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How Statistics Can Predict the Future November 10, 2016

Posted by stuffilikenet in Brilliant words, Geek Stuff, Science.
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The X Axis on the graph is the percentage of GDP spent on R&D and the size of the balls is the amount of spending. The Y Axis is the scientists and engineers per million people.

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Notice that the 2nd, 3rd, 5th and 6th largest amounts are spent by Asian countries.  And notice that Sweden, Denmark, Norway, Singapore and Finland have the largest number of scientists per capita, but look at the volume of South Korea and the number of scientists…those guys are going to eat the world.

Excuse me; I have to go buy a Samsung phone.

Better Neutrino Detection Through Beta Decay November 9, 2016

Posted by stuffilikenet in Awesome, Geek Stuff, Japan, Science, Toys.
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Once upon a time scientists studying the sun couldn’t have the faintest idea of the internal activity of the Sun. One bright (see what I did there) scientist realized that monitoring neutrinos, the massless, chargeless, non-interacting particles that zip through the universe barely interacting with anything at all, might give a useful clue to the machinations therein.  I mean, they knew neutrinos are part of the solar flux,so it’s just a matter of detecting massless, chargeless, non-interacting particles.

Oh, crap.

Well, luckily neutrinos do not remain neutrinos forever; they decay into detectable particles…eventually.  Not often to be sure, as billions pass through a square centimeter every second without leaving any decay particles. Those decay particles can be detected with rather elaborate photomultipliers in a huge cavern in Japan somewhere: “It consists of a tank filled with 50,000 tons of ultra-pure water, surrounded by about 13,000 photo-multiplier tubes. If a neutrino enters the water and interacts with electrons or nuclei there, it results in a charged particle that moves faster than the speed of light in water. This leads to an optical shock wave, a cone of light called Cherenkov radiation. This light is projected onto the wall of the tank and recorded by the photomultiplier tubes.1“ Despite the heavy hardware only a few thousand are detected every year, which should tell you something about the likelihood of a decay event…not very damn likely.

Thing is, the theoretical number and the actual number didn’t match; the experimental result was one-third of theoretical, indicating something must be wrong with the theoretical understanding, or the experiment is crap. It turned out that neutrinos oscillate among three forms (electron, muon and tau) and detectors were primarily sensitive to only electron neutrinos.

Here’s where science gets really intricate; pour another shot and I’ll tell you why. In a distantly-related field, other scientists observed variations in the rate of beta decay of radioactive elements.  Once again, either the data is crap or the theory, and the theory says the decay rate should be constant.  Looking at the data over time, they found that the beta-decay rate matched the neutrino data, indicating a one-month oscillation attributable to solar radiation. Many now believe that neutrino emissions from the Sun are somehow affecting beta decay.

If that’s not strange enough for you then feature this: the same guys who figured this out are going to use beta-decay experiments here on Earth to monitor massless, chargeless, non-interacting neutrinos, and thereby the Sun.

 

1. Sometimes I don’t feel like writing all that much.  It is 11:30p.m. and I’m tired. Sue me.

Homework:  P. A. Sturrock et al. Comparative Analyses of Brookhaven National Laboratory Nuclear Decay Measurements and Super-Kamiokande Solar Neutrino Measurements: Neutrinos and Neutrino-Induced Beta-Decays as Probes of the Deep Solar Interior, Solar Physics (2016). DOI: 10.1007/s11207-016-1008-9

Brain-Computer Interface Restores Locomotion November 9, 2016

Posted by stuffilikenet in Awesome, Brain, Science, Star Trek Technology, Toys.
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You heard me. Watch the video and be amazed.

The researchers think it could be ready for human trials by the end of the decade.

If it sounds familiar, it might be because Star Trek thought of it first:

Image result for spock's brain

Homework: Capogrosso, Marco, Milekovic, Tomislav, et. al, A brain–spine interface alleviating gait deficits after spinal cord injury in primates, Nature

もっと枝豆ください November 3, 2016

Posted by stuffilikenet in Awesome, Mutants, Science.
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Scientists at Washington State University have kicked up soybean yields 36% by increasing the number of genes coding for nitrogen-transporting proteins. They also believe the genetically-modified soybean plants may be drought-resistant and probably other stressors as well.

Soybeans have a unique ability to fix nitrogen from the air, rather than from their roots due to a symbiotic relationship with the bacteria rhizobia (Gram-negative, motile, non-sporulating rods).  This happy partnership will make my edamame appetizer in the local sushi parlor more profitable for the restaurant and me able to drink more beer with it.1  : )

 

1. Science really is the servant of man, isn’t it?

Homework:  Carter, Amanda M. and Tedeger, Mechthild. Increasing Nitrogen Fixation and Seed Development in Soybean Requires Complex Adjustments of Nodule Nitrogen Metabolism and Partitioning Processes, Current Biology Volume 26, Issue 15, 8 August 2016, Pages 2044–2051.,

Is it a Mutant if it’s Perfectly Adapted? November 3, 2016

Posted by stuffilikenet in Awesome, Mutants, Science.
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The bacteria Candidatus Desulforudis audaxviator has been discovered two miles  beneath the surface of the Earth in a gold mine in SouthAfrica.  It’s warm down there; a balmy 60 °C and completely devoid of light and oxygen.

D. audaxviator lives alone, without light or oxygen 2.8 kilometres down inside a South African goldmine

Being too far from light and oxygen has only made the little fellow more hardy; he seems to subsist on radioactive decay of uranium (sound familiar?) instead of grubbing for photosynthesis…or even eating other bacteria. Yes, in the water-filled cracks in which D. audaxviator lives, there are no other bacteria.

That’s right; no food at all. Sure, it has genes to extract carbon from dissolved carbon dioxide and other genes to fix nitrogen, which comes from the surrounding rocks, but that’s enough for this tough little bugger to synthesize all the amino acids it needs to grow and thrive.

It’s not the Andromeda Strain, though; oxygen will kill it—and it hasn’t seen oxygen for three million years, which give scientists (and even me) some idea of how old this strain must be.

The Homemade Muon Detector October 15, 2016

Posted by stuffilikenet in Awesome, Geek Stuff, Science, Star Trek Technology, Toys.
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Dazzling in complexity, the little chart above details the fate of cosmic rays (high-energy protons hurtled from the sun) which impact our atmosphere, leaving a byzantine collection of particles and EM emissions.  Some of these suckers are relatively easy to detect; the muon possibly the easiest.  Scientists studying the output of our sun can use more information about cosmic ray bombardment and an array of muon detectors would be really useful for this as muons (and other particles) are generated within a cone-shaped shower, with all particles staying within about 1 degree of the primary particle’s path.

Enter Spencer Axani, doctoral student at Massachusetts Institute of Technology who has whomped one up for a mere hundred bucks, and published a paper with detailed construction plans (no Instructables project yet, however.  I checked):

image

Straightforward as heck, a plastic brick and a photomultiplier tube are locked up in a light-tight box.  Muons hit the brick, generate a photon on decay and the photomultiplier generates enough juice to tell there’s been an event. An Arduino is used (yes, an Arduino) as a peak detector and a Python script crunches the time-stamped data for delivery to a PC.

He took it around Fermilab to test it out in Real Life:

image

Neat-o, right?

 

Homework:  The Desktop Muon Detector: A simple, physics-motivated machine- and electronics-shop project for university students , S.N. Axani, J.M. Conrad, and C. Kirby, Physics Department, Massachusetts Institute of Technology, Cambridge, Mass.

Extra credit:  http://www2.fisica.unlp.edu.ar/~veiga/experiments.html

Much Better Gluten Quantitation by GP-HPLC-FLD October 14, 2016

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Katharina Anne Scherf*, Herbert Wieser, and Peter Koehler combined gel-permeation high-performance liquid chromatography with fluorescence detection to develop a sensitive technique that can detect both gliadins and glutenins in purified wheat starch. The new method identified higher amounts of gluten in 19 out of 26 samples than the ELISA analyses did. And, according to the new test, 12 samples that had been labeled gluten-free contained between 25.6 and 69 milligrams of gluten per kilogram of starch. The U.S. Food and Drug Administration and the United Nations’ Food and Agriculture Organization have set the maximum limit for gluten in products labeled gluten-free at 20 mg/kg.

 

Homework:  Improved Quantitation of Gluten in Wheat Starch for Celiac Disease Patients by Gel-Permeation High-Performance Liquid Chromatography with Fluorescence Detection (GP-HPLC-FLD), Katharina Anne Scherf*, Herbert Wieser, and Peter Koehler, Deutsche Forschungsanstalt für Lebensmittelchemie, Leibniz Institut, Lise-Meitner-Straße 34, 85354 Freising, Germany J. Agric. Food Chem., 2016, 64 (40), pp 7622–7631. DOI: 10.1021/acs.jafc.6b02512

Mad Scientist Tutorial October 13, 2016

Posted by stuffilikenet in Applications, Geek Stuff, Science, Toys.
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An Electromagnetic Pulse (EMP) generator can overload various kinds of circuitry, causing all sorts of merry havoc among the pinks.  You can make a little baby one and overload poorly-protected circuits up close, although a hammer is more certain to succeed.

Universal Molecular Diagnostics by Affinity October 10, 2016

Posted by stuffilikenet in Awesome, Brilliant words, Science, Star Trek Technology, Toys.
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Rice University researchers have invented a technology that could potentially identify hundreds of bacterial pathogens simply, quickly and at low cost using a single set of random DNA probes. Richard Baraniuk, Amirali Aghazadeh and Rebekah Drezek whomped up a batch of five random probes and used them to identify 11 known strains of bacteria, providing a genomic-based test for identity of pathogens.  This is a big deal because usually each species required its own DNA probe.

Their new study includes several computer simulations, including one that shows how a random selection of five probes can identify 40 different strains of bacteria, and another that demonstrates how the system can accurately differentiate between 24 different species of Staphylococcus.

Rather than identifying a target strain based on a 100 percent match with a specific probe, Rice’s system tests how well the target DNA binds with several different random segments of complementary DNA. UMD uses a mathematical technique called compressive sensing, which was pioneered in the field of digital signal processing. With compressive sensing, the disease DNA need not bind with 100 percent of the probes. Instead, the new system measures how well the disease DNA binds with each of the random probes and creates a specific binding profile for the test organism. It then uses deductive reasoning to determine whether that profile matches the profile of any known pathogens.

With larger numbers of probes, it works even better:

No special hardware is required for this approach, other than the tried and true PCR with which we have become familiar over the last twenty years (thank you, Kary Mullis and LSD). The special sauce is the computer code which figures out the relative affinities.  This can be made available everywhere pretty cheaply, versus specialized DNA probes which require expensive facilities and a lot more regulatory testing.

Homework: Universal microbial diagnostics using random DNA probes, Amirali Aghazadeh1,*, Adam Y. Lin1,*, Mona A. Sheikh1,*, Allen L. Chen1, Lisa M. Atkins2, Coreen L. Johnson2, Joseph F. Petrosino2, Rebekah A. Drezek1 and Richard G. Baraniuk1, Science Advances  28 Sep 2016:Vol. 2, no. 9, e1600025 DOI:10.1126/sciadv.1600025

You Would be Smug, Too October 10, 2016

Posted by stuffilikenet in Awesome, Science, Star Trek Technology, Toys.
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https://cdn.arstechnica.net/wp-content/uploads/2016/10/bezos1-980x551.jpg

Jeff Bezos tweeted this picture of his boots and booze after completing a bucket of milestones in space exploration:

  1. Five flights of the same, reusable Blue Origin spacecraft within a year
  2. Separation of booster rocket and capsule with safe return for both
  3. Restart of booster rocket at only 3300 feet and safe return
  4. Safe return of capsule with one deliberately failed parachute.

The boots say “step by step, ferociously” in Latin. 

Smug and pretentious.  And well deserved.

Statcheck Checks PubPeer Stats and Conclusions October 10, 2016

Posted by stuffilikenet in Geek Stuff, Science, Toys.
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“When starting this project, I wouldn’t say [this was a big problem],” Nuijten tells me. “We’re detecting when people are making rounding errors, who cares?”

But she and some colleagues in the Netherlands were curious enough to check. They built a computer program that could quickly scan published psychological papers and check the math on the statistics. They called their program “Statcheck” and ran it on 30,717 papers.

Rounding errors, and other small potential mistakes in calculating the statistics, were rampant. “We found that half of all published psychology papers … contained at least one p-value that was inconsistent with its test,” Nuijten and her co-authors reported in 2015 in the journal Behavior Research Methods.

Most striking was that the errors weren’t entirely random. Most of the errors tipped the results in favor of statistical significance. And around 13 percent of the papers contained an error that could potentially change the paper’s conclusions.

–Shamelessly stolen from Vox.com

Experimental Design Review—Before Results September 25, 2016

Posted by stuffilikenet in Awesome, Brain, Brilliant words, Geek Stuff, Science.
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BMC Psychology has taken a novel (actually, a scorched earth) approach to the problem of irreproducible results in psych studies. Peer reviews of submitted studies will be checked for experimental methods only, until the end of the review process.  The thinking is, reviewers may be unconsciously biased by seeing results they agree with (or disagree with), rather than the value of the methods by which they were derived.

Given that as many as one-third of psych studies in a recent review (of a thousand studies) could not be reproduced, I think this is an excellent first step to cleaning house of cognitive biases.

Sadly, BMC Psychology is not one of the larger players in this field; it may be that this will enhance their prestige.

The Root of Salt Tolerance in Plants September 20, 2016

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A group of proteins in the roots of plants may be the route (see what I did there?) by which sodium ions enter.  Too much salt will, of course, kill many plants, so knowing the identity of the protein is critical.  It turns out the protein group in question is the same group responsible for admitting water, called aquaporins. 

"We discovered that it has characteristics similar to the properties previously identified for the pores responsible for sodium ion transport," says co-lead author Dr Caitlin Byrt, Postdoctoral Fellow in the School of Agriculture, Food and Wine. "This finding opens new possibilities for modifying how plants respond to high salt and low water conditions”—not to mention better fundamental understanding of plant water transport and potentially breeding salt-tolerant plants for Central California, when the soil gets completely poisoned Real Soon Now.

 

Homework:  Caitlin S Byrt et al. Non-selective cation channel activity of aquaporin AtPIP2;1 regulated by Caand pH, Plant, Cell & Environment (2016).

Graphene Nanoribbons in Spinal Recovery September 20, 2016

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Researchers at Rice University have caused rats with severed spinal columns to pass electrical signals 24 hours after “reapposition of the two sharply severed cords…re-establishes contact by regrowth.” There was a magic ingredient, however: polyethylene glycolated graphene nanoribbons, which were applied during the apposition. Two weeks later [ Video ], the rat could walk without losing balance, stand up on his hind limbs and use his forelimbs to feed himself with pellets. No recovery was observed in controls.

Christopher Reeves died a little too soon, apparently.

 

Homework:  Kim C, Sikkema WKA, Hwang I, Oh H, Kim UJ, Lee BH, Tour JM. Spinal cord fusion with PEG-GNRs (TexasPEG): Neurophysiological recovery in 24 hours in rats. Surg Neurol Int 13-Sep-2016;7:

Surface Chemistry Weekly Review September 19, 2016

Posted by stuffilikenet in Awesome, Science, Star Trek Technology, Toys.
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Things are happening in the thrilling world of surface chemistry (which I know you all care about deeply), so I will attempt to translate from Science to Normal and explain the usefulness of each advance (as I see it. I am never wrong).

First, and array of carbon nanotubes was created by drawing up a substrate from a solution of high-purity nanotubes, causing them to string out nicely.

Abstract Image

The resulting array of CNTs were etched with electrons scoring a resist coating, the remainder of which was washed off with acetone.  Not sure how they got the palladium contacts attached, but that may be just standard solution chemistry.  I can think of two ways to do it, if the CNTs can take it.

The upshot of all this is an array of CNT FETs (50 per micrometer!) with “quasi-ballistic conduction” (meaning really fast, almost effortless electron flow). As reported in Science “The saturated on-state current density is as high as 900 μA μm−1 and is similar to or exceeds that of Si FETs when compared at and equivalent gate oxide thickness and at the same off-state current density. The on-state current density exceeds that of GaAs FETs as well. This breakthrough in CNT array performance is a critical advance toward the exploitation of CNTs in logic, high-speed communications, and other semiconductor electronics technologies“, that last bit being a trifle understated.  This is equivalent to Silicon-based FETs, and more advances are coming.  This technology will most likely supplant silicon-base transistors in the not-too-distant future, giving you and me the ever-increasing computation speed and lower power demands that we associate with The Future of Computing.

Homework: Quasi-ballistic carbon nanotube array transistors with current density exceeding Si and GaAs, Science Advances  02 Sep 2016:Vol. 2, no. 9, Gerald J. Brady1, Austin J. Way, Nathaniel S. Safron1, Harold T. Evensen, Padma Gopalan and Michael S. Arnold

 

Next, Kiel University (Germany; it’s OK, I had to look it up, too) materials scientists found a way to microscopically etch metals so that they could be strongly joined by glue.  Their etching process results in a water- and grease-repellent metal surface which takes glue beautifully: “…the here described novel nanoscale-surface sculpturing based on semiconductor etching knowledge turns surfaces of everyday metals into their most stable configuration, but leaves the bulk properties unaffected.” Possible improvements to everyday life include surface prep for painting, aluminum removal from titanium implants and of course, using glue for metal parts assembly, which will save buckets of time and money, as welding is expensive and often impractical.

Not exactly surface chemistry, but I include it because I feel it’s a fundamental advance in materials science techniques.

Homework:  Making metal surfaces strong, resistant, and multifunctional by nanoscale-sculpturing, M. Baytekin-Gerngross et al, Nanoscale Horiz. (2016)

 

Materials researchers at North Carolina State University have developed a technique that allows them to integrate graphene, graphene oxide (GO) and reduced graphene oxide (rGO) on silicon at room temperature by using a nanosecond-pulsed laser.  They have foolishly tried to insist that this is to be used for medical sensors (and it may well be), but the reduced form of graphene oxide is a semiconducting material.  This could be an alternate route to large-scale manufacturing of graphene-based semiconductors, which means (once again) low-power, small devices for The Future of Computing.

Homework: Wafer scale integration of reduced graphene oxide by novel laser processing at room temperature in air, Anagh Bhaumik1 and Jagdish Narayan, J. Appl. Phys. 120, 105304 (2016)

That’s all for now.  Thanks for reading this far; you are very brave.

Gluten-free Bread Machine Adventures IV September 4, 2016

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wherein Pamela’s Amazing Bread for Bread Makers is used according to directions.

IMG_20160901_124504

It was awesome, and easily more tasty and has better bread-like consistency than Bob’s Red Mill Wonderful Bread. Recommended most highly.

However, as a dignified laboratory scientist and notorious cheapskate, I will attempt to improve Bob’s Red Mill by careful experimentation because I have six bags of it and will waste nothing if I can help it.

Zinc Oxide and You August 26, 2016

Posted by stuffilikenet in Japan, Science, Uncategorizable, Video.
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Japanese researchers at Tohoku University have created a special coating which reduces friction on high-speed, high-temperature bearings by 30%.  Made of a zinc oxide material, the coating has been integrated into bearings in a nifty jet engine-powered generator for emergency use capable of producing eight thousand watts, enough for two Japanese homes:

ZnO-coated high-performance bearings developed

Tiny, isn’t it?  Is there anything zinc oxide can’t do?

Gluten-free Bread Machine Adventures II August 23, 2016

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in which Our Hero tries Bob’s Red Mill Gluten Free Wonderful Bread Mix, using the package directions exactly.  The bread machine in question is the Black and Decker All-In-One Deluxe(tm) Automatic Breadmaker, set for Regular crust and Rapid rise.  This nominally takes 1:58 to bake.

 

IMG_20160823_164152

Delicious with butter so far.  Have not yet tried the toast  Update possible at breakfast.

A Theory of High-temperature Superconductivity August 18, 2016

Posted by stuffilikenet in Awesome, Geek Stuff, Science, Star Trek Technology.
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Scientists at Brookhaven National Laboratory have a potential  explanation for high-temperature superconductivity of cuprates, the superconducting breakthrough of the 1980s. They theorize that a certain density of electron pairs is required and when the density is too small or too great, superconductivity disappears.

They painstakingly created many different cuprates with different amounts of doping to create cuprates (actually, 2500 different compounds of lanthanum, strontium copper and oxygen) with differing number of electron pairs using an amazing beam epitaxy system to create each compound layer by layer. Because cuprates have 50 atoms per unit cell, it’s very easy to get a mixture of compounds, so it’s hard to know what kind of result you are seeing. They fixed that problem with this:

https://i0.wp.com/cdn.phys.org/newman/gfx/news/hires/2016/10-scientistsun.jpg

This beam epitaxy system builds compounds layer by layer and has some awesome built-in surface chemistry tools, like an absorption spectrometer and an electron diffraction gizmo to monitor surface morphology, thickness, chemical composition, and crystal structure of the resulting thin films in real time.

This is exceptionally elegant work, and points to potential understanding of  a general theory which may help in finding room-temperature superconductors.

Homework: Dependence of the critical temperature in overdoped copper oxides on superfluid density , I. Božović, X. He, J. Wu & A. T. Bollinger

Cheap Water Disinfectant From SLAC August 16, 2016

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A bunch of scientists as Stanford Linear Accelerator Laboratory have developed a thin-film composite which can disinfect  a liter of water with just 1.6mg in 20 minutes (99.999% inactivation).  It does this with a sandwich of MoS2 and copper and sunlight.  The MoS2 generates hydrogen peroxide and the copper promotes the hole-electron separation which multiplies the effectiveness six times.

FLV-MoS2 disinfection schematic.

The method is not a cure-all; for instance, it doesn’t remove chemical pollutants from water. So far it’s been tested on only three strains of bacteria, although there’s no reason to think it would not kill other bacterial strains and other types of microbes, such as viruses. And it’s only been tested on specific concentrations of bacteria mixed with less than an ounce of water in the lab, not on the complex stews of contaminants found in the real world.

Still, it’s a damned good start. I would like to point out that these materials are very cheap and found nearly everywhere.

Homework:

Nature Nanotechnology (2016) doi:10.1038/nnano.2016.138