Wednesday, September 28, 2016

Albuquerque 2016 Monsoon Season

From the ABQ NWS Homepage.
The monsoon began early in Albuquerque this year, with a week of good moisture at the end of June. But then June high pressure returned and most of July was hot and dry.  It wasn't until the beginning of June that the rains reliably returned.  Overall, the monsoon wasn't bad, but the hiccup in the beginning ended up dooming most annual plants.  Only perennials managed to reap the rewards of the late-breaking monsoon moisture.  Now, at the end of September, many monsoonal plants are still trying to finish flowering and set seed.  Many plant species are flowering late and show signs of stunted growth.

Monday, June 20, 2016


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Pathogenesis of atherosclerosis. (a) In the first stage, low density lipoprotein-cholesterol (LDL) is deposited in the endothelium and undergoes oxidative modification, resulting in oxidized LDL (oxLDL). OxLDL stimulates endothelial cells to express adhesion molecules (vascular cell adhesion molecule-1 (VCAM-1), P-Selectin) and various chemokines (e.g., Monocyte Chemoattractant Protein-1 (MCP-1), Interleukin 8 (IL-8)). This leads to a recruitment of monocytes, which transmigrate into the intima and differentiate to pro-atherogenic macrophages; (b) Macrophages harvest residual oxLDL via their scavenger receptors and add to the endothelial activation and, subsequently, leukocyte recruitment with the secretion of Tumor Necrosis Factor α (TNF-α) and IL-6; (c) The increasing plaque volume promotes neovascularization. Proliferating smooth muscle cells (SMCs) stabilize the nascent fibrous plaque. With deposition of fibrin and activated platelets on the dysfunctional endothelium that expresses tissue factor (TF) and von Willebrand factor (vWF), a pro-thrombotic milieu is formed; (d) Foam cells can undergo apoptosis and release cell-debris and lipids, which will result in the formation of a necrotic core. In addition, proteases secreted from foam cells can destabilize the plaque. This can lead to plaque rupture, in which case extracellular matrix molecules (e.g., collagens, elastin, TF, vWF) catalyze thrombotic events.
(PMC full text: Int J Mol Sci. 2015 May; 16(5): 9749–9769. Published online 2015 )
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Sunday, April 10, 2016

The Problem with Nutrigenomics

"Personalized nutritional counseling is a burgeoning field. Several companies, including Vitagene, Nutrigenomix and DNAFit, are already offering individualized dietary counseling.  Their efforts are based mostly on genetic testing, but scientists have only just begun to explore the links between DNA and good nutrition. “I think companies offering personalized dietary advice are probably running ahead of the evidence,” said John Mathers, director of the Human Nutrition Research Center at Newcastle University in Britain." [NYTimes Blog]


Science skeptics have recently reviewed these services, and found plenty of quackery. [Science Based Medicine] [Skeptical Raptor]

However, there is some research to back up the idea that genetic testing can provide insights into metabolic disorders.  There may be as many as 200 SNPs for which there are proven metabolic effects, and only a subset of these alter nutrient requirements in a significant portion of the population [e.g., the rs1801133 MTHFR SNP and folate requirement in 15–30% of the population (Solis et al., 2008) and the rs12325817 PEMT SNP and choline requirement in 20–45% of the population (da Costa et al., 2006)].

What do genetic testing services measure?

The human genome consists of about 3 billion nuceleotide bases, each of which is either A,C, T, or G.  A reference genome based on the similarities of all genotyped humans has been assembled, along with a corresponding reference database of all of the point "mutations" where individuals differ from that baseline.  So far, scientists have documented about 150 million of these single nucleotide polymorphisms, called SNPs.  The average person doesn't have all of these differences, however; most people have about 3 millions SNPs that differentiate them from the reference human genome.   Since 3 million is about 0.1% of the 3 billion base pairs, most humans differ from each other by about 0.1% of our DNA. Ancestry genomic testing services like 23andme test for a few hundred thousand SNPs for $100-$200.  For $1000-10,000 a complete genomic sequence can be obtained.  (there are about 3 billion bases total.  

Examples: MTHFR – metabolic pathways and nutrigenomics

In humans, SNPs in the gene MTHFD1 increase the demand for betaine as a methyl-donor, thereby increasing the dietary requirement for choline. Another SNP in the gene PEMT prevents the activation of this gene by estrogen, thereby decreasing endogenous production of phosphatidylcholine (a source of choline) in the liver and increasing the dietary requirement for choline. [Choline: Critical Role During Fetal Development and Dietary Requirements in Adults. Ziesel]

But note that it is not so simple.  There are several forms of the MTHFD1 gene, for example MTHFD1L and MTHFD2. If MTHFD1 is commonly mutated, it may be a pseudogene.

Complexities interpreting SNPs

No simple test can unravel the intricacies of the human genome, and consumers should be suspicious of anyone claiming to be able to interpret measurements of tens of thousands of genes, with millions of genetic variations, some of which have effects on hundreds or thousands of the small molecules of metabolism (and perhaps on thousands of peptides or proteins involved in metabolism).
[A grand challenge for nutrigenomics.  Steven Zeisel. 2010.]

Mistakes in genomics data

Note that 23andme data, like any large genome scan, can have mistakes in it.  For example, the Enlis genomics blog found more than 500 likely mistakes in a sample of 23andme raw data!  (Enlis)

Furthermore, many important nutritional SNPs are not testing by 23andme.

Solution: Metabolic Testing
There is a genetic test for MTHFR variations. But there’s also a cheaper and more accurate way to test for whetherMTHFR variations are causing disease. We simply check the levels of homocysteine in the blood...In other words, the homocysteine levels determine our actions, not the MTHFR test results.[Cleveland Clinic]

Tuesday, April 05, 2016

Portable Real-Time Measurement of Air Quality

I recently purchased a Uni-Trend Air Quality Meter.

It measures VOCs (both natural and man-made), PM2.5, and temperature and humidity.

Coarse particles (PM10) have a diameter of between 10 micrometers and 2.5 micrometers and settle relatively quickly whereas fine (PM2.5) (0.1 to 2.5 micrometers in diameter) particles remain in suspension for longer. To put things into perspective, human hair has a diameter of 50-70 micrometers and a grain of sand has a diameter of 90 micrometers.

Sources of fine particles include all types of combustion activities (motor vehicles, power plants, wood burning, etc.) and certain industrial processes.  Sources of coarse particles include crushing or grinding operations, and dust from paved or unpaved roads.

PM2.5 is made up of sulfates, nitrates, carbon, and soil.

Albuquerque reports the Air Quality Index for daily pollen and Fine/Coarse Particulates:

 But these numbers are reported as "Index" values, and have to be converted to ug/m3 to compare to measured values:

Over the last week, Albuquerque has reported AQI for PM2.5 of almost 50, which should be about 15 micrograms per square meter, whereas my unit typically reports 30-50 micrograms per square meter, indoors and outdoors.  It is possible that ABQ measures air quality higher from the ground than my unit, or that PM2.5 is lower during the night when I don't check it.

Here is an excellent resource for more information.  Most of the graphics on this page are from this source.

Monday, March 28, 2016

Metabolic Pathways

Say you want to know what the possible effects of taking a supplement might be.  You could research the supplement on the two high-quality websites that report supplement interactions based on human trials:

The Mayo Clinic - not as many supplements covered.

It would be great if there were reliable "trip reports" from patients on the effects and side-effects of drugs, but unfortunately side-effects are not reliably reported.

If you wanted more basic information, you could consult a metabolic pathway interaction diagram.  Note that the study of genetics and proteomics still has a long way to go:  we don't know what most of the essential genes even do, nor do we know the function of xx% of all genes.  No network diagram is complete....

SigmaAldrich offers a searchable poster:

According to this, NAC can increase glutathione, but also homocysteine. Important information from the network! has even more information.  Note that because the network diagram is again a poster, single compounds (e.g. cysteine) can occur in different places on the diagram.

Metacyc is the most detailed, but only shows one "pathway" at a time.

KEGG is another very good resource with drop-down menus to explore individual pathways.

A long list of other resources.

Friday, March 25, 2016

Testing a Relevant SNP?

A new study in Science Magazine by Simonti et al has linked this SNP to a rare condition known as protein-calorie malnutrition (PCM).  The study compared electronic health records (EHR) for 28,000 people with SNPs that are now known to derive from Neandertal DNA.

SNP rs12049593 is in an intron of SLC35F3, which means it does not change the actual structure of the protein, but instead alters the amount of protein produced.  SLC35F3 codes for a protein that helps transport vitamin B1 (thiamine) through the body to the mitochondria, where it can be used to generate and store energy from sugar. The linkage to PCM makes sense, because PCM is characterized by fatigue, malnutrition, and wasting even in the presence of adequate caloric intake.

"Humans depend on diet for their thiamine needs. Very little thiamine is stored in the body and depletion can occur within 14 days. Severe thiamine deficiency may lead to serious complications involving the nervous system, brain, muscles, heart, and stomach and intestines." (Mayoclinic)

"Thiamine is required for the assembly and proper functioning of several enzymes that are important for the breakdown, or metabolism, of sugar molecules into other types of molecules (i.e., in carbohydrate catabolism). Proper functioning of these thiamine–using enzymes is required for numerous critical biochemical reactions in the body, including the synthesis of certain brain chemicals (i.e., neurotransmitters); production of the molecules making up the cells’ genetic material (i.e., nucleic acids); and production of fatty acids, steroids, and certain complex sugar molecules.

Thiamine deficiency can lead to cell damage in the central nervous system through several mechanisms. First, the changes in carbohydrate metabolism, particularly the reduction in a–KGDH activity, can lead to damage to the mitochondria. Because the mitochondria produce by far the most energy required for cellular function, mitochondrial damage can result in cell death through a mechanism called necrosis. Altered carbohydrate metabolism can lead to oxidative stress, characterized by excess levels of highly reactive molecules such as free radicals and/or the presence of insufficient levels of compounds to eliminate those free radicals (i.e., antioxidants, such as glutathione). Oxidative stress can lead to various types of cell damage and even cell death."  (from Role of Thiamine Deficiency in Alcoholic Brain Disease)

Simonti et al state:
"Decreased expression of this transporter in the brain or GI tract could exacerbate malnutrition or its symptoms. It is possible that new dietary pressures may have caused changes in carbohydrate metabolism to be beneficial in early human migrants out of Africa; indeed, there is evidence suggesting that Neandertal-derived genes increase the efficiency of fat digestion. More recently, the reduction of thiamine present in foods from the grain-refining process, as well as an increased intake of simple carbohydrates, make this a potentially harmful allele, because it could reduce thiamine availability although modern diets increase demand."

I am homozygous for the recessive allele of SNP rs12049593.  I have a C where 95% of people have a G or T, courtesy of my Neandertal ancestry.  According to the Simnoti study, I may have some malnutrition symptoms if I do not express the B1 transporter gene.  According to my research, B1 can also passively diffuse if it is ingested at high enough concentrations.

I tested oral administration of 100mg/day of B1, which is more than 6000% of the US RDA but is the only size pill commercially available; apparently, this is a standard doze for supplementing B vitamins.  I weighed myself morning and night for 1 week and did not notice any change in weight.  Subjectively, I noticed some tiredness the first two times I took B1, then I noticed some energy, and after four or five days I do not notice any effect from supplementation.

UPDATE:  Figuring out what allele is variant and which is most common is difficult.  My information above was from 23andme raw data viewer, but when I loaded my data into the excellent Enlis Genome Personal software, I see that I actually have the reference allele, not the rare allele.  So that may explain why I don't respond to supplemental B1.

Thursday, March 24, 2016

Tama Hills and Environmental Consciousness in Japanese Anime Films

In 1994 Studio Ghibli produced Pom Poko, (directed by Isao Takahata) a trippy animated film about a community of magical shape shifting raccoons desperately struggling to prevent their forest home from being destroyed by urban development.  The movie draws heavily on traditional Japanese folklore (especially the reputed power of the raccoon's testicles), but the setting is the 1960's rapid conversion of the Tama hills rural farmland into planned suburbs of Tokyo (called Tama New Town).

In 1995, Studio Ghibli came out with a very different film.  Whisper of the Heart is a realistically-animated love story about a teenage girl who loves reading books, and the boy who had previously checked out all of the library books she chooses.  It was set in a peaceful suburb in the hills of West Tokyo.  Specifically, the Tama hills.

Development of Tama Hills, as depicted in Pom Poko.

Scenes from Whisper of the Heart:
Walking along Tama Hills, above Tama River.

Walking along Tama River, toward Tama Hills.
It is difficult to describe the cognitive dissonance these two films create.  The first, a story of animals defending nature against human development, and the second, a human-centered love story set in that very development.

Tama Hills (Tama New Town), Tokyo.  Yes, those are golf courses on the hills.  There is an amusement park, too.

The main character, Shizuku, in Whisper of the Heart even composes a song, set to the tune of "Country Road".  She and her friend Yuuoko sing it together.

"Konkuriito roodo, doko made mo
Mori wo kiri, tani wo ume
Uesto Toukyou, Maunto Tama
Furusato ha, konkuriito roodo

Concrete Roads, to everywhere
Cutting forests, burying valleys
West Tokyo, Mount Tama
My home town is a concrete road...

(both laugh)"

(transcribed by

Teenage lovers from Whisper of the Heart, overlooking Tokyo from Tama Hills.

It is possible to visit many of the locations that were used in Whisper of the Heart.

Young raccoon lovers from Pom Poko, overlooking Tokyo from Tama Hills.

More information about locations that inspired Japanese animated films.

Wednesday, March 23, 2016

Food4me study tested Nutrigenomics...and found no benefits

Food4me is a large online study designed to test whether personalized nutrition advice based on analysis of phenotypes (waist cicrumference, blood markers: glucose, cholesterol, carotenes, n-3 index ) or genotypes (SNPs in genes such as MTHFR, FTO, TCF7L2, APOE E4, FADS1 ) could perform better than standard nutritional advice.  The study recruited more than 1,600 volunteers from across Europe to take part.  Participants performed quantified health self-analyses such as biometric measurements and movement counts. They also used a do-it-yourself blood sampling technique that involves drying blood from a finger prick on absorbent paper, which can then be analyzed for more than 92 metabolic biomarkers in a lab.  They also submitted saliva samples that were checked for more than 36 genetic variants that have been linked to nutritional needs and health outcomes.

"A scientific knowledge base was developed, capturing the current knowledge in the field of nutrition
with a particular focus on the interaction of food consumption, nutrient intakes, biomarkers,
genetic variation to health. SNP information comprises risk allele frequencies as well as gene
symbols and functions. The collected scientific knowledge represented in the data base covers
currently 35 food items, 92 biomarkers, 36 genetic variations, 16 different health outcomes, and
180 established interactions based on scientific publications and an expert assessment."

After one year, the results are in.  Although their internet-based nutritional intervention was associated with positive outcomes, a recent whitepaper concluded that, after testing various diets, there were no improved health outcomes from phenotypic or genetic information.

The researchers state that, "despite enormous efforts over the last decade to identify gene variants that define the susceptibility of an individual to a life-style dependent disease, the outcomes of the large-scale profiling studies are rather disappointing. Although a large number of genes and variants have
been found (there are for example around 60 genes that carry a susceptibility risk to develop
type 2 diabetes mellitus (T2DM)), the effect sizes of each individual gene variant are generally
very low. In almost all cases, the risk-variant increases disease risks by only a very few percent..."

Complex Science: The Role of Vitamin D Receptor (VDR) Genotype Polymorphisms (SNPs)

Vitamin D regulates the expression of hundreds of genes, with widespread hormonal and immune effects.  But whether vitamin D is good for you may depend on your genes.  According to one hypothesis, supplemental vitamin D causes allergies and asthma.  [1]

But the biochemistry is complex.  The main circulating metabolite is 25-hydroxyvitamin D or 25(OH)D, a biomarker of vitamin D status.  The active vitamin D metabolite 1,25(OH)2D3 binds to nuclear vitamin D receptor (VDR), which exists from under 500 to over 25,000 copies per cell in many human tissues including thymus, bone marrow, B and T cells and lung alveolar cells.  Gene expression can be varied over a 100-fold range by subtle modifications of introns and promoter regions outside of the gene[1]

The SNPs that seem to affect VDR are not in the exon; they may affect RNA production in the promoter region. It is unlikely that increased or decreased vitamin D sensitivity is simply mediated by a genetic variation in the VDR. Vitamin D requires several enzymatic steps to be activated, transported and degraded; receptor signalling requires several co-factors and all of these may contribute additive or multiplicative effects on vitamin D sensitivity.

Possibly because of this complexity, progress in this field has been slow.  I reviewed several papers, most of which found very small or no effects from common SNPs.  For example, although most papers found insufficient or deficient levels of vitamin D throughout the population, a case-control study only found a small effect on circulating 25(OH)D from one of the SNPs tested. [2].  A randomized controlled trial found effects from more SNPs, but each contributed very small effect sizes. All SNPs tested had, at most, +/-5% effect on circulating 25(OH)D. : "Three SNPs had statistically significant interactions: rs10766197 near CYP2R1, rs6013897 near CYP24A1, and rs7968585 near VDR, with per allele effect sizes ranging from −4% to +3% differences in [25(OH)]."[3]

These complex and unimpressive results are representative of the difficulties inherent in assaying SNPs for clinically-relevant phenotypes.  Most SNPs slightly modify expression or binding of a protein, such that it takes the combination of dozens or hundreds of different SNPs to create any significant phenotype.  Biochemistry is complex, and it is always possible that other gene or protein interactions can ameliorate or exacerbate any small perturbation from any given SNP.

[1] Variants in the vitamin D receptor gene and asthma.  2005.  

[2] Vitamin D levels and vitamin D receptor gene polymorphisms in asthmatic children: a case–control study.

Sunday, March 13, 2016

Trying to Expose Sham "Nutrigenomics Testing"

Denise Minger published a post about her genetic MTHFR status that convinced me to test mine, but now I'm writing to expose this for scam it is. It took me an embarrassingly long time to realize that there is simply no scientific evidence for the claims on,, or any of the other websites that have sprung up around Dr. Yasko's unsupported claims about SNPs and the detox/methylation cycle.  I fell for, and many people are continuing to fall for it.

The idea of correlating individual genetic differences to different nutritional requirements seems scientifically plausible.  But searching Pubmed shows that the claims being made about specific SNPs are not backed up by published scientific research. This scam propagates on plausibility, confusion, and ultimately, apathy.  I was taken in and confused by the veneer of scientific credibility...and when it didn't make sense I assumed I just needed to spend more time on the research.

But there is no research backing up these claims. They can all be traced back to Amy Yasko, who runs a website promoting her personal interpretations and observations.  While she claims not to make any money from sharing her knowledge, she promotes products and testing sold by her husband's company.  Her bibliography appears to include extensive scientific work, but I was unable to locate any of the papers she claims to have published.  She states that she is now "too busy" to publish her results.  I also could not find any confirmation that she is a real doctor (JD or PhD).

The sad truth is that, whether she believes in her own theories or not, this is a classic snake oil supplement gimmick hiding behind a sheen of fake science.  Selling B vitamins as miracle drugs has a long history, because almost everyone feels better with a few B vitamins (that's why they put them in energy drinks).  If you try the more expensive supplements she promotes, you may or may not feel better.  If you do feel better, you're quite likely to promote the gimmick. Most of the people commenting write in to say that they are feeling better, or think that they will when they get their supplement combination dialed in.  If you don't fell better, you might be motivated to try a different high-priced supplement, or you might just give up and stop reading this (or other) blogs.  The result is a huge number of people who appear to have been helped by this approach, and a continuous supply of new customers.

While we all want personally-tailored miracle drugs, maybe the best we can say right now is to eat "whole foods, mostly plants, and not too much"...and skip the overpriced unscientific supplements.

More background on Amy Yasko's nutrigenomics scam.

A brief review of the state of the science for one of Yasko's claims.

My review of the complex problems involved in evaluating Yasko's incomplete metabolic diagrams.

Friday, February 26, 2016

Personality Types

Learning to appreciate diversity.

Clockwise from top left: Phlegmatic, Sanguine, Choleric, and Melancholic.Source.

link to myers brigg personality test

Keirsey Temperament Sorter:

Guardians (SJs)

Conservators (E/ISFJs): ProvidersProtectors
Administrators (E/ISTJs): SupervisorsInspectors

Artisans (SPs)

Entertainers (E/ISFPs): PerformersComposers
Operators (E/ISTPs): PromotersCrafters

Idealists (NFs)

Advocates (E/INFPs): ChampionsHealers
Mentors (E/INFJs): TeachersCounselors

Rationals (NTs)

Engineers (E/INTPs): InventorsArchitects
Coordinators (E/INTJs): FieldmarshalsMasterminds

Personality temperament artwork by Thomas Woodruff:


Wednesday, February 24, 2016

Wildlife Camera Photos - Winter 2015-2016

These photos were taken by a network of motion-triggered wildlife cameras in the Manzano Mountains, New Mexico:




Moore's Law Redux: Connectivity is More Important that Processing Power

While Moore's law continues to slow, traffic on international internet links continues to grow faster than capacity. 

Moore's law, which predicted a doubling of the number of transistors per chip every 18 months, lasted from the 1960's through the early 2000s.  Over the last 10 years, newer chips have cost less and use less energy, but they have not been noticeably faster. Yet, even as Moore's law has slowed, the rise of the internet has made individual computer chips less important.

Chip density is still increasing, but progress has slowed as chip designers bump up against fundamental physical constraints, like the size of silicon atoms.  Also, as chips get smaller and denser the problem of dark silicon has increased.  To combat these limitations, manufacturers have added multiple cores and specialized architecture for graphics processing and other specialized operations. But multicore processors are hard for software to use efficiently. (Ars Technica article.)

So the current state-of-the-art 14nm Broadwell chips will remain best for the next 18+ months.  Intel promises to go to 10nm and then 7nm with new non-silicon technology.  Non-silicon technology may also finally allow faster chip speeds.  3D chip architecture is the next big advance that will improve power efficiency.  

In the meantime, manufacturers have focused on building specialized chips for mobile applications and the internet of things.  It seems the brave new frontiers are really in new mobile and cloud-based applications where energy efficiency matters more than processing power.  Every person in the world will have, on average, three internet-connected devices by 2019.

Global peak Internet traffic volumes rose 37 percent overall in 2015.  In years past, peak  internet traffic increased in excess of 41 percent each year, a rate which implies that traffic is more than doubling every two years. Over the next three years, overall growth is projected to slow to 23% a year (Telegeography 2015 Annual Report, Executive Summary.)

Even with the relative slowing of internet growth, global internet traffic in 2019 will be equivalent to 64 times the volume of the entire global internet in 2005. Globally, Internet traffic will reach 18 gigabytes (GB) per capita by 2019, up from 6 GB per capita in 2014.

IP traffic is growing fastest in the Middle East and Africa, followed by Asia Pacific. Traffic in the Middle East and Africa will grow at 44 percent annually between 2014 and 2019. By 2019, there will be more internet traffic in east Asia than in North America.
(Cisco 2015 analysis.) (Ars Technica has an older analysis)

Saturday, February 20, 2016

Thinking with the Body - Eugene Gendlin's Breakthrough Embodied Cognition Philosophy

Gendlin is the heir to Heidegger and Lakoff.  His work bridges psychotherapy and philosophy.  I can't believe I haven't read him before.

Excerpts from "Thinking at the Edge":
"THINKING AT THE EDGE" (in German: "WO NOCH WORTE FEHLEN") is a systematic way to articulate in new terms something which needs to be said but is at first only an inchoate "bodily sense." It is the difficult task of getting students to attend to what they implicitly knew but could not say and never considered trying to say.

"Oh," one student exclaimed when he grasped what I was looking for, "you mean something about which we have to do hemming and hawing." Yes, that was just what I meant. Another asked: "Do you mean that crawly thing?"

An internally intricate sense leads to a series of statements with certain recognizable characteristics. Statements that speak-from the felt sense can be recognized by the fact that they have an effect on the felt sense. It moves, opens, and develops.

This is in contrast to what we normally call "thinking", which seems to require unitized things which are assumed to be either cleanly identical or cleanly separate, which can be next to each other but cannot interpenetrate, let alone have some more complex pattern. The unit model is regularly the reason why some new insights cannot be said. But to reject the unit model in general is not possible, because it inheres in our language, our machines and in all our detailed concepts. The capacity for breaking out of the unit model cannot be imparted simply by studying Heidegger, McKeon, etc. Critique does not prevent us from falling into the old model.

We must develop a new use of bodily-sourced language with which we can speak directly from the body about many things — especially about the body and language. . Language does not consist just of the words. The situations in which we find ourselves, the body, and the language form a single system together.

We find that when people forgo the usual big vague words and common phrases, then — from their bodily sense — quite fresh colorful new phrases come. There is no way to say "all" of it, no sentence that will be simply equal, no sentence which will simply "represent" what is sensed. One strand emerges from the bodily sense, and then another and another. What needs to be said expands! What we say doesn't represent the bodily sense. Rather it carries the body forward.

People live through a great deal which cannot be said. When the living body becomes able to carry itself forward by symbolizing itself, it acts and speaks from a vast intricacy. . Humans don't happen without culture and language, but with and after language the body's next steps are always freshly here again, and always implicitly more intricate than the common routines. You can instantly check this by becoming aware of your bodily aliveness, freshly there and implicitly much more intricate than the words you are reading.

We need to build new social patterns and new patterns of thought and science. This will be a mutual product no single person can create. On the other hand, if we work jointly too soon, we lose what can only come through the individual in a focusing type of process. Nobody else lives the world from your angle. No other organism can sense exactly "the more" that you sense.

Excerpts from "Three Assertions about the Body":
A felt sense comes. It isn't just there waiting. We have to let it form and come. That takes at least a few moments, sometimes longer. So we understand that a felt sense is a certain development, a certain bit of further life-process. What does it stem from? How can we think about ordinary events and experience in such a way that we could understand what a felt sense is and how it forms?

A felt sense is distinctly something there, something with a life of its own, that we attend to directly. If we attend to our bodies, in the middle of the body it comes, and then it is in an odd sort of space of its own. It brings its own space. In that space the felt sense is a direct object, that, there.

The kind of experience I mean is sometimes attributed to "the unconscious," although such a body-sense is, of course, conscious. We are aware of sensing it when it is there, yet it is true that much of the knowledge that can emerge from it was unconscious before. There is no such directly felt body-sense in the unconscious. When we invite it to come, we can feel it freshly forming. It is not already there, underneath. At most one could say that it forms itself from "the unconscious."

But calling it "unconscious" does not explain this kind of experience. It is only a mysterious name, just as "hunch," "intuition," and "instinct" are mysterious names for it.

What can we say about this kind of experience just from these two examples?

The experience is felt rather than spoken or visual. It is not words or images, but a bodily sense.
It does not fit the common names or categories of feelings. It is a unique sense of this person or this situation.
We must also notice one more characteristic of this kind of experience:
Although such a body-sense comes as one feeling, we can sense that it contains an intricacy. Let me explain that.

Your body-sense of the person you know contains all your past history with that person and what you hope for with that person. It also contains what that person rouses in you and some of your own unresolved troubles. In there as well is the exact way in which you[Page 24]do and don't like the person, and much more. Let me roll all that together and call it "an intricacy." You might be able to think three or four of those things, but most of them remain implicit. Such a body-sense contains an implicit intricacy.

We don't usually think of physical feelings as containing a whole complex mesh. Physical sensations are supposed to be simple. A pain or a sensation is just what it is. It is opaque. We don't expect a hidden complexity, for example, in the stabbing pain of a twisted ankle or in the sensation of red. A complex situation might have led to the twisted ankle, but we don't expect to find the intricacy of the situation inside the pain. What distinguishes the kind of physical sense I am discussing is that it does contain an implicit intricacy, "all that" about that person.

You can sense that it is implicitly complex, even if you don't find any of it out, even if you don't succeed in opening it and entering. I speak of "opening and entering." This kind of bodily experience is a door. If we open it and if we enter, we can go many steps into it...

Thursday, February 11, 2016

The Problem with Ecosystem Services

There is a controversy in the conservation community about monetary valuations.  A recent podcast on Freakanomics looked at rational altruism using a Consequentialist cost/benefit analysis.

The example was between treating HIV and malaria.  A person infected with HIV might cost $100,000, while a person dying of malaria might only cost $1,000 to cure.  Since we can help 100 people with malaria for every one with HIV, shouldn't we focus first on malaria, and only turn to HIV once we've helped everyone we can with malaria?

The logic is sound, but try telling that to a doctor working on HIV (let alone a patient with HIV).  But how else could we decide?

The big idea seems to be to add up the (monetary) costs of charities and look at some simple metric (like lives saved) to pick and choose the best charities.(link to bjorn lomberg's thinktank)  But do we only care about a single metric, a single value?  And how compare education to disease, senile dementia to juvenile delinquency?

The same problems bedevil conservation...

I think the simple answer is that there are no simple answers, and every approach has a place.  If some government minister will only listen to economic arguments, use them... but others will listen to other values, and those also matter.  Whether people care about the scariest diseases (terminal diarhea) or the cuddliest endangered animals (link to cockapo), these interests are meaningful.
There is a long tradition in decision science and economics of critiquing irrational human preoccupation with infrequent, but salient/scary crises (link to risk diagram disasters axis) as opposed to rational actors (link to behavioral economics discussion, maybe wikipedia) dispassionately evaluating statistics.  I try to avoid news sources because of our (link) well-demonstrated cognitive biases, but I don't think we can (or should) "fix" every element of human thinking.

Yes, every decision is a choice to focus on one priority over another, and yes it is not rational to make that decision without comparing and ranking all choices.  But pure rationality doesn't take account of the full richness of human life.  We care about many values, not just The Most Important. Is it absurd to try to save endangered species when many people don't have adequate nutrition?  (link to weird conservation stories, nature conservancy).

Monday, February 01, 2016

Osmotic Regulation of GI Tract

At its most basic level, diarrhoea results from an imbalance of absorption and secretion of ions and solute across the gut epithelium, followed by the movement of water in an attempt to restore the appropriate ion concentrations. Often, this imbalance is caused by the presence of bacteria that secrete toxins that disturb the organization of the epithelium.  NIH

The gut, known as the enteric nervous system, is located in sheaths of tissue lining the esophagus, stomach, small intestine and colon, and plays a key role in human emotions. But few know the enteric nervous system exists, and therefore gut health is often overlooked. Symptoms from the two brains can get confused....

The intestine absorbs nutrients while simultaneously forming a barrier to noxious substances and bacteria. Along its 7 metre length, the human intestine displays regional specialization, which is further marked by the presence of distinct cell types in different areas.

Osmotic laxatives, such as Fleet Phospho-Soda, Milk of Magnesia, or Miralax, and nonabsorbable sugars (such as lactulose or sorbitol), hold fluids in the intestine.  More info.

Wednesday, January 27, 2016

Future of blood testing?

Data is power, and these four potentially-revolutionary blood- or breath-testing companies could help generate next-generation medical insights:

University of Southampton, Sharp Labs Europe is developing a mobile lab-on-a-chip 5-10 years

Integrated Diagnostics has a "sniffer" test to look for lung cancer.

V-chip to test 50 different blood chemical markers with microfluidics is still in development. 5-10 years

Theranos lab testing is already cheap and easy online, but they have recently been investigated by the FDA for failing to prove that their tests are accurate.

Why Are You Interested in EDF's Chemical Wristband Study?

I'm interested in science and the environment. I think we need more science, more data, more documentation.

I've looked into the quantified self movement for personal health improvement and think that a similar focus could transform all of our environments -- especially the indoor spaces we spend most of our time in.

 I recently ordered a Air Quality Meter  to attempt to look at chemicals in the environment.

So I'm also interested in EDF's Chemical Detection Initiative, that recently documented our exposure to hundreds of chemicals in the environment.

The graphic above describes how this technology works.

I'm hoping to learn the identity, industrial use, and possible harm of chemicals from my environment. It would be a great opportunity to learn chemistry! I took the 23andme test last year for my wife and I -- and it was a great opportunity to learn about state-of-the-art genomics.

I'm also interested to connect with others who have similar chemical exposure patterns and join a growing community of people interested in improving their own health and become agents of change to all of society.

Level of Concern pre-test:

Pesticides -4

Air Pollution -3

Chemicals in cosmetics/skin care products - 2

Chemicals in cleaning products - 2

Chemicals in furniture and building materials - 4

Pharmaceuticals - 4

Monday, January 18, 2016

Ecosystem Art

I've previously blogged about cool ecosystem artwork, and wanted to recognize more amazing artists in this post.

The Nature of America stamp series featured the ecosystem artwork of John D. Dawson.

Dawson is one of the best-known artists featured in National Park ecosystem artwork, such as these brochures from Olympic National Park.

Larry Eifert may have done more ecosystem artwork for the NPS than any other artist.

The USFS has a series of posters featuring the ecosystem artwork of Steve Buchanan.

Traditional Chinese Medicine - 5 Phases Theory

Graphic from

Graphic from
For more archetypal correspondences, see

The Traditional Chinese Medicine (TCM) approach to health is based on categories (types, archetypes) and balance. The first thing to note is that stereotypes actually help individualize nutrition and health by putting human differences front and center. One size doesn't fit all when we acknowledge the obvious truth that humans can be more different than similar. Recognizing these differences and similaries is aided by categories. (see danger below).

Secondly, nutrition and health are pretty complicated. Even the simple dictum to "Eat whole foods, mostly plants."(Michael Pollan) hides a huge amount of confusion and contradiction about what is healthy and how to cook it.  Books like "The Perfect Health Diet" are a great place to start and I won't argue with their research showing the optimum ratio of the various macronutrients and amount of micronutrients to consume.  But which spices to eat, what recipes to make, how much exercise to get, and when to wake up in the morning are not covered.  A more intuitive approach is needed to comprehend the human condition.

Third, the importance of balancing constitutions and forces is absent from much of modern nutrition, which acts as if a simple summation of inputs is enough to insure health. Perhaps the most important insight of TCM-based approaches and Hippocratic humours is that health is the sum of harmonious balancing interactions (i.e. homeostasis, for the scientists). There are too many forces and nutrients to consider to balance every input and output analytically. A wholistic approach is needed.

However, one danger of the archetypal approach is the tendency toward simplification and identification. For example, saying that "I am a water-type", or "I am a phlegmatic". Many people resist such limiting classification, rightly so, and with good reason. The trick to using archetypes is to lean on them gently, maintain perspective, and flexibility.  No one is X.  They are themselves, a real, infinitely-complex human system.  But many of us manifest observable types, and recognizing those types gives us the three advantages described above.

 Another danger, perhaps part of the danger listed above, is the hermetic tendency to see all people, phenomena, etc within one system of thought.  No system can be complete. TCM cannot answer all questions, and it is unbalanced to rely on it obsessively. Another closely related danger is the esoteric tendency to compile endlessly complicated tables, enumerations, calculations, and the like, in order to fit all people and phenomena into a system. This is the inevitable result of the hermetic temptation to apply one categorical system to all phenomena.

 Pavlov encountered this when he tried to explain his dogs' behavior using Hippocratic types. He was forced to expand, and then expand again, endlessly redoubling the complexity of the system to attempt to fit a (probably infinite) range of idiosyncratic variation within a comprehensive system. Somewhat the same tendency can be seen in the 16 Type Indicators of Myers Briggs testing, which was an outgrowth of Pavlov's work. The system could easily be expanded to 32, or 64, or.. types, in order to continue to incorporate more degrees of variation. But the cost to understanding and ease of use is progressive.

 As any system becomes more baroquely complicated, it begins to lose the explanatory power of simplicity. In any analytical system, there must be a balance between conceptual simplicity and accuracy.

Traditional Chinese Medicine

"The logic underlying Chinese medical theory - a logic that assumes that a part can be understood only in its relation to the whole -- can also be called synthetic or dialectical.

The character for Yin originally meant the shady side of a slope.  It is associated with such qualities as cold, rest, responsiveness, passivity, darkness, interior, downward, inward, decrease, satiation, tranquility, and quiescence.  It is the end, completion, and realized fruition.

The original meaning of Yang was the sunny side of a slope.  The term implies brightness, heat, stimulation, movement, activity, excitement, vigor, exterior, upward, outward, and increase.  It is arousal, beginning, and dynamic potential.  

All things have Yin and Yang aspects....and any Yin or Yang aspect can be further divided into Yin and Yang.  

Yin and Yang mutually create, control, and transform one another.  Although Yin and Yang can be distinguished, they cannot be separated.   Yin and Yang are always subtly supporting, repairing, and transforming into one another.  This constant transformation is the source of all change.  Organic transformation can occur harmoniously in the normal course of events or sudden ruptures can occur. If Yin and Yang are unbalanced for prolonged periods of time or in an extreme manner, the resulting transformation can be drastic.  

Lao Tzu says:  
In order to expand, it is necessary to first contract.  In order to stregthen, it is necessary to first weaken.  In order to create, it is necessary to first destroy.  In order to give, it is necessary to first take.

In Chinese thought, events and phenomena unfold through a kind of spontaneous cooperation, an inner dynamic in the nature of things.  The key word is Pattern - people and things behave in particular ways not necessarily because of prior actions or impulses, but because their position in the cyclical universe and their endowment with intrinsic natures. 

The Chinese assume that the universe is continuously changing.  The cosmos itself is an integral whole, a web of interrelated things and events.  The desire for knowledge is the desire to understand the interrelationships or patterns within that web, and to become attuned to the unfolding dynamic.

A traditional Chinese landscape painting captures the essence of nature in balance and in flux.  The paiting is like the Taoist symbol, containing Yin and Yang in their proper proportions but constantly interacting and transforming into each other.  

The scene depicts a vast range of elements, from the towering mountain to the little trickling stream.  Nature is shown as a balance of the yielding Yin (foliage, water) and the unyielding Yang (rock, trees).  There are the dynamic (water, people) and the quiescent (mountains, houses); the slow (trees) and the fast (mist); the dark and the light; the solid and the liquid.  All things contain both Yin and Yang.  The water, for instance, is both yielding (Yin) and dynamic (Yang).

The picture is a totality, and each detail takes on meaning only as it participates in the whole.  The mountain is immense by virtue of its smaller foothills; the people are small by virtue of the vastness of nature.  All things are imbued with interactive qualities and dynamics in their relationships to the things around them.

The painting depicts a time and place that through their correspondence with the cosmos become timeless and placeless.  It rediscovers the elemental and continuous course of the cosmic pulsation through the figurative representation of a landscape...The tension created by the correlation between the lines and the washes, the visible and the invisible, fullness and emptiness, endows the landscape with a power to suggest more than the merely visible and open it to the life of the spirit. " 

(from p. 7-17 The Web That Has No Weaver by Ted Kaptchuk)

Friday, January 15, 2016

Why I Plan to Get the Seasonal Flu Vaccine Next Year

Introducing The Virus

Image of flu virus with antigen proteins on phospholipid(?) surface and RNA in the middle. From. Tamiflu works by binding the purple neurominadse proteins. Tamiflu was developed from shikimic acid, which was originally available only as an extract of Chinese star anise but by 2006 30% of the supply was manufactured recombinantly in E. coli.[54][55]

Vaccine viruses are chosen (i.e., February for the Northern Hemisphere flu vaccine) because it takes 6-8 months to grow them in chicken eggs. Health officials would like to grow them in human(?) cell culture, but that it not currently allowed. Eggs are problematic because viruses may adapt to the egg.

"As a result, Immunologically naïve ferrets) are the most sensitive method available for detecting antigenic differences between influenza viruses."(from

Evolution and Types of Virus

H3N2 (swine) flu and H1N1 (avian) flu are main lineages. Major outbreaks occur suddenly and unpredictably through transmission of new varieties from animal hosts. Seasonal (common) flus are derived from the same lineage, but generally evolve slowly and predictably. Each year, novel viruses make the leap from animal to human. For example, during the 2013–14 influenza season, one case of human infection with an new strain of H3N2v virus occurred in a child from Iowa with known direct exposure to swine. Birds seem to have co-evolved with the flu virus and do not mount an immune response to it. Therefore (luckily!) it appears to evolve much more slowly in resevoir species than in humans. This has important implications for the dynamics of seasonal and epidemic flu outbreaks.

Influenza A is the most common. It is highly likely that of all the seasonal influenza strains circulating at the present, one of them will multiply and give rise to the entire seasonal influenza populations in around 5 years. The descendants of all other viruses will most likely be extinct.

For example, the 2014–15 influenza vaccines used in the United States have the same antigenic composition as those used in 2013–14. The trivalent vaccines should contain an A/California/7/2009-like (2009 H1N1) virus, an A/Texas/50/2012-like (H3N2) virus, and a B/Massachusetts/2/2012-like (B/Yamagata lineage) virus. (

The lineage of evolutionarily successful viruses is usually termed the trunk of H3N2 influenza’s evolutionary treea:

The tree is based on hemagluttin protein sequence evolution, colored according to estimated geographic location, indicating high permanence of the trunk in China and Southeast Asia. The genetic changes occur on the neuroamidase and hemoagglutin virus surface proteins, causing antigenic drift. The truck of the H3N3 tree with a single dominant lineage contrasts with more branching trees of other flu types where different varieties often co-circulate, such as H1N1, and Influenza B and C. This graph and these findings are complicated by whole-genome sequencing: a new graph shows overall viral genome evolution in The evolution of epidemic influenza by Martha I. Nelson and Edward C. Holmes Nature Reviews.
Figure courtesy of Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, et al.

Current Trends - CDC FluNet

Is flu increasing...

This chart is from the same page.... The periodicity of flu seasons and epidemics is still being studied. Peaks occur during the winter in northern latitudes at ~2–5 year intervals, usually during H3N2-dominant seasons, since the 1968 pandemic. Recent phylogenetic analysis of viruses from single populations has shown that the virus does not ‘over-summer’, but dies out at the end of each seasonal epidemic, and that subsequent seasonal viral re-emergence is ignited by imported genetic variation.

Or decreasing?

Weekly Map

Wednesday, January 06, 2016

Welcome to the High Desert of New Mexico, USA

Surviving in the High Desert of New Mexico is like visiting another planet.

I suggest you find a house with a good airlock and sunshade, but you won't be able to filter out the cosmic rays; living up here is like being an airline stewardess.

The desert has a way of simplifying human needs: water, oxygen, respect (for the sun), oh, and more water.

The most important thing is water. You have to drink all the time. When you wake up in the morning you must drink a full nalgene; you've lost at least that much through exhalation during the night. I suggest miso bone broth soup to replace the electrolytes as well. Its dry here and you can't always tell when you're sweating because evaporation is so efficient.

Sometimes you can't drink enough water. The answer is coconut water. Always keep some at hand in case of emergencies.

High altitude. One of the commonest complaints (after dehydration, always check that first) is low oxygen. People forget to breathe. You have to really move that diaphragm! Ginseng and other tonifying herbs might help, too. Oh, and bone broth soup. Think like a sherpa.

Sun. I used to go without sunblock, but we're too close to the sun here. Respect the sun. Always wear sunblock when you have exposed skin - or wear a burkha. UV-blocking sunglasses are also, sadly, necessary. I hate wearing glasses, but if you don't the Light will wash away your world. Yes, it is possible to sunburn the back of your eyes.  8-(

Moisturizer. Dry skin is serious. One secret to prevent over-drying is to always end showers with cold water; it tones the muscles and closes pores in the skin so you don't lose all your hard-earned moisture. Never, ever use drying soap. I don't think that should be a problem, but I'm warning you now: Don't let cracks form on your hands or it will be Too Late, and you'll be covered in bandages like a mummy.

 Welcome to New Mexico!

Monday, January 04, 2016

Wetland, Stream, and Species Mitigation Banks

With the November 3, 2015 Presidential Memorandum "Mitigating Impacts on Natural Resources from Development and Encouraging Related Private Investment," mitigation banking has been getting more press.

Back in 2008 the US Army Corps of Engineers (USACE) and the Environmental Protection Agency (EPA) issued the 2008 Compensatory Mitigation Rule governing compensatory mitigation for activities authorized by Corps permits.  Each division of USACE has published Regional Compensatory Mitigation and Monitoring Guidelines.

Mitigation banks are restoration and conservation sites that preserve, enhance, or create important ecological functions that may be impacted elsewhere.  For example, since 2008 wetland banks can invest in the for-profit creation of new wetlands; developers can purchase credits in the bank to mitigate any impacted wetlands in the same watershed as the proposed development.

There are now over 2000 mitigation banks in the U.S.

USACE  runs the RIBITS website, which is their Regulatory in-lieu fee and bank information tracking system.
This map from RIBITS shows the distribution of mitigation banks in the continental U.S.  Some USAE districts already have dozens to hundreds of banks in operation, whereas some, such as the Albuquerque USACE district, have none.

This figure, courtesy of Kevin Janni, shows the distribution of mitigation banks and HUC watersheds in Texas for the Fort Worth and Galveston USACE districts.  Each bank may only be used to offset development within the same watershed.  Due to differing application processes and timelines for different USACE district, some districts have many more banks than others.

Mitigation banks are evaluated based on the quality of the wetlands created, using rapid assessments such as NMRAM.

The 2016 Mitigation Banking Conference will be held in Texas, May 10-13.

Ideal Amount of Potassium and Sodium Consumption to Minimize Mortality.

In the spirit of the type of analyses presented in the Perfect Health Diet, I wanted to post some correlations that appear to imply causation.  These two graphs plot Potassium and Sodium Excretion (which is assumed to be a good proxy for intake, assuming people in the study were at steady-state) versus the Odds Ratio of mortality. The odds ratio is a normalized measure of the probability of death.

The first graph illustrates that in this sample, the more potassium consumed (and hence excreted), the lower the odds ratio of mortality.

The second graph illustrates that mortality is higher for those consuming both more than, and less than, 4 g of Sodium per day.  Interestingly, the increase in mortality risk increases more slowly above 4 g/day than it does below 4 g/ day, suggesting that consuming slightly more than 4 g/ day is healthier than consuming slightly less than 4 g/day.

I think these types of analyses could be used to set standards for a whole range of vitamins, minerals, and perhaps other "Goldilocks" substances.  Goldilocks substances are things which are healthy in moderation, but either too much or too little can be harmful or hazardous.  Obviously, some substances such as toxins and radiation are inherently harmful, even down to the smallest dose (but see hormesis theory).

Source.  Urinary Sodium and Potassium Excretion, Mortality, and Cardiovascular Events N Engl J Med 2014; 371:1267 September 25, 2014.  This study looked at over 100,000 people from dozens of countries.

Bayesian Statistics

A recent post by Scientific American writer and blogger John Hogan got me thinking about Bayesian statistics again.

My favorite explanation of Bayesian statistics was by Nate Silver in The Signal and The Noise.  The basic approach involves incorporating prior estimates of probability into new measures of probability.  The opposing approach, which does not rely on prior knowledge, is termed "Frequentist" statistics and is exemplified Fisher's standard test used with p=0.05 (which implies that a given result would occur "by chance" only 5 in every 100 such tests).

Hogan uses the standard example of cancer tests to illustrate the importance and power of Bayesian thinking, but an astute commenter points out that the real power of Bayesian thinking comes when used in a process that tests, updates probabilities, and tests again, so that each test incorporates the learning from previous tests.

Silver offered a similar example in his book, but a review in the New Yorker points out that Silver got it wrong.   In Silver's case, he applies Bayesian statistics to the probability that global warming is occuring.  But the prior probability is estimated, and Bayesian approaches only improve on standard statistics when prior probabilities are well known.  So while Silver does present a rational means of updating beliefs, since the original belief is not based on statistical data, the resulting analysis cannot be called statistically valid.

Both the New Yorker review and Hogan's thoughts highlight the inherent power of confirmation bias to trump any statistical test, even Bayesian tests.

Friday, January 01, 2016

Top Conservation of Stories of 2015

Looking back on the year, I feel that victories and gained ground made good News:  US Congress acting(!) to ban microbeads,  Supreme court upheld Clean Power Plan to reduce emissions of  mercury by 1,000 million tonnes and thereby save more than 1,200 lives/year.  CO2 reduction plans from the 2015 Paris COP 16.  Administrative action to create a new office of ecosystem service financing (read: more support for restoration) and to standardize and promote mitigation banking.

However, there were some problems.  The gargantuan natural gas leak in S. Ca. highlighted the fact that natural gas leaks way too much to be a clean bridge fuel.  We either need to clean up natural gas or resolve to skip over it altogether.