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40Hz Light Pulses Stop Alzheimer’s May 10, 2019

Posted by stuffilikenet in Awesome, Brain, Geek Stuff, Science, Star Trek Technology.
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Neuroscientists at MIT have published a paper which demonstrates that 40Hz pulses of light can somehow inhibit the progress of neurodegeneration in mouse model. This study is designed to figure out how a flickering light could stifle cognitive decline, using two unique mouse models engineered to overproduced the toxic proteins that contribute to neurodegeneration. The animals were exposed to light flickering at 40 Hz for one hour every day for between three and six weeks. It worked a treat;  mice engineered to overproduce tau proteins (that usually cause neurodegeneration) displayed no neuronal degeneration after three weeks of treatment compared to a control group that displayed nearly 20 percent total neuronal loss. The other mouse model, engineered to produce a neurodegenerative protein called p25, displayed no neurodegeneration whatsoever during the entire six weeks of treatment.

At left is the brain of a mouse genetically programmed to develop Alzheimer’s disease. At right,...

The researchers then zoomed in on the light-treated animal’s neurons and microglia to study whether the treatment induced any unusual changes in gene expression. The light-treated mice revealed increased neuronal expression of genes associated with synaptic function and DNA repair. In microglia, the brain’s immune cells, there was a decrease in genes associated with inflammation.

Nobody understands how a 40 Hz flickering light can trigger these specific changes to gene expression deep in the brain, but human trials testing the sound and light treatment in Alzheimer’s patients have already begun.

Note: Adding a 40 Hz auditory tone to the process improved the efficacy of this treatment.  Your elderly parents can benefit from this by using gnuaural, an open-source generator of binaural beats for meditation and other psychological effects.

Homework: https://www.cell.com/neuron/fulltext/S0896-6273(19)30346-0

Manufactured Human Organs November 20, 2018

Posted by stuffilikenet in 3D Printing, Awesome, Brain, Science, Star Trek Technology.
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Scientists at Tel Aviv University have created human organs (little ones but, hey) from a bit of biopsied tissues.  They separated the cells from the rest, induced pluripotency and built up organs in differentiated cell layers on a gel scaffolding.  They were able to grow cardiac, spinal and cortical cells from the biopsy sample.

This is critical to success: the cells are the patient’s own cells, with little chance of immune system rejection.  These guys (Tal Dvir, Reuven Edri, NAdav Noor, Idan Gal, Dan Peer and Irit Gat Viks) are currently engaged in regenerating an injured spinal cord and an infarcted heart with spinal cord and cardiac implants. They have also begun to investigate the potential of human dopaminergic implants to treat Parkinson’s disease in animal models.

They have big plans for this technology: “We believe that the technology of engineering fully personalized tissue implants of any type will allow us to regenerate any organ with a minimal risk of immune response,” Prof. Dvir concludes.

Homework: Reuven Edri et al, Personalized Hydrogels for Engineering Diverse Fully Autologous Tissue Implants, Advanced Materials (2018). DOI: 10.1002/adma.201803895

Diagnosing Alzheimer’s with AI November 12, 2018

Posted by stuffilikenet in Applications, Awesome, Brain, Science.
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This is pretty good news if you think Alzheimer’s can be slowed or halted in some way (unproven, but a good idea): researchers funded by NIH have developed a (so far) 100% accurate method of diagnosing Alzheimer’s before any clinical symptoms appear.  The study seems pretty bullet-proof, too: Prospective 18F-FDG PET brain images from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) (2109 imaging studies from 2005 to 2017, 1002 patients) and retrospective independent test set (40 imaging studies from 2006 to 2016, 40 patients) were collected. 90% of the images were used as training data and the rest used as test data.  The learning algorithm developed for early prediction of Alzheimer disease achieving 82% specificity at 100% sensitivity, an average of 75.8 months prior to the final diagnosis.

Figure 2:

Example of fluorine 18 fluorodeoxyglucose PET images from Alzheimer’s Disease Neuroimaging Initiative set preprocessed with the grid method for patients with Alzheimer disease (AD). One representative zoomed-in section was provided for each of three example patients: A, 76-year-old man with AD, B, 83-year-old woman with mild cognitive impairment (MCI), and, C, 80-year-old man with non-AD/MCI. In this example, the patient with AD presented slightly less gray matter than did the patient with non-AD/MCI. The difference between the patient with MCI and the patient with non-AD/MCI appeared minimal to the naked eye.

I do recommend doing your homework (below), since the paper is pretty digestible for the alert layman, and the study itself well structured.


  1. Yiming Ding, Jae Ho Sohn, Michael G. Kawczynski, Hari Trivedi, Roy Harnish, Nathaniel W. Jenkins, Dmytro Lituiev, Timothy P. Copeland, Mariam S. Aboian, Carina Mari Aparici, Spencer C. Behr, Robert R. Flavell, Shih-Ying Huang, Kelly A. Zalocusky, Lorenzo Nardo, Youngho Seo, Randall A. Hawkins, Miguel Hernandez Pampaloni, Dexter Hadley, Benjamin L. Franc. A Deep Learning Model to Predict a Diagnosis of Alzheimer Disease by Using 18F-FDG PET of the BrainRadiology, 2018; 180958 DOI: 10.1148/radiol.2018180958


Training Neural Networks to Write Bach in a Day! March 24, 2017

Posted by stuffilikenet in Applications, Awesome, Brain, Geek Stuff, Toys, Video.
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Fascinating bit of video here as Our Hero (not me, in this case) takes Bach (and later Mozart) MIDI files, creates an 88-character ASCII-character alphabet from them and trains a Recurrent Neural Network to output similar sequences.

The results (and a lot of the process) is shown in the video above.  Take your time and watch the whole thing; I wonder how long he would have to train the RNN to start outputting Baroque Muzak continually?

Drawing the Wrong Conclusion March 6, 2017

Posted by stuffilikenet in Brain, Brilliant words, Science.
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…or, how we got to now.

Too Much Science to Read, Let Alone Review November 15, 2016

Posted by stuffilikenet in Awesome, Brain, Brilliant words, Geek Stuff, Science, Star Trek Technology, Toys, Uncategorizable.
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It’s been a banner week for science geeks, nerds, and squints. The locked-in lady gets to at least shout from her prison quietlyGoogle has radar sensitive enough to not only find objects but identify them by their radar signature and perovskite is once again breaking solar-conversion efficiency records.

Ordinarily I would give you a breakdown of each of these nifty developments, but more are coming and I may want to return to these later when I am not pressed for time.  Follow the links above; there are others as well that you will find more well constructed than my chicken scratchings, I’m sure.

Brain-Computer Interface Now in Use at Home!!! November 15, 2016

Posted by stuffilikenet in Applications, Awesome, Brain, Geek Stuff, Science, Star Trek Technology, Toys, Uncategorizable.
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A 58-year-old woman (“HB”) with ALS has had a functioning brain-computer interface (BCI) for a while now, and is able to communicate (slowly) with the outside world. She was facing total lock-in Real Soon Now, so any device which offers communication ability is welcome.

What it is:

A diagram illustrating the setup and use of the ECoG implant.

Electrode strips at the top laid across her brain like band-aids read faint electrical signals.  With training HB was able to “type” fairly quickly (words per minute, but still).  More work remains to be done on the interfacing software (I am imagining more inputs and a neural network to interpret her thoughts more and more efficiently), and HB is ecstatic to have a way t live in the world.  She would like to use the interface to control a wheelchair, for example, but that is a ways off.


Homework:  Vansteensel, Mariska J. et. al., Fully Implanted Brain–Computer Interface in a Locked-In Patient with ALS, New England Journal of Medicine November 12, 2016 DOI: 10.1056/NEJMoa1608085

Update: New Scientist has an excellent writeup as well.

Brain-Computer Interface Restores Locomotion November 9, 2016

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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

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.

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:

The Madness of Crowds September 18, 2016

Posted by stuffilikenet in Awesome, Brain, Brilliant words.
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A thoughtful dissection of crowd psychology is currently running in one of my feeds (ribbonfarm.com), which answers my questions about how persecuted folk end up in cultish groups.  It’s another long-form essay (and uh, book report : ) ), so only go there when you have time.

Why Your Life is Not a Journey August 25, 2016

Posted by stuffilikenet in Brain, Brilliant words, Uncategorizable, Video.
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Snippets from the film “Tree of Life”.  .

Science News Roundup August 12, 2016

Posted by stuffilikenet in Awesome, Brain, Geek Stuff, Science, Star Trek Technology, Uncategorizable.
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I haven’t had a lot of free time for stuff I like lately, but I didn’t want a few items from my science newsfeeds to go unnoticed by you, my adoring public. I expect most people don’t follow this kind of stuff closely, so pay attention:

First off, a team from the UK has found that a commonly available drug Fenamate can reduce the inflammation in a particular pathway to protect against a Alzheimer’s disease model in rodents. A mouse is not a man, but the results are intriguing enough (protected all rats in the study) that trials with humans are being strongly considered.  Because the drug is already approved for pain relief, the difficulty in getting into trials in the first place is enormously reduced. “In the USA, wholesale price of a week’s supply of generic mefenamic acid has been quoted as $426.90 in 2014. Brand-name Ponstel is $571.70. In contrast, in the UK, a weeks supply is £1.66, or £8.17 for branded Ponstan. In the Philippines, 10 tablets of 500 mg generic mefenamic acid cost PHP39.00 (or the equivalent of $0.88USD) as of October 25, 2014.”—Wikipedia.

Evil bastards? Well, sure. What do you expect from companies who can buy or sell legislators?

Next, paraplegic patients have had nerve and muscle function partially restored using a three-step training regimen in Brazil. Starting with VR to give them the sensation of walking through haptic feedback during brain-controlled maneuvering through a VR landscape, the patients then proceeded to move using a robotic walker on a treadmill with full support, also run through the brain-machine interface. Finally, they practiced walking with the robosuit used in that World Cup game a couple of years ago.  This took months, but the eight fully paralyzed patients who completed (one moved away) ALL showed some improvement.

This is a big deal.  None of these guys were ever supposed to get any sensation or control back.

This program is on-going, so we don’t know how much improvement will ultimately result from this innovative program, but I for one am pretty excited. Isn’t this why we work in computer science in the first place?

10% Happier, by Dan Harris July 10, 2015

Posted by stuffilikenet in Awesome, Books, Brain, Brilliant words, Science.
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10% Happier, by Dan Harris is the story of ABS anchorman Dan Harris’ journey through Buddhism to mindfulness in the most torturous of routes: trial and error from Eckhard Tolle, Deepak Chopra and a host of what he calls affectionately “Jew-Bus”, Jewish people who have come to embrace Buddhist practices (Harris is Jewish).  In his guise of newsman he cheats his way into getting real answers to the deep mystery: how do you meditate, and why (he even got face time with the Dalai Lama along the way, which is not that easy).

The real juicy part of this book is not so much who he met or how he learned this or that thing, but his blow-by-blow account of his thoughts and reactions as he began learning meditation.  Especially interesting was his reaction to a ten-day Zen retreat of six-hour daily meditation, wherein he finally felt he “got it” and later the emotional outpouring he experience when meditating upon compassion for the first time.

The reason I loved this book is that his story resonates closely with my own, especially the embarrassing awareness of the banality of my own thoughts, the ease of distraction and the lack of rigor in focus or awareness of anything but the voice in my head.  That, and I’m hoping to get a little guidance on my own practice, and I think this book helped.

The link above goes to the Audible audiobook version, but it is also available at sfpl.org.  I do recommend the audiobook, as it is read by him and guarantees his nuances will not be misunderstood (c.f., “Jew-Bus”, above).

The Antibody by Christopher Lukas June 28, 2015

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I haven’t been able to find it on Amazon1, but The Antibody by Christopher Lukas is a gripping tale of a man’s struggle with suicide, depression, cancer and loss.  Written, directed and starring only himself, it is hilarious, tragic and real. I cried at the end, and I don’t cry for much. Watch it at the link above; no telling how long it will last.


1. Seriously, Amazon?

The Singularity Started With the Wheel March 16, 2015

Posted by stuffilikenet in 3D Printing, Applications, Awesome, Brain, Brilliant words, Mutants, Science, Star Trek Technology.
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As difficult as it may be to comprehend, the wheel is the basic unit of technology. It made the repetitive business of carrying stuff easier. When tasks can be easily repeated (preferably automated), they can also be tweaked to do them better, maybe each time.

With computer controls, these tweaking steps can be automated, and the results don’t even have to be seen by a human.  These results can be used to produce new methods to experiment, ad infinitum. This is precisely why we should not allow AIs any autonomy whatever in creating new AIs.

But I digress.

The tools of automation are now cheaply available, giving everyone who wants it access to finely-controlled stepper motors which can be used in the trial and error methods heretofore mentioned.  Cheap microcontroller systems to run them combined with said stepper motors give us robotic assemblers, 3D printers and molecular assemblers.

Yeah, you heard me.

Usually, small-molecule synthesis usually relies on procedures that are highly customized for each target. Martin Burke, a Howard Hughes Medical Institute (HHMI) early career scientist at the University of Illinois at Urbana-Champaign, used a single, fully-automated process to synthesize fourteen distinct classes of small molecules from a common set of building blocks.

A broadly applicable automated process could greatly increase the accessibility of [this class of compounds] to enable investigations of their practical potential. More broadly, these findings illuminate an actionable roadmap to a more general and automated approach for small-molecule synthesis (he used Csp3-rich polycyclic natural product frameworks and developed a catch-and-release chromatographic purification method).

As a former chemist, I must say this is plenty difficult and detailed…but it only has to be done once and this genie is not going back into the bottle.  This will step up the pace of novel moiety experimentation, especially now that we have computational chemistry on a sound footing.  Picture this: computer cranks out theoretical molecule families for research.  Magic chemistry machine makes them.  Another automated machine tests them.  Potential drug candidates can be screened without human intervention, for conditions that currently have no treatment, but do have a good theoretical model.

Honestly, I have been thinking of this for thirty-five years, when one of my classmates described the room-temperature chemistry that was just being used for automated peptide synthesis, a hot subject in my college years1.

Now, with  automated synthesis producing testable quantities of continuously-varying drugs, we can start continuously comparing them with standard drugs for, say, antibiotic activity in a Petri-like environment (I hope it is no surprise that this technology exists already, although it is not in concert with the aforementioned molecular assembler), quickly finding optimal candidates in what could be an entirely automated process.  Promising candidates’ structures can be continuously varied by the molecular assembler under the watchful eye of an expert system (it is fun to imagine the expert system eventually deciding that chlorine bleach is the optimal antibiotic; obviously safety trials against mammalian cell lines need to run in parallel).

Aha, I hear you cry, what about diagnosis?  I’m pretty sure I covered this already2, when I  talked about brute-force cracking the human medical condition through big data: thousands of tests administered cheaply, regularly through millions of peoples’ lifetimes.  This data would be trawled for correlations between medical conditions and test results, telling us things clinicians would miss just because human heads can’t hold that kind of data well enough to draw statistical conclusions, or even reasonable inferences…but computers can.  Frustratingly, the legal problems here are beyond human comprehension as well; the intellectual property costs to create this many tests would be astronomical, although once acquired it could be quite cheap to administer (this is already possible, just not done for greed’s sake).  This will require a revolution in thinking which is not, alas, forthcoming soon3.

Other science can be brute-forced in a similar fashion by automation in other chemical reactions; I picked drug discovery for illustration since that’s where the most money can be found currently.

These are delightful speculations and become even more possible as long as things continue the way they are going, at least in terms of physical possibility.  Cheaper, faster processors make it possible to control all manner of laboratory  and industrial devices, not just your toaster, son.

It all makes me wish I were a better writer, because these ideas deserve better advocacy than I can bring to bear.



Synthesis of many different types of organic small molecules using one automated process Junqi Li, Steven G. Ballmer, Eric P. Gillis, Seiko Fujii, Michael J. Schmidt, Andrea M. E. Palazzolo, Jonathan W. Lehmann, Greg F. Morehouse, Martin D. Burke


EDIT: Somebody did it: “As proof of concept, we have demonstrated its capacity by optimizing the lycopene biosynthetic pathway. This fully-automated robotic platform, BioAutomata, evaluates less than 1% of possible variants while outperforming random screening by 77%. “–Mohammad HamediRad et al. Towards a fully automated algorithm driven platform for biosystems design, Nature Communications (2019). DOI: 10.1038/s41467-019-13189-z



1 We’re getting there, fellas.  Keep up the good work.

2 Please try to keep up.

3 If ever.

No Mud, No Lotus, by Thich Nhat Hanh February 23, 2015

Posted by stuffilikenet in Awesome, Brain.
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No Mud, No Lotus  is pretty much a simple manual for transforming suffering into mindfulness and perhaps joy by ancient (but not mysterious) practices: stopping, mindful breathing, and deep concentration.

The devil is in the details, and I urge readers to stop after this book.  Tibetan Buddhism is very, very busy with details which are (probably) unnecessary to enjoy a peaceful, enlightened life, or at least slow down and appreciate the life you have now.

Still, this particular book seems to me to strike a balance I can appreciate.  I do recommend it.

Cheap Complex Devices by John Sundman February 23, 2015

Posted by stuffilikenet in Awesome, Books, Brain, Brilliant words, Geek Stuff, Mutants.
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Cheap Complex Devices is a lovely slap on the head by the wet fist of surrealism.  It is a frothy coffee-like concoction with tentacles sticking out of it, and they are made of licorice.  Mmmmm…licorice.  And it is the story of the first (two) book(s) written by intelligent machines and delightfully complex and confusing. Cheap Complex Devices makes your sanity sit up and take notice, your grip on reality double its fists and say "Come at me! I can dish it out, too!"

I do love a book which confounds my expectations, and Cheap Complex Devices delivers.

What is Dark Energy? February 12, 2015

Posted by stuffilikenet in Awesome, Brain, Brilliant words, Geek Stuff, Science, Uncategorizable.
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On The List That Cannot Be Named, Joshua is perhaps the best exemplar of all our extended cocktail conversations held over the last twenty years by e-mail.  He recently had occasion to explain to a bright young man the current state of understanding of the nature of dark energy.  I asked him if I could reprint it here and (after redaction) I do so now:

Looking randomly through old email for something else, I stumbled on this attempt at "general relativity and beyond, for the bright 10th grader".  I’m rather pleased with it, and thought some folks on [The List Which Cannot Be Named] might enjoy it, as an example of "teaching science the student can’t actually do yet, without telling any lies."  The usual practice of science popularization, of course, is "tell entertaining lies that remind people who actually know of the science, while convincing the layman that he almost understands it."  I think the first way is better, and find it frustrating that no one else seems to agree.


> I’m a student in Mrs. [REDACTED]’s class and a member of QuarkNet, and
> I’m having some trouble researching for my physics expo project. I  also     > think we met for Shabbat dinner at the [REDACTED]’s a few weeks ago.
> My project is on Dark Matter and Dark Energy, and while I had no
> trouble finding sources that discussed why we know they exist, when it
> came to actually defining what Dark Energy is, most sources just said
> "we don’t know what it is but here are some wrong ideas ….". I was
> wondering if you could tell me what physicists today actually think
> Dark Energy is and why it’s causing the universe to accelerate.

Hi, [REDACTED].  Yes, certainly — I remember you from Linda [REDACTED]’s lovely Thanksgiving shabbat.
The basic idea of dark energy is a bit mathematical, and is therefore
going to require some handwaving, unless you want to skip ahead and
actually learn differential geometry.
(Aside:  calculus is all about limits and derivatives and integrals,
and Newtonian mechanics and calculus grew up together and were made
for each other.  Vector calculus extends those ideas to functions
that have direction as well as magnitude, so it’s all about gradients
and divergence and curl — Maxwell’s electromagnetism and vector
calculus were made for each other in the late 19c.  The next step
beyond that is doing geometry and calculus on "manifolds", which are
n-dimensional spaces that are curved, so that when you carry a vector
around a loop it doesn’t always come back pointing the same way.  If
you have ever seen a Foucault pendulum in a museum, this is the point
they are trying to get across; the old riddle about the man who walks
a mile south, shoots a bear, walks a mile east, then a mile north
and is back where he started — what color is the bear? white, of
course, because he must be at the north pole — is another simple
example.  Differential geometry, or "calculus on manifolds" as some
people call it, is the math that drives Einstein gravity, because to
study curved spacetime you need this kind of machinery.  But we can
talk about it, without actually teaching you to do problems.  If you
want to get a headstart on the actual math, I can point you at some
good texts, but really you should focus on getting one-dimensional
calculus well mastered before investing too much effort beyond it.)
So, the Einstein equations look like T_mn = 8 pi G_mn, where T_mn is
the local density of "stress-energy", or mass, energy, pressure,
energy flow, and momentum flow, at a given point.  That is, roughly,
T_00 is a function of position and time that gives the density of
mass and energy at that point at that instant, and the other 15
components, m=0..3 and n=0..3, are things like "how much x-momentum
is flowing through that point in the z-direction" and so on.  This is
sort of complicated because it has so many components, and you’re
not used to thinking about exotic things like momentum flow as a
source of gravity just like mass.  Partly this is because we are
used to speeds very much slower than c, so that in "natural" c=1
units (for example, time in nanoseconds and distance in feet, or
time in seconds and distance in light-seconds — that’s seven times
around the earth, or most of the way to the moon!) all the other T_mn’s
are basically zero for any matter less drastic than the interior of
an atomic nucleus or a neutron star.  Anyway, you can think of T_mn
as a complete description of the "stuff" at a given point at a given
moment in time.
G_mn is a complicated thing that describes the curvature of spacetime
at a given point; it turns out that you can completely describe the
curvature of a manifold by taking a vector, carrying it around a
circle, and seeing how it changes when it comes back.  I can
calculate G_mn for any set of coordinates you give me, but not every
different set of coordinates gives a different G_mn; for example, the
x-y plane is flat, and it’s still the same plane and just as flat
even if I describe it in polar coordinates as r, theta instead of
x, y.  This is a subtle point, because I can take a radial vector,
say pointing in the +r direction at r=1,theta=0 (that’s on the x-axis
in x-y coordinates), and carry it to r=1,theta=90 (on the y-axis)
where it is now pointing in the -theta direction!  So if I believed
the coordinates, I’d be tempted to say "this radial vector turned into
a circumferential vector when I moved it; the plane must be curved!"
But notice that if I bring the vector back where I found it, no matter
what path I walk to get there, the vector will once again be radial.
My polar bear hunter in the riddle was sort of a cheat, because he was
relying on the coordinates for his directions; when he walked "east"
a mile, he was going in a circle around the pole and he knew it.  But
let him do a 6,000 mile triangle instead of a 1 mile triangle, and
things get more interesting:  he walks down to the equator, along a
"straight" meridian — we can see that it’s curved in three-dimensional
space, but considering the two-dimensional surface of the earth as its
own thing, a meridian is straight, bending neither to right nor to
left — then along the "straight" equator, and back along a "straight"
meridian.  The existence of a triangle with three right angles proves
that the earth’s surface is curved; the "local" proof that doesn’t
rely on standing out in space and watching from afar is that if our
hunter carried a gyroscope or Foucault pendulum with him, he’d be able
to see that his coordinates turned by 90 degrees as he went around the
big triangle.
There is a thing called the Riemann tensor that completely describes
the curvature of any manifold; it’s written R_abcd, and it means,
roughly, if I carry a vector pointing in the "a" direction around a
small loop in the "c-d" plane, how much will it now point in the "b"
direction instead.  Since the two-dimensional surface of the earth
has only one "c-d" plane (longitude and latitude) to walk around on,
the curvature of a 2D manifold can be given by a single number.  For
3D manifolds, there are 6 numbers, for 4D, there are 20 — geometry
is complicated!  Of the 20 components of the Riemann tensor that gives
the curvature of spacetime, there are six that describe how much
space is "spreading" or "shrinking" over time, and 14 that describe
how much it is "shearing" in various directions without changing volume.
The six volume-changing components are called the Ricci tensor, given
by R_ab = (1/4)(R_a0b0 + R_a1b1 + R_a2b2 + R_a3b3).  And there is a
sort of "average" of the Ricci tensor called the Ricci scalar, which
is R = (1/4)(R_00 + R_11 + R_22 + R_33), which is a single number
that describes the curvature of spacetime as well as a single number
possibly could.  The Einstein tensor G_mn mentioned above is actually
G_mn = R_mn – (1/2)R.  I told you it was complicated, but don’t get
too intimidated by the preceding two paragraphs; really this is all
just bookkeeping.  The physics is coming now, so pay attention.
Einstein, after ten years of hard work 1905 to 1915, came up with a way
to generalize his theory of flat spacetime and constant motion into
a theory of curved spacetime, gravity and accelerated motion.  (Hence,
the name "general" relativity.  Special relativity is high-school
simple from a mathematical standpoint, once you’ve had the incredible
conceptual leap Einstein achieved in spring 1905; general relativity
needs the machinery of Riemann tensors, which wasn’t well understood
by physicists at that point in time, and requires some upper-division
college math even today.)  What he was trying to say was, "spacetime
is curved by stuff, wherever there is stuff; elsewhere, it may have
ripples caused by stuff in other places."  The final mathematical
formulation of that is T_mn = 8 pi G_mn.  The "stress-energy tensor"
T_mn is "stuff", and G_mn is "the part of curvature that actually
changes the volume of things."  For a practical example, if I put a
million fireflies in a sphere all around the earth, a mile up, and
suddenly stopped their wings and let them fall, the sphere would get
smaller as they fell, and that’s because there is mass (the earth)
inside the sphere.  If I put a million fireflies in a perfect sphere
formation next to the earth, say fifty thousand miles over the north
pole (and not in a moving orbit, just hovering there) and let them
fall, the ones closer to the earth would fall faster so the sphere
would elongate like a football, and the ones out to each side would
converge as they fell so the waist of the football would get narrower.
The volume of the sphere of fireflies wouldn’t change, because there is
no stuff (that is, no gravitating earth) inside the sphere.  The
converging sphere is firefly worldlines coming together, described by
the Ricci tensor part of spacetime’s Riemann curvature.  The constant
volume elongating sphere is described by the other 14 components of
the Riemann tensor (which also have a name, the Weyl tensor).  What
the Einstein equation says is "there is Ricci curvature wherever there
is stuff; to keep the universe from tearing, this means there will be
Weyl ripples, but no Ricci curvature, in empty space where there is
no stuff."
After that long setup, what is dark energy?  Well, a few years after
Einstein published general relativity, some smart mathematicians
pointed out that there are no static solutions to the Einstein equation;
that is, a universe made of stars and galaxies that have always been
there and never expand or collapse is not possible.  At that time,
there was a mostly unexamined prejudice in favor of an eternal static
universe, and Einstein was concerned that this was evidence against the
whole idea of general relativity.  (The observation of gravitational
bending of starlight in 1919, however, convinced many people that he
must be substantially on the right track.)  So, in a minor paper,
Einstein asked the question, "what is the minimal change to my
equations that will preserve all the good features, yet allow a static
universe?"  Later, he remarked to a biographer that lacking the courage
to stand by his equations and boldly predict the Big Bang here was
"my greatest blunder," but what an interesting blunder it was!
It turns out that about the only thing you can do to the Einstein
equation that doesn’t break everything is to add a term that looks
like this:  T_mn = 8 pi G_mn + lambda g_mn.  The g_mn here is the
simplest and humblest tensor in differential geometry:  it’s what we
use to make dot products, and in flat coordinates it’s just the unit
matrix.  We call it the "metric tensor" or just the metric.  It
obviously wouldn’t do to say, "spacetime curves where there is stuff,
and empty space curves slightly toward the Willis Tower", nor even
"…and empty space curves uniformly inward in all directions, but only
as seen by observers who are stationary relative to Ken’s Diner."  If
you’re going to break the simplicity of "spacetime curves where there
is stuff, you had better at least do it in a way that looks the same
to all observers in empty space, no matter where or when they are and
how they are moving.  This is what that lambda term with the metric
tensor does.  The revised Einstein equation reads "spacetime curves
where there is stuff, and empty space curves slightly, by an amount
given by lambda, in a symmetric way for all observers."  It’s ugly,
but it’s not as ugly as other alternatives.  The amount lambda is
called "the cosmological constant", and of course if lambda=0 we are
right back to honest general relativity.
Now it turns out that the effect of a cosmological constant is to give
the universe "an itch it can’t scratch" — because it’s curvature that
is caused by spacetime itself, rather than by "stuff" in spacetime,
any physical effect lambda may cause will continue eternally as long
as there is spacetime.  This should be enough to give you a clue what
a cosmological constant will do:  it causes an empty universe to expand
or to contract, depending on the sign of lambda, at an exponential pace,
because the growth in spacetime is proportional to how much spacetime
there is.  So, you could just about imagine a universe with matter and
energy that acts gravitationally to pull it into a big crunch, balanced
by a cosmological constant that expands spacetime just enough so the
crunch never happens.  It’s a delicate balance, and an unsatisfactory
solution to the original, obsolete problem of how to make the universe
endure forever at a static size.
Now that we know the universe is expanding, however, we can still
distinguish between matter and energy (which slow the expansion) and
a cosmological constant (which speeds it up).  Looking back at old
supernovae, we can see how fast the universe was expanding at various
times in its early history, and if we graph this carefully we can find
out whether the universe is slowing or accelerating in its expansion.
This was successfully done in the late 1990s, and the surprise result
is that the universe has been accelerating for at least the last eight
billion years of its 13.7 billion year history.  So the cosmological
constant wasn’t such a useless idea after all!
Now, notice that there are two ways to think about the cosmological
constant.  The one I presented went with the equation
T_mn = 8 pi G_mn + lambda g_mn,
which I read informally as "stuff (on the left) equals curvature plus
a constant, so the constant is the curvature of empty spacetime."
But consider moving the constant to the other side:
T_mn – lambda g_mn = G_mn
and now it reads "stuff minus a constant equals curvature, so the
constant is a funny kind of stuff that empty spacetime is full of."
It’s really semantics whether lambda is a kind of stuff that lives in
empty space, or a kind of curvature that happens in the absence of
stuff.  As a particle physicist, I’d rather think of it as a kind of
stuff, because then I can try to come up with a particle theory that
includes it and explains why spacetime is full of it!  Also, once I
think of it as "stuff that is proportional to the metric and seems
to be everywhere," I can entertain the possibility that it really
isn’t all-pervasive and eternal and everywhere; maybe the universe
has lambda a function of temperature, or of the age of the universe,
or something, instead of a constant.  It’s a cosmological *constant*
only in the sense that it’s proportional to the metric, so it doesn’t
vary asymmetrically from place to place or from a stationary
observer to a moving one.  It still might be a real substance that
obeys those laws and that only exists when the conditions are right.
Dark energy, to finally answer your question, is the stuff we infer
from the fact that the universe is accelerating, which behaves enough
like a cosmological constant in the Einstein equations to give that
behavior, but which might or might not be a true constant property
of the vacuum.  By contrast, dark matter is ordinary stuff that is
located some places and not others, that behaves just like atoms or
photons or neutrinos or any other kind of matter, except that it isn’t
made of stars because it doesn’t glow, and it isn’t even made of
atoms because we’d see it glow in star nurseries (and because we know
how various isotopes formed just after the Big Bang, and the numbers
come out wrong if most of the atoms are unaccounted for).
You asked what my guess was about what dark matter and dark energy
actually are.  For dark matter, I have lots of good candidates;
I think the obvious answer is that if supersymmetry is right, there
are some heavy exotic particles predicted that would have been
formed in the early universe, that interact very weakly with atoms,
and that have about the right properties to be the dark matter.
For dark energy, I truly have no guess — it could be a fundamental
property of spacetime (in which case the geometric picture with the
cosmological constant on the right side of the equation makes more
sense than the particle physics picture with lambda on the left),
or it could be something more dynamic.  To understand it, I would
sort of have to understand "what empty space is," which effectively
means I need to understand everything about all the particles in
not-empty space, whereas to understand dark matter I just have to
understand one kind of particle among who knows how many.
Does that help?

The Body Keeps the Score by Bessel van der Kolk February 3, 2015

Posted by stuffilikenet in Awesome, Books, Brain, Brilliant words, Science.
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The Body Keeps the Score: Brain, Mind, and Body in the Healing of Trauma is a fabulous up-to-date survey of what is currently known about psychological traumas and innovative, effective treatments for life-long sufferers of trauma. From war veterans to incest survivors to accident victims, Bessel van der Kolk in the JRI Trauma Research Center in Brookline, Mass. recounts painful case histories to illustrate creative approaches to trauma treatment and recovery, from neurofeedback to theater to EMDR, with often amazing results. Simple meditation can provide serious relief and often open doors to talk therapy that remained closed for many patients.

I have always held that about a third of humanity is seriously messed up inside, from unrecognized illness, child abuse, rape or simply absent parental figures. Given the huge numbers of trauma sufferers of so many kinds throughout the world, and the impact that even one damaged person can have on so many others, isn’t it time to learn more about trauma?

I found by the end of this book I was feeling quite a bit more charitable to strangers than heretofore.

Maybe I’m learning something about trauma.