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ref: -2018 tags: Michael Levin youtube talk NIPS 2018 regeneration bioelectricity organism patterning flatworm date: 04-09-2019 18:50 gmt revision:1 [0] [head]

What Bodies Think About: Bioelectric Computation Outside the Nervous System - NeurIPS 2018

  • Short notes from watching the video, mostly interesting factoids: (This is a somewhat more coordinated narrative in the video. Am resisting ending each of these statements with and exclamation point).
  • Human children up to 7-11 years old can regenerate their fingertips.
  • Human embryos, when split in half early, develop into two normal humans; mouse embryos, when squished together, make one normal mouse.
  • Butterflies retain memories from their caterpillar stage, despite their brains liquefying during metamorphosis.
  • Flatworms are immortal, and can both grow and contract, as the environment requires.
    • They can also regenerate a whole body from segments, and know to make one head, tail, gut etc.
  • Single cell organisms, e.g. Lacrymaria, can have complex (and fast!) foraging / hunting plans -- without a brain or anything like it.
  • Axolotl can regenerate many parts of their body (appendages etc), including parts of the nervous system.
  • Frog embryos can self-organize an experimenter jumbled body plan, despite the initial organization having never been experienced in evolution.
  • Salamanders, when their tail is grafted into a foot/leg position, remodel the transplant into a leg and foot.
  • Neurotransmitters are ancient; fungi, who diverged from other forms of life about 1.5 billion years ago, still use the same set of inter-cell transmitters e.g. serotonin, which is why modulatory substances from them have high affinity & a strong effect on humans.
  • Levin, collaborators and other developmental biologists have been using voltage indicators in embryos ... this is not just for neurons.
  • Can make different species head shapes in flatworms by exposing them to ion-channel modulating drugs. This despite the fact that the respective head shapes are from species that have been evolving separately for 150 million years.
  • Indeed, you can reprogram (with light gated ion channels, drugs, etc) to body shapes not seen in nature or not explored by evolution.
    • That said, this was experimental, not by design; Levin himself remarks that the biology that generates these body plans is not known.
  • Flatworms can sore memory in bioelectric networks.
  • Frogs don't normally regenerate their limbs. But, with a drug cocktail targeting bioelectric signaling, they can regenerate semi-functional legs, complete with nerves, muscle, bones, and cartilage. The legs are functional (enough).
  • Manipulations of bioelectric signaling can reverse very serious genetic problems, e.g. deletion of Notch, to the point that tadpoles regain some ability for memory creation & recall.

  • I wonder how so much information can go through a the apparently scalar channel of membrane voltage. It seems you'd get symbol interference, and that many more signals would be required to pattern organs.
  • That said, calcium is used a great many places in the cell for all sorts of signaling tasks, over many different timescales as well, and it doesn't seem to be plagued by interference.
    • First question from the audience was how cells differentiate organismal patterning signals and behavioral signals, e.g. muscle contraction.

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ref: -0 tags: third harmonic generation Nd:YAG pulsed laser date: 08-29-2015 06:44 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

Problem: have a Q-switched Nd:YAG laser, (flashlamp pumped, passively Q-switched) from ebay (see this album). Allegedly it outputs 1J pulses of 8ns duration; in practice, it may put several 100mJ pulses ~ 16ns long while the flashlamp is firing. It was sold as a tattoo removal machine. However, I'm employing it to drill micro-vias in fine polyimide films.

When focused through a 10x objective via the camera mount of an Leica microscope, 532nm (KTP doubled, second harmonic generation (SHG)) laser pulses both ablates the material, but does not leave a clean, sharp hole: it looks more like 'blasting': the hole is ragged, more like a crater. This may be from excessive 1064nm heating (partial KTP conversion), or plasma/flame heating & expansion due to absorption of the 532nm / 1064nm light. It may also be due to excessive pulse duration (should the laser not actually be q-switched... photodiode testing suggests otherwise, but I'd like to verify that), excessive pulse power, insufficient pulse intensity, or insufficient polyimide absorption at 532nm.

The solution to excessive plasma and insufficient polyimide absorption is to shift the wavelength to 355nm (NUV) via third harmonic generation, 1064 + 532 = 355nm. This requires sum frequency generation (SFG), for which LBO (lithium triborate) or BBO (beta-barium borate) seem the commonly accepted nonlinear optical materials.

To get SHG or THG, phase and polarization matching of the incoming light is critical. The output of the Nd:YAG laser is, I assume, non-polarized (or randomly polarized), as the KTP crystal simply screws on the front, and so should be rotationally agnostic (and there are no polarizing elements in the simple laser head -- unless the (presumed) Cr:YAG passive Q-switch induces some polarization.)

Output polarization of the KTP crystal will be perpendicular to the incoming beam; if the resulting THG / SFG crystal needs Type-1 phase matching (both in phase and parallel polarization), will need a half-wave plate for 1064nm; for Type-II phase matching, no plate is needed. For noncritical phase matching in LBO (which I just bought), an oven is required to heat the crystal to the correct temperature.

This suggests 73C for THG, while this suggests 150C (for SHG?).

Third harmonic frequency generation by type-I critically phase-matched LiB3O5 crystal by means of optically active quartz crystal Suggests most lasers operate in Type-1 SHG, and Type-II THG, but this is less efficient than dual Type-1; the quartz crystal is employed to rotate the polarizations to alignment. Both SHG and THG crystals are heated for optimum power output.

Finally, Short pulse duration of an extracavity sum-frequency mixing with an LiB3O5 (LBO) crystal suggests that no polarization change is required, nor oven control LBO temperature. Tight focus and high energy density is required, of course (at the expense of reduced crystal lifetime). Likely this is the Type-1,Type-II scheme alluded to in the paper above. I'll try this first before engaging further complexity (efficiency is not very important, as the holes are very small & material removal may be slow.)

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ref: work-0 tags: Cohen Singer SLIPPER machine learning hypothesis generation date: 10-25-2009 18:42 gmt revision:2 [1] [0] [head]

http://www.cs.cmu.edu/~wcohen/slipper/

  • "One disadvantage of boosting is that improvements in accuracy are often obtained at the expense of comprehensibility.
  • SLIPPER = simple learner with iterative pruning to produce error reduction.
  • Inner loop: the weak lerner splits the training data, grows a single rule using one subset of the data, and then prunes the rule using the other subset.
  • They use a confidence-rated prediction based boosting algorithm, which allows the algorithm to abstain from examples not covered by the rule.
    • the sign of h(x) - the weak learner's hyposthesis - is interpreted as the predited label and the magnitude |h(x)| is the confidence in the prediction.
  • SLIPPER only handles two-class problems now, but can be extended..
  • Is better than, though not dramatically so, than c5rules (a commercial version of Quinlan's decision tree algorithms).
  • see also the excellent overview at http://www.cs.princeton.edu/~schapire/uncompress-papers.cgi/msri.ps