Non-locality

A disclaimer about what follows: this is a substantial digression from any area I might claim knowledge of.

Quantum theory is counterintuitive in interesting ways. Many people emphasise the strangeness of indeterminacy and adduce it to argue that the mind contains or operates special causal levers. I don’t see a great benefit to uncaused causes for a free-will enthusiast or, for that matter, for first-cause mysticisers, so I tend to be sceptical of many popular claims of this nature. Indeterminacy is counterintuitive and interesting but determinacy isn’t a pin in the grenade of rationalism.

Non-locality  – or the capacity for state changes to propagate between entangled particles with no intermediaries and with no delay – has always seemed more interesting to me. This recent popular article emphasises its incompatibility with general relativity. It turns out that non-locality’s absolute simultaneity poses a significant challenge for physics and, given our ideas of the geometry of spacetime, for our understanding of causation.

Reading this stimulates in me the intuition that perhaps locality is in some sense incoherent. Just how close do two objects have to be (à la Zeno’s paradox) for interactions between them to be considered local? Is it necessarily all that peculiar that events in the future might determine events in the past?

I think that our concepts of locality and ontology are linked in such a way that revisions may be required in both. If X and Y make up the entity Z then any properties of Z will be shared by X and Y regardless of where and when X and Y are. This argument makes the description of instantaneousness redundant and I suspect that quantum entanglement is somewhere between the situation just described and one in which X and Y are truly separate entities. Perhaps the problem of non-locality cuts into ontology. I would very much appreciate any more expert thoughts on the matter…

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Pleiotropy

I’ve posted a few times on pleiotropy. Pleiotropy, or the multiple causal connections that a given gene is involved in, is the bête noire of evolution by selection because it increases the probability that a mutation at that gene will be deleterious (even though it may be beneficial within one context). Modularity is required at the gene level to allow functional change to occur by selection and this has motivated some to propose that cis-regulatory elements (CREs) are crucial to the evolution and development of form.

But modularity can also occur at the level of genetic networks and it is often asserted that such networks can be co-opted in their entirety to fulfill novel (non-homologous) functions. In the context of testing this idea, this recent article addresses the consequences of this for the pleiotropy of CREs. If network co-option really is that common, pleiotropic CREs will also be common at least among those genes that tend to be found within networks rather than upstream. This seems to be a nice example of entrenchment in evolution.

Creative thinking

There is a pattern in the way I respond to world events with high penetrance in the news. I tend to become emotional and ideologically minded, then analytical and anti-ideological. The financial and economic situation is no exception and it seems to offer plenty of opportunities for my sort of confusion. Here is a chance to push a social democratic agenda, to challenge market fundamentalism – the argument for market failure seems compelling. On the other hand, I am losing confidence in the stimulus: both as a concept championed by economic “science” and as a policy carried out by crony capitalists with friends in certain industries. I am entering my sceptical, anti-ideological phase – totally free markets are footling abstractions, real markets are fallible, real regulation inadequate, and the re-colonisation of the markets by governments not entirely benign. The disappointingly minimal conclusion seems to be that highly abstracted financial markets are negative sum or at least dangerously unpredictable (perhaps because of dangerous levels of prediction in them, after Nassim Nicholas Taleb). So while we can say that markets are engines of growth (and defend some level of abstraction in them), none of the big -isms offer much to add to or challenge this view and we must muddle along and cope with some of the absurd consequences of the dominance of betting in our economy (see this article for a specific and complex example).

But this recent piece has got me thinking about whether a more creative response is possible. The open source movement has made inroads beyond software into other social spheres (certainly into science where PLoS journals are flagships) and seems to offer a genuinely novel approach to production. Just as the market solves the tragedy of the commons, so open source approaches offer a solution to the tragedy of the anticommons (wherein production is limited because ownership of necessary components is distributed between companies each of which values their asset(s) at a price commensurate with sufficiency). And since open source approaches are decentralised they seem part of the solution for the burgeoning energy costs of the growing networks that support human society. The reduced transaction costs of the internet seem to offer a way to reinforce cooperation and more research is clearly needed to explore which factors drive and which factors limit this. Perhaps then we can take some of these ideas offline and into the wider world to produce robust and sustainable economies.

Adaptive acquired characteristics are genetically primed but not assimilated

Post Author: John Jacob Lyons

In their book, “The Four Dimensions of Evolution”, the Waddington ‘canalization’ explanation of the genetic assimilation of adaptive acquired characteristics is referenced (p.262) and tacitly accepted by Eva Jablonka and her co-author, Marion Lamb. I don’t find this explanation at all convincing and want to propose my own explanation. I suggest that adaptive acquired characteristics are always positively and causally correlated with concomitant, genetically generated propensities. These propensities gradually become more prevalent in the gene-pool because of the success of the positively correlated acquired characteristic. In time, the organism will appear to be primed to acquire the adaptive characteristic. It is suggested that examples in humans are language and religion.

Suppose that a particular mutation (M) that appears at generation n increases the capacity to learn an adaptive behaviour (AB). AB will have a selective advantage and consequently the relative frequency of M in the population will increase in generation n+1. This will, in turn, increase the frequency of AB in this generation. So long as AB remains adaptive, this positive feedback loop will, over evolutionary time, lead to all organisms in the population having mutation M and exhibiting adaptive behaviour AB. Additionally, selective pressure will result in AB appearing earlier and earlier in the lifetime of organisms. In due course, it will appear that all organisms in the species are primed to acquire the AB.

As stated, I believe that two examples of this process in humans are language and religion. This would account for the innate ‘Language Acquisition Device’ hypothesized by Noam Chomsky and Precocious Religious Belief hypothesized and empirically demonstrated by, among others, Justin Barrett (Centre for Anthropology and Mind, Oxford University). I don’t believe that an adaptive acquired characteristic is ever genetically assimilated as proposed by Waddington. In other words, I don’t accept that the Weismann Barrier between somatic and germ cells is ever crossed in these circumstances. Rather it is as if the constituents of the genetic soil, as it were, are gradually optimized to promote the germination and growth of the AB seed. In the case of religion, the seed of belief/ faith may be provided by the parent explaining to the child that their sadly expired pet kitten, Tiddles, is now “with god in heaven” and reinforced by similar references later on. In language, the innate universal grammar proposed by Chomsky and others, may be characterized in a similar way with the heard phonemes, words, syntax and grammatical exceptions of the native language providing the seeds.

It is also suggested that the niche construction and extensions to phenotype seen in many species of animal may also have a similar origin. These could well have originated as behaviours that proved to be adaptive and that, eventually, resulted in the concomitant, positively correlated and genetically mediated allele-sets becoming ubiquitous in the species. These would then have primed the young organism to reproduce the behaviour with minimal exposure to the behaviour by others.

Positively escaping pleiotropy

I recently attended a workshop at my institution covering a broad range of evolutionary topics (including many exciting hominin fossil finds in the offing it seems). The last talk of the day was Adam Siepel of Cornell University who gave a talk about positively selected genes reflecting this recent paper in PLoS Genetics. His group used well-sequenced genomes of human, chimp, macaque, mouse, rat and dog to infer positive selection in protein-coding genes using likelihood ratio tests. Bayesian methods were  used to establish likely selection histories (which suggested frequent state changes along the phylogeny implying that positive selection occurs and re-occurs over short intervals).

Interestingly positively selected genes tended to be expressed at lower levels and with more tissue-specific expression patterns. This mirrors inverse/positive correlations found elsewhere between substitution rate and expression level/tissue-specificity. More subtly, though, the inverse correlation between substitution rate and expression level was more pronounced in genes not subject to positive selection indicating that responses to purifying selection might be responsible for most of the trend. Thus: “It appears that genes may be more likely to come under positive selection if they are in a state of evolutionary flexibility brought on by reduced or tissue-specific expression, but once positive selection has taken hold their subsequent evolutionary course is not strongly dependent on their expression patterns.”

The inverse correlation with expression may relate to selection against protein-misfolding but the picture with tissue-specificity is about the costs imposed by pleiotropy and is interesting to me because I recently ran an argument about escaping pleiotropy in a recent paper with Samir Wadhawan and my advisor Anton Nekrutenko about the mammalian Gnas locus. The Gnas locus is formidably complex. Crudely it consists of multiple alternative transcripts which share downstream exons but which differ in first exons. These transcripts are subject to complex patterns of tissue-specific and imprinted gene expression with the non-canonical transcripts showing tissue-specificity. We observed an increased rate of evolution (by likelihood ratio testing of dN/dS) among exons unique to these alternative tissue-restricted and imprinted transcripts. I argued that the selection pressures commonly invoked to explain the evolution of imprinting were not sufficient to explain sustained elevated rates and that an escape from pleiotropy was also required in the explanation.

My point was that pleiotropic genes disproportionately attract imprinting (because are more likely to have phenotypes relevant to asymmetric kin interactions: see manuscript), while imprinting of widely expressed transcripts imposes heavier phenotypic costs, which may be avoided by imprinting of alternative tissue-specific forms or acquisition of tissue-specific imprinted expression (demonstrated by the canonical, near-ubiquitously expressed Gnas locus transcript). I used this to motivate an argument for the complexity of imprinted loci separate from Wilkins’ competitive signal discrimination argument for regulative complexity. From Siepel’s data it may be that the tissue-specificity alone is then sufficient to explain elevated rates (contra my thought that patrilineal/matrilineal arms races were involved at this stage). I wonder if this dynamic is generalisable – perhaps pleiotropic genes attract various forms of intragenomic conflict, which then favour the development of baroque modifications?

Siepel’s study had other interesting things to say about the functions of genes subject to positive selection (with some unsurprising targets such as immune system genes), but all-in-all the dynamical aspects seem very interesting to me.

Of trees and roots

I recently attended two talks by Professor Ford Doolittle of Dalhousie University. Doolittle’s argument is about the validity of phylogenetic trees. For prokaryotes specifically, his claim is that trees do not map onto natural kinds. Or more starkly the idea that there is a tree of life is a hypothesis which has now shown to be incorrect for the majority of life on earth.

In his first talk, he began by discussing classification as a common and useful practice and mentioned a paper by Jared Diamond (this one I think) showing that zoological classification by tribal peoples can correspond with scientific classifications. This inter-subjectivity seems to confirm the existence of real phenotypic gaps, but these days we are wont to think of our modified Linnean hierarchical system as reflecting something else: descent with modification (to use Darwin’s term). Creatures assigned to one taxon cannot also be assigned to another and higher level taxa are inclusive of lower level taxa.

Doolittle’s core point is that the prevalence of horizontal gene transfer (HGT) means that descent with modification needn’t produce a branching structure so much as a reticulate one. Perhaps the best known example of HGT is one Doolittle has been pivotal in establishing as a biological fact: the invasion of early eukaryotes by alpha-proteobacteria giving rise to mitochondria, but many more examples are now well known and these are mediated in bacteria by the processes of transformation, transduction and conjugation (loosely these are the uptake of naked DNA, viral DNA transfer and plasmid exchange, respectively). The key point is that the larger the segment of time considered, the smaller the proportion of a bacterial genome that has not been subject to HGT. He provided data in support of this.

In his second talk Doolittle gave details of his own research in the field of metagenomics where the concept of a metagenome is significant. Gene-level phylogenies frequently contrast with organismal phylogenies demonstrating HGT and in his study systems he provided evidence in support of exchange between halophylic archaea and eubacteria (organisms in different domains of life) with the former transferring salt-tolerant genes to the latter and metabolic genes flowing the other way. He gave some reasons for thinking that HGT can be recurrent in structured environments and that significant rearrangement of functional units can take place over periods of decades: i.e., that bacterial macroevolution is reticulate.

Doolittle’s principle philosophical claim flowing from this, and made with Eric Baptiste in this paper, is that while evolutionary biology now admits of multiple evolutionary processes besides natural selection, it needs to adopt a similarly pluralistic stance about the patterns produced by these. He calls those who accept (even implicitly) the tree of life idea, pattern monists. And he cited S. J. Gould’s criticism of process monists: those who attribute all of life’s complexity to natural selection alone.

This made me think of (and ask) a question. In this blog I have previously defended a kind of monism by emphasising that I am monist with respect to adaptation not the origin of species or diversity in general. I think most evolutionists would accept that selection (natural or sexual) is the only process able to generate adaptive change (though the details of any particular adaptive walk may involve drift or recombination as a key component). In brief I have defended this notion by pointing to the need for some sort of discrimination (something not provided in Lamarck’s alternative evolutionary theory for example). So I asked if monism/pluralism disputes about pattern might similarly be resolved by an analogous change of focus. Is the tree concept valid for some lower level unit? Let’s call it an atom. He suggested I might be able to wriggle in that direction but that he was betting against monism at any level of organisation (at least in prokaryotes; one questioner raised the interesting point that sex in eukaryotes might be a way of regulating HGT to largely within-group transfers).

Now an obvious candidate for the atom of analysis mentioned is the gene, particularly when you consider that HGT is often demonstrated using discordance between organismal and gene-level phylogenetic trees. But the trees used here are still arguably only instrumental and homologous recombination between similar genomes (which might also be counted a form of HGT) may be seen to occur across functional genes. This forces our atom definition into a unit of zero recombination or more generally and accurately anything that selection or linkage maintains in linkage disequilibrium. Ultimately we are referring to the selfish genetic element concept a la Dawkins and Trivers and much of this seems unsurprising from a neo-Darwinian perspective (contra Doolittle’s claim that his thesis represents a radical departure and, even more provocatively, one required to create a creationism-resistant evolutionary biology – I take issue with this as there is already evidence enough for evolution and for the processes posited to explain it).

I think that the timescale matters and that during microevolution it is reasonable to describe a tree of selfish genes, which include hyper-motile elements such as integrons. At the organismal level these trees may move in and out of phase with each other as the coalitions we call organisms shift about, but we can still validly describe a tree of life at lower levels. At the macroevolutionary level beyond the population dynamics and lifetime of particular selfish genetic elements, I am not so sure and there may be parts of the genome that are evolutionarily modular at a different scale from others (how this relates to function is interesting). The problem is that the birth and death of these elements seems to invalidate any claim to a universal tree of life. Fine, but remember this has the possible and interesting connotation that there is no last universal common ancestor (LUCA; which is not a statement about a unitary origin of life – this is about backward coalescence and all chemistries not extant are excluded).

Where I think I depart from Doolittle (if I represent his claim fairly) is in his saying, in answer to a question, that even the genetic code has no last common ancestor (LCA). There is basically one genetic code so far known with a few minor variants and given the combinatorial architecture of the transcription and translation machinery this amounts to a vanishingly small segment of the possible code space. It therefore seems likely that common descent explains code identity across the natural world. There are two objections to this: 1. the code may be the only optimal code and we have it thanks to selection and 2. it may itself be modular and hence derived from multiple lineages. With respect to point 1 it is well known that the code is highly optimised but it is not perfect and a better code is known to exist in a distant point of code space. With respect to point 2, it is reasonable to suppose gradual recruitment of tRNAs and competition between alternatives, but it is hard to imagine the de novo assembly of these sets of tRNAs into independent but identical codes in separate lineages. Once derived that would seem to be it.

In summary each of the major transitions in evolution may have fashioned a new set of replicators and the tree of life familiar to us in the eukaryote world is approximately correct but we must acknowledge its roots among the prokaryotes are highly reticulate.

Religion and morality

The idea that someone’s morality comes from a god is like the idea that their cellular structure is assembled by a god. Biochemistry describes a different process in which macromolecules from food are broken down and/or sorted into the structures in a process of self-assembly. This occurs over developmental and evolutionary time and the idea of assembly from extrinsic sources is not plausible.

My comparison suggests that a science of morality might yield or has already yielded similar conclusions, viz. that morality develops over developmental and evolutionary timescales by a process of self-assembly. Key theoretical pointers are theory of mind and game theoretic notions for the two timescales, respectively.  There is much to elaborate on here, but this is not the purpose of this post. Suffice it say that anticipating this general outcome of research is not unreasonable. It fits the pattern of scientific discovery in general, replacing implausible but intuitively appealing skyhooks with a multitude of cranes to do the heavy lifting of explanation (to borrow Dennett’s admittedly tendentious phrasing).

For those who disagree with me, there are several versions of what it means to say there is no morality without a god. First this might mean that if you do not believe in a god (or in this role for such an entity) then you cannot be a moral person (implying that atheists are necessarily nasty). Second it might mean only that a god plays this role regardless of whether you are aware of that fact (so atheists and theists are equivalent). But there is a third and intermediate position which posits that your being aware of a god’s role in planting morality’s seed in you in will enhance your access to it in some way. The details of this are not important, but the fact that there are several ways this can be imagined (e.g., that you accept a universal love invisible to others, that you can hear a god’s advice, etc.) makes it intuitively more appealing and plausible, at least to deists or theists. (For completeness, the supernatural realm is not always so appealing and it is plausible to be angry or frightened by powerful agents, like witches, and wish to be an unbeliever).

But for those who agree with me, there are also several versions of what it means to say that religion is not a source of morality. First it might mean that religion is essential for the development of morality but is not its source (so that to be good you must be culturally Christian, if not a theist, for example). Second it might mean that religion has nothing to do with morality (so theists and atheists are equivalent). But again there is an intermediate position: perhaps religion has an impact on the development of morality over developmental and evolutionary timescales though it is not essential. (For completeness, you might posit that religion has only negative effects on the development of morality too – more below).

I find the third non-theist position plausible and to explain why I return to the analogy of biochemistry and eating. While it is true that self-assembly, not outside-directed assembly, is responsible for cellular structures, chemicals we ingest do affect physiology. The most obvious class of things ingested which can do this is drugs though all aspects of diet are relevant over developmental and evolutionary timescales. What might this mean in the context of morality?

Religions generate plausible intuitions about morality the most obvious flowing from the concept of an all-access agent (of which the Christian god is an example): crudely, if He knows everything that everyone is thinking (not just doing), then He will know what is right and what is wrong (much of this follows from Pascal Boyer’s thesis in “Religion Explained”). Moral problems are problems of social coordination and are often caused by having only partial information about another’s motives. Now this concept might be too recent in history to have impacted the evolution of morality, but it can surely affect the development of morality in individuals at least as an intuitive framework for moral expression (and possible negative connotations if access to such an agent is claimed as a special privilege). Arguably the causation here is mostly in the other direction with the plausibility of the intuition driving hazy notions about the nature of the agent (e.g., God seems to be aware of all relevant strategic information such as that spoken of in confession, but people don’t make much of His knowing any particular detail of the physical universe unless it is relevant – it isn’t often subject to debate despite the implications for how this feat of memory might be achieved (none of which is to imply it could not)).

On whether believing in all-access agents has good or bad consequences, I suspend judgement. It may be that believing in one intensifies feelings of conscience, which seems like a good thing or it may be that it promotes a command-and-control morality possibly inappropriate after childhood when most fellow humans are on an equal footing as regards privileged information (but seemingly reinforced by fictive kin notions like “God the Father”). Hence the possibility that religion is less like opium, more like an amphetamine: a moral stimulant.

All-access agents aside, religion has been around for a while so there might be a story a bit like lactase persistence waiting in the scientific wings (again with neoteny being a feature). Perhaps notions of other worlds or of reincarnation or life after death have effects on intuitions that are now tolerated or even required by our moral intuitions. I am not sure, but if there are necessary components of religion it seems plausible they may already be dispersed outside of any particular religion in the form of intuitively appealing notions and moral fables and parables.

The take home point is that nobody should prejudge the matter. Religious people do give blood more (a measure which gets round the confounding fact that charities are often religious) and religions are effective at organising the distribution of club goods from social welfare to suicide terrorism. Religion has an impact and it is likely to be complex. Understanding this is important especially if as a social democrat you are interested in the forces responsible for social solidarity and want to move beyond the religious right’s “family values” (think Mafioso – amusing comparison made by Stephen Fry) and the atheist left’s tendency to throw the baby out with the authoritarian bathwater (see this article or this talk for a slightly hyperbolic version of this sentiment).