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ref: -1992 tags: evolution baldwin effect ackley artificial life date: 03-21-2022 23:20 gmt revision:0 [head]

Interactions between learning and evolution

  • Ran simulated evolution and learning on a population of agents over ~100k lifetimes.
  • Each agent can last several hundred timesteps with a gridworld like environment.
  • Said gridworld environment has plants (food), trees (shelter), carnivores, and other agents (for mating)
  • Agent behavior is parameterized by an action network and a evaluation network.
    • The action network transforms sensory input into actions
    • The evaluation network sets the valence (positive or negative) of the sensory signals
      • This evaluation network modifies the weights of the action network using a gradient-based RL algorithm called CRBP (complementary reinforcement back-propagation) which reinforces based on the temporal derivative, and complements (negative) when action does not increase reward, with some e-greedy exploration.
        • It's not perfect, but as they astutely say, any reinforcement learning algorithm involves some search, so generally heuristics are required to select new actions in the face of uncertainty.
      • Observe that it seems easier to make a good evaluation network than action network (evaluation network is lower dimensional -- one output!)
    • Networks are implemented as one-layer perceptrons (boring, but they had limited computational resources back then)
  • Showed (roughly) that in winner populations you get:
    • When learning is an option, the population will learn, and with time this will grow to anticipation / avoidance
    • This will transition to the Baldwin effect; learned behavior becomes instinctive
      • But, interestingly, only when the problem is incompletely solved!
      • If it's completely solved by learning (eg super fast), then there is no selective leverage on innate behavior over many generations.
      • Likewise, the survival problem to be solved needs to be stationary and consistent for long enough for the Baldwin effect to occur.
    • Avoidance is a form of shielding, and learning no longer matters on this behavior
    • Even longer term, shielding leads to goal regression: avoidance instincts allow the evaluation network to do something else, set new goals.
      • In their study this included goals such as approaching predators (!).

Altogether (historically) interesting, but some of these ideas might well have been anticipated by some simple hand calculations.

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ref: -0 tags: rogers thermal oxide barrier neural implants ECoG coating accelerated lifetime test date: 12-28-2017 02:29 gmt revision:0 [head]

PMID-27791052 Ultrathin, transferred layers of thermally grown silicon dioxide as biofluid barriers for biointegrated flexible electronic systems

  • Thermal oxide proved the superior -- by far -- water barrier for encapsulation.
    • What about the edges?
  • Many of the polymer barrier layers look like inward-rectifiers:
  • Extensive simulations showing that the failure mode is from gradual dissolution of the SiO2 -> Si(OH)4.
    • Even then a 100nm layer is expected to last years.
    • Perhaps the same principle could be applied with barrier metals. Anodization or thermal oxidation to create a thick, nonporous passivation layer.
    • Should be possible with Al, Ta...

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ref: -1977 tags: polyethylene surface treatment plasma electron irradiation mechanical testing saline seawater accelerated lifetime date: 04-15-2017 06:06 gmt revision:0 [head]

Enhancement of resistance of polyethylene to seawater-promoted degradation by surface modification

  • Polyethylene, when repeatedly stressed and exposed to seawater (e.g. ships' ropes), undergoes mechanical and chemical degradation.
  • Surface treatments of the polyethlyene can improve resistance to this degradation.
  • The author studied two methods of surface treatment:
    • Plasma (glow discharge, air) followed by diacid (adipic acid) or triisocyanate (DM100, = ?) co-polymerization
    • Electron irradiation with 500 kEV electrons.
  • Also mention CASING (crosslinking by activated species of inert gasses) as a popular method of surface treatment.
    • Diffuse-in crosslinkers is a third, popular these days ...
    • Others diffuse in at temperature e.g. a fatty acid - derived molecule, which is then bonded to e.g. heparin to reduce the thrombogenicity of a plastic.
  • Measured surface modifications via ATR IR (attenuated total reflectance, IR) and ESCA (aka XPS)
    • Expected results, carbonyl following the air glow discharge ...
  • Results:
    • Triisocyanate, ~ 6x improvement
    • diacid, ~ 50 x improvement.
    • electron irradiation, no apparent degradation!
      • Author's opinion that this is due to carbon-carbon crosslink leading to mechanical toughening (hmm, evidence?)
  • Quote: since the PE formulation studied here was low-weight, it was expected to lose crystallinity upon cyclic flexing; high density PE's have in fact been observed to become more crystalline with working.
    • Very interesting, kinda like copper. This could definitely be put to good use.
  • Low density polyethylene has greater chain branching and entanglement than high-density resins; when stressed the crystallites are diminished in total bulk, degrading tensile properties ... for high-density resins, mechanical working loosens up the structure enough to allow new crystallization to exceed stress-induced shrinkage of crystallites; hence, the crystallinity increases.

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ref: -0 tags: entropy life proteonomics transcription factors date: 07-08-2011 22:42 gmt revision:0 [head]

Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes -- read the article. These are my disordered, mesothermophylic notes.

  • Low and high temperature prokaryotes seem to have less protein disorder (as estimated by amino acid content, mostly, not actual structure) called IDR/IDP (intrinsically disordered regions or proteins).
  • IDR / IDPs seem essential in certain protein functions, such as transcription factors and ribosomal proteins.
  • hyperthermophyles have low genomic complexity and low protein disorder, possibly to combat the high disorder of their environment.
  • "life appears to be incompatible with less than about 1.5% disorder ". I would say that this is a rather conservative threshold.
  • transcription factors: "disorder is correlated with the number of genes they regulate, which suggests that their disorder is directly linked with functional complexity of the organism"
  • Transcription factor disorder is higher in psychrophiles (low temp) than hyperthermophiles, even though both show decreased genome size. Furthermore, disordered regions may confer temperature robustness at 40-50C as well as at low temperatures.
  • "...there is many evidence in the literature that structural disorder and complexity are correlated, both at the level of individual proteins, where IDP functions correlate with signaling and regulation, and whole genomes, where the frequency of disorder increases with increasing complexity of the organism [24], [25], [41], [52]. Thus, evolutionary changes (point mutations, deletions of regions, silencing of genes, etc…) that reduce disorder will tend to strip the organism of functions that increase its complexity, and leave functions that are required for its basic, non-regulated existence. In this sense, reduction in disorder is not a side-effect of selection for reduced complexity, rather the mechanism of this evolutionary drive."

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ref: -0 tags: rap poem life philosophy date: 04-07-2011 15:39 gmt revision:1 [0] [head]

so son why you looking so glum
why you not making that symbol with your index finger and thumb?
yea boy i know she couldn't kickit for real
true true puddin, if fun were a sale then she got quite a steal

the thing about the brain is with physical consequence
get computed with aplomb, clarity and consonance
when emotional matters get sucked into the fray
only a fool will guess where the causality will stray

it's almost fucking impossible to disentangle yourself
which is why im yappin to you rather than to cough cough to myself
dissatisfaction with her life is only slightly attached to angst in yer life
but blaming yourself is not what she did, so don't do it. 

externalize events, it's a common adult strategy
makes you feel a lot better irrespective of causality
titrating the blame like ah chemistry class
it's like the assholes are those who don't look at their own ass

speakin of which, point your telescope over there, 
no not the squirrel, check the thing that fills out the chair
now amusements can be had, amusements are given
the butcher is calling, high time to make a killin

you don't need to go to walking the Walden like Thoreau
to pick up the coinage that self questioning will throw
those who fail this will be a needle-nosed stasis
while you me and charley will be making a praxis

alright my brother time to show that squirrel who's bonafide
self-bootstrapping is best done while physically occupied. 

just having some fun :-)

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ref: -0 tags: fragment of a dream san francisco frustration life date: 01-07-2011 05:33 gmt revision:1 [0] [head]

Remembered fragment of a dream, letter never sent.

Probably it was ill-fated to ---. Eh. That didn't distract me from having a batshit insane dream last night, feat three army goons, myself, and the vivacious ---. The goons and I were soldiers in charge of some truck-mounted machine gun in a logged and dried-mud hillcountry - probably Serbia - but whenever we tried to get it ready, the part in question would instantly transform into crochet. When the ammunition roll was finally in the yarn gun, all the bullets would fall on the ground; look away and it would resume metallic reality. On cue to amplify our disorganization a officer sped in to harass us in a Honda S2000. Annoyed, I threw gravel at him; it transformed into a lamborghini, then a porsche, a tesla, a toyota. (I've seen a lot of fancy cars this past week).

Given the frustrated Daliesque nature of the battlefield, we retreated, I as a restrained but irked soldier. Montage in, montage out, you enter to this scene as an bit-played angry estranged woman, pissed at my lack of caring / perceived neglect. Bitch complain threaten whine, I guilt but look outside and the vegetation is gorgeous, lush, the sky a mild hazy blue. I am a little thirsty.

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ref: Friston-2010.02 tags: free energy minimization life learning large theories date: 06-08-2010 13:59 gmt revision:2 [1] [0] [head]

My letter to a friend regarding images/817_1.pdf The free-energy principle: a unified brain theory? PMID-20068583 -- like all critics, i feel the world will benefit from my criticism ;-) Hey , I did read that paper on the plane, and wrote down some comments, but haven't had a chance to actually send them until now. err..anyway.. might as well send them since I did bother writing stuff down: I thought the paper was interesting, but rather specious, especially the way the author makes 'surprise' something to be minimized. This is blatantly false! Humans and other mammals (at least) like being surprised (in the normal meaning of the word). He says things like: "This is where free energy comes in: free energy is an upper bound on surprise, which means that if agents minimize free energy, they implicity minimize surprise -- a huge logical jump, and not one that I'm willing to accept. I feel like this author is trying to capitalize on some recent developments, like variational bayes and ensemble learning, without fully understanding them or having the mathematical chops (like Hayen) to flesh it out. So far as I understand, large theories (as this proposes to be) are useful in that they permit derivation of particular update equations; Variational Bayes for example takes the Kullbeck-Leibler divergence & a factorization of the posterior to create EM update equations. So, even if the free energy idea is valid, the author uses it at such a level to make no useful, mathy predictions. One area where I agree with him is that the nervous system create a model of the internal world, for the purpose of prediction. Yes, maybe this allows 'surprise' to be minimized. But animals minimize surprise not because of free energy, but rather for the much more quotidian reason that surprise can be dangerous. Finally, i wholly reject the idea that value and surprise can be equated or even similar. They seem orthogonal to me! Value is assigned to things that help an animal survive and multiply, surprise is things it's nervous system does not expect. All these things make sense when cast against the theories of evolurion and selection. Perhaps, perhaps selection is a consequence of decreasing free energy - this intuitively and somewhat amorphously/mystically makes sense (the aggregate consequence of life on earth is somehow order, harmony and other 'goodstuff' (but this is an anthropocentric view)) - but if so the author should be able to make more coherent / mathematical prediction of observed phenomena. Eg. why animals locally violate the second law of thermodynamics. Despite my critique, thanks for sending the article, made me think. Maybe you don't want to read it now and I saved you some time ;-)

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ref: notes-0 tags: bjork music life date: 07-12-2008 15:46 gmt revision:0 [head]

Bjork has a special place in my heart - and not only because of stuff like this: http://www.youtube.com/watch?v=jX9y6AA5oOo ;) When I was in college - not so far back as Post, but before Selmasongs - we used to play a lot of pool. Not so much that we didn't get any work done, but enough that we started getting good. Near the end of that year we filmed a bunch of games & made a music video set to Underworld's remix of "Human Behavior". I don't know what happened to the actual end product, but I do clearly recall my mom complaining about the repetitive beats while I was cutting the shots so the ball collisions would align with snare/bass hits. Sometime later that year I was blown away by the real deal, the "All is full of love" music video, projected on the side of the art museum at ~ 2am when the mind is labile... Bjork & her music pervaded that period for me. I've found that music can 'tag' periods of life for me, such that when I remember the music first then the events. This winter it was Interpol, last fall was Metric, spring 2007 was Arca (you *have* to hear them!). When me and my brother went to Portugal for a few weeks we found two Pixies mix tapes in the tiny car that my friend generously let us use. Hence, Frank Black soaked our ears while the incredible Portuguese sun soaked our skin.

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ref: essay-0 tags: food life date: 05-13-2008 04:18 gmt revision:0 [head]

I have, minus some notable periods, been cooking for myself and at times others for about eight years now. It began after going off meal plan in college, something that my mother was rather concerned about (she violently opposed it). She needn't worry, though; huger is a powerful motivator, one that won't disappear without proper administration. At first I ate purely because of need -- an approach that is utilitarian, probably quite healthy, but ultimately depressing. I still revert back to this mode, sometimes, but feel that it is very self-defeating - we can subvert the natural hierarchies of value by placing work above food, but ultimately the (sometimes) illogical legacy of our subconscious will come back to bite. For most of evolution, a well fed animal was a happy animal, and, us humans can only ignore this for so long. If you allow me to (continue to) make broad generalizations that I'm not qualified to make, some people's problems may be traced to trying to control their reward system logically. Within my limited experience, it does not work that way; reward is from the outside world. Like food. (A learning system that is self-rewarding can be unstable).

So after about a year I began to trying to cook better, with the constraints that I had neither much money nor a car. Gradually, somehow, it got better! Most of this came by watching what others did, and some via experimentation. Both were rather slow, as the others in the equation were an odd mix of busy college students with a bias to the vegan and hippy, and my experimentation was very poorly informed. I knew roughly what was out there, but not how it could all fit together. With mimicry and fiddling, occasional good results were produced (and produced and produced until I got sick of that too), but progress was slow, because you never get better at anything unless you actually care about it. I cared about grades, and nobody was grading my food. (thankfully, my gpa would have suffered!)

Then I moved to Brooklyn, a translocation which hindered progress more: there was a Sicilian pizza parlor on my way home. My understanding of the culinary arts did not increase, but... my cholesterol sure did! I also developed the quick and filling habit of buying a big chunk of Jarlsburg & some bread from a bakery on the way home. The problem was that I really enjoyed what I was doing at the time, and unlike school with its segmented workflow with definite ends, the work was open-ended and like a gas. It ate up all my eating time, leaving no time for cooking.

Graduate school was (is!) a similar story, more interesting work to do and not enough time to do it. There were no longer excellent pizzerias on the way home, though there were plenty of accessible restaurants, and we did make use of this fact. When eating out, though, it is better if you leave with only a warm and amorphous recollection of the food. If you leave with a sharp recollection of the food, then either it was terrible, the conversation was dull, or you are well trained (you already know the last poses no problem for me). However, if you are eating with others - and you *cooked* the food, then the dinner table is reversed: flavor matters very much!

This happened, for me, upon moving into a rambling, old, drafty southern house with several others (I can't quote exactly how many -- it varied, some good, some bad, all interesting.) I think my peak moment in old 708 Parker was when cooking for a group of Brazilians - portobello mushrooms, potatoes, pork with apples. Probably I think so fondly of it because I was mostly unable to ask them what they thought of it, and they were unable to tell me. That was also shortly after having read Pat Conroy's "Recipes from my life", a book that filled me with a love of the south and cooking food. This book was just lying around somewhere in the house; finding it was no surprise, the house was positively filled with junk. Despite the good times and fruitful finds, that house liked natural gas to the tune of $500/month in the winter, so we ditched it. The kitchen was kinda crummy anyway.

Having enjoyed the taste of communal life, I secured a lease on an even bigger house and moved the crew over to it. At this time my dad's interest in cooking was also reaching new heights. Whenever I would go home, we were greeted with meals of increasing complexity and variety of ingredients. I liked it a lot, but to be honest I was beginning to get a taste for my own (mediocre but tuned to the target audience) cooking! My dad is an engineer, and the transfer of approach if not skill is not surprising in retrospect. Making a good meal can be very much an engineering problem, with the ingredients mixing together in generally learnable/predictable manner, and with an unusually simple objective criteria: it should taste good.

My period in the great big house (mode of occupancy:7) will end soon, but no worries: I still need to eat, and so do my friends!

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ref: notes-0 tags: two-photon laser imaging fluorescence lifetime imaging FRET GFP RFP date: 01-21-2008 17:23 gmt revision:0 [head]


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ref: life-0 tags: life diary portugal ana date: 07-08-2007 22:43 gmt revision:4 [3] [2] [1] [0] [head]

  • Thursday 28 June sat on runway for 5 hours, made it to NY but missed the connection to Lisbon so therefore had to wait in Newark for a Day. Slept in the meditation room and soiled the islamic rug.
  • Friday 29 June Called mom in the morning and went to NY, ate and slept, then went for a quick walk with the family & tux around little dam lake, ana liked the area alot, said it was super beautiful. Dad read my grant and said that i need to more clearly define Miguel's rights as a client/purchaser. Went back to newark, found the black ipod, got on the standby flight to lisbon, sat next to a really angsty portuguese.
  • Saturday 30 June Tired, picked up at airport by ana's parents, slept uncomfortably on the highway from Lisbon to Coimbra (ana's father drives very quickly). took a nap. went into Coimbra to go shopping at the big mall and later went to a oliveira family party where I spoke with Pedro (the elder).. too much portuguese, did not interact very much. Later went to Coimbra's republican square, to meet some of ana's friends, but i didn't have a great time - was too exhausted!
  • Sunday 1 July Went with the oliveira family to lunch in Figuiera de Foz, saw the ultralights, walked on the beach after a very long lunch & otherwise saw the town (pretty nice beachisde resort, Antonio went there frequently as a kid). Then went up to the Serra Boa Viagem, where it was damp, then to Praia de Mira where we rented paddle boats, walked along the boardwalk, and ate dinner after a long trip through the coastal wilderness. Went back and slept, slept, slept.
  • Monday 2 July - woke up late and went shopping for the stuff for our trip to the mountains (tent, sleeping mat, food). Left rather late, and traveled past Porto to Esposende where we had a long walk along the beach, coffee at the Bar de Praia. This eventually left us out of time, so we went to the orbitur camp site nearby, checked in late, then ate octopus black beans and flan at a nice local restaurant.. went to bed late, slept well.
  • Tuesday 3 July - Woke up late arg to a gray and rainy day. Discovered that we had put up the tent incorrectly late that night. spent a long time seaking out internet back in Esposende because ana wanted to meet up with her friends & tell them about the party she was planning for Friday. Eventually we were on our way to this area near the boarder of Portugal and Spain -- but then we ran out of gas! tried pushing the car up the slope, but it was too hard, too heavy, and ana called the road-rescue-crew then later we went into a absolutely beautiful farmhouse to locate some diesel. The people inside were rather affable, and gave us 5 liters of petrol, which was enough to get us to the next gas pump or 'bomba'. I managed to spill diesel on my shorts - not good because I only had two! Later we went to the beautiful village of Ponte Da Barca (I think) where we walked along the river , visited the public pool (absolutely gorgeous!), walked through the city, and eventually got hungry and started looking for somewhere to eat. We found a very nice place - Kibom i think - and i had steak and mushrooms. Left after yet another desultory meal, and went to the Dois Rios campismo, where we set up the tent (correctly, this time) and got some rest!
  • Wednesday 4 July - Awoke to a bright and clear day in the mountains; the campismo was much more interesting and nice during the day. Ate cereal and iogurte for breakfast, then traveled to Lindoso. Along the way we stopped to try a trail, but it turned out to be very overgrown and ana was afraid of vipers, so we did not go very far. In lindoso we visited a small ancient castle where ana's parents called to say that they were coming (this annoyed ana a bit), then went across the river up the hills , where we climbed pig hill and saw cows , horses, and feral dogs . it was really super incredible up there - wild, like scotland. I love that type of place. It was a clear day, too, so you could see at least 50km. we took the road further past many small vilages, winding through the hills, and saw many locals. Stopped for lunch by Lamas de Mouro, then continued to the small road by Castro Laboreiro, where we hiked for some 5 hours in the dazzling sunlight along the high plains of that region. It was truly incredible! I'll have to add photos: , , , , On the way there we had to go around a bunch of bulls and later we passed by a set of horses.. still later we crossed into Spain, as indicated by the Spanish no-trespassing sign (without needing to worry about border guards!). At the turnaround point we found a geyser of water .. in the middle of nowhere .. and ana called her parents to find out where they were. They had traveled all day & got stuck in the traffic around Porto, and eventually met us at the end of the trail in the high mountain pass. Ana and I then followed her parents through spain to a small restaurant in Campo do Geres (??), whence the subsequently left for Coimbra (Antonio had the day off - it was Coimbra day. Eventually got back to porto, found a campismo by Matosinhos. Got in too late to check in officially, so asked to pay later.
  • Thursday 5 July - Awoke early, too early, to take a bus to Porto to take the train to the boat trip down the river. Spent the little extra time in porto drinking cafe (of course!) and going to the river. Slept most of the trainride; ana slept almost all! The boatride was rather chill ; I liked the forest and ana liked the vineyards; we both liked to the small beaches along the way, some of which had people, especially as the day wore on. Stopped in Gaia to ride a small pedal kart (kinda the highlight of the day), and eat some spicy thai food (thank god - portuguese do not believe much in spices!). Then it was late, and we had to wait for the bus back to Matozinhos (10pm); eventually got back, but again too late to pay, but fortunately ana called ahead and the conta was filled out already. Drove back to Coimbra, once again at very high velocity ;)
  • Friday 6 July - woke up really late, like 1pm, and went shopping for the party, then later played in the pool and read calmly by the poolside, the waters of which had warmed up appreciably. Met Rita and Luisa (i think), who we met with Justin in NYC, then later Paulo and Vitor & their namoradas for dinner. This lasted until 3 in the morning, mostly because Paulos gf wouldn't shutup.
  • Saturday 7 July - Ana visited her grandfather whilest I fitzed with the computer; later Denisa and another Rita came over for lunch, after which we went into Coimbra. returned home @ 6, then went out again to see the graduation ceremony for 3 students in Pharmacy, after which we spent some time shopping and walking around the area near the university in Coimbra. Ate dinner and were too tired for further escapades in the city.