davi

Even low-dose ultrasound (what they use on pregnant woman) results in ultrastructural changes in brains [0], specifically at the nodes of Ranvier (the gaps between myelin along axons). See also [1] for a review.

[0] Ellisman MH, Palmer DE, André MP (1987), "Diagnostic levels of ultrasound may disrupt myelination," Experimental Neurology 98:78–92 https://pubmed.ncbi.nlm.nih.gov/3308504/

[1] Quarato, C.M.I., Lacedonia, D., Salvemini, M., Tuccari, G., Mastrodonato, G., Villani, R., Fiore, L.A., Scioscia, G., Mirijello, A., Saponara, A. and Sperandeo, M., 2023. A review on biological effects of ultrasounds: key messages for clinicians. Diagnostics, 13(5), p.855. https://pmc.ncbi.nlm.nih.gov/articles/PMC10001275/

In summer of 1997 I interned at the Santa Fe Institute. Barry McMullin was there as well, using swarm (an early cellular automata library) to reimplement and extend the original autopoiesis algorithm. His report: https://www.santafe.edu/research/results/working-papers/comp...

And a later study by him: https://pubmed.ncbi.nlm.nih.gov/15245628/

True. And this approach continues - the IARPA MICrONs program is trying to do a mm cube of mouse visual cortex: https://www.iarpa.gov/index.php/research-programs/microns

In the fruit fly, neuronal cell types are highly morphologically stereotyped and identifiable across animals. This means that for a given cell type, you can collect data on electrical synapses in animal A, on transmitters in animal B, and on electrophysiology in animal C, and in this fashion assemble a unified, multimodal view of the parts involved. Our whole brain EM volume lets you see how those parts are connected.

In the above examples dead brains are okay except for electrophysiology, where the brain needs to be alive.

Late to the party, but corresponding author on the paper here. Cool to see this on HN!

We have less than "half the picture" here. Not just weights; also missing electrical synapses, neurotransmitters, etc. We also don't know the spatial scale of neuronal arbor integration. Furthermore these are just the image data, not the complete connectome; people still have to trace circuits by hand in this dataset. Collaborators are starting to crack the segmentation problem, but it is still early days.

Necessary but insufficient class of information!

If anyone is interested you can browse the data live here:https://fafb.catmaid.virtualflybrain.org/?pid=2&zp=131280&yp...

"URL to this view" lets you share URLs to whatever you're looking at.

---- edit:

in mammals there is pretty good circumstantial evidence that post-synaptic density size correlates with evoked postsynaptic potential, but this hasn't been clearly and directly calibrated yet, and could vary from cell type to cell type

Hey cool, 3rd author Shane Gonin is now at Janelia (where my lab is) and I know a bit about this work. Funny to see it pop up here.

The kind of electron microscopy (EM) of brain tissue I do relies upon embedding the tissue in a resin called Epon. Epon has excellent cutting properties and low intrinsic contrast in EM. But in order to embed tissue in Epon it has to be completely dehydrated, which quenches genetically expressed fluorphores like GFP.

My fantasy for these genetically expressed buckyball-like proteins is that one could engineer their interior to be sufficiently hydrophilic that GFP fluorescence would survive complete dehydration of the surrounding tissue, instead relying on the polarized residues of the amino acids in the interior. This would let us combine highest quality EM with highest quality light microscopy in the same sample -- which would be very useful indeed.

"The day will come when David Bowie is a star and the crushed remains of his melodies are broadcast from Muzak boxes in every elevator and hotel lobby in town."

- Nancy Erlich, July 11 1971 New York Times (http://timesmachine.nytimes.com/timesmachine/1971/07/11/9130...)

Whups, forgot the email in my HN profile isn't visible, and now too late to edit the post; here are some links:

- website & email: https://www.janelia.org/lab/bock-lab; bockd@janelia.hhmi.org

- more on our approach to electron microscopy: http://reid.med.harvard.edu/pdf/Bock-Lee-etal-Reid-2011-Natu...; http://reid.med.harvard.edu/pdf/Bock-Lee-etal-Reid-2011-Natu...

Bock lab, Janelia research campus, Howard Hughes Medical Institute (HHMI) | Ashburn, VA | ONSITE

Data scientist / Neurogeometer

We recently finished acquiring an electron microscopy dataset encompassing the entire brain of a fruitfly (120 million images, 115 TB on disk, voxel size 4 x 4 x 40 nanometers). A team of tracers is manually skeletonizing portions of this animal's nervous system, and we are starting to see interesting circuit motifs emerge.

We are looking for someone to help build and use tools supporting this analysis (neurogeometry), as well as help wrangle the millions of images continuing to flow from our three microscopes (~500 TB of primary image data anticipated in the next two years). During this time we expect to switch from RAID-based file systems to an object store (likely Scality), with substantial support from a team at Janelia outside the lab.

Desirable attributes:

- Education: B.S. or M.S. in Computer Science or related field (or an equivalent in education and experience)

- Strong familiarity with Linux, including command line wizardry and detangling dependency nightmares

- Proficient in Python and at least one other programming language (e.g Java or C/C++)

- Experience with utilizing SQL and/or NoSQL data stores (e.g. MongoDB, PostgreSQL, Microsoft SQL Server)

- Experience with image processing (ImageJ, SciPy, Matlab, OpenCV, etc.)

- Comfortable working with new programming languages and tools when necessary

- Familiar with RESTful web services

- Experience using an HPC cluster (MPI, SGE/OGE, Spark, etc.)

- Follows current trends in industry and academia

- Willing to get hands dirty with hardware

- Ability to concentrate in a fast paced and dynamic environment

- Ability to communicate effectively, orally and in writing

- Ability to take initiative, prioritize tasks, use good judgement and monitor completion of assigned duties.

- Experience or strong interest in working in an interdisciplinary environment.

Classic quote: “Harald is much smarter,” Betzig said. “When I left Bell Labs, I said ‘fuck you.’ When Harald left, he took all his equipment.”

I wrote about this here five and a half years ago, before it went "sour so quickly": https://news.ycombinator.com/item?id=470181

As a grad student back then, I saw a pyramid scheme. Training programs were (and are) funding way more students than there is room at the top. If funding at the top level stops expanding, the current scenario unfolds.

If I have undergrads in my lab who want to go on to graduate school, I give them sufficient information on these numbers that they can provide "informed consent". If they still want to go ahead, they receive my full support.

Given the hosts and the venue, the best topic to bring up could be software patent reform. This is something pg has written about in the past [0] -- I wouldn't be surprised to learn this issue is the driving reason for hosting the dinner.

[0] http://paulgraham.com/patentpledge.html

Fascinating idea: insane society-scale bureaucracies make puzzle solvers out of everyone.

Sokoloff was Russian, born and raised in a city on the Volga River. He had an explanation for why so many of his countrymen wound up in high-frequency trading. The old Soviet educational system channeled people into math and science. And the Soviet-controlled economy was horrible and complicated but riddled with loopholes, an environment that left those who mastered it well prepared for Wall Street in the early 21st century.

“I don’t know what they think I do,” Minsky said. “I make up theories of how the mind works and when I’m lucky enough, I have some students who make careers out of that.”

As a guy with a lab, the idea of thinking of how the mind works from time to time and then having students make a career of that idea is fairly humbling.

the availability of energy to the individual almost exactly correlates with economic growth

A corollary might be that the more energy available per capita, the greater the environmental footprint of per capita. E.g. the McMansions of the megasprawl: rolling hills of former farmland are graded and leveled off, enormous balloon-like, energy inefficient stick frame houses pop up, and twice a day their inhabitants wait in lines of SUVs on the clogged roads between the exurbs and the suburban office parks. The entire enterprise is completely dependent on vast quantities of energy being available to participants in the system. People are comfortable in their SUVs and McMansions, and aspire to this lifestyle. But the environmental footprint per capita is enormous. Without some penalty for the external costs (which are long latency and hard to measure), there is nothing to slow the spread of this pattern of economic development.

In this light, when you say:

Energy very well may be the 20th century's internet. The more everybody has it, the better off we all are.

I suspect it is more like an upside-down U-shaped curve. People are indeed better off when we have sufficient energy per capita, but when we have a massive superabundance of energy, we negatively affect our environment to the point that real consequences start to kick in. Unfortunately, it is hard to know where we are on that upside-down U, and it is hard (impossible?) to distinguish overwrought hand-wringing about impending environmental doom from the real thing, until the real thing has started to have obvious, severe, and sustained effects.

Am I anything more than a junkie seeking the ultimate fix? I don’t know. I may never know. I’m committed though.

Good line. Feel the same way in science, sometimes.

This reminds me a lot of Ars Digita's bootcamp (http://philip.greenspun.com/teaching/boot-camp, which I attended, back in the day. It's up there amongst the more interesting experiences of my life).

Except that instead of being a recruitment mechanism for the host company, it is an environment to give people skills and match them up with external companies, and in return get a referral fee.

Really a good idea; I wonder if it is scalable. They will have to figure out a way to assess coding ability objectively?

Ashburn, VA/Heidelberg, Germany

Scientific Software Developer

http://hci.iwr.uni-heidelberg.de/Jobs/

Ilastik (http://ilastik.org) is a collaborative open-source project with the aim of providing a scalable image analysis platform for the neurosciences and beyond. Current ilastik development seeks to bring the power of interactive machine learning to very large data sets.

Janelia Farm (http://www.janelia.org), one of the premier centers for biomedical research worldwide, is funding a Scientific Software Developer (Janelia Farm Research Campus, Ashburn, VA with visits to Heidelberg University, Germany) to reach that goal quickly. Tasks include the refinement of the architecture, the integration with existing tools and the design of a graphical user interface for handling of very large microscopic data sets using image analysis and machine learning algorithms. The software developer will also support proof-of-principle studies on pioneering applications from the neurosciences, and liaise between experts at Janelia Farm and ilastik core developers at the University of Heidelberg.

The position requires a strong background in C++, experience in software engineering applied to large projects, and the skills to integrate existing algorithms and functionality into a unifying biomedical processing framework. Experience with python, Qt, numpy, scipy and scientific parallel programming is a plus. Good communication skills are essential to make for good cooperation both with local experts and with other programmers working remotely. Salary is commensurate with prior experience and will be highly competitive for extremely well-matched candidates.

The principal work place is on the beautiful campus of Janelia Farm, with regular visits to Heidelberg. The successful candidate will be in a position to help shape a project that is becoming an enabling technology in one of the most interesting fields conceivable: the deciphering of the inner workings of the brain.

see also:

http://janelia.org/, http://www.hhmi.org/research/fellows/bock.html

good and non-obvious (at the time) advice, at the end: "Whatever name you choose, be careful. Names stick."

With a color lookup table: http://davibock.net/111025_quasicrystals/l3LL3_colorized.gif

Full interview audio available on linked page. Topics:

- NeXT WebObjects and dynamic web programming

- Visit to Xerox PARC

- Difference of Apple from other companies

- NeXT lessons learned

- First computer Jobs used

- Meeting Woz and starting Apple

- Being ousted from Apple

- Apple's current (1996) problems

- Work/life balance

- Pixar

etc.

watch 'til the end, Woz chokes up (and made me do the same)

I think the idea is that different categories of science might occur at different scales of funding.

50 junior faculty will likely do 50 safe-ish projects which will lead to tenure. 1 senior faculty with 25 million dollars might do something qualitatively different: ambitious, risky, long-term. Or might not, no guarantee. But I think it's a valid exploration of parameter space.

The goal is to make great science happen, not fund the maximum number of scientists.

I subscribe to the Disposable Soma theory of aging. http://medicine.jrank.org/pages/1758/Theories-Biological-Agi... [1]

In this scheme cancer is just one example of the balance between somatic maintenance and reproduction rate.

[1] The disposable soma theory of aging predicts that species and cohorts in a population expecting, on average, to have high survival and low reproductive rates should invest more heavily in protecting their somas than species and populations that expect a short lifespan and to reproduce rapidly

To that extent, the answer to the OP's question is likely "See the essays I've written since Hackers and Painters came out."

1. [2001]

2. What he's up to these days: http://blogs.law.harvard.edu/philg/

3. One specific is helping with patent litigation (see comments at http://blogs.law.harvard.edu/philg/2011/08/16/anyone-have-a-...)

I think of certain quiet people I know as having high signal-to-noise. When they start to emit, I listen carefully, because my attention will be rewarded with lots of signal per unit time.

There is a new field of extracting wiring diagrams from brains at the level of individual neurons. This is what I work on.

http://openconnectomeproject.org has some introductory material. (This is not my site, it is by some people at JHU who picked up our data set and are working on it.) Massive image data sets, lots of need to develop workflow. You can browse the image data here: http://openconnectomeproject.org/catmaid/?pid=4&zp=40635...

Concretely, look at the plugins being developed by the Fiji project and pitch in, especially on the electron-microscopy-centric plugins: http://pacific.mpi-cbg.de/wiki/index.php/Category:Plugins

edit: also think about contributing to the CATMAID project, which is the software serving the browsable data set above, and perhaps will someday enable crowd-sourced markup: http://fly.mpi-cbg.de/~saalfeld/catmaid/

What are some examples of "seat belt" and "airbag" changes you see shops making?

You give some good feedback but maybe you could have struck a stance of, "Hey, do you know you could be alienating a large fraction of your readers with the style of your job posting? Here is why."

These guys are trying to do a startup. It's a hard thing to do. Why grouse at them? Perhaps their posting is unprofessional because they are unprofessional, in the sense of not having had lots of professional experience yet. Maybe cut them some slack instead instead of increasing the concentration of venom in the commons.