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A.I. and Gene Regulation December 27, 2019

Posted by stuffilikenet in Applications, Brain, Geek Stuff, Mutants, Science.
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Understanding gene regulation is a bitch. Seriously, this is one of the thornier problems of science today and it is because the complexities of living cells, with the thousands of proteins in each cell, make tracing a single protein’s regulation just as complex as hell. Smart guys Tareen and Kinney have figured out a way for AI to interpret (some) interactions using massively-parallel reporter assays to figure out the biophysical basis for (some) gene regulation…which is more than we have had heretofore. They did this by assigning nodes and weights with explicit physiochemical interpretations. This last is the important bit; many AI algorithms are very difficult to interpret, so the underlying “logic” is impenetrable to humans.  The smart guys made many of the decisions explicit, so they would be better able to understand the “logic” by which the characterizations were derived.

 

 

Homework: Biophysical models of cis-regulation as interpretable neural networks, Ammar Tareen, Justin B. Kinney BioRxiv,

Nanowired Brain-like Functions December 25, 2019

Posted by stuffilikenet in Awesome, Brain, Mutants, Science.
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Nation Institute of Material Science geeks have created a complex metallic nanowire structure that mimics brain-like functions, such as memorization, learning, forgetting, becoming alert and returning to calm.

"figure: (a) Micrograph of the neuromorphic network fabricated by this research team. The network contains of numerous junctions between nanowires, which operate as synaptic elements. (b) A Human brain and one of its neuronal networks." Image

This indicates that self-organizing structures can be built from random arrangements of conducting fibers. This suggests that many different types of brain-like activity can be induced from stuff other than the kind of materials from which you and I are made.
Intelligent life on other worlds might be made of very different stuff indeed.

 

Homework: “Emergent dynamics of neuromorphic nanowire networks” by Adrian Diaz-Alvarez, Rintaro Higuchi, Paula Sanz-Leon, Ido Marcus, Yoshitaka Shingaya, Adam Z. Stieg, James K. Gimzewski, Zdenka Kuncic and Tomonobu Nakayama, 17 October 2019, Scientific Reports.
DOI: 10.1038/s41598-019-51330-6

Chemistry Class Graduation Photo December 24, 2019

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Multi-dimensional Blood Testing and A.I. December 23, 2019

Posted by stuffilikenet in Applications, Awesome, Brain, Brilliant words, Geek Stuff, Science, Star Trek Technology.
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I suggested long ago that sufficiently-comprehensive blood tests could effectively predict a person’s risk of developing a broad array of different diseases. We would use artificial intelligence to find patterns of varying concentrations of blood proteins to predict and/or diagnose disease. Someone much better funded than me has a newly developed platform called SomaScan which can scan five thousand individual proteins from a single blood sample.

In a new study testing the efficacy of predicting 11 different health indicators using these protein expression patterns some models were much more effective than others, such as the protein expression model predicting percentage body fat. The cardiovascular risk model was cited as only modestly predictive, however, the researchers do suggest the protein-pattern-based system is generally more convenient, and cheaper, than many traditional tests currently available for evaluating health conditions.

The study in Nature Medicine was funded by SomaLogic which owns SomaScan, so grain of salt, people. But it’s exciting to see that someone is actually looking into what I feel will be the method of the future for maximizing health…also, the study used ~85 million protein measurements in 16,894 participants, which is a pretty damn good sample size.  Plenty of data there for an A.I. to examine for hidden relationships.

Homework:

Plasma protein patterns as comprehensive indicators of health, Nature Medicine, Stephen A. Williams, Mika Kivimaki, Claudia Langenberg, Aroon D. Hingorani, J. P. Casas, Claude Bouchard, Christian Jonasson, Mark A. Sarzynski, Martin J. Shipley, Leigh Alexander, Jessica Ash, Tim Bauer, Jessica Chadwick, Gargi Datta, Robert Kirk DeLisle, Yolanda Hagar, Michael Hinterberg, Rachel Ostroff, Sophie Weiss, Peter Ganz & Nicholas J. Wareham

The Everything Box, by Richard Kadrey December 23, 2019

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The Everything Box, by Richard Kadrey is a macguffin chase done in neo-noir style with snappy dialogue and pretty unique characters..except they are all kind of snappy dialoguers. That’s a minor quibble and you don’t even notice it as the book hums along with charm, wit, pathos and a bit of terror tossed in for fun. The macguffin is stolen not once, not twice, not three times but four (tying with The Hot Rock’s record for ripped-off treasure). Problem is, this particular macguffin is an apocalypse engine lost by an angel right after The Flood, and being hunted by, well, everyone: gangsters, a fake Russian, two rival demon cults, The Government and probably others I have forgotten[0]. Along the way the burglar (our hero) meets, fights, partners with or robs a Caspar Gutman sort of character, a dragon, thousands of enchanted spiders, a frightened ghost, two mind-clouding women, a magical locksmith, the deedholder to Earth, the angel who lost the macguffin in the first place, vampires, werewolves, tentacle monsters from hell (by which I mean The Government), demonic pets, a revenant and a particularly unpleasant government operative.[1]

Very entertaining read, and admirably read as audiobook. The narrator gets the dialogue just right.

At Amazon, but I got mine at sfpl.org.

 

[0] Just kidding.  I think that’s all of them.

[1] I am not at all sure I mentioned everybody.

Two-headed Bearded Dragon December 23, 2019

Posted by stuffilikenet in Awesome, Mutants, Photography.
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Enchanting Furby Toy Hack December 20, 2019

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Toys.
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I do wish I had thought of this.

Sacre Blue, by Christopher Moore December 19, 2019

Posted by stuffilikenet in Awesome, Books, Brilliant words.
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Sacré Bleu is the story of a muse, her enslaver, several Impressionist painters, multiple murders, syphilis, spelunkery, immortality, immolation and the possibly gratuitous use of the word “penis”. As with all Christopher Moore works, it has a hint of mythology which forms the center of the narrative but take off quickly from such staid constraints to a flighty soufflé featuring Henri Toulouse-Latrec as a detective hunting an impossibly ancient shaman (immolation comes into play here).

It’s hilarious. Amazon, or sfpl.org

Octobrella December 11, 2019

Posted by stuffilikenet in Awesome, Mutants, Octopus, Photography, Publishing Tools.
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Purloined from reddit.

Moore’s Law, and Progress December 11, 2019

Posted by stuffilikenet in Awesome, Brilliant words, Geek Stuff, Video.
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An Accelerated Pace of Change

Moore’s Law has translated into a faster rate of change for society as a whole.

A new idea, like the smartphone, can get immediate traction because of instantaneous communication, increased global connectivity, and the ubiquity of information. New tech advancements can now change business or culture in a heartbeat:

The accelerating rate of technology adoption

Further, since software is a “layer” built upon the foundation of computing, it means that digital products can be replicated at almost no marginal cost. This is why a phenomenon like Pokémon Go was able to captivate 50 million users in just 19 days.

Imagine this kind of scalability, when applied to things like artificial intelligence or virtual reality.

–stolen freely from Visual Capitalist. I’m sure they’ll ask me to take it down soon. But look at the possibilities, people!

Catfishing on Catnet, by Naomi Kritzer December 9, 2019

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This piece of classic AI fiction is unusual in that the AI is not evil. S/he/it/they [insert politically-corrected grammar item here] is an empathetic intelligence that also likes cat pictures (an obvious sign of empathy and sentience). The AI is involved in fugitive children, gender discussions, assault with a deadly weapon, murder, robot rampage and gratuitous cat pictures and is unrepentant about most of it.
Great fun. I read it straight through. I am a little bit old for the target demographic for this one (by about fifty years), but loved it like twelve-year-old me would have. Highly recommended.

Available on Amazon, but not yet on sfpl.org

Meanwhile, at Hydra HQ November 10, 2019

Posted by stuffilikenet in 3D Printing, Mutants, Octopus, Toys.
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Moby Duck November 9, 2019

Posted by stuffilikenet in Awesome, Toys, Uncategorizable.
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IMG_20190630_161313250_HDR.jpg

That sucker is five feet long, children. Suitable for adults of all childish ages.

Capable Modular Robots November 9, 2019

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Science, Star Trek Technology, Toys, Video.
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 MIT’s Computer Science and Artificial Laboratory’s M-Block robots can self-assemble into different structures. The little cubes (in development over the last six years) have gained the ability to jump, flip, spin, and recognize each other. A barcode-like system on each face of each cube, allowing them to identify the other cubes around them.

The engineers wanted to see if the M-Blocks could (for example) form a straight line or form a random structure using the new communication algorithms. They waited to see if the blocks could determine how they were connected, and then what direction they would need to move to create that line. They found that 90% of the block swarm knew which motion and guidance to move to accomplish the task. I’m curious to know what the other 10% did…

Engineers hope to create a more substantial swarm of blocks (>16) that can assemble to form more complex structures with new capabilities.

3D Scanning to Print (Photogrammetry) October 8, 2019

Posted by stuffilikenet in 3D Printing, Applications, Awesome, Geek Stuff, Photography, Publishing Tools, Star Trek Technology.
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Due to an unfortunate incident while moving from the ver parted lips of Hell (Greenville, CA) I have had to replace a few parts on my Casio CDP-120 piano keyboard. Basically, the highest key (C for those who need to know) was/is smashed and needs a replacement. Aha! I have this iPrusa printer and can whip up a new key post-haste using
Fusion360 to measure and design a new key.  Right?

No. It’s a part with surprisingly complex geometry, so I thought I would try photogrammetry to create a model and see how that works.  I never tried this before, so what could it hurt? Can’t be any harder than Fusion360 to master. Right?

No. There seems to be no (free as in beer) software which can do this which is simple enough for me to install (grumble, grumble) on this company Mac, and I’m not sure company policies built into the security suite on this company Mac would permit it (grumble, grumble) anyway. Since my replacement Windows box isn’t here yet (grumble, grumble) I have to pay for a cloud-based solution…Altizure.com.  So I took 56 pictures of the C key an octave down with my cellphone camera, submitted them to Altizure.com‘s loving embrace and was rewarded with a fairly competent render of my key:

Screen Shot 2019-10-08 at 11.06.36 AM.png

I say “fairly competent” because it has lots of hole in the sides.  No matter; I can probably fix it in software modify it in Fusion360 to fill in the holes.  I will likely need to use Fusion360 to get the dimensions useably correct in any case.

Now I have to steel myself to pay the subscription rate of something like $70 per project. It would be worth it if I was a company making a prototype with great prospects for the future…but I’m not (grumble, grumble).

The key costs about five bucks from Casio’s parts subcontractor, plus six or so to ship it. I know which I am going to choose.

It’s a shame, really; I was looking forward to monkeying around with it. Maybe next time.

However, I don’t give up easily; I got 3DF Zephyr and used the (limited to) 50 pictures in it at the highest defaults in the wizard to create this render:

c-key-3df zephyr

My army of loyal and discerning readers may notice a bit of degradation here and there…yeah.  I will try again, but this took an hour or so and was NOT automatically rendered, but went through stages. In all fairness it would have been shorter if my graphics card had CUDA…but I don’t have a graphics card, just whatever Lenovo thought was cheap but still enough to get by on. Still, it needs work, and it’s midnight.  Possibly updates to follow, if I get any sleep.

EXCITING UPDATE:

I got a better render with 50 pictures and the most extreme settings I could figure out:

c-3df-zephyr-2-extra tasty

It’s got the holes that Altizure’s render had, but 3DF Zephyr is free to use.  Now I have to figure out how to make the save-able form of this (an .obj file) into an .slt and thence to gcode. With luck, I will have a hideous key to use before my real one arrives.

 

 

 

Exhalation, by Ted Chiang October 2, 2019

Posted by stuffilikenet in Books, Brilliant words.
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A most exhilarating collection of short stories by Mr. Chiang, Exhalation has several completely captivating stories, both in concepts and characters. In one, an archeologist/paleontologist in a Biblically-literal world discovers that their Earth is not the center of the universe, throwing her into a crisis of confidence of, yes, Biblical proportions. In another, a father’s memory is supplemented with electronics and allows him to review his relationship with his daughter, throwing him into a crisis of conscience. In a third, quantum mechanics/many worlds dopplegangers find ways to communicate with highly mixed results.

There are more, but this should be enough to whet your appetite. Link above goes to Amazon, but sfpl.org has it also.

Potential MRSA Treatment August 15, 2019

Posted by stuffilikenet in Awesome, Science.
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Scientists from UNC (North Carolina, not Northern Colorado) School of Medicine, in a study published in Cell Chemical Biology, found just adding molecules called rhamnolipids to aminoglycoside antibiotics, such as tobramycin,

Tobramycin.svg

makes them hundreds of times more potent against Staphylococcus aureus, including the strains that are otherwise very hard to kill.

We’re talking about MRSA here, folks.  This is a big damned deal. CDC says there were 119,000 cases of serious bloodstream Staph infections in the United States in the last year for which data is available (2017), of which more than 20,000 were fatal.

Take time to process that.

These rhamnolipids effectively loosen up the outer membranes of S. aureus cells so that aminoglycoside molecules can get into them more easily. In a new study, Conlon, Radlinski and colleagues tested rhamnolipid-tobramycin combinations against S. aureuspopulations that are particularly hard to kill in ordinary clinical practice. The researchers found that rhamnolipids boost tobramycin’s potency against:

  • S. aureus growing in low-oxygen niches;
  • MRSA (methicillin-resistant S. aureus), which are a family of dangerous S. aureus variants with genetically-acquired treatment resistance;
  • tobramycin-resistant S. aureus strains isolated from cystic fibrosis patients;
  • and “persister” forms of S. aureus that normally have reduced susceptibility to antibiotics because they grow so slowly.

They found this effect works in related families of antibiotics including gentamicin, amikacin, neomycin, and kanamycin, for the same reason and on Clostridioides difficile, which is a bit of a killer in its own right.

 

Homework:

Chemical Induction of Aminoglycoside Uptake Overcomes Antibiotic Tolerance and Resistance in Staphylococcus aureus; 

Giggling Maniac with Gatling Gun July 16, 2019

Posted by stuffilikenet in 3D Printing, Awesome, Geek Stuff, Toys, Uncategorizable, Uncategorized.
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It’s lovely what you can do with 3D printers. It is, of course, best illustrated by a cackling madman with a Gatling Gun.

 

EXCITING UPDATE: I tend to forget the excellent work done in a related space by Jeorg Sprave, a happy German fellow who specializes in rubber-driven devices for impelling various projectiles:

As the video shows, he is also a giggling maniac, just this time with an electric fully-automatic crossbow.

Pandoc Conversion to Markdown July 15, 2019

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pandoc -s example.docx -t markdown -o example.md

 

For converting from MS .docx to .md files in a hurry.  I usually do this manually, but file bigness.

Oh, crap. July 15, 2019

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EXCITING UPDATE:

triceratops-femur.jpg