02:20:15 *** nsh (n=nsh@eduroam-80.uta.fi) has joined #bioinformatics 02:25:11 *** pingou_ (n=pingou@AMontsouris-158-1-9-119.w92-128.abo.wanadoo.fr) has joined #bioinformatics 02:28:06 *** pingou has quit (Nick collision from services.) 02:28:11 *** pingou_ is now known as pingou 03:39:46 *** Splicer (n=p@h89n1c1o261.bredband.skanova.com) has joined #bioinformatics 03:56:11 *** biopunk has quit (Read error: 110 (Connection timed out)) 03:56:56 *** biopunk (n=p@h211n1c1o261.bredband.skanova.com) has joined #bioinformatics 04:05:25 *** Splicer has quit (Read error: 110 (Connection timed out)) 04:18:59 *** Splicer (n=p@h211n1c1o261.bredband.skanova.com) has joined #bioinformatics 04:34:08 *** biopunk has quit (Read error: 110 (Connection timed out)) 04:58:56 *** biopunk (n=p@h98n2c1o261.bredband.skanova.com) has joined #bioinformatics 04:59:44 *** biopunk has quit (Client Quit) 05:14:30 *** Splicer has quit (Read error: 110 (Connection timed out)) 05:49:23 kanzure: I would guess the eyes are a pretty fundamental sensor in what ever algorithmic implementation the spider has embedded 05:54:33 This is weird : First there is the fact that such a specific mental behaviour as looking for an egg sac could be wired into a spider’s genome. And then there is the realisation that this is a population-specific, not species-specific, trait! It is a bit of locally acquired genetic knowledge. How does any simple hardwiring story account for that? 05:55:17 OK, I see... its just an argument for certain kinds of complex cognative behaviour 05:55:40 because the trivial model fails to explain the observation. 06:02:57 So what do the researchers conclude? Does Portia have a mind, some inkling of an inner mental life? Or can every behaviour eventually be explained away in terms of simple cues and instinctive responses? Harland replies that what would be exciting would be if science could recognise some halfway position between the two conventional extremes of conscious and mindless behaviour. 06:03:50 This reminds me of a lecture I saw about consciousness in rats - its like the mechanics of looking and sniffing are a part of the rats cognative process... it couldn't chose 'left or right' at a particular point in a maze without physically looking left and right 06:04:16 by looking left and right, it is literally thinking about the two choices 06:10:20 so are there any spider colondies? The end of that article is giving me the creeps! 06:16:26 *** faceface has quit ("leaving") 06:27:06 *** dbolser (n=dbolser@bioinformatics.org) has joined #bioinformatics 06:32:08 *** dbolser is now known as faceface 06:41:52 hi 07:45:22 * nsh smiles 07:45:29 , directs HAET at faceface 07:46:03 (for juxta-position of 'behavior', 'wired', and 'directly [...] into genome' 07:46:04 ) 07:46:46 oh ok, you were expressing incredulity not accepting-amazement? 07:46:59 (then i can retract my HAET rays) 07:47:02 wierd :D 07:47:09 weird even 07:47:34 context: 07:47:36 This is weird : First there is the fact that such a specific mental behaviour as looking for an egg sac could be wired into a spider’s genome. And then there is the realisation that this is a population-specific, not species-specific, trait! It is a bit of locally acquired genetic knowledge. How does any simple hardwiring story account for that? 07:47:49 referring to: http://www.dichotomistic.com/mind_readings_spider%20minds.html 07:48:04 * pingou reads 07:48:34 itself referring certain hunter-spiders hunting certain other hunter-spiders using 'instinctive' tactics of a nuanced nature (from a human [i.e. distorted] perspective) 07:50:29 (nitpick: anaeophagic just means 'eating spiders', not spider-eat-spider) 07:51:49 oh, and faceface was quoting 07:54:50 Oo " 07:54:52 Undoubtedly many of Portia’s cognitive abilities are genetic. " 07:55:00 "The same species of Portia trapped a few hundred miles away doesn’t show any evidence of seeing the egg sac." 07:55:11 is there not a contradiction there ? 07:56:51 depends the when-of-the-how you understand the term genetic 07:56:51 ok I quote the same thing just the paragraph above ^^ 07:57:11 a few decades ago or more, that would be a contradiction, i gues 07:57:12 s 07:57:47 nowadays, we have a better appreciation of the ability of the genetic code to interact in 'real-time' with its environment 07:57:51 well assuming it is species specific there is a contradiction, but since it seems to be population specific it makes sense 07:58:14 nsh: do you have any article that explain that a bit more ? 07:58:26 mm, kanzure linked to it originally; i'd have to search 07:58:36 just follow the researcher names, i guess 07:58:49 I'll have a look as soon as I finish to read :) 07:59:27 http://scholar.google.com/scholar?q=Harland+portia+spider&hl=en&lr=&btnG=Search looks promising 07:59:55 * nsh has to go for cake and sparkling wine 08:00:01 lab's losing a slave today 08:00:03 hmm sounds hard ! 08:00:05 bbiab 08:00:12 doi 08:37:21 nope 08:37:40 I think the statement was made to challenge the assumption that the 'behaviour' was 'genetic' 08:38:03 showing that the observation is not consistent with our current interpetation of spider cognition 08:38:28 i.e. something more complex is happening... i.e. certain groups of spiders learngin certain behaviours 'in real time' 08:38:47 * faceface proposes 'real-time genomics' just to annoy nsh 08:38:53 hello pingou 08:44:40 stupid western metaphysical tradition 08:44:50 * nsh goes back in time and kills aristotle 08:45:28 hello faceface 08:46:29 saying behavior is genetically determined is like saying a chess game is written in the rules 08:46:39 it's true in some trivial sense, but completely misinformed 08:46:43 yes I think they started by mentionning that their behaviour was genetics but then they contradicted it by saying that this cognitive behaviour varies among localization 08:46:59 nsh: yes and no 08:47:09 elabpls 08:47:11 philosoply is all foot notes to nsh 08:47:27 * nsh is all footnotes to philosophy 08:47:30 well cognitive behaviour are supposed to be genetically determined rught ? 08:47:30 well... the rules of chess are fixed... 08:47:39 imagine that the rules evolved too 08:47:46 well, they did 08:47:56 then the games, although overlapping, could be 'on average' different 08:48:11 but in any one game, or instance of an organism, they 'rules' of sequence are fixed (to a first approximation) 08:48:18 certainly the brain of the spider is the result of its genome... 08:48:28 nsh: sure 08:48:41 but it's the level of contribution that's up for debate 08:48:52 OK 08:49:01 back in 1990, almost 100% of what happened in my computer was determined by the hard-drive 08:49:13 perhaps 3-4 percent of the data came from my interaction 08:49:13 nature vs. nurture? (to boil the issue down into a nice neat (and disposable) category) 08:49:25 today, the greater part comes from the network 08:49:37 nature via nurture :-) 08:49:54 nsh: you should publish ;_) 08:49:59 it's an off-loading to transcend memory limitations.. 08:50:01 * nsh mehs 08:50:02 I mean ... my nose isn't hat wokny 08:50:12 nsh: sure - I totally get that 08:50:16 from genome to brain-ome 08:50:21 neur-ome 08:50:23 right, and thence to cultrome 08:50:26 is also faster 08:50:37 nsh: yup 'semiol-ome' 08:50:39 well, at certain scales 08:50:41 * nsh smiles 08:50:57 I heard a great track about language... 08:51:04 regail, good sir 08:51:36 its weird, but there is a lot of good stuff ... esp. in the first bit http://music.yellowgrey.com/Dan/NumberTwo/010-Leandro-Katz--Animal-Hours.mp3 08:51:56 prolly best to wget 08:52:13 wcan't :-/ 08:52:19 stream? 08:52:27 * pingou weget... 08:52:29 -e 08:52:30 well, i'm vistacapped until i get an external 08:52:45 which I *will* do right soon now (tm) 08:52:48 vlc 08:53:06 * nsh smiles 08:53:28 'first postulate' 08:54:19 hmm 08:55:02 * nsh tries to think where he's encounted Leonard Katz previously 08:55:04 it takes a few listens 08:56:18 parallel anaphora 08:56:34 fancy pants 08:58:14 anaphora is when the interpretation of an expression depends on another 08:59:03 the key point that I like from that scramble is that language encodes knowledge 08:59:19 and that modern language is the result of 1000's of years of acruing knowledge 08:59:28 right 08:59:52 when we bable today, we are actually reflecting our cultural, ideological, philosophical heratige 08:59:53 i've been thinking intermitantly lately that learning anything (conceptual) is merely a matter of accruing a language 08:59:58 whether it is explicit or not 09:00:11 "every word is a fossilised poem" 09:00:28 nice 09:00:41 aparently nice derives from 'dumb' 09:00:54 I'll call it divergent :-) 09:00:58 etymologically? 09:01:02 * nsh smiles 09:01:02 yeah 09:01:16 i found something similar in english class, aged 12 09:01:18 it was one of those - lets look at genes like words 09:01:24 lectures 09:01:36 "c.1290, 'foolish, stupid, senseless,' from O.Fr. nice 'silly, foolish,' from L. nescius 'ignorant,' lit. 'not-knowing,' from ne- 'not' (see un-) + stem of scire 'to know.' 'The sense development has been extraordinary, even for an adj.' [Weekley] -- from 'timid' [...]" - http://etymonline.com/?term=nice 09:01:45 funny i didn't remember that; sure i must have read it before 09:01:48 mmm 09:02:19 you read the whole thing? 09:02:38 nsh: have you read hofstdater? 09:02:44 oh no, but i check about 20 etymologies a day 09:02:52 * nsh read half of GEB 09:02:53 just thinking about the idea of the chess game 09:02:58 then the library wanted it back 09:02:59 bastards 09:03:03 go on 09:03:09 he has a nice analogy based around chess 09:03:15 (i was getting pissed off at him, anyway. but i won't get into that..) 09:03:21 nsh: yeah, they wanted it back on the shelves where it should be! 09:03:27 * nsh smiles 09:03:45 its about game vs. rules as you were talking 09:04:14 combinatorial explosion? 09:04:31 one chess board in the middle, with the game going on, surrounded by 8 chess boards in a square. 09:04:41 the surrounding 8 encode the rules of the inner game 09:04:56 mmhmm 09:05:02 instead of making a move on the inner game, you can make a move on the outer table to change the rules 09:05:32 I think his point was that, either you have a fixed set of rules encoding the way the pieces move on the outer tables... or... you have loopy hell 09:05:41 * nsh smiles 09:05:52 well, i'm not suprised that was his conclusion 09:05:54 and we are back on cybernetics... 09:06:25 the psychology of horror at such phenomena is well-rooted in the western psyche 09:06:33 wel... talking of conclusions... I shoudl go work... interesting chat thoug! 09:06:37 nsh: perhaps 09:06:39 (which psyche now encompasses most of the world) 09:06:47 like the fear of an out of body experience... 09:06:50 right 09:06:58 or the disillusionment of individuality 09:07:16 that accompanies many activities which are traditionally persecuted and stamped out with a virulence unmatched 09:07:24 but another matter for another time 09:07:28 * faceface extends his consciousness onto the internet by means of extended electronic sensory systems... 09:07:56 its cool, but the dreams it gives you are weird 09:08:01 bbl 10:06:45 *** highvoltz has quit () 10:12:32 faceface, metabase appears to be broken 10:13:00 (Can't contact the database server: Too many connections (localhost)) 10:13:02 same here 10:13:10 MetaBase has a problem 10:57:27 * faceface weeps 10:57:42 works for me 10:58:00 pingou nsh - seems fixed? 10:58:22 I wish my memory worked... now you made me forget why I opened this window 11:00:31 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 11:13:30 *** synthasee (n=synthase@68.63.20.12) has joined #bioinformatics 11:20:03 *** synthase has quit (Connection timed out) 12:07:30 *** mib (n=mib@r124-19-38-81.cpe.unwired.net.au) has joined #bioinformatics 12:07:34 hi 12:07:44 anyone used before Al-AML dataset? 12:32:05 faceface, yeah worked here a little while ago 12:32:35 and now 12:33:07 * nsh wonders about hypogogic-recall improvement techniques 12:33:19 the most interesting thoughts, evanescent as the wind.. 12:33:29 bbiab, flies 13:29:36 I heard of hypnopompic halucinations 13:29:49 anyway, _dan where is the php2fasta found? 13:30:07 I got phred and phrap... but seems I am missing consed... 13:31:53 I see... back to my 'out of body' comment 13:32:03 I got terrified and gave up exploring ;-) 13:38:42 isn't consed available via download, they have to open up a specific ip or something along those lines 13:40:03 http://bozeman.mbt.washington.edu/consed/consed.html#howToGet point 5 13:46:01 flu: they won't give me a download until I fill in the form 'properly' 13:46:42 aah 13:47:06 I used my gmail email not an 'academic' one 13:48:05 like that means that I'll run off and start a biotech company and use their code in my commercial apps... 13:49:31 and even if I did use their code commercially, what do they really loose? 13:49:42 they loose their 'email' system... 13:49:54 their precious 'oooh ask us first!' 13:58:55 *** nsh has quit ("a culture gets the mythology it deserves") 14:02:11 heh... seems they have it at 'my old place'; 14:03:17 hmm... but not phd2fasta 14:18:13 intellectual property man...don't disrespect it 14:45:38 *** kushalsejwal (n=kushal@59.178.202.99) has joined #bioinformatics 14:45:46 hello guys anybody there? 14:54:41 No. 14:55:16 any active pathogens :D 14:57:26 *** kushalsejwal has parted #bioinformatics () 16:39:37 *** deeku (n=telppa@c1.ucalgary.ca) has joined #bioinformatics 16:40:02 *** deeku has quit (Client Quit) 17:39:55 *** highvoltz has quit () 18:28:48 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 19:13:14 *** mercutio22 (n=htorres@c95181ec.virtua.com.br) has joined #bioinformatics 19:32:08 *** nsh (n=nsh@87-94-146-186.tampere.customers.dnainternet.fi) has joined #bioinformatics 19:44:17 *** nsh has quit (Read error: 104 (Connection reset by peer)) 19:44:31 *** nsh (n=nsh@87-94-146-186.tampere.customers.dnainternet.fi) has joined #bioinformatics 19:56:42 *** pingou_ (n=pingou@AMontsouris-158-1-61-164.w92-128.abo.wanadoo.fr) has joined #bioinformatics 20:08:33 *** pingou has quit (Read error: 110 (Connection timed out)) 20:59:19 *** mib has quit (Read error: 110 (Connection timed out)) 20:59:53 *** Iskr (n=i@host188-82-dynamic.54-82-r.retail.telecomitalia.it) has joined #bioinformatics 21:14:51 *** kanzure has quit (Remote closed the connection) 21:26:35 *** nsh has quit (Connection timed out) 21:46:15 *** Iskr has quit ("Leaving") 21:57:45 *** deeku (n=telppa@c1.ucalgary.ca) has joined #bioinformatics 21:57:47 *** deeku has quit (Remote closed the connection) 23:28:07 *** fakingfantastic (n=franklak@pool-71-172-62-204.nwrknj.fios.verizon.net) has joined #bioinformatics 23:28:36 hi, is it possible someone can explain to me an example of using density-based clustering?