--- Log opened Wed Feb 27 00:00:01 2019 00:13 -!- ebowden_ [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 240 seconds] 00:19 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 00:49 -!- Urchin [~urchin@unaffiliated/urchin] has quit [Read error: Connection reset by peer] 01:06 -!- Urchin [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 03:42 < fenn> that "NEM relay" is 25 microns long 04:21 -!- Gurkenglas [~Gurkengla@unaffiliated/gurkenglas] has joined ##hplusroadmap 04:42 < nsh> .wik NEM relay 04:42 < yoleaux> "A nanoelectromechanical (NEM) relay is an electrically actuated switch that is built on the nanometer scale using semiconductor fabrication techniques." — https://en.wikipedia.org/wiki/Nanoelectromechanical_relay 04:42 < nsh> gotcha 04:47 < ebowden> Maybe it's big, but has nanoscale features? 04:49 < archels> I like the idea, but frankly their implementation looks kinda dodgy 04:50 < archels> easy to get into a "half state" between 0 and 1 04:52 < nsh> in fairness, that's where all the fun is 05:57 -!- Gurkenglas [~Gurkengla@unaffiliated/gurkenglas] has quit [Ping timeout: 255 seconds] 06:14 -!- arisum [sid283163@gateway/web/irccloud.com/x-ukgdqaayobnhizct] has quit [] 06:14 -!- arisum [sid283163@gateway/web/irccloud.com/x-qxwkrghulmheveqj] has joined ##hplusroadmap 06:28 -!- Urchin [~urchin@unaffiliated/urchin] has quit [Ping timeout: 255 seconds] 07:08 -!- Gurkenglas [~Gurkengla@unaffiliated/gurkenglas] has joined ##hplusroadmap 07:43 < kanzure> .tw https://twitter.com/JimDMiller/status/1100141160784375811 07:43 < yoleaux> China's easy path to world domination: secretly create numerous CRISPR-enhanced babies that will grow into super-intelligent adults 25 years before anyone else tries. https://www.statnews.com/2019/02/25/crispr-babies-study-china-government-funding/ @zoltan_istvan (@JimDMiller) 07:44 < kanzure> .tw https://twitter.com/bitcoin_bolsa/status/1100147363790966784 07:44 < yoleaux> @JimDMiller @zoltan_istvan China has scientists who will risk gulags for breakthroughs, we have whiner bioethicists. (@bitcoin_bolsa, in reply to tw:1100141160784375811) 07:44 < kanzure> .tw https://twitter.com/antonioregalado/status/1100548361978023938 07:44 < yoleaux> Geneticists found a gene variant in Peruvians that knocks 2.2cm off of height. Partly explains very short stature. https://twitter.com/joe_pickrell/status/1100520568741421058 (@antonioregalado) 07:48 < kanzure> https://motherboard.vice.com/en_us/article/ezp8me/genetic-editing-could-cause-the-next-cold-war 07:56 -!- yashgaroth [~yashgarot@cpe-66-27-127-185.san.res.rr.com] has joined ##hplusroadmap 08:05 < fenn> "Shenzhen Armed Police Hospital Reproductive Centre" sounds like something out of THX-1138 08:43 -!- qu1ck_57udy [~qu1ck_57u@191.193.255.219] has joined ##hplusroadmap 10:10 -!- qu1ck_57udy [~qu1ck_57u@191.193.255.219] has quit [Quit: Leaving] 10:25 -!- Gurkenglas [~Gurkengla@unaffiliated/gurkenglas] has quit [Ping timeout: 255 seconds] 10:51 -!- Gurkenglas [~Gurkengla@unaffiliated/gurkenglas] has joined ##hplusroadmap 11:22 < nmz787> ebowden: if you look at the scale bars, the main rod is around 300nm 11:22 < nmz787> ebowden: across the width anyway 11:35 -!- NikopolSohru [~Nikopol_@5.79.79.41] has joined ##hplusroadmap 11:45 -!- Gurkenglas [~Gurkengla@unaffiliated/gurkenglas] has quit [Ping timeout: 255 seconds] 12:42 -!- NikopolSohru [~Nikopol_@5.79.79.41] has quit [Read error: Connection reset by peer] 13:23 < nsh> IN ROD WE TRUST 13:23 -!- ebowden_ [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 13:26 -!- ebowden_ [~ebowden@unaffiliated/ebowden] has quit [Read error: Connection reset by peer] 13:26 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 240 seconds] 13:26 -!- ebowden_ [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 14:31 -!- sachy [~sachy@91.146.121.5] has quit [Quit: Leaving.] 14:46 -!- Cory [~Cory@unaffiliated/cory] has quit [Ping timeout: 246 seconds] 14:54 -!- Cory [~Cory@unaffiliated/cory] has joined ##hplusroadmap 15:45 -!- CryptoDavid [uid14990@gateway/web/irccloud.com/x-zknsmgeyadolntyy] has joined ##hplusroadmap 16:22 -!- fltrz [~fltrz@212.71.7.172] has joined ##hplusroadmap 16:22 < fltrz> can anyone tell me if there occurs exactly one crossover per homologous chromosome pair per single meiosis event? 16:24 -!- cluelessperson [~cluelessp@unaffiliated/cluelessperson] has quit [Remote host closed the connection] 16:29 < fltrz> wikipedia states (for humans) there are about 30,000 hotspots per genome, and that the average crossover rate is one crossover per 1,300 meiosis per hotspot. I wanted to estimate the expected number of crossovers per single meiosis so 30,000 / 1,300 = 23.0769230769 = approx 23 (number of homologous chromosome pairs!). If my conjecture is right, then not only should the exact sum over all crossover frequencies equal exactly 23 per meiosis, but also each 16:29 < fltrz> sum over all the crossover frequencies for all the hotspots within the same homologous chromosome pair should equal 1 16:33 < fltrz> of course it could also be coincidence that the total crossover rate happens to be so close to 23... 16:33 < fltrz> but to me it strongly suggests one crossover on each homologous chromosome pair per meiosis event 16:47 < yashgaroth> https://link.springer.com/content/pdf/10.1007/s10577-007-1140-3.pdf "at least one 16:47 < yashgaroth> CO is formed per chromosome arm both in humans 16:47 < yashgaroth> and mice"; apparently it's not as stringent a rule as in C. elegans, where there is exactly one crossover per chromosome 16:47 < yashgaroth> oh no, invisible linebreaks 16:49 < nsh> hey, i'm 2.7% invisible linebreaks, mr judgey 16:49 < fltrz> thanks yashgaroth 16:49 < fltrz> im not sure what is meant with "per chromosome arm" 16:49 < yashgaroth> chromosomes have two arms 16:51 < fltrz> but then how can the average be 1 CO per 1,300 meiosis, for 30,000 hotspots? 16:53 < yashgaroth> ehh there's two meiosis divisions, so maybe they're just doubling the number of COs? that'd fit pretty well with the numbers in that paper, e.g. ~2 COs per chromosome pair 16:53 < fltrz> oh I see 16:54 < fltrz> per lineage that makes one CO per chromosomme pair? 16:55 < fltrz> I still suspect that apart from abnormal events, this is exactly 1 (or 2 in the other perspective) 16:56 < fltrz> can I find a list of the crossover frequencies of the 30 000 hotspots? and the homolog they are present on i.e. 1...23 ? 16:57 < yashgaroth> I am sure the many hundreds of postdocs who poured years of their primes into that research are gleeful that someone's finally asking, so yes it's probably out there somewhere 17:06 < fltrz> Question nr 2: obviously a literal interpretation of blending inheritance is false, but lets take a small detour and use the genetics code ~ computer code analogy / trope 17:07 < fltrz> when we wrote physics simulations, or math procedures, say for simulating galaxies of stars, we gave the stars variables like position and speed, and we effectively pretended we assigned real numbers as vector coordinates, but as we all know they are just approximations, and we are using floating point numbers 17:08 < fltrz> so fundamentally the illusion of continuous parameters are implemented as binary bits, but nobody defines their variables as strictly booleans to then reimplement floating point arithmetic 17:09 < fltrz> similarily, in the genome it would seem advantageous to not just have presence or absence of a specific gene or variant, but to also be able to relatively smoothly encode parameters like transcription rates 17:10 < fltrz> without having to change the actual protein catalytic properties 17:11 * nsh mutters "you'll get my primes when you pry them from my cold dead hands..." 17:12 < fltrz> so in genetics there is this "transcription factor affinity" 17:14 < fltrz> I interpret this as a form of "blending inheritance", which is literally and fundamentally false of course, but the affinity as a function of a sequence of bases can be seen as a relatively smooth function 17:14 < fltrz> am I wrong to view this as a form of *effectively* blending inheritance? 17:15 < nmz787> isn't any sexual reproduction blending inheritance? 17:16 < fltrz> nmz787, well the historical discussion was particulate inheritance vs blending inheritance 17:16 < fltrz> and it turns out of course that fundamentally it is particulate, i.e. there is a smalles piece of information, a base 17:17 < nmz787> .wik particulate inheritance 17:17 < yoleaux> "Particulate inheritance is a pattern of inheritance discovered by Mendelian genetics theorists, such as William Bateson, Ronald Fisher or Gregor Mendel himself, showing that phenotypic traits can be passed from generation to generation through "discrete particles" known as genes, which can keep their ability to be expressed while not …" — https://en.wikipedia.org/wiki/Particulate_inheritance 17:17 < fltrz> and above bases theres genes etc..., so it is highly particulate 17:17 < nmz787> well sure, but there are a bunch of rules that guide such things 17:18 < nmz787> .wik gene linkage 17:18 < yoleaux> "Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction." — https://en.wikipedia.org/wiki/Gene_linkage 17:18 < nmz787> other factors influence besides just proximity though 17:18 < nmz787> like binding proteins, etc 17:18 < nsh> unfortunate or at least confoundingly many traits are still viewed relative to some continuous measure. it's hard to imagine a discrete combinatorial understanding of height for instance 17:18 < nsh> or longevity 17:19 < fltrz> but the DNA binding sites, at least in my view (and I am looking for confirmation, or at least understanding that it is not too far from blending inheritance), the affinity as a function of sequence (motif, logo) seems to be a false but effective approximation to blending 17:19 < nsh> *unfortunately 17:19 < nsh> how do you mean motif or logo? 17:19 < nsh> oh okay of the base sequence 17:19 < nmz787> it's all system dependent... if that binding co-factor wasn't inherited, then the new organism won't pass on it's genetics in the same way it's parent passed on to it 17:20 < fltrz> sequence motif, sequence logo, i.e. the sequence for a specific binding site that occurs the most in a population (i.e. the fittest or fitter such sequence) 17:20 * nsh nods 17:20 < nmz787> .wik demoscene 17:20 < yoleaux> "" — https://en.wikipedia.org/wiki/Demoscene 17:20 < nmz787> pfft 17:20 < nmz787> what a shit synopsis 17:20 < nmz787> anyway, demoscene is the best equivalent in my mind of how to relate genetics to programming 17:20 < nsh> (the infobar or something fucks up the introsentence parsing) 17:20 < nsh> good analogy nmz787 17:21 < nsh> but it's more like 17:21 < nmz787> doing wonky frameshift stuff to pack more data into the same sequences, etc 17:21 < nsh> say oyu had to make a demo, and then you had to make another demo that is built entirely from salvaged/cannibalised code of the previous demo 17:21 < nsh> and then you layered this some exponential amount of times 17:21 < nmz787> says nothing about reproduction tho 17:21 < nsh> it's like that 17:21 < nmz787> yeah 17:22 < nsh> and then actually it's also like if you had to make demos based on how humans reacted to watching demos 17:22 < nsh> where their reactions to your demo become more code oyu can use 17:22 < nsh> (epigenetic enfolding of rich complexity from environmental interactions) 17:22 < nsh> *unfolding 17:22 < nsh> we don't really have a direct coding analogy for this 17:22 < fltrz> I have the impression that the recombination hotspots that determine the gene-linkage associations are such that the "API" is very stable, i.e. humans that were separated for thousands of years over different continents are today perfectly able to have functioning offspring 17:23 < nsh> even dogs that have been hyperspeciated beyond interreproduceability tend to be part of a ring-species 17:23 < nsh> or whatever you'd call it 17:23 < nsh> you can mate pairs of breeds and that way cover the whole dog species 17:23 < fltrz> i.e. while there is some variation in exact protein sequence, for the "same protein", that increased and decreased affinities of a DNA binding site are very similar 17:24 < nsh> you're expect some things to 'fix in' sooner than others 17:24 < nsh> ones that relate to how the DNA/RNA/protein/regulator metasystem operates would be earliest 17:24 < nsh> or early at least 17:25 < nsh> the most variable would be the most contingent so probably vaguely correlated with duration of existence or the "outermost" layers of the adaptation of adaptations of adaptations 17:25 < nsh> vaguely *inversely correlated 17:26 < fltrz> I guess my question or remark was simply that, it seems logical to concentrate the fine tuning settings to DNA binding sites (where variations in transcription can explore different settings of transcription rates), instead of having to explore variations in the protein itself to find a variation with a different catalytic property, which would be slower and more dangerous since an attempt to modify the catalytic property you might turn the protein 17:26 < fltrz> disfunctional 17:27 < fltrz> better to leave the protein and modulate the binding site 17:28 * nsh nods 17:28 < nsh> there's probably over a dozen ways to affect the activities of proteins other than changing their direct functional properties 17:28 -!- strages [uid11297@gateway/web/irccloud.com/x-bivqvlzmlcakwdnm] has quit [Quit: Connection closed for inactivity] 17:28 < nsh> but binding sites would be one of the main ones 17:29 < nmz787> well, embryos that fail to compile, simply get flushed down the toilet 17:29 < nsh> (others would be of course regulatory networks, pH, transportation, relative frequency, colocation with other proteins, etc. etc.) 17:29 < nmz787> it's not really too obvious aside from "we haven't had a kid yet" 17:29 < yashgaroth> ehhh you're only slightly tweaking the expression of a gene up/down, and expression levels are already pretty stochastic 17:29 < nsh> the cost of earlier errors is less than the cost of later but still fatal/serious errors 17:30 < fltrz> and it was in this sense, if we have a maternal and paternal variant of most genes, and *also* the maternal and paternal DNA binding site sequence, that if we make the simplifying assumption of identical transcriptionn factor, and identical protein, that the total transcription rate would be an interpolation or blend of the transcription rates of the maternal and paternal copy 17:30 < nsh> but the value of variations that might result in earlier errors is probably low when you have high complexity 17:30 < fltrz> which sounds a lot like blending 17:31 < nsh> sure 17:31 < nsh> is it like a doctrinal problem that blending is demurred at? 17:32 < nsh> there's often this problem in the development of science that an idea has currency, then turns out not to hold water, but then later turns out to obtain again for more subtle reasons 17:32 < nsh> and there's an annoying pendulum swing momentum against the idea when it's been 'debunked' in a facile or superficial sense 17:32 < nsh> like lamarkian inheritance was debunked but then it was subsequently found that acquired characteristics can be passed on due to epigentic factors 17:33 < nsh> and many more examples in other fields 17:33 < nsh> but i haven't studied genetics formally so i don't know what the fashionable biases are really 17:33 < yashgaroth> blending has been discredited for simple gene inheritance, but there is some aspect of it that's relevant wrt polygenic traits 17:33 < nsh> except i was very annoyed at the central dogma when i was working in a genetics lab 17:33 < yashgaroth> epigenetic inheritance applies to a very narrow subset of genes, like that 'starving parents have obese kids' thing or w/e it was 17:33 < fltrz> nmz787, yes, I also even think that both sperm and egg cells do some kind of POST (power on self test) that relies on a large number of genes or associating domains to early abort 17:33 < fltrz> yashgaroth, I agree they are stochastic, but you are changing the average expression level 17:34 < nsh> (and nobody i asked about how a few hundred megabytes can result in an organism with seemingly vastly more complexity had a reasonable answer) 17:34 < fltrz> so now that you understand my interpretation, would you guys go so far as comparing this to or even calling it "blending inheritance"? 17:34 < nsh> sometimes you have to be a bit politic about choosing names 17:34 < nsh> so that you're doing science and not fighting sociological battles 17:34 < yashgaroth> fltrz, you are, but you'd be surprised by how easily you can survive only having one functional copy of a gene, and that'll mess with relative transcription far more than tweaking the regulatory region of a gene 17:35 < nsh> yashgaroth, we have scant examples atm but i'm not sure that we've exhausted the space of possibilities 17:35 < nsh> idk 17:35 < nsh> maybe there's some mechanism that compensates for having only one functional copy of the gene 17:35 < nsh> that would seem like a very common issue that would be mitigated 17:36 < yashgaroth> no doubt, but full-on lamarckian is right out; it's limited to genes that are affected in the germ cells, so glucose sensitivity is one, but not height or something 17:36 < nsh> oh sure, i'm not trying to revive it 17:36 < nsh> i'm just saying that often in science when we're wrong it turns out later we were almost right in a more subtle sense 17:36 < yashgaroth> that's part of the reason we've got (theoretically) two copies of a gene, and why inbreeding is so dangerous - people are walking around with a bad copy of one gene or another, and it's usually fine since a random mate will compensate for that deficiency 17:36 * nsh nods 17:37 < nsh> it's an interesting self-referential statistical problem 17:37 < yashgaroth> as long as there's enough enzyme X to catalyze enough substrate Y, you don't really notice 17:37 < nsh> probably some budgetary cost 17:37 < nsh> that manifests in some manner or other 17:37 < nsh> but not terminally 17:37 < nsh> or below some threshold of difficulty-production 17:38 < yashgaroth> there's a lot of that, hell we lost vitamin C synthesis pretty quick 17:39 < fltrz> but if my interpretation is right, I would also expect a mechanism to encourage variation on the DNA binding site region more than in the protein coding region, and I know of no such mechanism 17:39 < fltrz> i.e. during meiosis or mitosis 17:40 < yashgaroth> that variation would usually only occur from mutation, rather than crossover 17:40 < nsh> can we not measure whether crossover events are uniformly distributed? 17:40 < nsh> i'd have thought there'd be data on that 17:40 < fltrz> yes, is there some way to have a sequence be more susceptible to mutation than another sequence? 17:40 < yashgaroth> I'm sure mutation in the regulatory (DNA binding site) region is more common, since you're less likely to have a deleterious mutation there vs. the coding region 17:41 < nsh> anything is possible. we don't have exactly solvable models for meiosis 17:41 < fltrz> the crossover events occur on hotspots in humans 30 000 17:41 < nsh> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105470/#S4title 17:41 < nsh> .title 17:41 < yoleaux> Variation in Patterns of Human Meiotic Recombination 17:42 < yashgaroth> homopolymer stretches (e.g. GGGGGGG) are more likely to experience insertions/deletions, otherwise there's probably been studies on what sequences are more likely to spontaneously mutate - thymine dimers are another example 17:42 < fltrz> interesting 17:43 < yashgaroth> there's probably quite a lot of data of recombination hotspots, but it's biology so don't expect rigorous statistics 17:43 < nsh> the former is probably due to increasingly difficulty of accurate location with homopolymer sequences. liek it's harder to count a long stretch of the same letter than it is to count the letters in the words i am writing now 17:43 < nsh> because of contextual subitisation 17:44 < nsh> or something analogous 17:44 < fltrz> yeah it doesnt have to be rigorous, i.e. if I group them by homolog, I'm expecting to see 1, but that question (number 1) was already answered 17:44 < yashgaroth> mhm, it's mostly polymerase slippage iirc, but it's probably the reason nature tends to avoid homopolymers in general 17:45 < nsh> i think slippage is an analogous mechanism/mistake for when humans lose count when counting a long sequence of similar things 17:45 < fltrz> I came here with 3 questions in mind, 1: the one crossover per homolog pair, 2: the binding sites sequence as "floating point" variables / blending inheritance, and question 3 I forgot :( 17:45 < nsh> but perhaps i'm oversimplifying/analogising 17:45 < fltrz> perhaps after my cigarette I remember 17:46 < nsh> :) 17:47 < yashgaroth> as much as one can anthropomorphize biochemistry, that's a fair analogy nsh 17:48 * nsh smiles 17:49 < jrayhawk> don't anthropomorphize enzymes; they hate it when you do that. 17:53 < fltrz> I remember my 3rd question 17:54 < fltrz> space is 3 dimensional, so volume concentrations can be enclosed in 2dimensional surfaces (vacuoles) 17:54 < nsh> (bulk) space is 3-dimensional 17:54 < nsh> (other theories are available) 17:55 < fltrz> then we have the discovery of TAD domains, i.e. if theres a problem with a TAD domain boundary proteins from one domain turn out to be willing to interact with DNA binding sites of what should have been a different TAD domain 17:56 < fltrz> i.e. TAD domains shield "namespaces" and limit to some extent the regions of interaction of genes 17:56 < fltrz> but DNA is linear, so how does that happen physically? 17:58 < fltrz> does each TAD domain get its own 2D vacuole wall? or are the transcription factors that are supposed to stay within one TAD domain somehow restricted by attraction to stay very close to DNA such that instead of a volume concentration they have a linear concentration on the DNA string, in that way you don't need a vacuole wall and a DNA loop as in TAD domains would be sufficient 18:00 < fltrz> is that a poorly phrased question? or is it clear what disturbs me? it disturbs me that we know about TAD domains and recognize their boundaries in the genetic code, but that currently the interaction restriction is in word salad, and is not chemically or physically explained, what prevents chemical species from diffusing in the nucleus from one TAD domain to the other? 18:03 < fltrz> we see that in individuals where theres a problem with the TAD domain that they have defects, so there is *some* isolation mechanism but I see no description of the physical isolation, is it an undiscovered vacuole wall that encapsulates each TAD domain? or there are no 2D TAD domain boundary surfaces, and instead the "local intended" species are constrained to move strictly along the DNA string, such that the TAD domain loop is sufficient to isolate 18:03 < fltrz> the "local intended" species and prevent them from interacting with neighbouring domains 18:05 < fltrz> if it is a 2D surface that forms the actual boundary, the question is what is this surface and why is nobody talking about this surface in the context of TAD domains, OR in case there is no such surface, what constrains the species to stay in the TAD domain DNA loop? 18:06 < fltrz> if they are constrained to stay close to the DNA helix, it would mean using linear concentrations to model the transcription dynamics 18:06 < fltrz> i.e. instead of particles per nanoliter, particles per nanometer... 18:15 < nsh> .wik Topologically associating domain 18:15 < yoleaux> "A topologically associating domain (TAD) is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD. These three-dimensional chromosome structures are present in animals as well as some plants, fungi, and bacteria." — https://en.wikipedia.org/wiki/Topologically_associating_domain 18:16 < nsh> are you a grad student, fltrz? 18:16 < fltrz> nope, I am an amateur gynaecologist 18:16 < nsh> ah cool 18:16 < fltrz> jk, I am a physics dropout 18:16 < nsh> i like how you think anyway 18:16 < nsh> even better 18:16 < nsh> (as am i) 18:17 < nsh> so are 2d surfaces necessarily boundaries? in physics... 18:17 < fltrz> those questions had been bugging me over the last few months 18:17 < nsh> at short scales 18:17 < fltrz> I know nothing about the potential 2D boundaries regarding the TAD domains, I never see them even conjectured 18:18 < fltrz> but other 2d boundaries in cells are the different vacuole membranes 18:18 < fltrz> typically with their own types of pore proteins 18:19 -!- ebowden__ [~ebowden@103.75.117.55] has joined ##hplusroadmap 18:19 -!- ebowden_ [~ebowden@unaffiliated/ebowden] has quit [Read error: Connection reset by peer] 18:19 < fltrz> since it's already been discovered that the TAD domains form loops, I am inclined to think that the "local intended" species are somehow constrained to stay close to DNA by their mutual properties 18:20 < nsh> chromatin is implicated certainly 18:20 < fltrz> and that a 2D surface is not involved 18:20 < nsh> but there are probably also... knotty type things going on 18:20 < nsh> or rather twisty molecular dynamics and entropic interactions 18:20 < nsh> .title https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937343/ 18:21 < yoleaux> Entropy gives rise to topologically associating domains 18:22 < nsh> the dynamics of the DNA molecule twisting and folding and compaction and loop availability are possibly problems closer to physics than biology 18:22 < fltrz> yes, but chemistry is not my strong point, I can imagine things like hydrophobic vs hydrophilic or electronegative vs electropositive to constrain the "local intended" species within the domain 18:22 < nsh> yeah but even these are emergent properties 18:22 < fltrz> oh yeah absolutely 18:22 < nsh> the density of information means that emergent statistical properties become somewhat treacherous abstractions 18:22 < fltrz> but it seems possible that nearly everything can be interpreted entropically 18:23 < nsh> oh sure, i mean it's another word for information 18:23 < nsh> and we assume that all dynamics is encapsulated by some kind of information 18:23 < nsh> because we don't have anything else really 18:23 < nsh> information is what you put into maths and physics and computers that do either 18:23 < nsh> but it just means you have to stop abstracting the information 18:24 < fltrz> right, it's just that it disturbs me that we know quite a bit about the TADs but that the exact mechanism that keeps the "local intended species" in its proper TAD domain is never discussed 18:24 < nsh> so you can't necessarily treat every segment of the DNA molecule as though it's going to react uniformly according to how a protein or surface or a chemical gradient or an electrostatic potential insists 18:24 < nsh> i suspect nobody has produced a reasonable candidate explanation 18:24 < nsh> that has gotten any traction 18:25 < nsh> but there are probably a few ideas at the fringes of the literature 18:25 < fltrz> nsh, are you currently studying biology? 18:25 < nsh> ah no i am an unemployed parasite on society 18:25 < nsh> and general menace to law and order 18:25 < nsh> but i used to think about these things a lot 18:26 < fltrz> ah just like me then, well I'm not really a parasite, I do actually work when I need money... not that I consider others parasites, imho we should reconsider the world as common property and rent each parcel out to the highest bidder and continuously divide the incoming rent equally over all humans 18:26 < nsh> i was being sarcastic of course 18:26 < fltrz> that way we would all get the average rent unconditionally, and anyone who wants more should work to get more 18:27 < nsh> i feel perfectly entitled to be subsidised as an independent scholar 18:27 < nsh> i believe everyone should have a basic universal income to facilitate their actualisation 18:27 < nsh> but that's a separate discussion :) 18:27 < nsh> right 18:28 < nsh> anyway it's a bit of a joke for society to say certain citizens of subjects are not paying my dues when humans as a whole are significantly overdraft on our ecological current account 18:28 < nsh> if anything the layabouts are the least culpable 18:28 < nsh> and the titans of industry have a heck of lot to answer for 18:28 < fltrz> the reason I prefer "system of average rent" is that it can't be diluted over time, while "basic income" prompts a lot of questions like how much exactly? and how can we assure the value over time if more money is printed etc 18:28 < nsh> but that's not perhaps the best received perspective here :) 18:28 < nsh> this is the first i've heard of this idea but i'm warming to it 18:29 < fltrz> and how do we sponsor it, while with average rent it's really clear where it comes from, and maintains a certain value, your virtual proper share of the world 18:29 * nsh approves 18:30 < fltrz> it would cover not just housing, but also food, and natural resources, since farmland would also be rented, as would mines etc 18:30 < fltrz> also, if employees don't like the way an organisation is managed, they can just outbid the manager of the local macdonalds or whatever 18:31 < fltrz> so it is simultaneously libertarian and simultaneously communist 18:31 < fltrz> the highest bidder gets to rent a place 18:32 < fltrz> we don't need to source the money from income tax 18:32 < fltrz> lots of people would be happy staying home, whereas now populace can become violent if there is not enough jobs 18:35 < fltrz> kids can run away from their parents before they get traumatized, and move to a aunts/uncles or perhaps older brothers and sisters without becoming a burden since the kids bring their own share of average rent 18:35 < fltrz> the fact that kids *can* do this automatically changes the power dynamic in families so that parents take care to treat their children right 18:35 * nsh nods 18:36 < fltrz> but also among partners, since you can just leave for a while and cool down 18:36 < nsh> is this an established proposal or something you've thought up? 18:36 < nsh> was discussing in another channel the tendency for family units to harbour abusive dynamics 18:36 < fltrz> something I have thought long about, if you want I can add you to the list if I ever finish writing this out in full 18:36 < nsh> or domestic arrangements generally 18:36 < nsh> ah please do 18:36 < nsh> worth writing up 18:37 < fltrz> where do you live? 18:37 < nsh> UK 18:38 < nsh> you're in belgium? 18:42 < fltrz> correct 18:43 < nsh> cool 18:43 < fltrz> if I ever finish writing it up, I tell you via IRC? I'm not on IRC much, just a couple of periods or times per year 18:44 < nsh> or you can email lauri.love@gmail.com or message @xeb@mastodon.social 18:44 < nsh> but i'm here always or my znc is 18:45 < fltrz> are you *the* lauri love? 18:45 < nmz787> duh 18:46 < fltrz> yeah I mostly live under a rock but that name rang familiar 18:46 < fltrz> I will send you a copy if I ever finish writing it out 18:47 < fltrz> the average rent is but a part of a larger vision, but perhaps one that is most dear to me 18:52 * nsh nods 18:53 < nsh> if there were another lauri love i'd happily be the more obscure one 18:53 < nsh> hmm, maybe that's an option 18:54 < nmz787> hehe 18:54 < nmz787> "best baby names of 2019" 18:55 < nsh> lol 18:55 < nsh> (there is actually at least one buxom blond who lives in florida that has my name) 18:55 < fltrz> lol 18:55 < nsh> (and a few dubious looking others on facebook) 18:55 < nsh> i get her emails occasionally 18:56 < nsh> they're not that interesting 19:00 < fltrz> nsh, was it a bit off topic in the other channel, or was the other channel related to concepts of UBI? 19:03 < nsh> oh it was in ##politics and the general topic was whether families are a good or bad thing and what would replace them for the purposes of child-rearing 19:03 < nsh> it split off from a discussion of the factors tending towards reunification or harmonisation in the korena peninsula 19:03 < nsh> i suggested the families split by the war would exert a pressure towards ending the partition 19:04 < nsh> and there was a sentiment in response to the effect that families are shit 19:04 < nsh> which i thought needed elaboration or qualification 19:04 < nsh> but it's undeniable that most abuse happens within families 19:04 < nsh> it's just that so far tried alternatives to the family as the basis unit of reproduction and rearing haven't been able to replace it 19:04 < nsh> or when they have there have been similar problems of abuse just at bigger scales 19:05 < nsh> it's a tough one 19:05 < nsh> also it depends highly on whether you value autonomy or consistency of quality or the minimisaiton of potentiality of abuse 19:05 < nsh> or the conservation of useful combinations of alleles or ... 19:05 < fltrz> ah I see.. I think individualism is more important than families but does not *necessitate* abolishing families, as long as individuals have the power to leave, but historically centralized governance has emphasized the idea of owning children so that parents teach them to become (at least implicit) obedient slaves 19:06 * nsh nods 19:06 < nsh> it's be nice to progressively emancipate children but there's no denying that they are not capable of independent decisions for quite a few years 19:06 < fltrz> the system designer should not a priori decide if people should be either forced together or forced apart 19:06 < nsh> and then only progressively within the constraints of their worldview sophistication 19:06 < nsh> oh sure 19:08 < fltrz> right, well to start receiving the average rent the child would have to prove it understands how to minimally interface with the average rent platform etc, i.e. yearly exams and attendance (and school trips should take the form where the class go to some city and the kids independently form groups or individually bid on some room for a week etc) so they get acquainted with the process 19:09 < fltrz> only if the child keeps up with this knowledge does it receive its average rent (which initially the child will nearly always pass on to its parents), so as to motivate the parents financially to make them as independent as soon as possible 19:10 < fltrz> i.e. a shady parent who wants an artificially dependent child is losing out on extra income 19:11 < nsh> there's a danger of over-protocol-ising :) 19:11 < fltrz> but since most traumatic perpetrations were not premeditated long in advance, a child would typically already have passed (or regularly passing) such qualifications 19:12 < nsh> maybe 19:13 < fltrz> it wouldn't be very complicated, basically the child must understand and repeat every year on its own that his share of average rent is *his alone* and that he should not share the credentials with his parents and so on, but that he is *free* to forward (part of) the rent to his parents 19:13 < fltrz> but that the average rent is *ultimately his*, that he knows where and how to bid on rooms, etc 19:14 < fltrz> a lot of conflicts also build up slowly, and the mere knowledge that a child can leave its parents will change the power dynamics *before* they run out of control 19:18 -!- cluelessperson [~cluelessp@unaffiliated/cluelessperson] has joined ##hplusroadmap 19:24 * nsh nods 19:26 < fltrz> in a wider sense, it liberates human decisions in relationships in general, for example employer employee: if the wage for a job is not high enough, you can just stay at home and let price communication work 19:28 < fltrz> every interaction should be consensual = free, but a lot of "consent" today are forced forms of "consent", if you don't and work you don't get your average rent, and you'll end up on the street 19:30 < fltrz> for example (adult) prostitution: I am not against it a priori, but it is ludicrous to pretend these women consent, in a system of average rent, they don't have to, but if they want to make a quick buck sure they can, and today you can't know if this specific women would also be in prostitution in a truly free society, while in a system of average rent you are sure that if she consents it is true consent, for she does not *need* to sell sex to survive 19:31 < fltrz> they will probably make more money too, since fewer women who artificially need to sell sex means higher wages, and the men can reach higher wages (if they work on top of receiving their average rent) 19:35 < fltrz> regarding climate change, for example a south american nation demanding money for not cutting down swathes of rain forest, ... if all humans get average rent we can just make some parts of the world like rain forest off limits, and the concept of citizenship is unnecessary 19:35 < fltrz> its much easier to reach agreement, while it will take a *long* amount of time to reach agreements between nation states with competing interests 19:38 < fltrz> in the current system you even get ridiculous situations like when a woman really loves a man, but the man despises her for he (incorrectly) suspects she is only with him for the money... basically theres unnecessary paranoia on one hand, and necessary but lacking paranoia on the other 19:40 < fltrz> only when humanism is truly respected (through equal rent rights for the accessible universe), can we be sure to have not only consensual relations, but also only then can we *enjoy the fact that we know it is consensual* 19:41 < fltrz> whereas today the unconsensualness is constantly suspected (sometimes rightly so, sometimes unnecessarily so) 19:42 < fltrz> so I believe even the richer will lead happier lives 19:43 < fltrz> the certainty that something is consensual can not be bought with money! 19:50 < fltrz> you also no longer need pension funds (and all the scams associated with them like inflation, privatized pensions, "savings accounts" which are essentially accounts that permit the banker to speculate/gamble with the money) 19:52 < fltrz> when you are an aging old fart you don't really need your own private swimming pool, or a garage for a car etc, so the average rent should suffice even if you are no longer able to work, ... i.e. live when you are young instead of postponing, saving and then possibly dying prematurely... 20:03 < fltrz> SSR site specific recombination could potentially exchange halves of a DNA binding site from a paternal and maternal chromosome, and end up with an affinity inbetween 20:03 < fltrz> such that the interpolation is inheritable 20:41 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 20:45 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 246 seconds] 21:45 -!- yashgaroth [~yashgarot@cpe-66-27-127-185.san.res.rr.com] has quit [Quit: Leaving] 22:10 < cluelessperson> I have an idea for website 22:10 < cluelessperson> Basically a display/UI of humanity's tech tree 22:10 < cluelessperson> and how we've worked up to certain things 22:11 < cluelessperson> and how we imagine other things to come in the future 22:33 -!- Cory [~Cory@unaffiliated/cory] has quit [Ping timeout: 240 seconds] 22:42 -!- Cory [~Cory@unaffiliated/cory] has joined ##hplusroadmap 22:52 -!- Cory [~Cory@unaffiliated/cory] has quit [Ping timeout: 246 seconds] 23:01 -!- Cory [Cory@unaffiliated/cory] has joined ##hplusroadmap --- Log closed Thu Feb 28 00:00:02 2019