My microbes made me do it...

This week, the 40th anniversary of the first moon landing, there’s much talk of exploring other worlds. Which is exciting and grand; such is the stuff that dreams are made on. Yet we don’t need to go abroad to find amazing new life forms. We just need to look at the palms of our hands, the tips of our fingers, the contents of our guts.

The typical human is home to a vast array of microbes. If you were to count them, you’d find that microbial cells outnumber your own by a factor of 10. On a cell-by-cell basis, then, you are only 10 percent human. For the rest, you are microbial. (Why don’t you see this when you look in the mirror? Because most of the microbes are bacteria, and bacterial cells are generally much smaller than animal cells. They may make up 90 percent of the cells, but they’re not 90 percent of your bulk.)

This much has been known for a long time. Yet it’s only now, with the revolution in biotechnology, that we’re able to do detailed studies of which microbes are there, which genes they have, and what they’re doing. We’re just at the start, and there are far more questions than answers. But already, the results are astonishing, and the implications profound.

Even on your skin, the diversity of bacteria is prodigious. If you were to have your hands sampled, you’d probably find that each fingertip has a distinct set of residents; your palms probably also differ markedly from each other, each home to more than 150 species, but with fewer than 20 percent of the species the same. And if you’re a woman, odds are you’ll have more species than the man next to you. Why should this be? So far, no one knows.

But it’s the bacteria in the digestive tract, especially the gut, that intrigue me most. Many of these appear to be true symbionts: they have evolved to live in guts and (as far as we know) are not found elsewhere. In providing their habitat — a constant temperature, some protection from hostile lifeforms and regular influxes of food — we are as essential to them as they are to us.

And they definitely are essential to us. Gut bacteria play crucial roles in digesting food and modulating the immune system. They make small molecules that we need in order for our enzymes to work properly. They interact with us, altering which of our genes get turned on and off in cells in the intestinal walls. Some evidence suggests that they are essential for the building of a normal heart. Finally, it seems likely that gut bacteria will turn out to affect appetite, as well as other aspects of our behavior, though no one has shown this yet. (Imagine the plea: I’m sorry, sir, my microbes made me do it.)

Together, your gut microbes provide you with a pool of genes far larger than that found in the human genome. Indeed, the gut “microbiome,” as it is known, is thought to contain at least 100 times more genes than the human genome. Moreover, whereas humans are extremely similar to one another at the level of the genome, the microbiome appears to differ markedly from one person to the next.

What determines these differences? Good question. Diet has some effect: a diet rich in sugars and fats reduces the diversity of gut bacteria, and shifts the balance towards those that are more efficient at extracting energy. Start eating more plants and you can shift the balance back, and increase the diversity of your gut microbes. Your own genetic background may play a role as well, though we are far from understanding how, or how much. It probably also matters which other microbes are present: as in any ecosystem, relationships among different inhabitants are likely to be complex.

(At this point, I’d like to introduce a caveat. We know that the diversity of microbial species differs between your gut and mine, and that the less related we are, the more that will be true. Family members tend to have more similar gut microbes than nonrelatives, and preliminary evidence suggests that geography matters, too. So the gut microbes of people in China are different from those of people in the United States — though whether this is due to diet, human genes or geography is entirely unknown. But despite this variation at the species level, we don’t yet know how much variation there is at the genetic level. It may be that different sets of gut microbes provide broadly equivalent sets of genes.)

Naturally, a huge effort is now under way to see whether differences in gut bacteria are responsible for differences in health. But what interests me most about all this is that it suggests another mode of human evolution. Bacteria evolve quickly: they can go through many thousands of generations for every human one.

This has two potential consequences. First, during your lifetime, your bacteria can change their genes even though you cannot change yours. (You do have some flexibility: your immune system has a built-in capacity to change.) It may be that gut bacteria evolve in response to short-term changes in the environment, especially exposure to food-borne diseases. They may thus act as an evolving supplement to the immune system.

The second potential consequence is further reaching. Because bacteria can evolve so fast, it may be that some of what we think of as human evolution — like the ability to digest new diets that accompanied the invention of agriculture — is actually bacterial evolution. We know that hostile bacteria — those that cause diseases in ourselves and our domestic plants and animals — have undergone dramatic genetic changes in the last 10,000 years. Perhaps our friendly bacteria have, too.

Notes:

For human cells being outnumbered by microbial cells by a factor of 10, see Savage, D. C. 1977. “Microbial ecology of the gastrointestinal tract.” Annual Review of Microbiology 31: 107-133. For new techniques in analyzing microbes that we cannot grow in the laboratory see, for example, Marcy, Y. et al. 2007. “Dissecting biological ‘dark matter’ with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.” Proceedings of the National Academy of Sciences USA 104: 11889-11894.

For bacteria living on hands, see Fierer, N. et al. 2008. “The influence of sex, handedness, and washing on the diversity of hand surface bacteria.” Proceedings of the National Academy of Sciences USA 105: 17994-17999. For gut microbes not being found elsewhere, see Ley, R. E. et al. 2008. “Worlds within worlds: evolution of the vertebrate gut microbiota.” Nature Reviews Microbiology 6: 776-788.

For a summary of the essential roles that gut microbes play, see Turnbaugh, P. J. et al. 2007. “The human microbiome project.” Nature 449: 804-810. For estimates of the number of genes contained in the microbiome, see Gill, S. R. et al. 2006. “Metagenomic analysis of the human distal gut microbiome.” Science 312: 1355-1359.

For diet affecting human microbial diversity, see Ley, R. E. et al. 2006. “Human gut microbes associated with obesity.” Nature 444: 1022-1023. For “obese” microbes harvesting more energy, see Turnbaugh, P. J. et al. 2006. “An obesity-associated gut microbiome with increased capacity for energy harvest.” Nature 444: 1027-1031. For initial evidence that the genetic background of the host affects which microbes are present, see Rawls, J. F. et al. 2006. “Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection.” Cell 127: 423-433.

For differences in gut microbes between people in China and the United States, see Li, M. et al. 2008. “Symbiotic gut microbes modulate human metabolic phenotypes.” Proceedings of the National Academy of Sciences USA 105: 2117-2123. For evidence that different sets of gut microbes can provide broadly equivalent sets of genes, see Turnbaugh, P. J. et al. 2009. “A core gut microbiome in obese and lean twins.” Nature 457: 480-484.

For recent and dramatic genetic changes to our hostile bacteria, see Mira, A., Rushker, R. and Rodriguez-Valera F. 2006. “The Neolithic revolution of bacterial genomes.” Trends in Microbiology 14: 200-206.

Many thanks to Rob Knight and Jonathan Swire for insights, comments and suggestions.

On the evolution of altruism ~ the role of conflict

Dawkins gene based view doesn't allow for group selection but here is a work around. Evolution, in genes or culture operates on many levels, imo.

People are altruistic because they are militaristic, and cultured because they are common. At least that is the message of a couple of new studies


TWO of the oddest things about people are morality and culture. Neither is unique to humans, but Homo sapiens has both in an abundance missing from other species. Indeed, that abundance—of concern for the well-being of others, (even unrelated others), and of finely crafted material objects both useful and ornamental—is seen by many as the mark of man, as what distinguishes humanity from mere beasts.

How these human traits evolved is controversial. But two papers in this week’s Science may throw light on the process. In one, Samuel Bowles of the Santa Fe Institute in New Mexico fleshes out his paradoxical theory that much of human virtue was forged in the crucible of war. Comrades in arms, he believes, become comrades in other things, too.


In the other paper, Mark Thomas and his colleagues at University College, London, suggest that cultural sophistication depends on more than just the evolution of intelligence. It also requires a dense population. If correct, this would explain some puzzling features of the archaeological record that have hitherto been put down to the arbitrary nature of what has survived to the present and what has not.

Dr Bowles’s argument starts in an obscure cranny of evolutionary theory called group selection. This suggests that groups of collaborative individuals will often do better than groups of selfish ones, and thus prosper at their expense. It is therefore no surprise, according to group-selectionists, that individuals might be genetically predisposed to act in self-sacrificial ways.

This good-of-the-group argument was widely believed until the 1960s, when it was subject to rigorous scrutiny and found wanting. The new theory does not pitch groups against groups, or even individuals against individuals, but genes against genes. It does not disallow altruistic behaviour, but requires that this evolve in a way that promotes the interest of a particular gene—for example by helping close relatives who might also harbour the gene in question. The “selfish gene” analysis, so called after a book by Richard Dawkins, makes good-of-the-group outcomes almost impossible to achieve.
War and peace

A few researchers, of whom Dr Bowles is one, have been unwilling to give up on group selection completely. They note the word “almost” in the argument above and contend that humans, with their high intelligence and possession of language, and their tendency to live in small, tightly knit groups, might be exceptional. They also think people could be subject to a form of group selection that is genetically selfish.

Dr Bowles has focused the argument on war, since it is both highly collaborative and often genetically terminal for the losers. In his latest paper he puts some numbers on the idea. He looks at the data, plugs them into a mathematical model of his devising and finds a pleasing outcome.

To gather his data, Dr Bowles trawled through ethnographic and archaeological evidence about warfare between groups of hunter-gatherers. This is rarely war in the modern sense of planned campaigns. It is more a matter of raids, ambushes and fights between groups who have met accidentally. It is, nevertheless, quite lethal. Dr Bowles identified eight ethnographic and 15 archaeological studies that met his criteria of reliability and abundance of data. They suggest that 12-16% of mortality is the result of such low-level warfare. This is a figure much higher than, for example, the mortality caused in Europe by two world wars, and is certainly enough to drive evolution. But the question remained of whether it could drive group selection.

It was to test that idea that Dr Bowles devised his model. Although it pitches group against group, it is strictly based on the idea of selfish genes. It looks at the benefit to a notional gene that promotes self-sacrifice. The question is, does such a gene do well if individuals having it belong to a group that takes over the territory and resources of a similar, neighbouring group, but at the risk of some of those individuals losing their life in the process? What is the maximum self-sacrificial cost that can evolve in these circumstances?

In the absence of war, a gene imposing a self-sacrificial cost of as little as 3% in forgone reproduction would drop from 90% to 10% of the population in 150 generations. Dr Bowles’s model, however, predicts that much higher levels of self-sacrifice—up to 13% in one case—could be sustained if warfare were brought into the equation. This, he contends, allows the evolution of collaborative, altruistic traits that would not otherwise be possible. Moreover, although warfare is an extreme example, other, less martial forms of self sacrifice may have similar group-strengthening virtues.

Dr Thomas and his colleagues also rely on a mathematical model. They are trying to explain the pattern of apparent false-starts to modern human culture. The species is now believed to have emerged 150,000-200,000 years ago in Africa and to have begun spreading to the rest of the world about 60,000 years ago. But signs of modern culture, such as shell beads for necklaces, the use of pigments and delicate, sophisticated tools like bone harpoons, do not appear until 90,000 years ago. They then disappear, before popping up again (and also sometimes disappearing), until they really get going around 35,000 years ago in Europe.

The team drew on an earlier insight that it requires a certain number of people to maintain skills and knowledge in a population. Below this level, random effects can be important. The probability of useful inventions being made is low and if only a few have the skills to fabricate the new inventions, they may die without having passed on their knowledge.

In their model, Dr Thomas and his colleagues divided a simulated world into regions with different densities of human groups. Individuals in these groups had certain “skills”, each with an associated degree of complexity. Such skills could be passed on, more or less faithfully, thus yielding an average level of skills that could vary over time. The groups could also exchange skills.

The model suggested that once more than about 50 groups were in contact with one another, the complexity of skills that could be maintained did not increase as the number of groups increased. Rather, it was population density that turned out to be the key to cultural sophistication. The more people there were, the more exchange there was between groups and the richer the culture of each group became.

Dr Thomas therefore suggests that the reason there is so little sign of culture until 90,000 years ago is that there were not enough people to support it. It is at this point that a couple of places in Africa—one in the southernmost tip of the continent and one in eastern Congo—yield signs of jewellery, art and modern weapons. But then they go away again. That, Dr Thomas suggests, corresponds with a period when human numbers shrank. Climate data provides evidence this shrinkage did happen.

According to Dr Thomas, therefore, culture was not invented once, when people had become clever enough, and then gradually built up into the edifice it is today. Rather, it came and went as the population waxed and waned. Since the invention of agriculture, of course, the population has done nothing but wax. The consequences are all around you.

http://www.economist.com/science/displaystory.cfm?story_id=13776964