blog evolution

toward a mash between life-related stuff and random science stuff. don't fear that this will just be a dumping ground for things read . . . it just lets me get excited about random new discoveries in science. something i used to do much more. back before i was channeled along whatever random path of research i followed. this new, well, closed-mindedness (closed because full of doing other stuff) really hits home when going through all my old papers during a move. i used to know so much about so many things. c'est la vie.

possibly the winner for best Nature/Science paper title this year...

from the title itself, i couldn't tell if this was some unknown realm of quantum chromodynamics or an anthropological study of a race of rainbow people. an important question - whether non-kin-based altruism can evolve. although it always seemed like language what was missing from many a model of altruism evolution, because it can create and spread knowledge of the kinds of 'tags' discussed in the abstract below. makes you wonder, though, about how many papers are framed in an idea that came from the bar. "eh! what about 'beard chromodynamics'!" (highlighting mine)

also - a quick note on a really cool study done on chinese frogs. "Ultrasonic communication in frogs" - Nature, 3/23. Basically, only bats, rats, and sea mammals were known to communicate ultrasonically. researchers recorded communications in an amphibian, the concave-eared torrent frog. the frequencies making up male calls spread into the ultrasonic, and when these parts of the call are played back, they reply. so - hearing and sound production have evolved together, presumably separate from the evolution of ultrasonic capacities in other animals. the neat (well, i think) explanation of why this would happen is simply because the frogs live near torrential streams with dominant low-frequency sounds. they evolved to be heard above the roar. it's stuff like this that highlights how fantastic natural selection can be . . .

ok, beards!..

Altruism through beard chromodynamics

Vincent A. A. Jansen and Minus van Baalen

The evolution of altruism, a behaviour that benefits others at one's own fitness expense, poses a darwinian paradox. The paradox is resolved if many interactions are with related individuals so that the benefits of altruism are reaped by copies of the altruistic gene in other individuals, a mechanism called kin selection. However, recognition of altruists could provide an alternative route towards the evolution of altruism. Arguably the simplest recognition system is a conspicuous, heritable tag, such as a green beard. Despite the fact that such genes have been reported, the 'green beard effect' has often been dismissed because it is unlikely that a single gene can code for altruism and a recognizable tag. Here we model the green beard effect and find that if recognition and altruism are always inherited together, the dynamics are highly unstable, leading to the loss of altruism. In contrast, if the effect is caused by loosely coupled separate genes, altruism is facilitated through beard chromodynamics in which many beard colours co-occur. This allows altruism to persist even in weakly structured populations and implies that the green beard effect, in the form of a fluid association of altruistic traits with a recognition tag, can be much more prevalent than hitherto assumed.

from the title itself, i couldn't tell if this was some unknown realm of quantum chromodynamics or an anthropological study of a race of rainbow people. an important question - whether non-kin-based altruism can evolve. although it always seemed like language what was missing from many a model of altruism evolution, because it can create and spread knowledge of the kinds of 'tags' discussed in the abstract below. makes you wonder, though, about how many papers are framed in an idea that came from the bar. "eh! what about 'beard chromodynamics'!" (highlighting mine)

molecular biology and kuhn . . .

Microparadigms: chains of collective reasoning in publications about molecular interactions. A Rzhetsky, I Iossifov, JM Loh, KP White. (bio and gen people from columbia and yale) PNAS 2006

i respect modeling more and more after taking the math modeleing class in my last semester (even though my own model was a big unsuccess [push that thing toward submission again, or muck it?])

the authors analyzed millions of published statements about molecular interactions (apparently all these things are stored in a searchable database of papers, and the extraction process was pretty much automated). then they constructed strings of related statements over time. simple logical relationships between molecules (protein A activates protein B) in these statements were tagged with 1's and 0's (for true/false), and then the dependence of future links on prior links can be modeled.

"We found that published statements, regardless of their verity, tend to interfere with interpretation of the subsequent experiments and, therefore, can act as scientific "microparadigms," similar to dominant scientific theories [Kuhn, T. S. (1996)..."

the authors dub the positive influence of existing findings on subsequent findings "experimental momentum." how this works: prior results frame the conceptions of a new 'space' of molecular interactions, so that alternative interpretations are irrationally deweighted priors. reviewers only will accept findings framed in prior findings, making repetition more likely. positive results are much more likely to be published than negative results (e.g. we found that my eyebrows do not interact with molecule x) - though the authors take this into account in their model.

they put forth several model scenarios to demonstrate the effectiveness of their model, and then move on to the results when using real data. dozens of 'experiments' are initialized at timepoint 1 and these are then more-or-less repeated in subsequent steps. they basically can model something like the coupling between prior and current work by measuring how much subsequent expertimental statements are influenced by prior statements, and how much this influence deviates from chance (chance of many repeated same results, etc.) e.g. if error is 5% on any experiment, the chances of 20 similar experiments reproducing the same result is .05^20 - rather unlikely, unless the "momentum" of prior results is high.

-one, where each experiment was conducted in complete isolation, not influenced at all by any others. results: each experiment is predictably as accurate as a normal p<.05 error rate.

-two, where each experiment is stronly influenced by prior results. strong conformity. resulting long strings of replications and infrequent opposing findings - which are not themselves replicated.

-three: super anti-conformism, where each finding has a net negative effect on replications. "believe no one (but yourself)."

-four, where each experiment is strongly influenced by prior results, but when a contrary finding is made, everyone jumps onto that bandwagon immedialy. ("anticonformism with an inferiority complex")

-five: the ideal scientific universe, "mild scepticism", where subsequent results are positively influenced by prior results (experimental momentum is greater than zero) but this influence is weak. experimenters trust their data much more than others, but try to align it with existing work. in this version, the model allows the authors to pick the optimal variables that ensure the fastest convergence on the correct result.

findings from modeling the millions and millions of interactions: an optimist's universe and a pessimists universe:

An evaluation of the optimum parameters under our model (see Model Box) indicated that the momentums of published statements estimated from real data are too high to maximize the probability of reaching the correct result at the end of a chain. This finding suggests that the scientific process may not maximize the overall probability that the result published at the end of a chain of reasoning will be correct. ... our computations indicate that our data set can be interpreted in two very different ways (two "alternative universes"): one is an "optimists’ universe" with a very low incidence of false results (<5%),>90%). Our computations deem highly unlikely any milder intermediate explanation between these two extremes.
...
If the problem of convergence to a false "accepted" scientific result is indeed frequent, it might be important to focus on alleviating it through restructuring the publication process or introducing a means of independent benchmarking of published results."

? i want more discussion of their conclusions. the paper ends very briefly with talk of their models. maybe more discussion of the meat in online supplements

? this hits on something that has always interested me in the philosophy of science, strongly influenced by Kuhn and Paul Churchland (and maybe stu kaufman?): how ideas evolve in societies. Churchland, translated into this realm (most of his stuff is about individual minds/neural networks) is all about random walks through a space of theories. random in a sense, but influced by force of natural selection - weak survival biases dependent upon chance, a bully pulpit, etc, etc. hell, i even hacked together an Anthro model about evolutionary dynamics in a population of minds analogous to evolutionary and population dynamics in ecosystems on connected but separated “archipelagos of minds.” but this is, to my knowledge, the first attempt at a quantification.

? applications to other sciences. i.e. mine. well, we don't really replicate stuff. too f'ing expensive to redo someone else's imaging study, and we don't get published again if we do anyway. so i would conservatively estimate the error rate in the neuroimaging field to be 20%.

note to self: after moving, dig up old feyerabend.
note to others: check out the guy's crazed eyebrows on the backjacket of, say, 'the end of reason'.

i was waiting for a sign

to direct me in my indecision, and here it is: X-Phi.
no more affect, no more 'neuroeconomics', we're doing experimental philosophy (i think it's 'x'-phi, and not 'chi'-phi, though if the latter my former roomate was was ahead of the times)! the possibilities are endless.

Experiment 1: we take a just born infant - let's call her mary - and put her immediately, before a second of experience of the world outside the womb, into a sterile, white, soundproofed room. she learns everything that science has to offer - and by the time she is 20 this is a lot, 'cause in 20 years we'll have solved, like, everything. but the catch is she won't ever experience color! ha! even though she knows what color is from her reading (and understands the neuroscience to a degree we mere present mortals cannot imagine). the question: is there something about mary that is missing? something she doesn't know?

Experiment 2: we do phone surveys. asking unbiased questions like 'do you think in organized, literate, almost logical sequences of sentences, or in pictures that look like they were taken from a children's book?' to settle the age-old (or at least decades-old, damnit) question of whether or not there is useful picture-play in people's heads. i'm guessing NOT! oh, and another good one - is your Language Acquisition Device (LAD) functional, or wonky?

Experiment 3: ok, so this is a good one. zombies have recently been a problem in philosophy, probably because one of the current old poo-bahs had a fear of them when he was wee or something. but to settle the issue. people watch classic zombie movies (you know what i'm talking about) to acclimate them to the terrain upon which their clouds of imagination will scruffle. then, we have subjects imagine a case where their neighbor bill suddenly is replaced by an exact replica of him that arose from the local dump. exactly - exactly! - everything is the same about him, down to the quark. but this bill - call him bill' - doesn't actually experience anything. question: is this possible? if bill molests his cows before killing and eating them, does he not enjoy it? and regardless, is zombie bill' at fault here - is he free? or just some pile of atoms moving according to pseudo-probabilistic mechanics? is there some kind of essence that is lacking in your zombie neighbor that prevents him from really experiencing things? i think so! materialism: 0. x-phi: 1

and this is just 10 minutes into my new career! imagine decades and decades of these rigorous questions! i apologize in advance, but i'll probably be throwing new schtuff out like this for a while. talking to people is going to be so much more fun from now on, too, because the whole conversation will be just a x-phi experiment in disguise. oooh, maybe i'll get a costume!