anyone could know anything about the event of abiogenesis — the “Origin of Life”, when the fuzzy boundary between chemicals and life was first breached — that happened on this planet. I’ve agreed with them on a number of points, including Anthony’s main thesis, that there was exactly one way that this universe’s past has unfolded, exactly one “truth” to any event in history, and that as a result, figuring out that exact truth is nearly impossible short of having been there to witness it yourself. He accuses the current scientific establishment of “decadence” (belittling our blog friend DuWayne in the process), and of “ideological materialism” wherein the elite of the scientific world are beholden to assume materialism lest their entire epistemology crumbles beneath them.

Luckily, science doesn’t work that way or we’d have stopped investigating this universe long ago.

The scientific method can be implemented to attempt to model events that it cannot prove with 100% certainty happened in exactly one way. By learning about the past, through the physical and inferential evidence we have available to us, we can develop hypotheses which are testable today. If our hypotheses about the past are correct, we can then correctly predict the results of these experiments, and if the experiments are carefully enough crafted, they can disprove the hypotheses and force us to start over. In the specific case of the abiogenesis event that occurred on this planet, we might never know the exact formula that resulted in our exact lineage. This should not stop us from taking the evidence we have available to us, the direct and inferential physical evidence that shows how this planet was very likely composed chemically in the early pre-biotic environment, and extrapolating from that knowledge that perhaps self-arranging lipids and amino acids might have formed.

The Miller-Urey experiment in 1953 took some of our best guesses about the pre-biotic environment and attempted to verify the Oparin-Haldane hypothesis that it would allow for amino acids to self-arrange. When the experiment was complete, they were proven correct. Amino acids — the building blocks to life itself — formed spontaneously, without direction, in an environment that was like science’s contemporary understanding of the early Earth. If this experiment had failed, it would have put a nail in the coffin of the abiogenesis theory, though not the last one, certainly. The fact that it succeeded suggests one of two things: 1) amino acids might spontaneously emerge in a number of environments, or 2) we got lucky and hit upon the correct way to create amino acids but did not replicate the early Earth, thus disproving abiogenesis. The former is far more likely, for obvious reasons — not ideology, but pure math. If there are a near infinite set of environments that the planet could have had, then there are a near infinite set of environments to test. The problem comes down to one of narrowing — if we know the early Earth had to have ammonia (to provide the organic compounds necessary), then we’ve excised all models that do not include ammonia. Scientists later discovered a photochemical reaction of nitrogen that would provide this ur-Earth with the necessary ammonia. Meanwhile, we narrow our options down significantly with each new piece of evidence.

The fact that better evidence turned up suggesting that the early environment was actually significantly different from the conditions replicated in the Miller-Urey experiment should thus hardly come as a surprise, though the actual early environment is still hotly debated among scientists. Miller tried again in 1983 with the newer data, but came up empty — hardly any amino acids to be found. However, Professor Jeffrey Bada repeated the experiment with an even better approximation of the early environment, e.g. that Miller’s second test had omitted iron and carbonate, and amino acids were once more formed spontaneously through nothing more than pure chemical interactions in the simulated environment. And that certainly isn’t the only such related test.

Two different environments, both resulting in amino acids. Certainly the later test benefits from the extra evidence collected about the early Earth, but getting amino acids in multiple different environments bodes well for our ability to show that every step in the grand staircase toward biology is plausible. We know that the lipid bilayer necessary to create a cell membrane can self-arrange as an emergent property of the lipid’s intrinsic hydrophobia (fear of water) on one side, hydrophilia on the other. They’ll form up all by themselves without prompting, given the right environment. So will RNA nucleotides, meaning if the RNA-world hypothesis is correct, we’re well within our rights to suggest that the hypothesis is the one that best fits the available evidence and make further predictions and experiments from there.

None of this is, you’ll notice, an attempt at building a narrative of “how things definitely happened”. People will often demand such a thing, knowing that they cannot themselves replicate experiment results, nor comprehend their interconnectedness with other such experiments if they’re even aware of these other experiments, nor suss out how all the pieces of the puzzle ultimately fit together. I understand this drive — the drive to build a narrative that is easily digested — because every human being has it. It is that drive that frees up one’s mind to contemplate other things, like immediate survival concerns or reproduction or the pursuit of leisure. It is that drive that one combats when arguing with people who cling tenaciously to their received dogmas. The temptation is great to replace one dogmatic narrative with another. But the scientific worldview demands that we understand that our understanding of this universe may never reach 100% certainty about any single topic or event, but as we slowly polish and chip away at the theories we have built, we can bring them to within impressive degrees of certainty that put any former, more dogmatic, effort at explaining the universe to shame.

The level of certainty that Andrew believes we are expressing about the study of abiogenesis is galling, and his repeated insistence that scientists are engaging in myth-making betrays his lack of understanding of the process. That we don’t know a great many things about the actual abiogenesis event on this planet means nothing, ultimately, in the study of how it might have happened. It is like asking that we know everything about the daily life of the very first ape to climb down out of the trees, or else the theory of evolution is about building a just-so narrative. I’m personally content to allow the process of scientific investigation to grind down all the possibilities until there are but a few left, and we can choose which one fits all the evidence best, until such time that new evidence overturns the model and we are forced to revisit.

That’s how science works, you see. And science does indeed work.

(To within a reasonable degree of confidence.)

Abiogenesis is not spontaneous generation. Period.

During a brief skirmish I had the other day on Twitter with young-Earth creationist Joe Cienkowski (of self-published anti-atheist tract fame), he asserted that the theory of abiogenesis is the same as the now-disproven hypothesis of spontaneous generation. This is, of course, as with pretty well every other assertion about science ever made by Joe, patently false.

Spontaneous generation held that life in its present form today could form from non-life, and did so all the time — for instance, aphids sprang from dew on plants, maggots emerged from rotting meat, and mice were created from wet hay. In 1859, Louis Pasteur performed experiments that put the final nail in the coffin of the hypothesis. He proved definitively that life does not spring, fully formed and unbidden, from any recipe of inorganic or dead organic matter. So the question of the origin of life was reopened for the first time in centuries.

Abiogenesis, on the other hand, does not predict that life in any form known today — not even the simplest single-celled life forms — were created in some flash of magic or through some arcane recipe of components. That would be creation, in the sense of a personal creator deity. Rather, it predicts that, as life is made up of chemical reactions, and the constituent components of life can self-arrange given certain conditions, there is some point in Earth’s early history wherein a chemical chain reaction went runaway and breached the fuzzy barrier between chemistry and biology. All biology is is one single long, unbroken chemical reaction that can be traced back to whatever initial condition sparked it billions of years ago.
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Tyson on abiogenesis

Please note that he does not talk about evolution *at all* until after life has formed. That’s because, as Neil de Grasse Tyson put it, abiogenesis is chemistry, not biology, and only becomes biology after the chain reaction starts. Yes, abiogenesis was once called chemical evolution (as chemicals do have a process by which they will become altered given certain specific catalysts), but just as stellar evolution is a wholly different use of the word evolution, so too is chemical evolution a total misuse of the word which means (and ONLY means) the process by which life has diversified over time.

httpvp://www.youtube.com/view_play_list?p=27DA63FC8AB8DFD9

An interesting addendum on the Miller experiments is that years later, when scientists figured out the initial conditions of life were much different than Miller anticipated, the experiment was redone with even better results, indicating that abiogenesis can occur in a variety of conditions. And the results from the original experiment were revisited fifty years later, and some totally brand new and wholly unexpected amino acids were discovered. Isn’t that fascinating? Don’t the implications boggle your mind?

The 2011 Lousy Year in Review

Happy new year, everyone! Hope 2012, the Year Of Doom, finds you hale and hardy. Remember, rinse your mouth out with water and wait fifteen minutes before brushing your teeth after you’ve vomited, or you’ll wreck the enamel on your teeth. Of course, the same advice goes for after eating an orange, so there’s that.

This is my first time trying something like this. I’ve been blogging since May 2008, and yet I don’t think I’ve ever once gone through my previous posts and highlighted a few things per month like most other bloggers have a habit of doing. This lack of introspection is inexcusable, of course. So, I’ll try right now.
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How strawman arguments and shitty authors undermine #atheism

I haven’t read anything by Anthony DeStefano aside from his anti-atheist screeds on various news journals like USA Today, but I have no doubt merely by looking through the title list that he is a man of deep conviction in that which he cannot see. He’s written a book for children called Little Star, all about how the baby Jesus is very tiny but is our Lord. He’s written a book for grown-up children about how awesome a place Heaven is. And he’s written a book about all those things you can’t see but that the Bible assures you are really really real. And since you know other people believe it, they must really really REALLY be real.

So today we have a Serious Author writing a Serious Article in a Serious Journal about how atheists are superstitious “Materialists” who are simply incapable of comprehending that the parts of this natural world that we haven’t figured out yet are actually impossible to decipher, because God wants it that way.

Of course, it’s not quite fair to say that atheists believe in nothing. They do believe in something — the philosophical theory known as Materialism, which states that the only thing that exists is matter; that all substances and all phenomena in the universe are purely physical.

What nonsense.

We’re off to a running start.
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Scientists investigate ammonia meteorites; science media claims we’re all aliens.

This is a story about meteorites. Well, meteorites, and life. WELL, meteorites, life, and totally misleading headlines.

Pictured: a perfectly normal human wormbaby.
(via some photoshop goon at Worth1000)

I know what you’re thinking. No, this isn’t about the Orgueil meteorite, which in the 19th century caused a ruckus when a conman embedded some grass seeds in it and claimed it proved exobiology. Nor is it about Richard Hoover’s claims, referencing the exact same meteorite, for the third time in his career (first in 2004 then in 2007!). This time around, he’s gaining news traction despite not actually having a discovery. I have precious little to say about it that isn’t already said elsewhere. The Orgueil meteorite is not news, nor is it alien life, no matter how desperately I wish it was.

No, this is, instead, about this science-ish pablum written by the good folks over at The Independent, a UK-based newsish organization. I use the “ish” to denote my skepticism that either adjective fits the subject. In putting together what I can only assume was intended to be a thought-provoking science piece, they’ve succeeded not only in making a mockery of the hunt for life elsewhere in the universe, but also for the hunt for the reasons life exists back at home base. They’ve succeeded also at one more thing, incidentally — in provoking my ire for the unthinking hyperbole that passes for science media these days.

The piece in question begins with the blaring headline: “We’re all aliens… how humans began life in outer space”. Sound like we’re setting up an argument for panspermia, where life itself began elsewhere in the universe and was carried via meteor to Earth by some cosmic happenstance in the projectile ballet we call our cosmos’ set of physics? That’s because other hypotheses have argued for exactly what I’ve described, though they multiply entities unnecessarily and thus Occam’s Razor slices them neatly down to the low probabilities they enjoy presently. And as the rest of the article will soon make clear, they’re not talking about us being aliens at all — only that our constituent components may have extraterrestrial origins. Knowing what we already know about this universe, I have to rebut with: “DUH.” And also: “You’re not an extraterrestrial if you’re born on this planet, asshole.”

The article proceeds from its already rocky start, to making a number of claims that are hardly news and that put the lie to the assertion in the title: the chemicals that make up our planet’s biosphere probably come from outer space.

In fact, a growing body of evidence is now pointing to deep space as the possible source of the raw materials that formed the building blocks of life. The latest study, which focused on a class of meteorites that fell on to the Antarctic ice sheet, also suggests that life’s origins may have been extraterrestrial.

An analysis of the meteorites has revealed that these rocks can be induced, under high pressures and temperatures, to emit nitrogen-containing ammonia, a vital ingredient for the first self-replicating molecules that eventually led to DNA, the molecule at the heart of all life.

Know what else is needed for life? Carbon. Since the only atoms created during the Big Bang were hydrogen and helium, every carbon atom on the planet was built in a star’s supernova billions of years ago. So does that make us “aliens”? Like hell it does. Water probably came from orbital bombardment too — at least, that’s the frontrunner for hypotheses about its origin, but it’d be farly difficult to find the remains of an ice comet billions of years after the fact. The origin of nitrogen, or any other constituent element of the amino acids that are capable of self-arranging and eventually evolving into life as we know it, is certainly an important factor in determining with any level of confidence Earth’s early history.

I will give the scientists a pass. They’re working some pretty detailed experiments that border on the very furthest edge of what we can hope to ascertain about Earth’s early history. They’re not the ones making the odious claims I dislike about the science “reporting” in the Independent. They claimed this:

“What is important is the finding of abundant ammonia. Nitrogen is an indispensable ingredient for the formation of the biopolymers, such as DNA, RNA and proteins, on which life depends, and any theory that tries to explain life’s origin has to account for a supply of ‘usable’ nitrogen,” Professor Pizzarello said. “Therefore, its direct delivery as ammonia and in relatively large amounts from the nearby asteroids could have found a ‘prebiotic venue’ on the early Earth.”

It’s this pullquote that was so obviously mangled not only by the paper’s editor in the ridiculously overinflated headline to pull views, but also by the author of the piece, Steve Connor, in his initial paragraph: “As scientific mysteries go, this is the big one. How did life on Earth begin? Not how did life evolve, but how did it start in the first place? What was the initial spark that lit the fire of evolution?”

He’s describing abiogenesis. While that’s certainly the best theory we have right now, the one that fits all available evidence with the least amount of shoehorning or multiplying entities unnecessarily, that doesn’t mean the people investigating how all this nitrogen got here are even looking sidelong at that aspect of the planet’s history outside the pullquote. Even if abiogenesis wasn’t the accepted theory, there’s every reason to ask “why’s all this nitrogen here to begin with?” It doesn’t have nearly the implications that Connor feels it does, nor that Prof. Pizzarello is quoted as explaining. The galling part about this is, I realize that Pizzarello very likely intended to play science populist in explaining things as he did to Connor. Not every scientist can be their own publicist. Media types evidently have this uncanny knack for pulling the most interesting soundbite from any sentence and blowing the whole story out of all manner of proportion, and I strongly feel the professor was wronged here. I sympathize completely with his excitement, and with his explanation of the implications of his research and why it should continue.

Understanding the nitrogen’s origin, or the origin of any other constituent atom in our biosphere, is a necessary component of any fully formed theory of life’s origins, whether abiogenesis or some other better explanation should one ever come along. It is not, however, a sufficient condition, by any stretch of the imagination. This constant stretching of the truth in science reporting is deplorable in its lack of nuance, and directly leads to much of the mistrust and ill will toward science in general harbored by those people that are burned time and again by the “maybe it’ll cure cancer!” headlines they’re bombarded with daily.

Not every investigation of every phenomenon or historical event is going to unearth the deepest mysteries known to mankind. Sometimes an ammonia-filled meteorite is just an ammonia-filled meteorite.