Saturday, March 27, 2010

Driven to speciate- meiosis and PRDM9

Many crossover sites in meiosis are selected by the protein PRDM9, which has been evolving extraordinarily rapidly, contributing to the speciation of humans. (Warning... this post is unusually technical.)

Analysis of the human genome is picking up speed. A recent issue of Science provided two examples, one paper describing dramatic advances in the search for human genes with variants whose prevalence in the population has risen recently due to strong selection. Another set of papers each found the same gene, PRDM9, to act in crossover hotspot selection, converging from two separate mouse genetics studies and one computational study which I will focus on.

One of the more subtle processes of reproduction among sexual organisms is chromosome crossing-over at meiosis. Typically each chromosome arm, as it goes through the meiotic division that reduces the diploid genome inherited from the two parents into one haploid genome found in gametes, ends up not as a pure copy of either parent's chromosome, but as a patchwork, with some portions from one parent and the rest from the other. Sort of a contra dance, with a choreographed do-si-do of DNA recombination.

Getting there requires one or more crossover events per chromosome whose core is direct recombination between DNA from the two parents somewhere along the chromosome arm, and involves complicated chromosomal dynamics which can also influence cell division. To whit, if any single chromosome fails to have such a connecting crossover, it also fails to align at the center of the cell during metaphase I and floats off in the cytoplasm, stopping cell division at a point called the pachytene checkpoint, usually fatally. You don't want those gametes!

One might imagine that these crossovers occur randomly across the genome, but they don't. They occur primarily at what are called "hotspots", distributed unevenly over each chromosome. Hotspot locations change dramatically from species to species. We have almost completely different ones from chimpanzees, even though most of our DNA is the same. Why is that?

The reason seems to be an even more subtle process called "biased gene conversion", which is the engine behind all the phenomena of this article, causing in this case something called "meiotic drive". Crossover events begin with breaks in the DNA: double-stand breaks that are repaired using the information from the undamaged, homologous strand of DNA. The sound DNA physically invades the duplex of the damaged DNA, allowing both duplexes to be filled out by polymerases, i.e. repaired, (as diagrammed below) based on the sequence of the undamaged DNA.

Diagram of gene conversion- the repair of one homolog suffering a break with information from the other DNA/chromosome homolog.
But some of the time, this repair resolves not a clean invasion and retreat of the "good" DNA, (which process is called gene conversion), rather it resolves by the crossed DNA getting cut the other way, one DNA strand of the "good" chromosome staying with the opposite arm/strand of the damaged chromosome. In the diagram, this takes place after the "New DNA Synthesis" stage, where, if you just swing the arms around and cut the products a little differently (up and down, in line with the gray arrows), you end up with a crossover rather than two cleanly repaired original chromosomes. These crossover events are the ones that meiosis relies on (and regulates) to end up with properly inter-joined homologous chromosomes in meiosis I, where one homolog comes from each parent. However meiosis involves plenty of gene conversion as well- only a minority of induced double strand breaks end up as cross-overs.

If an organism has a mechanism to cause double-strand breaks during meosis, (as they do), and that mechanism relies on signals on the local DNA as targets of these breaks, (as it does- those are the hotspots), then it follows that the activating signal will tend to get erased when it is heterozygous and attracts repair by undamaged DNA lacking that particular local hotspot sequence. This process of eliminating the very markers that start the events of DNA repair / gene conversion / crossing over represents a bias, since one sequence variant tends to lose out over time and get erased- not just from the gametes, but from the population as a whole. Thus the term "biased gene conversion". Thus also the term "meiotic drive", since it is an example of selection based on the peculiarities of the molecular system, which "drives" the genetic composition of the population in a non-random direction.

In this paper (with review), the hotspot of interest contains the sequence CCTCCCTNNCCAC, where N stands for any nucleotide. They claim that this sequence is at the core of 40% of human meiotic recombination hotspots, while not being involved in chimpanzee hotspots at all. While other papers in the issue arrive at the protein that binds this sequence from painstaking genetic mapping of loci that affect hotspot usage in mice, the current paper gets there from computational analysis of zinc finger proteins.

Humans have about 691 zinc-finger proteins, which typically bind DNA with their zinc-finger domains, and do something else with the rest of the protein, like regulate transcription, or as in this case, direct the double-strand break apparatus. One reason the family is so large is that its members have a modular design where each finger, which is a protein loop that coordinates one zinc ion inside while its outward-facing amino acid residues touch the DNA, touches about four nucleotides in the major groove. Zinc-finger proteins typically have multiple fingers, up to thirty in some cases, enabling them to recognize lengthy and specific sequences. This modularity allows them evolve easily by shuffling around pieces of their genes. They are also interesting from a biotech standpoint, in the quest to develop technical ways to regulate arbitrary DNA sequences with injectable or gene therapeutic agents.

The modularity is also a boon to bioinformaticists, who, as this paper demonstrates, can predict from a target sequence what zinc-finger protein might bind to it. Given the target sequence mentioned above (which is set within an additional 30 base pairs of influential context), these authors estimated that the binding protein had about 12 fingers, and could also estimate what the key residues of these fingers probably were. Scanning the human genome data, they came up with one protein that closely fit the bill- PRDM9. Below is their diagram of the critical fingers/residues of this protein, aligned along the human target DNA sequence to which it binds, also aligned with its homologs from other species.
"In silico prediction of the binding consensus for PRDM9 ... Below the text is the sequence of four predicted DNA-contacting amino acids for the 13 successive human PRDM9 zinc fingers (one oval per finger, differing colors for differing fingers, and the separated finger is gapped N-terminal from others) and their predicted base contacts within the motif. (C) Sequence of four predicted DNA-contacting amino acids for the PRDM9 zinc fingers in seven mammalian species, presented as in (B). Distinct fingers are given different colors; fingers present in at least two species have a black border."
Note that the same protein in different species has almost completely different DNA-binding residues and thus target specificity. This rate of change far surpasses that in the rest of the genome, where very little change typically separates us from any of these other mammalian species, and  most of that change is random. This data (combined with other work that confirms the connection between PRDM9 and crossover hotspots) accounts for why hotspot locations differ so dramatically between humans and chimpanzees, at least those that are directed by this protein.

So here we have it- an inexorable genetic process by which the targets of meiotic recombination continually change under the pressure of biased gene conversion, matched with a targeting protein which seems to evolve rapidly in response, as though the actual sequence it binds to is of minor significance, just as long as it has something to bind to as the rug is continually pulled out from under it.

How does this relate to speciation? Speciation depends on mating/fertility barriers between populations, either geographic, behavioral, biological, etc. A typical example is hybrid infertility- the inability of individuals from different protospecies to mate and have offspring, or the infertility of those offspring. Mules come to mind, for instance.

Problems in meiosis result in infertility. Specifically, reduction of meiotic crossovers below the one-per chromosome level is fatal to the resulting gametes, as outlined above. As the PRDM9 gene races to keep up with gene conversion that erases its targets, it will diverge between populations, leading to changes in hotspot locations and sequence. The arrival of two incompatible parental genomes, one of which lacks the ability to recognize the crossover hotspots of the other, is a recipe for catastrophe- specifically, for meiosis I non-synapsis. This indeed is how one of the other papers in this issue found PRDM9- by locating a genetic variant in mice directly responsible for the hybrid infertility between Mus domesticus and Mus musculus.

These findings advance considerably knowledge and theory about speciation in animals whose genetic variation can be quite low (on average), whose generation times may be quite long, and whose populations can be quite small. It is very exciting to be able to synthesize, using the modern toolchest especially including the human genome, these strands of cell, molecular, and evolutionary biology.

  • Another discussion of the PRDM9 gene, authored before its molecular function was understood, and focusing on its role in speciation.
  • On girls, real girls, and equality.
  • Great news from Iraq.
  • Nice quote from Gregor.
"We have lost touch with the hurdles faced by our not-too-distant forbears who, in a world of wood and coal, found waterway transport a kind of miracle. What kind of a nut, for example, would blast through all that granite in upstate NY to build a canal? A nut who did not have oil, that’s who."
"This insight allows us to see another dimension of taxation which is lost in orthodox analysis. Given that the non-government sector requires fiat currency to pay its taxation liabilities, in the first instance, the imposition of taxes (without a concomitant injection of spending) by design creates unemployment (people seeking paid work) in the non-government sector. The unemployed or idle non-government resources can then be utilised through demand injections via government spending which amounts to a transfer of real goods and services from the non-government to the government sector.
So it is now possible to see why mass unemployment arises. It is the introduction of State Money (which we define as government taxing and spending) into a non-monetary economics that raises the spectre of involuntary unemployment."

Saturday, March 20, 2010

I am a program

On programming and being

As a programmer by trade and a biologist by training, I am afforded an endlessly fascinating perspective on the question of being, since organisms turn out to be (via the magic of DNA) enormously complicated learning and self-reproducing programs.

Now that we are all dependent on computers and comfortable with various analogies between computation and biology, (memory, viruses, language, bugs(!)), it might seem unproblematic to see ourselves as programs, instantiated in messy wetware and programmed with glacially slow evolutionary optimization. But of course there is a great deal of resistance, since one of the features of our program is that we see outwards, not inwards, and thus customarily don't have the faintest appreciation of our psychological or bodily inner workings. Indeed, our program creates a brain that militantly resists thinking of itself as a program, enjoying instead an illusion of sovereign freedom and a sovereign view over its flowing experience, as though its own basis were immaterial.

While some nerds revel in the computational analogy, and hope that they may shortly "download" their brain contents into immortal mechanical devices, it is fair to say that most people resist the analogy, whether instinctively or behind the smokescreen of elaborated theology. Unfortunately, science has relentlessly chipped away at these superstitious defenses, starting at the outer perimeter of humanity's geographical place in the cosmos, proceeding to kill the knights of vitalism through biochemistry, then breaching the sanctum of our mental sovereignty through Freud and the later work of psychology.

Really, there is nothing sensible left of the idea that subjectivity is as it naively seems- an immaterial soul with intuitive powers to communicate with the foundations/founders of the universe. But then, a final mechanistic account of subjectivity is not at hand either. At least the problem of consciousness is on the research program in earnest, at last, but solving it will take a few more years- decades at most.

On the silicon side, programs have become behemoths of complexity, though remaining well short of "artificial intelligence". Language translation on the web has become a great example of mini-intelligence, however. What is the barrier to true intellegence? It is learning. Humans are voracious learning machines, pulling in and storing vast amounts of information, but more importantly, interlinking it all organically in our neural nets, so that connections between near and far facts and ideas arise instantly as the need (or "inspiration") arises via related ideas, creating an integrated "world" for us to inhabit.

Despite all the databases, no computer yet inhabits this kind of world. Current programs are nowhere near learning at this high level and structure. It is a bit like the "total information awareness" project of John Poindexter, which was supposed to bring Big Brother to life across the federal government. Which was killed not because it worked, but because the concept itself was so disturbing.

But these capabilities will develop. That is the basis for Kurzweil's "singularity"- a point when machines can really learn and inhabit general conceptual worlds effectively, to the point of driving technological development faster than humans can (not to mention reproducing themselves!). Of course, there is the countervailing trend of diminishing returns to technology as the real limits of science and sustainability are reached. But at any rate, just as we have relegated half our minds to Google already, we may relegate the rest at some point in the future, and just enjoy life.

On the philosophical level, silicon is more benign and interesting. When I am looking for a so-called "bug" and puzzling over a program's mystifying behavior, the temptation to pray to unseen beings glimmers across the screen. But one thing you learn is that there is always, always, a definable cause. It may be a single character out of place in an enormous program, a well-hidden bug in infrastructure you have relied on for years, or a machine physically melting down. In philosophy, this is called the principle of sufficient reason (PSR), (in physics, it is Newton's third law, or many other conservation laws), and to come up against it day after day, on a relentless basis, can be most sobering.

Biology has similar moments, science being predicated on the PSR as well- the observation and assumption that causes can be found for any phenomenon. But cells and organisms are complicated systems, often more persistent in their inscrutiblility than we are in unlocking their secrets. Thus the triumph when the gene is found that causes a dramatic phenotype or syndrome, or the virus that causes a disease.

The science of genetics, and especially the discovery of DNA with its endless transmission through the generations, creating discardable somatic bodies as it goes along, brought the subject of biology down to a matter of programming, in the sense of heredity and evolution. How is the program propagated, preserved against accidents, read to create bodies, and divided to mate with partner DNAs? Most critically, how does this DNA make a brain and mind?

Obviously, DNA does not program the brain in the same explicit way that Microsoft programs Windows. The programming is indirect, generating and regulating complex proteins that have small lives of their own, which in turn generate dynamic metabolic, regulatory, and developmental processes, (an example in neuronal patterning), which in turn generate complex structures like brains. It's a messy process, built on a haphazard basis. It relies on many forms of homeostasis- feedback regulation- to maintain "normal" operations in the face of genetic and environmental variability, as well as to leverage normal obstacles and challenges into learning and development.

It's a bit like the Sims/SimCity game. There are discrete units of basic structure- people with various roles, furniture, urban fixtures, needs to fulfill. Once everything is working together, and combined with other players, you may end up with a city that behaves in complex ways, built out of relatively simple reproducible parts. Most theories of brain development rely on similar self-organizational behaviors to do much of the heavy lifting, for instance Edelman proposes massive neuron growth followed by function-induced testing/weeding/death to come up with properly structured networks, once the basic anatomy is in place.

Finally, there is the being of a program, rather than the making of programs (playing god, in a way) and the analysis of biologically given programs. Through the amazing alchemy of DNA, development, and neural brainwave patterns, we are the program, feeling the programmed instincts to learn, to live, to reproduce. We also feel the programmed need to imbue it all with inspirational meaning that is worth living for, and worth dying for, chosen freely with no influence from the programming.

"But an economic system should be about enhancing the prospects for the people. What other reason would there be to organise production and work in the way we do? That is actually the nub of all this ideological debate. The mainstream is not about people – the people are just “factors of production” (as they are referred to in the mainstream microeconomics textbooks) and are there to create profits."

Saturday, March 13, 2010

Mr. Toad's wild ride

An evolutionary reconstruction of the world-wide radiation of toads speaks to the process of speciation.

What makes toads so successful? They arose sixty million years ago in South America from frogs that had existed for 200 million years before, and had spread all over the world by twenty million years ago. In our day, cane toads have become pests in Australia, arriving from Hawaii and showing their awesome evolutionary fitness.

A recent paper in Science (with comment) attempts to classify traits among toads and deduce which traits were present in those lineages that spread most rapidly, arriving at a suite of traits that promoted both radiation and speciation.

The distinction between toads and frogs is a bit hard to define. Proper toads are a phylogenetic lineage (Bufonidae). But many frogs which convergently evolved similar dry-tolerance traits are commonly called toads, while some rainforest toads (harlequin frogs) are called frogs. This paper sticks to the lineage-based definition, however.

Traits allowing toads to spread rapidly over the terrestrial globe are relatively obvious, involving independence from water- to live in drier areas outside rain forests; fat storage and large size- also for portability; secretion of toxins for protection; and high fecundity- large numbers of small eggs, with larvae that feed themselves rather than living off egg reserves.

The authors deduce these traits from current conditions- traits common in the most widely-distributed toads, relative to those toads with smaller geographic distribution. The authors then take this method back in time, creating a DNA-based family tree (phylogeny) of toads, aligning it with paleontological data for time estimates, and deducing which toads had which traits at which times in the past.

They use paleontological data and various statistics to estimate which toads had which traits back in the day. For instance, poison glands appear in toads shortly before their entrance into North America ~47 milion years ago- no toads from lineages branching prior to this point have them.

Their key conclusion is that those lineages that spread to new areas (entering North America, for instance, or Asia) shared a high number of these portability traits. Thereafter, these lineages generated a radiation of species, many of which were more specialized again and restricted in range. The figure shows what they are talking about, with color codes indicating the proportion of portability traits at each divergence.

Phylogenetic tree of toads, color coded with inferred range-expansion traits (click for larger size).
The authors conclude that toads have repeatedly evolved both range-expanding and range-restricting traits, and it is the range-expanding traits that led not only to range expansion (obviously) but also to speciation, since arriving in new continents and climates generates speciation (sometimes called range-edge speciation).

An important corollary is that lineage representatives at the range edge tend to both colonize new areas and to generate new species. "We hypothesize that these reciprocal effects [of range expansion, leading to better adaptation to diverse habitats] have caused the rapid global colonization of bufonids and produced the enhanced genetic drift at the expanding frontier, with consequent high levels of population differentiation and speciation."

Something similar happened in the human lineage. Absolute genetic diversity is highest in the ancestral homeland of Africa, hosting lineages far more ancient than those that migrated to other parts of the world. Yet migration to range edges and distant continents led to new traits and population differentiation, and may have involved range expansion traits as well. What have been traditionally been viewed as "races" would have become incipient species, had hundreds of thousands more years elapsed with sufficient isolation (as apparently was true for past hominid lineages, which ramify as more fossils are unearthed).

Perhaps our instinctive xenophobia is a related mechanism of speciation by which miniscule differences between virtually identical populations is psychologically enforced, preserving whatever small advantage or peculiarity a successful population embodies. This would operate in delicate tension with our other strong tendency to seek novel experiences, resources, and marriage partners in other lands.

  • Galbraith gets it- and writes an excellent primer on government spending and deficits.
  • Great pair of articles on Afghanistan in TNR. I'd reiterate that the Afghan people would probably welcome NATO replacement of Karzai and a guarantee of 10 years of federal administration.
  • Interesting notes on Jung and antisemitism.
  • A small reminder of what Republicans do with power.
  • Moral sentiments and morals.
  • Bill Mitchel quote of the week:
"But on more substantive matters, today I have been thinking about how much momentum the conservative lobby has at present and that history is being continually re-written to give these characters the oxygen they need to warp public opinion. We are now in danger of an even greater shift to the right in the coming years than was represented by the “neo-liberal” era. It is an ugly thought. But the macroeconomics is clear – if these ideas really take over the policy making process – then we will be facing a lengthy period of economic malaise."

Saturday, March 6, 2010

Parallels between Trotsky and Paul

Yes, I am reading the final volume of Isaac Deutscher's excellent biography of Leon Trotsky, and it is inspiring me to utter things like "Proletarians, to horse!", and "death to the imperialist capitalist running dogs!", and "all hail the international revolutionary vanguard".

It also reminded me strongly of the biography of the semi-apostle Paul, oddly enough!

Both sent epistles far and wide to cult members urging loyalty, good behavior, settling squabbles, and urging a world-wide revolution (Trotsky during his final decade of exile, which this book covers).

Both proselytized on behalf of prophets from two generations before, who had been beaten down and ignored in their own time.

Both were outsiders to the power centers of their cult (the Jerusalem church in the case of Paul, the Soviet Union under Stalin in the case of Trotsky). In response, both took their message to an international audience.

Both believed in a second coming of their ideology- changing the world through revolutionary means towards a glittering future of righteous harmony.

Both are recognized as animating spirits and organizers of what ultimately became totalitarian institutions that lived on long after them- eighty years in the case of the USSR, and 1300 years in the case of Catholic hegemony in the West. Institutions that, incidentally, spent generous portions of their energies spinning "orthodox" doctrines and hounding and killing heretics.

Both were ultimately executed for their pains- by, or with the connivance of, their own cult leaders.

And, of course, both believed unshakeably in an ideology that makes no sense whatsoever in the rational light of day. One remarkable aspect of Deutscher's work, for instance, is his  constant valorization of struggle. His hero is in constant political struggle, hurling thunderbolts of epistolatory brilliance, dashing off books, pamphlets, and articles. The proletarian revolution is always on a knife's edge, whether from its enemies like Hitler, or from its friends, like Stalin. He had fought a civil war to defend the revolution, and now from exile fought on to the end to preserve its principles, amidst ever fewer followers and dwindling interest from the larger world.

One would think that the philosophical core of Marxism would take this heroism and constant struggle into account, as do, say, evolutionary biology and conventional economics. But no- the wiki page on communism sums it up as ...
"Pure communism" in the Marxian sense refers to a classless, stateless and oppression-free society where decisions on what to produce and what policies to pursue are made democratically, allowing every member of society to participate in the decision-making process in both the political and economic spheres of life.
It is hard to tell what relation this has to the titanic struggles, not to mention deception and force of arms, involved in establishing every actual communist state, or with the theory of the dictatorship of the proletariat, or to human nature at large. Democracy is a wonderful thing, when honestly implemented. But it is no way to run smaller and more personal affairs, where personal ownership and initiative are the more effective and natural principles. So the idea of extending democracy -writ large- to questions like how to run one's farm or office, is completely counter-productive, especially when the democracy in question is of Stalin's (or Trotsky's) ilk.

All this is richly reinforced by Trotsky's own career, since he gained power not through democratic means, but at the head of an armed worker's insurgency, had little use for democracy after gaining power, relied on (capitalist) royalties on his published works for income during exile, ran his household along conventional autocratic lines, and employed all means at his disposal- charisma, discipline, and intellect, for one aim, which was power. The true communist society was just as much a mirage as the second coming and last judgment of Jesus, now almost two thousand years overdue.

In theory, the communist ideal was predicated on an over-abundance of material goods, so that all would get according to need, and material competition would be a thing of the past. But this completely misreads human psychology. Not only are human material needs bottomless, (witness the ability of billionaires to spend their money endlessly and want still more), but in the end, material objects become symbolic of desires that lie closer to our hearts- status and power, with which Trotsky was so familiar. Society benefits from policies and structures that promote egalitarianism, but not from the erasure of all differences and distinctions, which requires oppression in very large doses.

Man does not live by bread alone. Indeed, the less plausible the ideal, the more devoted and fanatic the followers. In our time, it is Al Queda that carries the banner of world revolution, in hopes of a dream world of totalitarian Islam. Yesterday, it was Communism with its dictatorship of the proletariat. And the day before that it was Christianity with its messiah coming back from the dead to rule the earth and separate the believers from the damned. The pattern is clear, from these and many other movements- that millennial visions are humanity's deepest and most persistent danger, which needs to be perpetually opposed by cosmopolitanism and true democracy.

  • Early warning gives a stunning climate report the once-over.
  • Even honest right wing economists can figure out Keynesianism.
  • But the Chicago school has no shame whatsoever, apparently.
  • Track your electricity.
  • Watch a minicooper being built, using lots of robots.
  • Brave words from the NYT about economic recovery... 
"But those very overreactions may have set the stage for a recovery that will turn out to be stronger and faster than those after the two previous downturns."
I will put my understanding of macro-economics on the line and say that this isn't going to happen. Mr. Norris is simply guessing at trends, and not showing his data, other than saying that "order books are filling up", rather hopefully. Indeed, the statistics he charts indicate that we are at bottom, not that we will be going up any time soon.

Unless the US returns to the debt binge days of the mid-2000's, we are in for a protracted slump of high unemployment and capacity under-utilization. Commercial real estate has yet to bottom out, for instance. This is due to an overall demand implosion, driven by loss of wealth and higher savings desires, combined with a continuing strong dollar and trade balance deficits, combined with insufficient federal deficit spending to offset the first two. Many banks, including the largest, remain insolvent, rigging accounting rules to hide that fact. So another debt binge is hardly in the cards.

  • Mitchell quote of the week, on the Russian default of 1998, after interest rates were raised to >100%, and the central bank had spent almost $30 billion defending the ruble's dollar peg against speculators.
"On September 2, 1998, the government floated the ruble.
First, this was not a bank crisis. It was the result of the currency peg and the massive exposure to foreign-denominated debt.
Second, at any time they wanted to they could have floated which would have stopped the need to hike interest rates and kill their economy.
Third, they never needed to default on domestic debt. That was the act of sheer stupidity and the poor advice they were getting. There was never a solvency risk in their own currency. The IMF were in there telling the Russian government that they had to implement an austerity plan and convincing them that they needed to “raise money” to fund the deficit – both erroneous propositions."