--- Log opened Sun Mar 03 00:00:05 2019
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00:47 < nmz787> fltrz: well super-resolution microscopy is a thing, and I just visited a team at Boise State University using that in conjunction with DNA origami scaffolds with 'address
00:48 < nmz787> fltrz: 'address tethers' which are to complement various small oligo sequencens, localizing the address in a know place in a CCD/CMOS camera field of view
00:48 < nmz787> fltrz: they're seeing single molecules of photons
00:48 < nmz787> not quite extracting phase information from a piece of DNA itself, as I think you're looking for though
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03:47 < nsh> nice
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11:23 < nmz787> err, I should say they're seeing single-molecules of dye affixed to the DNA
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12:57 < fltrz> nsh, I'm surprised the quantum holography paper doesn't mention the Poinsot construction, it seems as irrelevant as the correct but irrelevant reminder about hodographs concerning Keplerian orbits...
12:58 < fltrz> if it was written more recently I'd be convinced it was written by an AI
13:00 < fltrz> the main reason I think coherent imaging and holography are not at all applicable is rather simple: all lifeforms are dissipative structures, we seek free energy, and we require a cold heat bath to dump the garbage heat. Of all solid angle around us, there is a small speck of high temperature and high energy light in a small solid angle coming from the sun, and then there is a huge solid angle of cold cold space.
13:01 < fltrz> life requires natural selection, and natural selection requires a copying mechanism that is perfectly reliable most of the time (to propagate the genome), and erroneous part of the time (to explore variations))
13:03 < fltrz> so this is dissipative, and not coherent. every time information is copied in the cell (DNA replication, transcription, translation) information is copied, energy is consumed and heat is necessarily generated in the process
13:03 < nsh> .wik Poinsot construction
13:03 < yoleaux> "In classical mechanics, Poinsot's construction (after Louis Poinsot) is a geometrical method for visualizing the torque-free motion of a rotating rigid body, that is, the motion of a rigid body on which no external forces are acting. This motion has four constants: the kinetic energy of the body and the three components of the angular  …" — https://en.wikipedia.org/wiki/Poinsot_construction
13:03 < nsh> nice, didn't know of that. thanks!
13:04 < fltrz> do you know the author personally or indirectly?
13:08 < fltrz> if you forced me to make any analogy between quantum information and biology it would be nonlinear optical processes: for example light amplification, when a laser is powered up, the first photons are incoherent, and filtered by the mirrors such that only the photons that satisfy the environmental constraints (longitudinal modes) survive and multiply
13:09 < fltrz> the wavelength and phase is in some interpretation copied into the state of the stimulated photons
13:09 < fltrz> and theres also multiple populations (multiple longitudinal modes) surviving in parallel
13:10 < nsh> i don't know Walter Schempp, but i have corresponded with a few people in his 'set' and know one or two personally
13:10 < fltrz> but is that really useful? no because we can simply have the gillespie algorithm as a "fundamental picture"
13:10 < fltrz> i.e. plain old chemistry
13:11 < nsh> plain old chemistry is making use of a lot of quantum... superspace of trajectories
13:12 < nsh> which is why it's so hard to simulate on classical computers
13:13 < fltrz> I'm *not* saying quantum chemistry is not important, I'm saying *coherent* optics effects like holography is not relevant
13:13 < nsh> QM is really a kind of extension of stochastic methods in a way
13:13 < nsh> well, i don't know on what basis you make that claim :)
13:14 < nsh> because you can roughly get some outcomes of a coherent process using stochastic algorithms it doesn't mean that you are encapsulating everything thereby
13:14 < nsh> or a potentially coherent process
13:14 < nsh> i'm not sure, seems harder to obviate or rule out than that
13:14 < nsh> the laser analogy is useful though i think
13:14 < fltrz> OK, so humans are trying to build quantum computers of nontrivial sizes, the reason we fail at larger qubit sizes is mostly incoherence / dissipation / ...
13:16 < fltrz> cellular life is built on top of dissipation, it uses dissipation, then obviously the operation of life is closer to the operation of computers than to quantum computers, that said in order to design classical computer parts like transistors, diodes, ... a quantum understanding of matter is definitely important
13:17 < fltrz> but one does not need quantum mechanics to understand classical software
13:18 < nsh> biological organisms are clearly infinitely better at... life... than classical computers
13:18 < fltrz> the very act of copying state in transcription, translation means that there can be no coherence / unitary transformation / ... such that it makes no sense to view the higher level dynamics as a quantum system
13:18 < nsh> i would not use the classical computer as a model for anything except classical computing
13:18 < nsh> and not even that if i could avoid it at all
13:18 < nsh> they are terrible things, mostly useless
13:19 < nsh> it's one of the worst things that has happened to humanity over the last 80 years that we've started thinking everything is like classical data
13:19 < fltrz> the similarity is that a computer needs energy to operate, and that information can be erased and copied, which generate heat
13:19 < nsh> almost nothing is
13:19 < nsh> if anything it's an aberration :)
13:19 < fltrz> in a quantum computer you can not copy information (unless you use redundant inputs)
13:20 < fltrz> the mere observation that cellular processes and life in general involve copying information implies that it can not behave as a quantum computer
13:21 < fltrz> while it can display behavior similar to classical computers (and questions of relative efficiency comparing life with computers are only of technological interest, like building DNA memory technology)
13:22 < nsh> only if you think of DNA as being classical data
13:22 < nsh> which is useful until it's not
13:22 < nsh> but yes, there is replication
13:22 < fltrz> not of fundamental interest, since the moment one copies information, coherence is destroyed
13:22 < nsh> so there is something that has the properties of the quantum-as-we-know-it but not some of the limitations
13:22 < nsh> ie, a better theory
13:22 < nsh> a deeper reality
13:22 < fltrz> quantum with copying lol
13:23 < nsh> you're viewing everything through two bad and provisional lenses
13:23 < nsh> it's a habit to get out of :)
13:23 < nsh> all advances come from getting out of the habits of previous understandings
13:23 < nsh> and their limitations and hidden assumptions and "it must be so"s
13:23 < nsh> everyone goes about living in their box constantly redrawing their box and making it harder to see out of their box
13:23 < fltrz> quantum mechanics *relies* on unitary transformations
13:23 < nsh> because it's a hack
13:24 < nsh> for simulating the effective evolution of an ensemble of states because you don't know the precise microstate
13:24 < nsh> so you get rid of the exponential divergence by creating a collection of possible systems in superposition that can evolve unitarily
13:24 < nsh> it's a hack
13:24 < fltrz> so now we are trying to interpret genetics in terms of an undisclosed underlying theory beneath not only classical but also beneath quantum mechanics?
13:24 < nsh> sure why not
13:24 < nsh> i'm not saying you have to :)
13:25 < nsh> i'm saying it's a thing that might be tried
13:25 < fltrz> how does such a comparison help in any way if the other comparee is unknown?
13:25 < nsh> but people are very welcome to stay where it's comfortable and proceed by painstakingly small steps in known directions
13:25 < fltrz> we might as well say that genetics should be interpreted in terms of *that mechanism that underlies alien life forms*
13:25 < nsh> well that's how you triangulate the direction you haven't gone in yet
13:25 < nsh> you say "it's not tihs, we've done that. it's not t'other, we've done that to death"
13:25 < nsh> and then you eventually find a new way to og
13:29 < fltrz> ok, suppose someone claims we should take into account relativistic effects of the speed of the protein molecules, ... great that will be slightly slightly more accurate and complicate the picture,... since v << c we can safely ignore relativistic effects
13:29 < fltrz> this is not a random shortsightedness, once you know the distribution of velocities of molecules at a certain temperature
13:30 < nsh> the meme that relativity is only germane at high velocities or high gravitational gradients is a psychological comping mechanism
13:30 < fltrz> then we *know* we can ignore relativistic effects... similarly by knowing that genetics relies on copying information, we can exclude coherence effects... (try making a hologram with incoherent light)
13:30 < nsh> and is not a proven result of any physics :)
13:31 < nsh> which theorem says this?
13:31 < nsh> can you derive that nothing non-classical happens at what we imagine are low velocities?
13:31 < fltrz> relativity itself says this, you can simply see the terms that involves v/c
13:31 < nsh> you think this is 3+1 dimensional air your breathing?
13:31 < nsh> :P
13:32 < fltrz> ...
13:32 < nsh> it's a thing we can construe because of the average properties of a more complex dynamics
13:32 < nsh> nothing is moving slowly
13:32 < nsh> all electrons are relativistic
13:32 < fltrz> yes, electrons
13:32 < nsh> so therefore nucleons
13:32 < nsh> trivially
13:33 < nsh> so therefore all hadronic matter
13:33 < nsh> trivially
13:33 < nsh> it's a coping mechanism. nothing is that simple
13:33 < nsh> it's simple on average
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13:33 < nsh> when you ask classical questions
13:33 < fltrz> their behavior we model and isolate in chemistry, so we use chemistry as an *effective theory* to take into account quantum mechanical effects and some relativistic effects
13:33 < nsh> obviously you get the answers that are allowable by the kinds of questions you ask
13:33 < nsh> but nothing tells you biology is interrogating or interacting with physics that way
13:33 < nsh> the cell did not have a newton
13:34 < nsh> it never invented classical mechanics
13:34 < nsh> it was using something beyond that all the time
13:34 < fltrz> its not about averaging, it's about asymptotic behavior, it's just math really
13:34 < nsh> that's more fair
13:34 < nsh> effective theories are the limits of conformal theories
13:34 < nsh> which include physical infinities or at least very large finitary values
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13:36 < fltrz> OK, suppose you have 2 quantum computers with a classical computer in between, the classical computer takes the output of the first Q computer, copies some bits of the result to overwrite some other bits of the result, and then hands this to the second quantum computer for further computation
13:36 < nsh> k
13:36 < fltrz> copying destroys coherence
13:37 < nsh> entanglement is monogamous is fairer to say
13:37 < fltrz> the new pipeline can not be used as a longer quantum computer
13:37 < nsh> so an informational cascade will make coherence difficult to see
13:37 < nsh> due to diffusion like effects
13:37 < nsh> it doesn't actually go away
13:37 < fltrz> no the coherence is destroyed
13:37 < nsh> that's just another coping mechanism
13:37 < nsh> lol
13:37 < nsh> what physics destroys it?
13:37 < nsh> wavefunction collapse is a story
13:37 < nsh> it's not physics
13:38 < nsh> it's part of the interpretation of QM
13:38 < nsh> no correlations are harmed in the making of this motion picture
13:38 < fltrz> the dissipation of the classical computer inbetween
13:39 < nsh> what classical computer?
13:39 < fltrz> the opamp for the fanout copied the voltage state onto multiple lines
13:39 < nsh> you mean the computer in a quantum reality that does very wasteful things to make it seem like oyu can copy data
13:39 < fltrz> the classical computer inbetween the 2 quantum computers
13:39 < nsh> by incredibly redundantly interpreting a lot of different modes as the same bit
13:39 < fltrz> right
13:39 < nsh> you still think there's a classical world
13:39 < nsh> there isn't
13:39 < nsh> it's just what we construe
13:40 < nsh> so a classical computer is itself working by coherence
13:40 < nsh> it's holographic.  it's just shite at it
13:40 < nsh> all of the actual electrons and holes, i think 10^6 or so per bit, are quantum mechanical and relativistic
13:41 < nsh> we just abstract over them
13:41 < nsh> maybe less than 10^6 i just pulled that out of my arse
13:41 < fltrz> nsh, can I simulate a classical computer with another classical computer?
13:41 < nsh> well, that's turing universality
13:41 < nsh> but it's a result that masks a lot of other things
13:42 < nsh> if you ignore efficiency and assume infinite tape head
13:42 < nsh> then sure
13:42 < nsh> but if you build it you're just simulating one classical computer with the quantum system you call a classical computer
13:42 < nsh> one simulation is more or less the same as another, they're all incredibly wasteful
13:42 < fltrz> would you agree that proper cellular behavior relies on cellular homeostasis?
13:43 < fltrz> cells are very resilient to perturbations thanks to homeostasis
13:44 < fltrz> all of the perturbations (of those that recover to the same homeostasis equilibrium point) well recover to the same equilibrium point
13:44 < fltrz> this is characteristic of classical systems, not quantum systems, cells require dissipation to function
13:45 < fltrz> all this is reflected in our need for food, and drive for reproduction
13:47  * nsh nods
13:47 < nsh> homeostasis is an attractor.  it's a thing you can achieve in any nonlinear system in which you can create basics of attraction and bend trajectories back towards the fit state for minor-to-moderate perturbations
13:48 < nsh> but already even despite linearity and unitarity we have quantum chaos so probably attractor systems are possible
13:48 < nsh> i haven't read much about it tbh
13:49 < fltrz> you agree that a flip flop relies on homeostasis?
13:52 < nsh> that's pushing it a little
13:52 < nsh> it relies on autopoeisis. it self-recreates its state until flipped
13:52 < fltrz> its a bistable system
13:52 < fltrz> that *is* homeostasis
13:52 < nsh> well, depends how much you wanna dilute that term :)
13:52 < nsh> but sure
13:52 < nsh> so's a toggle switch but i think the cell would get offended at the equivocation :)
13:53 < nsh> so's a coin
13:56 < fltrz> ok let me put it this way, we can use quantum mechanics to predict the evolution of a known initial state, and then we can predict the outcome of a measurement on the final state. The final state is a quantum state, but the measurement can not be predicted, neither by us nor by cells/genes/life, we can however predict the probability instead of the result itself, and these probabilities can be viewed as the classical effective theory on top of quantum
13:56 < fltrz> mechanics
13:57 < fltrz> it is these probabilities that determine the behavior of a system in a versatile and reliable way
13:57 < fltrz> it is through shaping such probabilities that we can engineer the flipflop to perform homeostasis on a voltage
13:58 < fltrz> the moment you have these probabilities you can classically describe the analog behavior of the flipflop
13:59 < fltrz> to say that not the probabilities but the exact quantum state is relevant to genetics, is to say that life relies on exact quantum states, is to say that it can predict quantum states!
13:59 < nsh> that's fine as far as it goes, but the error is assuming there is a loss of information
13:59 < fltrz> how can a thing rely on an outcome without having an expectation? that expectation would be the prediction of an exact outcome
13:59 < nsh> then a continuously evolving variable is projected along a measurement axis into a binary spin +/- state or any other
13:59 < nsh> *when
14:00 < fltrz> while we observe cells to be very resilient to perturbations
14:00 < nsh> it's not that there is a loss of information, it's that there is an underdeterminacy of coordinate frames. this is quite different
14:00 < nsh> when you have something rotating in a more abstract space and you create/construe a laboratory frame that is not determined in that abstract space of rotations then ask what is the orientation of spin
14:01 < nsh> then you will get one of two results which will seem statistical or random
14:01 < nsh> but of course the continuousness of the rotations never went awy
14:01 < nsh> you didn't reduce the information in the physics
14:02 < nsh> well, i think cells have expectations, indeed any system that is maintaining itself has and is finding its expectations met by its continued existence over time
14:02 < nsh> and when it's continued existence changes it can tend it back towards its preferred state, or rather a subspace of states that it preferences
14:02 < nsh> which we call at some level of abstraction "healthy"
14:02 < fltrz> oh we are back to the discussion of reversing scattering light through frosted glass! that works on one condition: that the scattering is *elastic*, i.e. if the light was UV, and the frosted glass is replaced with a mirror covered with semitransparent phosphors and fluorescent materials, then it will again be impossible to invert
14:03 < nsh> dunno
14:03 < nsh> half-silvered is the usual term, not frosted
14:03 < nsh> or if you're talking about the scattering
14:03 < nsh> aye, sorry
14:04 < nsh> so yeah if you have things go into inaccessible modes then you lose some fidelity of reconstruction of course
14:04 < nsh> and that's hwat happens in inelastic scatterings
14:04 < nsh> but it's still just a diffusion or a confusion phenomenon
14:04 < nsh> the information is still there in a modes of the dye molecules or whatever
14:04 < nsh> it's just taken out of the photonic EM field
14:05 < fltrz> the reason we can invert scattering through frosted glass is because it is elastic, each photon kept its original wavelength, the reason the relatively recent (few decades) result of inversion was spectacular was mostly the advance in measurement and digital storage to store large matrices
14:05 < fltrz> i.e. it was a tour de force more than a conceptual breakthrough
14:07  * nsh nods
14:14 < nsh> .wik Single-electron transistor
14:14 < yoleaux> "A single-electron transistor (SET) is a sensitive electronic device based on the Coulomb blockade effect. In this device the electron flows through a tunnel junction between source/drain to a quantum dot (conductive island)." — https://en.wikipedia.org/wiki/Single-electron_transistor
14:15 < nsh> Exploring the Influence of Variability onSingle-Electron Transistors IntoSET-Based Circuits - https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8090539
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18:28 < kanzure> nr2b memory stuff https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007486
18:28 < kanzure> "Scientists created Hobbie-J and Doogie by making them over-express CaMKII, an abundant protein that works as a promoter and signaling molecule for the NMDA receptor, something that likely could not be replicated in humans. In October 2008, they reported in Neuron that they could also safely and selectively erase old and new memories alike in mice by over-expressing CaMKII while the memory ...
18:28 < kanzure> ...was being recalled"
18:41 < kanzure> .tw https://twitter.com/eonian10/status/1102211624755068928
18:41 < yoleaux> @EricTopol @NessaCarey @guardianscience @ObserverUK Don't worry, off-target will keep it out of use for quite some time. (@eonian10, in reply to tw:1101873849006665730)
18:41 < kanzure> unsequencable dark matter on a chromosome is the main constraint prohibiting a solution to off-targets; otherwise, just use sequencing for everything else.
18:43 < kanzure> .tw https://twitter.com/wilbanks/status/1101874989865885696
18:43 < yoleaux> many / most biologists are in deep, deep denial about this type of thing. biology's physical resource requirements kept it in the academy, but it's escaping that gatekeeper pretty damn fast. https://twitter.com/EricTopol/status/1101873849006665730 (@wilbanks)
18:43 < kanzure> .tw https://twitter.com/wilbanks/status/1101876173854916609
18:43 < yoleaux> sometimes i wonder if all the stuff we do is going to be looked back on like debating how best to allocate PDP line computers, while the personal computer revolution took flight. (@wilbanks, in reply to tw:1101875945722527749)
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--- Log closed Mon Mar 04 00:00:06 2019