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.