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I’m reading philosopher Thomas Nagel’s most recent book, Mind and Cosmos
in which he argues that the “neo-DarwinianMind and Cosmos Cover conception of nature is almost certainly false” – in fact, that is the subtitle of the book. Key to his argument is that it doesn’t appear that the cornerstone of neo-Darwinism, namely random mutation to genes that turn out to be fitness enhancing, could ever come up with the vast variety of large scale variations in body morphology and physiological systems we see in the world, many of which are argued to be “irreducibly complex” (i.e. all-or-nothing from an evolutionary fitness perspective). The architecture of the eye, and the molecular motor that powers flagellum in bacteria are examples of these complex biological structures that would seem (to some) impossible to evolve through simple random mutation.

Nagel, and others (and not just  intelligent design (ID) folks, some of whom think God orchestrates evolution) see the need for some more directed form of evolution to explain the diversity and complexity of life on our planet. Nagel seems to think mind / consciousness, and not God in the traditional conception of the term, might fit the bill. But to me that seems rather extreme, and goes against “reductive materialism / naturalism” that has been so successful at explaining how the world works over the last few hundred years.

One wonders if a less drastic solution that tweaks the mechanism of neo-Darwinian evolution, might be invoked to save the day for materialism / naturalism.

As discussed elsewhere (see this post for details), I’ve recently been studying epigenetics, where gene expression can be modulated by methylation (among other mechanisms). In methylation, a methyl groups can attach to a particular DNA base pair, causing the gene to “wrap up” around a histone, preventing it from being transcribed into RNA, thereby suppressing expression of the protein that the gene codes for. This methylation can be driven by environmental factors, is quite localized, specific, and repeatable, and can occur not only in somatic cells, but also in germ-line cells (eggs and sperm), and thereby get passed down to several subsequent generations.

While the epigenetic changes can be adaptive both for the organism in which they first occur, as well as their progeny, they aren’t permanent changes to the base-pair sequence of genes, so they aren’t heritable variations over thousands or millions of years, like we see across species in the world. So they are “Lamarkian” to a point, but not in the true sense of the world – giraffe necks could get longer for a generation or two after (hypothetical) epigenetic changes occurred as a result of a giraffe stretching to reach the high leaves on a tree, but eventually the epigenetic changes would “wear off” and subsequent generations would go back to having short necks.

But what if epigenetic changes via methylation not only silences genes, but also made those silenced genes more prone to mutation? The methylation would not only be a signal that “this gene isn’t worth expressing in the current environment”, it would also be signaling “this gene is not very useful in is current form in the current environment, so target it for mutation”. With an elevated mutation rate specific to maladaptive genes lasting several generations, new variations should more readily arise in subsequent generations, accelerating experimentation with parts of the genome where changes would be mostly likely to be beneficial in a rapidly changing environment.

This sort of elevated mutation rate in parts of genes that have been methylated (silenced) is exactly what this study [1] found. To quote the abstract:

Our results … provid[e] the first supporting evidence of mutation rate variation at human methylated CpG sites using the genome-wide sing-base resolution methylation data.

It’s not clear that this targeting of random mutations to specific maladaptive genes could result in the type of big changes Nagel and others point to when criticizing neo-Darwinian evolution. But it seems like a way to facilitate a sort of “semi-Intelligent Design”, without an explicit designer, by focusing “random tinkering” with the genome in places where genetic changes could do the most good in the current environment.

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[1] BMC Genomics. 2012;13 Suppl 8:S7. doi: 10.1186/1471-2164-13-S8-S7. Epub 2012 Dec 17.

Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome.

Xia J1, Han LZhao Z.

Full text: http://www.biomedcen…1-2164/13/S8/S7

Abstract

BACKGROUND:DNA methylation, which mainly occurs at CpG dinucleotides, is a dynamic epigenetic regulation mechanism in most eukaryotic genomes. It is already known that methylated CpG dinucleotides can lead to a high rate of C to T mutation at these sites. However, less is known about whether and how the methylation level causes a different mutation rate, especially at the single-base resolution.

RESULTS:In this study, we used genome-wide single-base resolution methylation data to perform a comprehensive analysis of the mutation rate of methylated cytosines from human embryonic stem cell. Through the analysis of the density of single nucleotide polymorphisms, we first confirmed that the mutation rate in methylated CpG sites is greater than that in unmethylated CpG sites. Then, we showed that among methylated CpG sites, the mutation rate is markedly increased in low-intermediately (20-40% methylation level) to intermediately methylated CpG sites (40-60% methylation level) of the human genome. This mutation pattern was observed regardless of DNA strand direction and the sequence coverage over the site on which the methylation level was calculated. Moreover, this highly non-random mutation pattern was found more apparent in intergenic and intronic regions than in promoter regions and CpG islands. Our investigation suggested this pattern appears primarily in autosomes rather than sex chromosomes. Further analysis based on human-chimpanzee divergence confirmed these observations. Finally, we observed a significant correlation between the methylation level and cytosine allele frequency.

CONCLUSIONS:

Our results showed a high mutation rate in low-intermediately to intermediately methylated CpG sites at different scales, from the categorized genomic region, whole chromosome, to the whole genome level, thereby providing the first supporting evidence of mutation rate variation at human methylated CpG sites using the genome-wide sing-base resolution methylation data.

PMID: 23281708

The Edge.org question for 2010 is How is the Internet Changing the Way We Think? The site has lots of interesting answers including quite a bit doom and gloom about how we’re distracting ourselves to death, penned by smart people like Clay Shirky, Danny Hillis, and Dan Dennett.  But I was particularly intrigued by a couple passages from the response of evolutionary biologist Richard Dawkins.

Like many of the other respondents, Dawkins has observed a dumbing down of the individual as a result of the lower quality of media we’re exposed to, and the information firehouse that seems to be preventing us from focusing too hard or too long on anything that requires deep thought.  But at the same time, Dawkins (and other respondents) see room for optimism. As Dawkins put it:

But I want to leave negativity and nay saying and end with some speculative — perhaps more positive — observations. The unplanned worldwide unification that the Web is achieving (a science-fiction enthusiast might discern the embryonic stirrings of a new life form) mirrors the evolution of the nervous system in multicellular animals. …

I am reminded of an insight that comes from Fred Hoyle’s science fiction novel, The Black Cloud. The cloud is a superhuman interstellar traveller, whose ‘nervous system’ consists of units that communicate with each other by radio — orders of magnitude faster than our puttering nerve impulses.

But in what sense is the cloud to be seen as a single individual rather than a society? The answer is that interconnectedness that is sufficiently fast blurs the distinction. A human society would effectively become one individual if we could read each other’s thoughts through direct, high speed, brain-to-brain radio transmission. Something like that may eventually meld the various units that constitute the Internet.

I agree with Dawkins and many of the other experts who give their opinion to the Edge.org question. The jury is still out on just how the Internet is impacting the thinking of individuals. It gives us the opportunity to be aware of so much more than has ever been possible. But whether this will translate into knowledge individuals can employ to lead better lives isn’t yet certain.

What is indisputable is that the Internet is affording opportunities for collective intelligence, and coordinated action on a scale that has  never before been possible.  But is less certain is whether we will find ways to effectively nurture and harness this collective energy.  That seems to be what Web 2.0 is all about.  At the moment, we appear to be going through the equivalent of a Cambrian Explosion of projects & startups trying to capitalize on web-enabled collaborative systems. There are literally hundreds of big and small apps trying to leverage Twitter alone.

As Jeff Stibel (@Stibel) suggests in his new book Wired for Thought (which I highly recommend), we are likely to soon see a period of mass extinction of social media startups as the novelty of this new form of collaboration and communication wears off.  Such a die off will resemble  the massive pruning of connections that occurs in the human brain to eliminate redundant and unhelpful connections during childhood.  The human brain’s synaptic down selection during maturation is astonishing and quite draconian, going from about 10 quadrillion connections in a three year-old to a mere 100 trillion by adulthood, which means than only 1 in 100 synapses survive (source: Edelman’s book Neural Darwinism).

Hopefully the fittest & most useful (as opposed to the most amusing) will survive, and the result will be a set of sites and services that will facilitate true collective intelligence and collaborative action to move humanity forward, pulling we overstimulated and distracted individuals along with it.

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Ever feel like you're part of a big machine?

This blog is an exploration of what being part of a collective might mean for each of us as individuals, and for society.

What is it that is struggling to emerge from the convergence of people and technology?

How can each of us play a role, as a thoughtful cog in the big machine?

Dean Pomerleau
@deanpomerleau

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