Monthly Archives: December 2016

Open Source Magnet Holder Stand

I built a magnet stand today. It’s comparable to a $100 Thermo Fisher product but only costs about $2 in materials. Maybe $10 if you have a service like ponoko cut the acrylic. The holes in the top hold a 1.5 ml centrifuge tube. The  center column has a receptacle for a 12 mm disc magnet. The design source file available in a github repository. I’m still learning github, but hopefully that makes it easily accessible.

The laser cut out these five pieces:

2016-12-30 12_05_32-OSSHmagnetholder_magnet holder stand 003.svg at master · drhex_OSSHmagnetholder.png

Then I assembled them into the stand and added a bit of superglue to the joints to hold it all together. It turns out that cyanoacrylate glue works really well on this material.


While assembling my fist prototype, the teeth were a little too big for the holes. One piece split apart and jabbed into my finger. It turns out that cyanoacrylate glues will also stop a cut from bleeding .

The use of cyanoacrylates to close wounds is nothing new. Cyanoacrylates are used in surgery and were used on the battlefield in the Vietnam war. I went searching for other blogs talking about this use of superglue and found this old Lifehacker article from 2012. So, yeah: you can close a wound with a little superglue. It’s not the best way, but it’s  it’s good to know in a pinch.

And now I need to digress a little.The top comment on this article is a pedant literally starting his comment with “uuummm, NO.” I read it in a nasal voice like droopy dog. It’s so stereotypical it’s funny.

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Whatever, Droopy McProperface. Rub some dirt glue in it. There’s SCIENCE to be done.

EROEI dictates coal will go extinct as an energy source

The energy return on energy invested (EROEI) is just a measure of “bang for your buck.” It tells you how much energy you deliver relative to how much energy it took to deliver it. Let’s say running a drilling rig takes a gallon of fuel. The oil extraction pump takes another gallon. Plus, the delivery truck takes another gallon (I’m simplifying). That’s three gallons of fuel to deliver fuel to the station. If that truck delivers 12 gallons, then the EROEI is 4:1.


Back in 1962 when the Beverly Hillbillies debuted, the EROEI on oil was about 10. In the opening for that show, Jed Clampett accidentally strikes oil with an errant gunshot. It bubbles out of the ground for free. That kind of oil has a very high EROEI (very little drilling or pumping, and its location requires less transport than, e.g. Prudoe Bay). Oil with very high EROEI is part of the American Mythology. Back in 1940, the EROEI for American oil was over 200. Today it’s closer to 5.

People die mining coal. People die drilling oil. Those fuels make a huge amount of pollution. I’m not even talking about CO2. Why did we tolerate a dangerous, polluting energy source? Because those energy sources used to have the biggest EROEI. The EROEI of coal electricity was about 9 in 2009 (in some cases closer to 3 depending on source and pollution reduction strategies). As we dig deeper to get coal, the EROEI necessarily decreases.

So, if some other energy source has a better EROEI than fossil, it wins. Economics follows thermodynamics. The efficiency of PV systems has increased and production methods have become more refined. Where conditions are favorable, the EROEI of solar PV has passed 8 and is rapidly approaching 10. Solar Technology is getting better continuously. Fossil fuels are getting harder to extract. In the longer term, solar will eat their lunch.

Biomarkers for Chronic pain 2

A great article published in diagnostics by Emmanuel Bäckryd highlights the need for a good mechanism based diagnosis for clinical pain medicine.

Everyone understands that pain is unpleasant. Pain is nonetheless necessary information: humans need to know when they are doing things that will injure their body. People who lack the ability to feel pain are at very high risk for injury or death. The sad case I member reading about was a little girl who was born without the ability to feel pain. When her eye itched, she rubbed her eye until she went blind. She lacked the painful feedback to warn her that what she was doing was damaging her eye.

The trouble is that in some cases pain persists even when there is no injurious condition. This kind of pain does not help people avoid injury. In fact, this kind of pain may actually increase injury. Because of chronic, uninformative pain, people avoid healthy activities like physical therapy or exercise. In some cases, pain may interfere with hygiene and self-care. These are expensive problems.

Additionally, many forms of pain are not well treated by opiates. Patients seeking care for chronic, unmanageable pain may end up on high doses of opiates to compensate for their low efficacy. I suspect that this significantly contributes to the opiate epidemic in the United States. Pharmaceutical marketing campaigns have led doctors to feel that they can prescribe opiates for chronic pain. According to Frontline, MDs were reluctant to do so until fairly recently. Prescribing opiates for chronic pain is a fine idea when they work. When opiates are available, but don’t work, it is a gateway to addiction.

If we had a good blood test to determine if a person would respond well to opiates (or any other kind of pain medication, for that matter) we could guide treatment more effectively. A blood test for the existence of pain seems unlikely (pain is a subjective experience). But I think that guiding treatment by biochemistry instead of by subjective assessment is usually a good idea.

The review discusses several interesting candidates that have failed as biomarkers for pain. Cystatin C was a potential biomarker identified in animal studies. A study in humans did not confirm biomarker as correlating with acute labor pain. Bäckryd notes that their group did not detect a significant differences between patients and controls in any of the other potential biomarkers listed (e.g. neurotrophic factors, cytokines, neuropeptides, beta endorphins, and substance P). And of course, none of these biomarkers are listed in the common blood panels used by pain management physicians. Perhaps no single protein is adequate to give useful information to guide pain treatment.

Ultimately, Bäckryd confirms my view that the field of biomarkers for pain conditions is still young. He also shares my view that it would be good to have a blood test to help guide the prescription of pain medicine or disease modifying drugs. He brings up an interesting point of skepticism: if pain is sensitized or mediated by central nervous system conditions, it’s not clear that the blood brain barrier would allow for biomarkers to enter the blood. In such a case, it might be more reasonable to look for degradation products or other downstream effects. Undoubtedly, this would complicate diagnosis.

Biomarkers for chronic pain

Chronic pain is an important quality of life issue for millions. The current epidemic of opiate use underscores the struggle to cope with chronic pain. Diagnosing chronic pain is usually done by self-report. Obviously, people know when they are in pain. Discovering the root cause of pain is not trivial. Diagnosis may require a great many tests and every delay is misery for the patient. Blood tests exist but (from what I can tell) track complications from treatment and do not greatly help diagnosis. One pain management organization uses the following panel of blood tests for new patients:

AM Cortisol
AM Pregnenolone
Erythrocyte Sedimentation Rate (ESR)
C-Reactive Protein
Total Testosterone

In reading the rationale for these tests, it is not clear how all of these are related to the physiology of pain. It’s not clear if there is any blood work that can be done to help assess the source of chronic pain.

Cortisol and blood pressure may be elevated if the patient is already experiencing extreme pain. Ideally, these conditions would be reduced in the case of successful treatment. How does pain change cortisol or blood pressure? Maybe through the psychological stress that pain causes. Maybe something else.

Pregnenolone and cortisol are adrenal hormones. They can correlate with pain, but possibly be increased or reduced as a result of pain induced stress. Likewise, C-reactive protein may report inflammation, and inflammation may be the cause of pain. On the other hand, pain itself may cause C-reactive protein or erythrocyte sedimentation rate to be elevated through mechanisms that are largely unknown.

A testosterone test is administered in order to screen for an underlying hormonal problem, determine whether the patient is already on a dose of opiates that is suppressing testosterone production, and to establish a baseline so that this complication can be detected and avoided later on in the course of treatment.

My point is that none of these tests will tell a physician that pain is definitely neurological/inflammatory/CNS-related. They won’t tell the physician with any certainty if the patient is an addict who needs a fix. At best, these tests might rule out inflammatory problems as the root cause of pain.

What are the biomarkers of specific pain causes? More tomorrow.

Basis supplement: pterostilbene and niacinamide

I took Elysium’s Basis supplement for a month but didn’t notice a dramatic effect. Basis is a supplement, a combination if pterostilbene and nicotinamide riboside. I switched to a cheaper combination of generic  pterostilbene and niacinamide. After two months, I think maybe there’s a small effect? I have very strange dreams if I take it before bed. I take it in the morning instead and maybe I feel a little more energetic.

Pterostilbene is the methylated version ofresveratrol. Resveratrol is derived from red wine. Pterostilbene is found in blueberries. It’s the subject of a lot of study for its antioxidant and supposed anti-aging properties. The methylations may make it easier to absorb.
pterostilbene and resveratrol.png
I can’t vouch that it works, but the Basis brand combination has some strong scientific support. Several Nobel prize winners are on their scientific board of advisors. Their hypothesis is that  NAD+ declines with age and that these two components might increase production of NAD+.
The supplement industry is largely marketing and deception. On the other hand, it would be hard to organize a proper clinical trial. If this company can follow the effects of their unregulated supplement product on their customers, it might give enough data to justify a proper trial. I wish them luck, but I’ll go with the generic product, given the price.