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Fantastic optimism!

In my younger days I had a soft spot for well crafted “space opera,” with David Brin’s “Uplift” series being an excellent exemplar. And yet the reality is that part of me always felt that these were more akin to space fantasy than science fiction. The reason is that a world such as the one you see in Star Trek, where aliens often meet each other at technological parity, just did not seem intuitively plausible to me. Rather, much more likely was the dark universe Gregory Benford outlines in Great Sky River. In this imaginging intelligent life forms meet across a chasm of technological sophistication which makes the idea of a broad class of organisms with the term “intelligent life form” laughable; humans were to the “higher intelligences” in this universe as ants are to us. Benford’s novel was depressing from a human perspective, and its coldly Malthusian universe reflects the pessimism of many biologists. I first encountered this in Jared Diamond’s The Third Chimpanzee, where the author suggests that optimism in regards to “First Contact” promoted by astronomers such as Carl Sagan in his work Cosmos was incredibly naive. Diamond’s basic contention was that if the universe was full of intelligent life forms, then we had better be glad that they weren’t here yet, because it probably wouldn’t end well for human beings, using our own planet’s encounters between different civilizations as models.

But I no longer even hold to the position that the cosmos is teeming with intelligences of varied levels of sophistication. Rather, I would guess that we humans are all there is in this galaxy.* I don’t speak of this often because I haven’t thought about this issue in great depth. And with these incredibly big picture inferences deduced from sparse data points one has to admit (at least I do!) that one’s confidence is just not high. What can a puny human truly grasp?

So why would I suggest that we are the only intelligence? Basically, the Fermi paradox. Rather that outlining my inchoate thoughts I’ll point you to Nathan Taylor’s posts at Praxtime, Life on Wet Planets, and Intelligent life is just getting started. With the appropriate caveat that we don’t really know much about this in any deep sense, it strikes me that major bottleneck for the emergence of intelligent life is the transition from simple unicellular life forms to multicellular organisms. Therefore the prediction from this model is that the universe is filled with life, but of the single celled kind. As Taylor lays out time almost ran out for the emergence of intelligent life on this planet (the sun is getting brighter, and it seems like that runaway greenhouse is inevitable ~1 billion years into the future).

Yet please note that we are likely just the first intelligent life form. If we go extinct soon before developing a form of automaton which can populate the galaxy there is plenty of time for other organisms similar to ourselves to emerge. The local universe is relatively young when measured in terms of the future existence of G (or K) class stars. That means the “responsibility” of being the first intelligent galactic species is somewhat attenuated on a cosmic scale.

Addendum: It is possible that the universe is teaming with intelligent non-technological life forms, and the upward ratchet of cultural complexity of Homo sapiens is a major bottleneck. I doubt that, therefore I have omitted a qualifier of technological intelligences, because I do think that if intelligences were numerous then many would have become technologically sophisticated.

* The whole space of possibilities is so much larger than our galaxy that I am somewhat wary of making broad assertions about the universe.

• Category: Science • Tags: Contingency, Futurism 
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Graph of hominin encephalization by Luke Jostins

Graph of hominin encephalization by Luke Jostins

After my post, Functions oh So Random, which comments on old arguments about contingency in evolutionary biology, a reader pointed me to an excellent feature in Nautilus, If the World Began Again, Would Life as We Know It Exist? It explores the question in greater depth, and reviews many of the contemporary players. The primary representative for the idea that evolutionary processes will tend to converge upon a finite set of specific adaptive peaks is still Simon Conway Morris, who seems to argue that experimental evolutionary results which indicate the likelihood of contingency just haven’t gone on long enough (I wonder, how many generations, Dr. Conway Morris?). It strikes me that Conway Morris is unlikely to ever be satisfied unless we discover life on another planet, which has the potential to falsify his model. But his comments probably did push me more toward the power of contingency, in particular:

Conway Morris believes that, over time, natural selection leads organisms to evolve a limited number of adaptations to the finite number of ecological niches on Earth. This causes unrelated organisms to gradually converge on similar body designs. “Organisms have to configure themselves to the realities of the physical, chemical, and also biological world,” he says. In Conway Morris’s view, these constraints make it all but inevitable that if the tape of life were replayed, evolution would eventually reproduce organisms similar to what we have today. If humans’ ape ancestors had not evolved big brains and the intelligence that goes with them, he believes that another branch of animals, such as dolphins or crows, might have, and filled the niche that we now occupy. Gould disagreed.

The idea that physics implies particular body plans strikes me as plausible. Here there seem to be limits to contingency. But the assertion that intelligence is in some way a niche is a jump too far for me, at least to an extent. More on that later. First, let’s note that it seems highly unlikely that organisms adapt to a niche which exists in a Platonic sense as a fixed idea in the firmament. Organisms evolve in the context of each other, adapting not only to the physical world, but inter and intra specific pressures. Ergo, the idea that sex persists among complex organisms despite its cost because of co-evolutionary pressures of infection by pathogens.* But when it comes to intelligent life forms we can extend the complexity further, because arguably one of the primary adaptive feedbacks of these organisms is going to be their own cultural production. In other words, one would have to also argue that cultural production itself exhibits some level of inevitable convergence upon a fitness peak.

But I don’t want to get carried away. Obviously there are some cultural forms which are not adaptive. Shaker obligate celibacy comes to mind. But the range of possibilities for cultural expression is still complex. And going back in time I think it is important to suggest that even if contingency rules over the macroscale, it may not be as powerful over a shorter timescale. A few years ago Luke Jostins produced the above figure to show that distinct hominin lineages, which we believe were genetically isolated by and large, nevertheless were all increasing in cranial capacity over the Pleistocene. We do not know why, but the chart suggests that there are some powerful common forces which can overcome phylogenetic divergence.

41wehNqV33L._SY300_ Ultimately though the argument about contingency is fascinating, it strikes me that it is not entirely scientific in its deepest level. It reminds me of an argument I encountered in Cultural Evolution: How Darwinian Theory Can Explain Human Culture and Synthesize the Social Sciences. Recounting the emergence of the neo-Darwinian synthesis in the 1930s and 1940s the author suggests that it took so long partly because geneticists and naturalists were focusing on different evolutionary scales (micro vs. macro) and utilizing unintelligible languages. Because of the discrete Mendelian nature of inheritance geneticists were skeptical of Darwinian gradualism in evolutionary process and phenotypic characteristics. While naturalists had difficulty conceiving of how isolated mutations could result in the panoply of diversity they saw around them. The conflict was resolved with the development of a formal language which could translate the two scales, population genetic theory. Population genetics illuminated quite elegantly how numerous genes of discrete effect could combine to produce quantitative traits and gradual evolutionary change, and, how low rates of mutation might nevertheless allow for rapid change on a geological scale through selection pressures. Without a formal language the two groups had to rely on intuition and kept talking past each other.

We’re at a similar juncture when it comes to nearly meta-scientific questions such as contingency. We can’t even know who is right until we know the right questions to ask. At that point the write up will be in Nature Reviews Genetics, rather that long popular science books or features.

* Obviously the physical world itself can be changed by biology. Oxygen producing bacteria totally reshaped the biosphere.

• Category: Science • Tags: Contingency, Evolution 
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adaptivelandscape150 years after Charles Darwin’s The Origin of Species there are many open questions in evolutionary biology. For example I have been wavering between the possibility that on the molecular genomic scale evolutionary process is predominantly neutral and stochastic, and a new possibility that selection is pervasive (a new possibility that is actually old). The nice aspect of this area of study today is that empirical data can be brought to bear upon ancient arguments. Previously the dialogues were fruitless in terms of actually resolving opposing viewpoints, as interlocutors dug into their presuppositions, and the same theoretical paradigms flew through data free debates.

One area where this was clear was in relation to the of whether evolutionary process is deterministic or stochastic on the most general level. More prosaically, is evolution an experiment which one can broadly reproduce genetic and functional outcomes over and over? Stephen Jay Gould was the most famous proponent of the position that evolution is not a reproducible experiment. Rather, it is a contingent historical process. You can’t rewind the clock and expect the result to resemble what came before. In contrast Richard Dawkins has tended to defend the stance that there are broad inevitabilities as evolution explores the adaptive space of possibilities (see The Ancestor’s Tale for his detailed position). Over the past few years Joe Thornton’s lab has been looking at this issue by examining the evolutionary genetic trajectory of steroid receptors. This may seem abstruse, but obviously these are functionally significant, and, they’ve been able to utilize ingenious biophysical methods to “rerun” evolution. The general conclusion seems to be that steroid receptors as we understand them are subject to path dependence in a fashion where the outcome is sensitive to unlikely sequences of mutations.

The group now has a paper in Nature, Historical contingency and its biophysical basis in glucocorticoid receptor evolution (ungated). Let me jump straight to the conclusion:

If evolutionary history could be replayed from the ancestral starting point, the same kind of permissive substitutions would be unlikely to occur. The transition to GR’s present form and function would probably be inaccessible, and different outcomes would almost certainly ensue. Cortisol-specific signalling might evolve by a different mechanism in the GR, or by an entirely different protein, or not at all; in each case, GR—or the vertebrate endocrine system more generally—would be substantially different. Because GR is the only ancestral protein for which alternative evolutionary trajectories to historically derived functions have been explored, the generality of our findings is unknown. The specific biophysical constraints, and in turn the degree and nature of contingency, that shape the evolution of other proteins are likely to depend on the particular architecture of each protein and the unique historical mechanisms by which its functions evolved.

170px-Type_C_OrcasThe issue about generality is important. Read the whole paper and you’ll be struck by the level of experimental detail that went into making the inferences they arrive at. There’s a reason that these papers get into glamour journals. But is this just a story about a particular class of proteins, or the story of evolution writ large? When molecular evolutionary neutralism became ascendant in the 1980s some responded that though stochasticity might dominate on the sequence level of A, C, G, and T, there was no such randomness when it came to morphology. The power of this argument seems most evident when it comes to the body plans of some metazoans which are clearly dictated by the laws of physics. Marine mammals have evolved toward a morphology which has clear parallels with that of species of the fish lineage which occupy the same niche. Similarly, the elephantine legs of ancient sauropods were no coincidence. As land animals become large their massive bulk becomes unwieldy for more gracile body plans, and there is a tendency toward stout builds, as the cross-section of bone and muscle attempts to race up to the massively increased volume and mass.

The same tension seems to be at play in these sorts of results, which focus on the contingencies of a specific piece of biological machinery. Is there only one way to construct a particular a component due to biophysical constraints? Perhaps. But what does this tell us about the construction of the whole organism, which is the stitching together of innumerable biomolecular parts? In science fiction is not peculiar to imagine worlds where gross morphology is broadly recognizable, but none of the organisms are edible to humans because of divergences in biochemistry. Ultimately as implied in the paper above other groups have to reproduce this sort of work on other families of proteins to see how ubiquitous contingency really is.

• Category: Science • Tags: Contingency, Evolution 
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Hominin increase in cranial capacity, courtesy of Luke Jostins

A few years ago a statistical geneticist at Cambridge’s Sanger Institute, Luke Jostins, posted the chart above using data from fossils on cranial capacity of hominins (the human lineage). As you can see there was a gradual increase in cranial capacity until ~250,000 years before the present, and then a more rapid increase. I should also note that from what I know about the empirical data, mean human cranial capacity peaked around the Last Glacial Maximum. Our brains have been shrinking, even relative to our body sizes (we’re not as large as we were during the Ice Age). But that’s neither here nor there. In the comments Jostins observes:

The data above includes all known Homo skulls, but none of the results change if you exclude the 24 Neandertals. In fact, you see the same results if you exclude Sapiens but keep Neandertals; the trends are pan-Homo, and aren’t confined to a specific lineage….

In other words: the secular increase in cranial capacity for our lineage extends millions of years back into the past, and also shifts laterally to “side-branches” (with our specific terminal node, H. sapiens sapiens, as a reference). This is why I often contend as an aside that humanity was to some extent inevitable. By humanity I do not mean H. sapiens sapiens, the descendants of a subset of African hominins who flourished ~100,000 years before the present, but intelligent and cultural hominins who would inevitably construct a technological civilization. The parallel trends across the different distinct branches of the hominin family tree which Luke Jostins observed indicated to me that our lineage was not special, but simply first. That is, if African hominins were exterminated by aliens ~100,000 years before the present, at some point something akin to H. sapiens sapiens in creativity and rapidity of cultural production would eventually arise (in all likelihood later, but possibly earlier!).

This does not mean that I think humanity was inevitable upon earth. For most of the history of this planet life was unicellular. I do not find it implausible that life on earth may have reached its “sell by” date due to astronomical events before the emergence of complex organisms (in fact, from what I have heard the end of life is going to occur ~1 billion years into the future due to the persistent increase in the energy output of Sol, not ~4 billion years in the future when Sol turns into a red giant). But, once complex organisms arose it does seem that further complexity was inevitable. This was Richard Dawkins’ case in The Ancestor’s Tale based simply on the descriptive record. But did the emergence of complex organisms necessarily entail the evolution of a technological species? I don’t think so. It took 500 million years for that to occur (it does not seem that coal resources formed hundreds of millions of years ago were tapped before humans). Given enough time obviously a technological species would evolve (e.g., extend the time of evaluation to 1 trillion years), but note that the earth has only ~5 billion years. Homo arrived on the scene in the last 20% of that interval.

Here I am positing at a minimum two not excessively likely or inevitable events over a 5 billion year time span which would lead to a hyper-technological and cultural species:

- The emergence of multicellular life

- The emergence of a lineage with the propensities of Homo

One Homo evolved and expanded outside of Africa I suspect that something of the form of a technological civilization became inevitable n this planet. We see parallelism in our own short post-Pleistocene epoch. Multiple human societies shifted from hunter-gatherers to agriculturalists over the past 10,000 years. The experience of the New World civilizations in particular illustrates that human universal tendencies are real. Not only were “game changing” cultural forms such as agriculture and literacy invented independently during the Holocene, but they were not invented during earlier interglacials (at least in all likelihood).

Khufu, Necho, Augustus and Napoleon

Why not? Well, consider the cultural torpidity of Paleolithic toolkits, which might persist for hundreds of thousands of years! I suspect some of this due to biology. But even over the Holocene we do perceive that cultural change has proceeded at a more rapid clip as time has progressed (i.e., at a minimum cultural change has been accelerating, and it may be that the rate of acceleration itself is increasing!). Consider that the civilization of ancient Egypt spanned at least 2,000 years. Though there are clear differences, the continuity between Old Kingdom Egypt and the last dynasties before the Assyrian and Persian conquests is very obvious to us, and would be obvious to ancient Egyptians. In contrast, 2,000 years separates us from Augustan Rome. The continuities here are clear as well (e.g., the Roman alphabet), but the cultural change is also clear (if you wish to argue that the early modern and modern period are sui generis, the 1,500 year interval from Augustan Rome to the Neo-Classical Renaissance would still be a stark contrast when compared against an ancient Egyptian reference*, despite the latter’s aping of the forms of the former).

So far I have focused on the vertical dimension of time. But there is also the lateral dimension, of cross-fertilization across the branches of the hominin family tree. The admixture of a Neanderthal element into non-Africans has started to become widely accepted recently, thanks to the confluence of archaeology and genomics in the field of ancient DNA. Even if one rejects the viability of Neanderthal admixture, the solution to the conundrum of these results must still entail stepping away from a simple model of recent exclusive origin of humans from a small African population. There are also hints of admixture with other archaic lineages on the Pacific fringe, and within Africa.

Until recently it was common to posit that modern humans, our own lineage, had some special genius which allowed it to sweep the field and extinguish our cousins. The qualitative result of Luke Jostins’ plot was known; that other hominin lineages also exhibited encephalization. In fact, it was a curious fact that Neanderthals on average had larger cranial capacities than anatomically modern humans. But the reality remained that we replaced them, ergo, we must have a special genius. Until the lack of distinction between Neanderthals and modern humans on loci implicated in the necessary (if not sufficient) competency of language that trait was a prime candidate for what made “us” special. But now I put “us” in quotation marks. The data do point to an overwhelming descent from an African or near-African population for non-Africans over the past 100,000 years. But the “archaic admixture” is not trivial. What was they are us, and we have become what they might have been.

For over two centuries there has been a debate in the West between monogenesis and polygenesis. The former is the position that humankind derives from one single pair or population (the former a straightforward recapitulation of the standard Abrahamic model). The latter is the position that different races of humans derive from different proto-humans, or, for the Christian polygenists that only Europeans descent from Adam and Eve (the other races being “non-Adamic”). Echoes of this conflict persist down to the present era. Many of the earlier partisans of “Out of Africa” have claimed that the proponents of multiregionalism were latter-day polygenists (not without total justification in some cases).

But the conflict between monogenism and polygenism is not the appropriate frame for what is being unveiled by reality before our eyes. What we see in the creation of modern humanity is a monogenic base inflected with the flavors of polygenism. Modern humans descend, by and large, from an expansion of an African population over the past 200,000 years. But on the margins there are other strands and filaments of ancestry which tie disparate populations back to lineages which branched off far earlier from the main trunk. At a minimum hundreds of thousands, and perhaps an order of 1 million years, before our own age. Today genomics avails of us the statistical power to extract out these discordant signals from the fluid “Out of Africa” narrative, but I would not be surprised if in the near future we stumble upon more and more “long branches” of less noteworthy quantity. Admixture is likely to be an old and persistent story in the hominin lineage, with only the most recent substantial bouts of separation and hybridization being of notice and curiosity at this moment in time.

What does all this mean? And why have I juxtaposed deep time natural history across the tree of life with inferences of relatively recent paleoanthropology? Let’s start with two propositions:

- Technological civilization, an outward manifestation of radically complex sentience, is not inevitable, though it is probable given certain preconditions (I believe that the existence of Homo increased its probability to ~1.0 over a reasonable time period)

- Radically complex sentience is not the monopoly of a particular exclusive lineage which accrues its genius from a particular specific forebear

John Farrell has pointed out the possible issues that the Roman Catholic church may have with the new model of human origins. But the Catholic church is only but a reflection of more general human strain of thought. Descent-groups, whether real or fictive, loom large in the human imagination. The evolutionary rationale for this is not too hard to explain, but we co-opt the importance of kinship in many different domains. Like evolution, human cultural forms simply take what is already present, and retrofit and modify elements to taste.

So why are humans special? And why do humans have inalienable rights? Many of us may not agree with the proposition that we are the descendants of Adam and Eve, and therefore we were granted the divine grace of eternal souls. But a hint of this logic can be found in the assumptions of many thinkers who do not agree with the propositions of the Roman Catholic church. Recently I listened to Sherry Turkle arguing against a reliance on “robot companions” which are able to exhibit the verisimilitude of human emotions for those who may be lacking in companionship (e.g., the aged and infirm). Though Turkles’ arguments were not without foundation, some of her arguments were of the form that “they are not us, they are not real, we are real. And that matters.” This is certainly true now, but will it always be? Who is this “they” and this “we”? And what does “real” mean? Are emotions a mysterious human quality, which will remain outside of the grasp of those who do not descend from Adam, literal or metaphorical?

If there arises a point where non-human sentience is a reality, do they have the same rights as we? Though the difference is radical in terms of quantity to some extent I think we know the answer: they are human by the way they are, not by the way their ancestors were. The “taint” of admixture with diverse lineages across the present human tree of life has not resulted in an updating of our understanding of human rights. That is because the idea that we are all the children of Adam, or the descendants of mitochondrial Eve, is a post facto justification for our understanding of what the rights of humanity are, adn what humanity is. And what it is is a particular ecological niche, a way of being, not being who descend down in a line of biological relationship from a particular person or persons.

* The cultural fundamentals of Old Kingdom Egypt arguably persisted in a living fossil form in the temple at Philae down to the 6th century A.D.! Therefore, a 3,500 year lineage of literature continuity.

Image credits: all public domain images from Wikpedia

(Republished from Discover/GNXP by permission of author or representative)
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Ornithomimosaurian dinosaur & ostrich, image credit Nobu Tamura & James G. Howes

ResearchBlogging.orgThe Pith: This post explores evolution at two different scales: the broad philosophical and the close in genetic. Philosophically, is evolution a highly contingent process which is not characterized by much replication of form and function? Or, is evolution at the end of the day aiming for a few set points which define the most optimal fitness positions possible? And how do both of these models relate to the interaction across genes, epistasis? In this post I review a paper which shows exactly how historical contingency could work through gene-gene interactions on the molecular genetic scale.

Imagine if you will a portal to another universe which you have access to. By fiat let’s give you a “pod” which allows you to move freely throughout this universe, and also let’s assume that you can travel fast enough to go from planet to planet. What if you see that on all the planets there’s a sludgy living “goo” of some sort? To complexify the issue imagine that upon further inspection the goo is divided between a predominant photosynthetic element, and “parasitic” heterotrophs. But aside from these two niches there’s little diversity to be seen in this cosmos. The “climax ecology” of all the planets resemble each other, in case after case convergent evolution toward the one-morphology-to-out-fit-them-all. We could from these observations construct a general theory of evolution which deemphasizes the role of contingency. In other words, there are broad general dynamics which shape and prune the tree of life in this hypothetical universe so that there is always a final terminal steady-state of the most fit morphology.

A model of evolution as a process of very general principles which converges upon a small finite range of optimal solutions has been promoted by paleontologists such as Simon Conway Morris. Stephen Jay Gould was a famous expositor of the inverse position, which emphasized chance and contingency. Gould’s suggestion was that if you ran the evolutionary experiment anew the outcomes each time would likely differ. In The Ancestor’s Tale Richard Dawkins leans toward the former position, insofar as he does assent to the proposition that evolutionary dynamics do inevitably forward certain broad trends, irrespective of the specific historical sequence of states antecedent to the terminus. More fanciful and speculative extrapolations of this logic are used to justify the ubiquity of a humanoid morphology in science fiction. The theory goes that a bipedal organism whose upper limbs are free to manipulate tools is going to be the likely body plan of intelligent aliens (though they will also have easy to add nose frills and such).

Until we meet those aliens these speculations are going to remain just that. And the debates about morphology, in particular body plan, are constrained by the fact that we have only one “natural experiment” to go on. So that’s why it is interesting to look at genetics, which is after all the modern fundamental characterization of the basic of evolutionary process in regards inheritance of traits. In particular looking at molecular genetics and evolution can be illustrative of the grounding of broader process. Neutral theory, which was stimulated by an understanding of evolution on the molecular level, has reordered our perception of the nature of larger scale morphological characters, in terms of both their potential utility and ultimate origin. Similarly, an inspection of the interactions of genotypes can put a spotlight on the adaptive landscape, an abstraction of the dimension of fitness explored by combinations of genetic variants.

A new paper in PLoS Genetics explores the specific question of the role of epistasis in the dance between contingency and determinism. The more common conceptualization of epistasis is mechanistic or biophysical, describing concrete gene-gene interactions on a molecular genetic scale. In this context we are more curious about the fitness and phenotypic implications of gene-gene interactions. This is evolutionary or statistical epistasis. You can think of this sort of phenomenon as simply the non-linearities in the mapping from genotype to phenotype.

Evolutionary genetics in the early 20th century was formulated by R. A. Fisher to avoid these non-linearities. Rather, it fixated on a model of change of allele frequency one locus at a time, averaging the “genetic background.” These were evolutionary genetic architectures which were additive and independent (multiplicative effects remain linear, and can be rescaled easily). Statistical epistasis is describing genetic architectures which are not additive and independent. Fisher’s intellectual rival Sewall Wright was more concerned with these interaction effects in his “Shifting Balance Theory,” but even Will Provine, Wright’s biographer, admitted that there was a certain incoherency and lack of clarity in his thoughts on gene-gene interactions and adaptive landscapes.

So where are we now? In the PloS Genetics paper, Initial Mutations Direct Alternative Pathways of Protein Evolution, the authors suggest that interlocking gene-gene interactions can shape the path of evolution via the constraints which prior states place upon later ones. In other words the adaptive landscape is not simple in its topography, characterized by a clear and distinct fitness peak, but is rugged so that there are multiple points upon which the populations may converge upon.

Here’s the author summary:

A long-term goal of evolutionary biology is to understand the factors that govern the outcome of evolution. Epistasis (i.e. the situation in which the fitness effect of a mutation depends on its genetic background) is one such factor. Epistasis not only affects the dynamics of evolution, it may also direct its outcome by affecting the type and order of selected mutations. This effect is particularly strong under sign epistasis, which occurs when the sign of a mutation’s fitness effect depends on its genetic background. Here, we demonstrate how epistasis causes divergence of mutational pathways of an antibiotic resistance enzyme, TEM-1 β-lactamase. First, we use in vitro mutagenesis followed by selection for cefotaxime resistance to demonstrate that alternative mutational pathways towards highly resistant variants exist in addition to the main pathway that was previously described. Next, to test whether negative interactions between alternative initial substitutions govern this diversification, we start identical evolution experiments with alleles containing initial substitutions from the deviating lines. These alleles consistently evolve to lower adaptive peaks and acquire different mutations than those in the main pathway. Our results demonstrate that sign epistasis between alternative initial substitutions may force evolution to follow different mutational pathways.

This is not a paper gifted with easy to comprehend figures. The one to the left though is rather informative. It shows what we should expect in regards to evolutionary arcs: populations converge upon a fitness peak and enter a phase of stasis after rapid evolution. Each of the lines denotes different mutational lineages, and the height on the y-axis illustrates how resistant these lineages are to antibiotics. The x-axis is time. In this series of directed evolution experiments they seem to have increased the mutation rate so that genetic variation was not a limiter on the action of evolution through natural selection (remember, the power of selection is proportional to genic variance). This is to some extent old school genetics. We’re not talking thousands of SNPs. But I honestly had a hard time keeping in mind the alphabet soup of different loci. But the broad insights are derived from a narrow range of results:

- An initial set of experiments which allowed for the evolution of antibiotic resistance show the emergence of a similar genetic profile in most of the lines. This illustrates the power of convergence given the same exogenous adaptive pressure, the antibiotic. The authors argue that this highlights epistasis’ role in constraining the mutational space across the genome which can be modified to allow for antibiotic resistance.

- But, there were exceptions in several lineages. Two lack the G238S substitution. These two lines had reduced ability to resist the antibiotic. Forcing the G238S variant onto the background of the lineages which lacked it resulted in the finding that this substitution did not have a fitness improving impact, in contrast to the other cases. This shows the importance of genetic background, as the nature of other genes affects the selective advantage or lack thereof of a particular allele. Additionally, the lineages which lacked G238S tended to plateau at a lower of level of resistance. These would be lower fitness peaks, but separated from the higher G238S peak by “valleys.”

- Also, in these lineages there seem to be an excess of mutations as opposed to the G238S bearing trials. The authors offer the hypothesis that this selection of mutants in this novel background is evidence that the evolutionary process is taking a different route to solving the same problem because of shifted initial conditions (i.e., genetic variants which block the selection of G238S).

- Aside from the key initial mutations the authors also noted that there was a tendency to specific joint mutational pairs, as well as negative correlations across others. In other words, if mutation X was present, mutation Y tended not to be present, and vice versa. This suggests that the mutational path toward a fitness peak is not a series of independent steps, but a varied set of circumlocutions until an avenue toward the goal is sighted.

- Finally, forcing different pairs of negatively epistatic variants also resulted in different outcomes contingent upon the magnitude of the interaction. In a case where there was very strong negative epistasis (sharply reduced fitness, and reduced expression of the phenotype) there was a rapid reversion back to a state where such epistasis was mitigated. Remember, the mutational rates here were high, so back mutations are possible. But a second case with far weaker epistasis showed that such reversions were not always inevitable. In these cases weak epistatic interactions may eventually have been masked by modifier variants in the genetic background.

So is evolution contingent, or is it inevitable? Do gene-gene interactions play a major long-term role in evolution, or is epistatic variance inevitably converted to additive genetic variance? I think the answer is that it depends. Instead of dichotomously binning the possible space of answers one just has to acknowledge that the nature of the parameters are important. In a universe of near infinite population size and stable environmental conditions one suspects that contingency is rather less important, as natural selection can explore an enormous range of genotypic combinations over long periods of time. A contrasting situation would be one where environmental pressures are protean, and populations constrained in size. If evolution by natural selection is thought of as a tinkerer, you’d naturally see a lot more ad hoc contingent creations when you limit the raw materials (population size) and reduce the time to create (by changing selection pressures).

Citation: Salverda ML, Dellus E, Gorter FA, Debets AJ, van der Oost J, Hoekstra RF, Tawfik DS, & de Visser JA (2011). Initial mutations direct alternative pathways of protein evolution. PLoS genetics, 7 (3) PMID: 21408208

(Republished from Discover/GNXP by permission of author or representative)
🔊 Listen RSS One of the most persistent debates about the process of evolution is whether it exhibits directionality or inevitability. This is not limited to a biological context; Marxist thinkers long promoted a model of long-term social determinism whereby human groups progressed through a sequence of modes of production. Such an assumption is not limited to Marxists. William H. McNeill observes the trend toward greater complexity and robusticity of civilization in The Human Web, while Ray Huang documents the same on a smaller scale in China: A Macrohistory. A superficial familiarity with the dynastic cycles which recurred over the history of Imperial China immediately yields the observation that the interregnums between distinct Mandates of Heaven became progressively less chaotic and lengthy. But set against this larger trend are the small cycles of rise and fall and rise. Consider the complexity and economies of scale of the late Roman Empire, whose crash in material terms is copiously documented in The Fall of Rome: And the End of Civilization. It is arguable that it took nearly eight centuries for European civilization to match the vigor and sophistication of the Roman Empire after its collapse as a unitary entity in the 5th century (though some claim that Europeans did not match Roman civilization until the early modern period, after the Renaissance).

It is natural and unsurprising that the same sort of disputes which have plagued the scholarship of human history are also endemic to a historical science like evolutionary biology. Stephen Jay Gould famously asserted that evolutionary outcomes are highly contingent. Richard Dawkins disagrees. Here is a passage from The Ancestor’s Tale:

…I have long wondered whether the hectoring orthodoxy of contingency might have gone too far. My review of Gould’s Full House (reprinted in A Devil’s Chaplain) defended the popular notion of progress in evolution: not progress towards humanity – Darwin forend! – but progress in directions that are at least predictable enough to justify the word. As I shall argue in a moment, the cumulative build-up of compelx adaptations like eyes strongly suggest a version of progress – especially when coupled in imagination with of the wonderful products of convergent evolution.

Credit: Luke Jostins
Credit: Luke Jostins

One of those wonderful products is the large and complex brains of animals. Large brains are found in a disparate range of taxa. Among the vertebrates both mammals and birds have relatively large brains. Among the invertebrates the octopus, squid and cuttlefish are rather brainy. The figure to the right is from Luke Jostins, and illustrates the loess curve of best fit with a scatter plot of brain size by time for a large number of fossils. The data set is constrained to hominins, humans and their ancestors. As you can see there is a general trend toward increase cranial capacities across all the human populations. Neandertals famously were large-brained, but they exhibited the same secular increase in cranial capacity as African Homo. On the scale of Pleistocene Homo and their brains the idea of the supreme importance of contingency seems ludicrous. Some common factor was driving the encephalization of humans and their near relations over the past two million years. This strikes me as very strange, as the brain is metabolically expensive, and there are plenty of species with barely a brain which are highly successful. H. floresiensis may be a human instance of this truism.

But what about the larger macroevolutionary pattern? Is there a trend toward larger brain sizes in general, of which primates, and humans in particular, are just the most extreme manifestation? Some natural historians have argued that there is such a trend. But, there is a question as to whether increased brain size is simply a function of allometry, the pattern where different body parts and organs tend to correlate together in size, but also shift in ratio with scale. The nature of physics means that very large organisms have to be more robust because their mass increases far faster than their surface area. By taking the aggregate relationship between body size and brain size, and examining the species which deviate above or below the trend line, one can generate an encephalization quotient. Humans, for example, have a brain which is inordinately large for our body size.

And yet there are immediate problems looking at relationships between body and brain size, and inferring expectations. Different species and taxa are not interchangeable in very fundamental ways, and so a summary statistic or trend may obscure many fine-grained details. A new paper in PNAS focuses specifically on various mammalian taxa, corrects for phylogenetics, and also relates encephalization quotient by taxa to the proportion of social animals within each taxon. Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality:

Evolutionary encephalization, or increasing brain size relative to body size, is assumed to be a general phenomenon in mammals. However, despite extensive evidence for variation in both absolute and relative brain size in extant species, there have been no explicit tests of patterns of brain size change over evolutionary time. Instead, allometric relationships between brain size and body size have been used as a proxy for evolutionary change, despite the validity of this approach being widely questioned. Here we relate brain size to appearance time for 511 fossil and extant mammalian species to test for temporal changes in relative brain size over time. We show that there is wide variation across groups in encephalization slopes across groups and that encephalization is not universal in mammals. We also find that temporal changes in brain size are not associated with allometric relationships between brain and body size. Furthermore, encephalization trends are associated with sociality in extant species. These findings test a major underlying assumption about the pattern and process of mammalian brain evolution and highlight the role sociality may play in driving the evolution of large brains.

A key point is that the authors introduce time as an independent variable, so they are assessing encephalization over the history of the taxon. This is clearly relevant for humans, but may be so for other mammalian lineages. The table and figures below show the encephalization slope generated by using time and body size as the predictors and brain size as the dependent variable. A positive slope means that brain size is increasing over time.

[nggallery id=21]

Two major points:

- Note that the slope is sensitive to the level of taxon one is examining. A closer focus tends to show more variance between taxa. So, for example, humans distort the value for primates in general. Bracketing out anthropoids paints a more extreme picture of encephalization, a higher slope. In contrast, the lemurs and their relatives exhibit less encephalization over time.

- The correlation between proportion of species which exhibit sociality and encephalization of the taxon is strong. From the text:

Encephalization slopes were correlated with both the proportion of species with stable groups (order R = 0.92, P = 0.005, n = 6; suborder R = 0.767, P = 0.008, n = 9; Fig. 2 A and B) and the proportion in either facultative or stable social groups (order R = 0.804, P = 0.027, n = 6; suborder R = 0.63, P = 0.04, n = 9).

The last figure makes it is clear that the correlations are high, so the specific values should not be surprising. Don’t believe these specific figures too much, how one arranges the data set or categorizes may have a large effect on the p-value. But the overall relationship seems robust.

A highly encephalized “alien”

What to think of all of this? If you don’t know, one of the authors of the paper, Robin Dunbar, has been arguing for the prime importance of social structure in driving brain evolution among humans for nearly twenty years. The relationship is laid out in his book Grooming, Gossip, and the Evolution of Language. Robin Dunbar is also the originator of the eponymous Dunbar’s number, which argues that real human social groups bound together by interpersonal familiarity have an upper limit of 150-200. He argues that this number arises because of the computational limits of our “wetware,” our neocortex. Those limits presumably being a function of biophysical constraints.

One interesting fact though is that the median cranial capacity of our species seems to have peaked around one hundred thousand years ago. The average human today has a smaller brain than the average human alive during the Last Glacial Maximum! (see this old post from Panda’s Thumb, it’s evident in the charts) This may be simply due to smaller body sizes in general after the Ice Age. Or, it may be due to the possibility that social changes with the rise of agriculture required less brain power.

Ultimately if Dunbar and his colleagues are correct, if social structure is the most powerful variate in explaining differences in brain size when controlling for phylogenetics and body size, then in some ways it is surprising to me. After all, it does not seem that ants have particularly large brains, despite being extremely social and highly successful. Clearly the hymenoptera and other social insects operate on different principles from mammals. Instead of
developing “hive minds,” it seems as if in mammals greater social structure entails greater cognitive structure.

Citation: Susanne Shultz, & Robin Dunbar (2010). Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality PNAS : 10.1073/pnas.1005246107

(Republished from Discover/GNXP by permission of author or representative)
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"