--- Log opened Sat Aug 01 00:00:27 2015
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00:14 < fenn> xtalmath> what if cancers were just accidental organoids?  <- that's called a "teratoma" and happens sometimes with stem cell therapy, very difficult to deal with because they are human cells
00:15 < xtalmath> I thought most human cancer cells were human cells (with the "non human" cells being dna damaged cells?)
00:15 < fenn> yes that's also why cancer is difficult to deal with, but cancer often expresses a lot of extra surface proteins that normal cells don't
00:16 < fenn> so you can target those proteins and kill the cancer
00:16 < xtalmath> perhaps the question should be rephrased: what if all non-DNA damage cancers were in fact organoids? and not just the ones recognized as teratoma
00:17 < xtalmath> perhaps embryonic cells also express similar surface proteins? and further down the cell lineage less surface proteins are expressed?
00:18 < fenn> yes
00:18 < xtalmath> once it is recognised as teratoma, the organoid development might have progressed far enough so that typical extra surface proteins aren't found to that extent?
00:19 < fenn> i guess the difference is that a teratoma has structure similar to normal organs
00:19 < fenn> whereas cancer is just a blob
00:19 < xtalmath> well the average body part is very different from the uterus
00:20 < xtalmath> some cancers get lucky and succeed in growing their organoid?
00:23 < xtalmath> pure speculation though
00:25 < xtalmath> also, I think cell suicide, or cell death penalty in the body for rogue cells might be functioning fine, and is low risk once the body is grown (its just one cell of the many in the tissue), but in embryonic stage I expect the system to be more tolerant lest it not deprive the future body of an arm or a leg...
00:26 < xtalmath> so perhaps cells that somehow end up in a state closer to stem cells in the cell type lineage, will be less cooperating with cell suicide
00:26 < xtalmath> since it genuinely thinks to be part of a developing embryo
00:28 < xtalmath> I guess there is some transition from finite, countable cell instances in the embryo, to non-exact count density-feedback of cells in the adult tissue.
00:28 < fenn> a lot of cells undergo apoptosis during development... it's how most structure happens
00:29 < fenn> division and apoptosis is like plus and minus
00:29 < xtalmath> sure, but the apoptosis is probably a cooperative act, and not in response to adult tissue "plz kill yourself, trust us, you misbehave" signal molecules
00:30 < xtalmath> with cooperative I meant more like, consensual
00:31 < xtalmath> like apoptosis in embryo, so that handblob becomes fingers, those cells expected to kill themselves
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00:38 < fenn> this article about organoids is pretty cool, i hadn't heard of these yet
00:40 < fenn> it seems like they need to add a circulatory system to get anything bigger than a pea
00:57 < fenn> this "deceullularized heart" doesn't look anything like the "ghost heart" at counter culture labs: http://www.nature.com/polopoly_fs/7.11286.1372788772!/image/heart_0037.jpg
00:57 < fenn> it's very droopy
01:17 < fenn> http://www.nature.com/news/stem-cell-scientists-mourn-loss-of-brain-engineer-1.15679
01:18 < fenn> sasai (the guy who made the artificial brainlets) was involved in the STAP paper retraction and committed suicide
01:27 < fenn> such a japanese thing to do
01:33 < fenn> http://www.nature.com/news/crumb-of-mouse-brain-reconstructed-in-full-detail-1.18105
01:33 < xtalmath> hmm, wish I could access "Design and characterization of a multisource hand-held tandem mass spectrometer"
01:39 < fenn> xtalmath: fennetic.net/irc/ac801275x.pdf
01:40 < xtalmath> how did you find that?
01:41 < fenn> visiting the doi page from somewhere with access
01:42 < fenn> basically clicking around on a bunch of search results until something worked
01:42 < fenn> this is a topic i'm also interested in
01:43 < fenn> i would like to see an open source inexpensive mass spectrometer
01:45 < fenn> i think a large part of that is getting the size of tubing/chambers down to smaller than the mean free path of a reasonably attainable vacuum
01:45 < fenn> nobody can afford a turbomolecular pump
01:45 < fenn> also portability is nice
01:58 < fenn> "The cube of tissue was too small to contain an entire cell, but large enough to contain fragments of more than 1,600 neurons and of other brain cells of at least six different types, as well as around 1,700 synapses."
01:59 < fenn> well that doesn't seem particularly useful
02:11 < jrayhawk> xtalmath: http://med.stanford.edu/ludwigcenter/overview/theory.html might interest you
02:12 < xtalmath> I was wondering how much the turbomolecular pumps cost nowadays?
02:13 < xtalmath> jrayhawk: that is interesting
02:13 < fenn> $10k
02:14 < jrayhawk> https://en.wikipedia.org/wiki/Cancer_stem_cell oh there's a wikipedia article
02:15 < xtalmath> $10k is not a fair price :(
02:15 < jrayhawk> usually alternative medicine crap gets killed pretty fast
02:15 < fenn> 2-5k used
02:15 < fenn> anyway it's more than i want to pay for PART of an instrument
02:16 < xtalmath> true
02:16 < fenn> jrayhawk: i thought cancer was 100% "stem cell" in that they can proliferate indefinitely
02:17 < fenn> is that just the type used for tissue culture?
02:18 < xtalmath> I wonder what happens if one taps a deep hole, with a valve on the other end of the hole, then opens the valve, screws in a bolt, then closes the valve, then partially unscrews the long bolt to create a vacuum?
02:18 < fenn> bolts don't seal along the threads
02:18 < xtalmath> lubricated with oil?
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02:18 < fenn> not even close
02:19 < fenn> some hydraulic pipe threads seal along the thread, but i'm not sure how they work
02:19 < fenn> it seems like you've just reinvented the piston but with all sorts of complications
02:20 < xtalmath> how about ferrofluid droplets, multiple in series in a tube , each withstanding about 3-4 psi (https://en.wikipedia.org/wiki/Ferrofluid#Electronic_devices)
02:20 < fenn> most oils and liquids have high vapor pressure
02:20 < xtalmath> dragged along by magnets
02:21 < xtalmath> according to https://en.wikipedia.org/wiki/Ferrofluidic_seal ultra high vacuum operation
02:21 < fenn> you could probably pump mercury droplets around with induction magnetism
02:21 < xtalmath> I think the problem is you cant recirculate the droplets
02:22 < fenn> i'm surprised the ferrofluid seals work in "ultra high vacuum"
02:23 < xtalmath> so am I
02:23 < fenn> they probably are shielded by hard seals so they don't have very much surface area exposed to hard vacuum
02:23 < xtalmath> but diffusion pumps use oil
02:23 < fenn> whereas a pump made of ferrofluid would have a lot of surface area exposed
02:24 < xtalmath> I think you are right
02:25 < fenn> i don't know very much about high vacuum technology unfortunately
02:25 < xtalmath> im also amazed the turbomolecular pump and the rest of the system operating at what was it 35W?
02:25 < fenn> the article on diffusion pumps makes it seem like stationary oil never comes into contact with the hard vacuum side
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02:27 < xtalmath> fenn: but this looks like it is :S https://upload.wikimedia.org/wikipedia/commons/thumb/f/f6/Diffusion_pump_schematic.svg/250px-Diffusion_pump_schematic.svg.png
02:27 < fenn> "One major disadvantage of diffusion pumps is the tendency to backstream oil into the vacuum chamber. This oil can contaminate surfaces inside the chamber or upon contact with hot filaments or electrical discharges may result in carbonaceous or siliceous deposits. Due to backstreaming, oil diffusion pumps are not suitable for use with highly sensitive analytical equipment or other applications
02:27 < fenn> which require an extremely clean vacuum environment, but mercury diffusion pumps may be in the case of ultra high vacuum chambers used for metal deposition. Often cold traps and baffles are used to minimize backstreaming, although this results in some loss of pumping ability."
02:27 < xtalmath> in my mind that would just boil oil into the chamber
02:28 < fenn> it goes angled downwards because it's a molecular flow
02:28 < xtalmath> oh ok, so it stays liquid in vacuum, but it messes up the walls everywhere
02:28 < fenn> no
02:28 < fenn> it's individual molecules flying around in straight lines
02:29 < xtalmath> like kinetic gas theory?
02:29 < fenn> sort of, but when talking about gases you think of the molecules bouncing off each other, but these are too sparse for that to happen
02:32 < xtalmath> "Unlike the more numerous and problematic leukemia cells, a relatively  few of these rarer cells could transfer a leukemia from a sick mouse  into a previously healthy one." wow cancer is contagious
02:33 < fenn> https://en.wikipedia.org/wiki/Transmissible_cancer
02:34 < fenn> this is actually really weird https://en.wikipedia.org/wiki/Canine_transmissible_venereal_tumor
02:34 < xtalmath> fenn: what I dont understand then in the straight line analogy: so pretending the "fans", walls are like mirrors and the molecules reflect like rays, then for every ray the path is reversible, and instead of chamber particles being dragged downwards it could be upwards?
02:35 < fenn> uh, you can't un-boil the egg
02:36 < fenn> i don't understand what you're asking
02:36 < fenn> you can pump small amounts of gas into the vacuum chamber if you wanted
02:36 < fenn> but what would be the point of that
02:38 < xtalmath> no I mean how does the diffusion pump work, if you imagine the particle traveling in the opposite direction on the schematic picture?
02:40 < fenn> the oil jet is directed downwards, so when it collides with some other molecule going upwards they both tend to go down because the oil molecule is heavier
02:40 < fenn> also they stick to the sides that are cold
02:41 < xtalmath> ok
02:50 < fenn> wow images of pluto: http://www.nature.com/polopoly_fs/7.28153.1437413329!/image/tn-p_lorri_fullframe_color_web.jpg
02:53 < fenn> http://www.nature.com/news/vibrant-pluto-stuns-scientists-1.18022
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03:08 < fenn> even more images http://pluto.jhuapl.edu/soc/Pluto-Encounter/index.php?page=1
03:58 < fenn> and SETI is getting $100 million from yuri milner, a 2000% budget boost
03:58 < fenn> time to dust off the allen array
03:59 < xtalmath> how can those be cosmic rays at http://pluto.jhuapl.edu/soc/Pluto-Encounter/index.php?page=1 ?
03:59 < xtalmath> multiple pictures at different times have the same 2 artifacts, or is there 2 strong beams of multiple cosmic rays?
03:59 < fenn> cosmic ray artifacts are a sort of sensor noise that only occurs in the presence of heavy ion bombardment
04:00 < fenn> oh you might be seeing the saturation streaks from pluto and charon
04:00 < xtalmath> that is way more reasonable than cosmic rays
04:00 < fenn> the page "about these images" mentions them also
04:01 < xtalmath> they seem more like normal saturation streaks, yet the accompanying descriptions claim its cosmic rays pfft
04:02 < fenn> "some of the more interesting SETI signal candidates (such as SHGb02+14a) appear to emanate from interstellar space rather than a star" https://entersingularity.wordpress.com/2014/06/10/dark-extraterrestrial-intelligence/   an essay about the implications of thermal noise on the probable location of computronium
04:09 < xtalmath> I think particles are topological handles ("wormholes"). At some point lifeforms discover how to stretch them open, or make pairs and stretch them open and can place both ends wherever they want for quick and cheap transport (everything in their world is now close connected). To explore the universe they open random particles and use starmaps to locate whereabouts that is.
04:09 < xtalmath> Every time they hope they dont connect their intimately connected world with a particle near a black hole. someday it happens...
04:11 < xtalmath> every trace of their society is removed. except perhaps for a few self-reliance hippies, but they dont have big societies to discover
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04:43 < xtalmath> fenn: is this like a complete vacuum system? one of the markings says -101.3 kPa ... I don't really find a vacuum pump in there, is it more like a vacuum distribution system? http://www.ebay.com/itm/170845030304?item=170845030304&rmvSB=true
04:45 < fenn> it's just valves and driver electronics, no vacuum pump
04:46 < fenn> this is for moving stuff around or degassing liquids, not high vacuum
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05:27 < xtalmath> hmm would PtW (tungsten) wire be a W wire coated with Pt?
05:28 < xtalmath> or more like an alloy? I have some lying around, not sure what it is
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05:30 < xtalmath> I see lots of Pt 92% W 8% wires in search engines, I guess the W is added for rigidity? thinking of making an STM now..
05:34 < kanzure> i wonder if the seti money is going to fund the "let's look at more binary star systems" plan
05:36 < kanzure> e.g. http://diyhpl.us/~bryan/papers2/physics/astrophysics/Starivore%20extraterrestrials%20-%20Interacting%20binary%20stars%20as%20macroscopic%20metabolic%20systems%20-%20Clement%20Vidal.pdf
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05:53 < kanzure> ebola vaccine got licensed out to some company for $200k https://news.ycombinator.com/item?id=9982005
05:55 < kanzure> "I grew a heart by mistake once. I was studying the way cells move, and to make cells that moved, we would dissect hearts out of seven-day-old chicken embryos, shread them into chunks, and put the bits down on a layer of matrigel in a dish full of tissue culture medium. After several hours, the cardiac muscle cells would start to dedifferentiate into fibroblasts (not really fibroblasts, but people call them that) and start zooming ...
05:55 < kanzure> ... around, at which point you can do science on them. I painstakingly prepared one of these dishes, then forgot about it, and left it in the incubator for a week. When i got back to it, the initial chunk of heart muscle had completely gone, turned into fibroblasts - which had then spread out over the dish, and turned back into cardiac muscle cells. There was a thin sheet of muscle strung out across the width of the dish, and it had ...
05:55 < kanzure> ... started beating."
05:55 < kanzure> .title https://news.ycombinator.com/item?id=9984660
05:55 < yoleaux> The boom in mini stomachs, brains, breasts, kidneys and more | Hacker News
06:07 < cluckj> oh neat, power's out
06:22 < xtalmath> kanzure: thats just gross
06:25 < kanzure> you sound like someone that would enjoy gurochan
06:26 < JayDugger> Yes, he does.
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06:33 < JayDugger> Junji Ito has a new book out in English, "Fragments of Horror." Ought to be a good start.
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06:37 < JayDugger> Ha! and the publisher recommends DBZ to go with it.
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06:43 < kanzure> if you have seen that then you would also like teamfourstar's parody of dbz
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06:49 < kanzure> greetings zadock
07:16 < JayDugger> Assuming I like dbz enough to enjoy a parody of it.
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09:43 < juri_> nmz787: which SEM do you have?
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09:48 < CaptHindsight> who is selling femtosecond lasers for <$5K
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11:01 < QuadIngi> lw-exile
11:01 < QuadIngi> sorry, trying to find that channel
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12:30 < kanzure> "More recently, targeted strategies have been employed where one bacterium is engineered to perform a very specific function in the gastrointestinal tract. These functions range from secreting a therapeutic molecule (mostly peptides and small proteins) to detecting a particular signal, such as small molecules derived from other bacteria, food, or cancerous or inflamed tissues (Claesen and Fischbach, 2015)."
12:30 < kanzure> http://www.cell.com/cell-systems/fulltext/S2405-4712(15)00011-3
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13:53 < archels> http://www.dx.com/p/colorful-micro-usb-2-0-data-sync-charger-wrist-bracelet-cable-grey-22cm-379962#.Vb0ySHWUdhE
13:53 < archels> http://www.dx.com/p/micro-usb-2-0-data-sync-charging-wrist-bracelet-style-cable-black-22cm-379960#.Vb0ySXWUdhE
14:15 < kanzure> "Saturated Reconstruction of a Volume of Neocortex" http://www.cell.com/cell/abstract/S0092-8674(15)00824-7
14:16 < kanzure> "We describe automated technologies to probe the structure of neural tissue at nanometer resolution and use them to generate a saturated reconstruction of a sub-volume of mouse neocortex in which all cellular objects (axons, dendrites, and glia) and many sub-cellular components (synapses, synaptic vesicles, spines, spine apparati, postsynaptic densities, and mitochondria) are rendered and itemized in a database. We explore these data to ...
14:16 < kanzure> ... study physical properties of brain tissue. For example, by tracing the trajectories of all excitatory axons and noting their juxtapositions, both synaptic and non-synaptic, with every dendritic spine we refute the idea that physical proximity is sufficient to predict synaptic connectivity (the so-called Peters’ rule). This online minable database provides general access to the intrinsic complexity of the neocortex and enables ...
14:16 < kanzure> ... further data-driven inquiries."
14:16 < kanzure> "•Tape-based pipeline for electron microscopic reconstruction of brain tissue; •Annotated database of 1,700 synapses from a saturated reconstruction of cortex; •Excitatory axon proximity to dendritic spines not sufficient to predict synapses"
14:16 < kanzure> http://www.openconnectomeproject.org/#!kasthuri11/c12r2
14:17 < kanzure> http://openconnecto.me/catmaid/
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14:21 < kanzure> "We built an automatic tape-collecting ultramicrotome (ATUM) that retrieves brain sections from the water boat of a diamond knife immediately as they are cut via a continuous submerged conveyor belt (Figure 1A ; Movie S1). The tape’s pulling motion and its adhesiveness cause the caught sections to lie flat on the tape’s surface (Figure 1A, inset). To generate the cerebral cortex image dataset in this paper, we collected 2,250 29-nm ...
14:21 < kanzure> ... coronal brain slices (each section ∼1 mm2, total volume 0.13 mm3) from somatosensory cortex of a young adult mouse on ∼6.5 m of Kapton tape (Figure 1B). We generated 1,000 sections per 24 hr. We chose 29 nm as section thickness in order to trace the finest neuronal wires (Mishchenko, 2009), and with a sharp knife we have successfully sectioned >10,000 sections from a small block without missing a cut and importantly manual ...
14:21 < kanzure> ... segmentation is nearly flawless at this thickness (see below). Following section collection, the tape was cut into strips and placed on silicon wafers that were then photographed (Figure 1C)."
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16:50 < kanzure> "Synthetic multicellularity" https://emslhub.emsl.pnl.gov/resources/28/download/Maharbiz_TICB2012.pdf
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--- Log closed Sun Aug 02 00:00:28 2015