On the origin of life

First of all, you may have notied something a little different here. I am now a member of Field of Science, a new network of science blogs. You can investigate the other blogs in this network through the links at the top and bottom of this page. All the content from the original blog has been imported here (including your lovely comments), and the original address redirects here, so no need to update your links. At the moment, we're looking a little plain in the visual department, but some massive redecoration plans are in the works.

On to today's topic: life. How exactly did a collection of random chemicals give rise (eventually) to sentient beings? Where did it start?

This question supposes that at some point, a collection of chemicals that were "not alive" found a way to organize themselves into an entity that was "alive." But we immediately run into another, more fundamental issue: what, exactly, is life? How can we distinguish life from whatever came just before it?

Some researchers (see this Wikipedia article, for instance) consider chemicals such as DNA or RNA to be the distinguishing feature of life, and reduce the question of life's origin to looking at how these chemicals were synthesized.

But this perspective, in my opinion, misses the point. Life is a process, not a chemical. The distinguishing feature of life is not what it's made of but what it can do: namely, it can reproduce itself. More precisely, we can define the process of life by this picture:



Or in words:

An entity is alive if it can produce copies of itself using the free energy and materials that are available in its environment.

There are other caveats we may want to add, such as that living entities can tolerate a certain amount of mutation or environmental change without losing their reproductive ability. But self-replication is a good starting point.

Now the question becomes, how could such a process have arisen? Scientists have managed to synthesize a few self-replicating molecules, but the sponaneous formation of such molecules from inorganic matter seems highly unlikely.

On the other hand, nature is full of chemicals that do this:



In this diagram, A plays the role of a catalyst, helping to synthesize B from other chemicals in the environment. The ubiquity of catalysts led Stuart Kauffman to hypothesize that life may not have started with a single self-replicating molecule, but with a collection of catalysts, each catalyzing another in a cycle:



or in a more complex network:



Kauffman called such collections autocatalytic sets. If such a set of chemicals were able to surround themselves with a membrane, and eventually produce enough of themselves so that the membrane would split in two, we could have our very first example of a living cell.

This idea has a number of interesting implications, which I intend to explore in the very near future. In the meantime, enjoy the new site!

Why Darwin?

Charles Darwin turns 200 today. His birthday is the occasion for worldwide celebrations by scientists, and also a few protests by those who still dispute the theory of evolution. 150 years after this theory was published in "Origin of the Species," it remains the primary flashpoint of what some call a war between science and religion. I'd like to take this day to explore exactly why evolution has sparked such a passionate debate, and why even those of us who have no use for the concepts of creation or God might find value in considering the philosophical implications of evolutionary theory.

First, why is Darwin such a hero to the world of science? Before Darwin, biologists could only describe the "what" of nature. Evolutionary theory provided them with the tools to ask "why?" The whole nature of biological inquiry was changed. Beyond that, he showed how every living thing on Earth is connected by a common heritage. Evolutionary ideas have found application in almost every other area of science. An argument could be made that no other single idea has had such an impact on the history of science.

Secondly, why exactly is evolutionary theory so threatening to those who take the Bible literally? It's hardly the only scientific theory to contradict the literal truth of the Bible: scientists knew for decades before Darwin that the earth must be much older than 4000 years. The Big Bang theory has generated much less controversy than evolution, despite its obvious differences from the biblical creation story.

I think that the hidden thread underlying the evolution/creation debate is the question of meaning. Genesis doesn't just give a story for how the earth started, it gives humans a special place and purpose on the earth. It tells us that we are made in God's image, and that we are to fill the earth and be its stewards. Evolutionary theory upends this picture, saying instead that we are the product of a random process, following our genetic impulses, whose only purpose is to ensure the survival of our species.

Of course, it is not the role of science to provide meaning in people's lives. But I do think scientists should ackowledge the philosophical implications of their work, if for no other reason than that it significantly affects how that work is recieved. Having deflated the Judeo-Christian idea of meaning in life, can scientists, in their alternate roles as human beings, help provide an alternative?

My life partner is taking a class at Harvard Divinity School, taught by complex systems guru Stuart Kauffman and theologian Gordon Kaufman, exploring this very idea. Kauffman holds that notions of the "sacred", and even "God" itself, can and should be reclaimed without any reference to the supernatural, that the natural word itself can be our source of spirituality and meaning.

I won't say any more now about Kauffman's ideas because I haven't read his book yet. But I will over the course of the semester, and I'm sure I'll have much more to say about it soon.

Brits and Yanks on the Titanic

Discovery News Top Stories: Manners Lowered Brits' Chances of Survival on Titanic, said my Gmail ad banner. Intrigued, I clicked the link.

It seems behavioral economists David Savage and Bruno Frey, looking through historical records, found that Britons had the highest death rate of any nationality aboard the Titanic, even though the ship's crew was British. There is anecdotal evidence that British politeness contributed to their mortality: Witnesses heard the captain saying "Be British, boys, be British!"--meaning for them to "queue up" and wait for women and kids. Meanwhile, Americans, whom some saw elbowing their way forward to board the lifeboats, had the highest survival rate of any nationality.

Behavior in all animals reflects a delicate balance between cooperative and selfish instincts. Human history, in particular, shows extreme examples of both greed and selflessness. These behaviors, like all others, are evolved; and reflect the multilayered incentives for selfish and altruistic behavior that run throughout evolutionary history.

Assuming Savage and Bruno are correct, it appeared the jerks took the day in this instance. If we suppose that evolutionary history contained many such "Titanic moments", in which the self-interested could elbow out the polite in the struggle for survival, one might conclude that only the selfish would emerge from evolution unscathed.

But there's more to the picture. We'll never know if more could have survived the Titanic had everyone on board worked together. Certainly fewer would have survived had everyone been fighting for a spot on the lifeboats. If we imagine many Titanics sinking in simultaneous, independent events, it's possible that more altruists would survive overall, because boats of mostly altruists would save a higher percentage of passengers than boats filled with arseholes. So there is a sense in which, while selfishness works on an individual level, cooperation may do better on a large scale. (This is essentially the group selection argument I refered to in this post--one of many explanations for why both altruism and selfishness are seen in the products of evolution.)

One can also ask how the social norms in America and Great Britain evolved to be this way. British and American people separated far too recently to have diverged genetically, but the two nations have certainly evolved culturally along different paths. An argument could be made that America, with its vast expanses of open (except for Native Americans) land and looser socioeconomic hierarchy, rewarded bold and individualistic behavior more than old, statified Britain.

Neither British nor American social norms were evolved specifically for the Titanic. Behaviors adapted for one context played out in another, resulting in a higher proportional survival for Americans, perhaps a lower total survival than if all the passengers were British.

In considering the behaviors we'll need to survive in a world of global interconnection and environmental fragility, it's important to remember that behavior evolves in context. If we can anticipate the kinds of behaviors we'll need in the future, can we also anticipate the changes we'll need to make to start evolving these behaviors now?

Update: The Emerging Field of Cultural Evolution

In my last post I asked how a society that evolves through its ideas would differ from one that evolves through its genes. Today I came across a cache of Wired Science blog posts highlighting recent efforts to address this very idea, in a new field that is being called "cultural evolution."

• Paul Ehrlich studied the evolution of canoe design in Polynesia, as a model system for how cultural evolution works in general. He found, not surprisingly, that artistic variation occurred rapidly, whereas variation in the the canoes' functional design was slower (due to the need to be sea-worthy.) (blog post,journal article)



• Simon Kirby et. al. simulated the evolution of a new language. Human subjects were shown a collection of nonsense words, and a picture associated to each word. They were then asked to recall these word-picture associations. Whether or not these recollections were correct, they were used as the basis for a new set of words-picture associations, which were then shown to a new set of subjects. As the associations changed each round based on what people could remember, a structred language began to develop.
  
  In other words, human memory was the environment in which the language was evolving. The more structure in the language, the easier it was to remember, and therefore the more it got passed on. Very cool! (blog post, journal article)



• Arne Traulsen et. al. (the et. al. includes Nowak) found that if you assume a much higher rate of "mutation" in ideas than in genes (a reasonable assumption), you get qualitatively different results. For example, cooperation can become viable in situations where it wouldn't otherwise be. (blog post)

The Future of Human Evolution

For much of the history of life, evolution worked a certain way. Organisms competed for the chance to reproduce. An individual with an advantageous mutation would produce more offspring, which would inherit the advantageous gene, and in this way life continually improved upon itself.

But I would argue that for humans, in the world as it is today, this process is more or less defunct. We are not, by and large, competing with each other to produce more offspring. It's true that some people lack reproductive ability or die before their time, but most people who reach adulthood with their health intact can have as many babies as they want. It is a matter of choice more than a competition. Furthermore, people with genetic defects, who may never have survived in times past, can now (sometimes) lead healthy procreative lives thanks to modern medicine.

This means that the best genes no longer produce more copies. There is no longer a way for advantageous mutations to spread through the population. If these trends continue, we can expect that our gene pool will no longer improve, and may even degrade a bit thanks to advanced health care. The human body and mind are currently as good as they will ever get.

So have humans stopped evolving? As individuals, I would say yes. But our society is clearly still evolving, due a mechanism we evolved in the past million years (back when we were still evolving the normal way): language.

Language allows for the evolution of ideas rather than genes. A person with a good idea can communicate it to others, who, if they like it, can communicate it further. In this way good ideas, rather than good traits, spread through the population.

Here's another way of seeing the difference: for conventional evolution, DNA carries information about traits that successfully spread themselves. For this new form of evolution, language (both oral and written) carries information about ideas that successfully spread themselves.

I don't think any of the above ideas are terribly original. But it occurred to me today that while there are many mathematical models for genetic evolution, I don't know of any good models for the evolution of ideas. And more generally, how does a society that progresses by idea-based evolution differ from one that evolves genetically? The question is so vague I can barely conceive of how to frame it, but it seems very important to the study of humanity's future.

The Punishment Paradox

Why do attempted murderers get less jail time than murderers? Why is a drunken driver who hits a tree punished less than one who hits a person? If our laws are set up to correct behavior, why do they punish according to the outcome of an action rather than the intention?

Questions like these were raised in a talk I heard today by Fiery Cushman who, in addition to having an awesome name, has done some fascinating research on this subject.

It turns out the phenomenon of punishing by outcomes rather than intentions is reflected not just in our legal system, but in our individual behavior. In a variety of experiments, (see his publications page for details) Cushman found that people's decisions to reward and punish, even amoung children as young as five, are based on the result of someone's actions rather than on what the person was thinking.

Interestingly, when asked if they want to be friends with a person, or whether that person is "good," intentionality becomes much more important. Thus, if you throw a rock at me and miss, I'll think you're a jerk, but I won't chase you down the way I would if you'd hit me. (Hah, I'm actually a wimp. I'd go home and cry. But you get the point.)

This talk being part of an evolutionary dynamics class, Cushman turned to the question of how this punishment instinct might have evolved, and why it evolved so differently from moral judgments.

The answers to these questions are still cloudy, but they may have to do with our interactions with the natural (non-human) environment. Consequences in the natural world are based on outcomes: If you climb a dangerous cliff but don't fall, you aren't punished, even though it was still a bad idea. So from these non-social interactions, we're "used" to being punished based on outcomes; in evolutionary terms, we've adapted to it. And according to some of Cushman's experiments, we learn better from outcome-based punishment, because it's what we expect. So punishment evolved to fit our already-established learning patterns. I think. If you're having trouble following this, it's tricky stuff. I can barely follow it myself.

The Evolution of Cooperation

First of all, a personal triumph: I've had my first academic paper accepted! "A New Phylogenetic Diversity Measure Generalizing the Shannon Index with Application to Phyllostomid Bats" is tentatively accepted for publication at the American Naturalist, a venerable biology journal. Whooo!

But on to our main topic: It's one of evolution's oldest riddles. If evolution is a brutal battle for survival, in which only the fittest survive, why do we see so much cooperation in nature? Why, in extreme cases, do some animals sacrifice themselves to help others of their species? In the competition between individuals, genes, and species, what kind of advantage does this altruistic behavior confer?

This question is quite deep and has generated an array of possible answers, whose implications go beyond evolutionary biology. I'll outline the history of how this question has been explored, and offer something of a synthesis to conclude.

• Reciprocation-It pays to help someone else if that person will help you in return. This fact is incontrovertible, and helps explain many of the interactions we see in nature, like monkeys grooming each other. However, reciprocation does not explain the acts of extreme altruism sometimes seen in nature, such as cellular slime moulds that sacrifice themselves to help others find food. So it can’t be the whole story—some actions really are selfless.



• Group selection-This is the idea that Darwinian evolution acts on groups of organisms as well as on individuals. If the members of a group cooperate well together, then the group as a whole may survive, while other less cooperative groups die off. This idea fell out of favor in the 60's as mathematical analysis showed group selection is generally a much weaker evolutionary force than individual selection. New models, however, show that group selection can be important in some circumstances.



• Kin discrimination-This view holds that the real unit of Darwinian selection is not organisms or groups but genes. Since genes are the material that is passed on through generations, the genes that help themselves out will survive the best. So if your gene “sees” that another individual has the same gene, your gene will “want” to help that person out in order to further its own interests. Of course, genes can’t really see each other. But your genes can tell you to help out your relatives, who are likely to have the same genes as you. This is the kin discrimination theory: our genes tell us to help our immediate family members, and thereby further their own gene-centric interests. Preferential behavior toward relatives is commonly observed in animals, and one study even found closely-related plants helping each other out.



• Repeated interactions-Axelrod’s tournaments of Prisoner’s Dilemma games show that, while it may be beneficial to act selfishly in the short run, more cooperative strategies are better if you know you’ll be interacting with someone repeatedly. The best strategies for repeated interactions are those which reward others who cooperate with you and punish those who don’t.



• Spatial structure-Cooperators do best if they’re surrounded by other cooperators. One way this can happen is in ecosystems where offspring are born close to their parents and don’t move much. In this case, the children of cooperators stay and cooperate with their relatives, while the children of selfish bastards hang out with their selfish bastard relatives and be miserable. Thus, systems with a strong spatial structure and little movement tend to favor cooperators. The system breaks down if the selfish bastards can move fast enough to find the cooperators and exploit them. Robert Austin found that spatial separation could help "altruistic" bacteria survive coexist with their "selfish" bretheren.



• Punishment-Evolutionary biologists have also explored the idea that punishment can help enforce cooperative behavior. Punishment can be “vigilante-style”, where any individual who sees someone else acting unethically can hurt them, or there can be some kind of agreed-upon authority whose job it is to punish misbehavers. The question of if and how punishment works in nature seems still up for debate.

Bottom line is, it doesn’t pay to be a nice guy in a world of assholes. But if you can find other nice people to interact with, and some mechanism for keeping the assholes out of your little nice-people club, then you’re on to something.

Each of the proposed mechanisms for cooperation has interesting implications for human society. I’ll highlight just one of them for now: spatial structure. When humans first evolved, long-distance travel was difficult, and so different societies could develop independently with their own norms of cooperation or selfishness. But now we can travel across the world in a day, so the spatial separation is gone. Any thoughts on the implications of this change for the stability of human cooperation?

Further reading