Sunday, December 28, 2014

Heart Disease and Blood Lipid Panels

Cholesterol is present in the diet and in the blood, and the difference bears repeating: cholesterol in the diet has very little effect on cholesterol in the blood. While cholesterol blood levels are often talked about as "less is more", we would argue that having values too low can be problematic too. For example, based on WHO data, total cholesterol between 200 and 240 is associated with lowest all-cause mortality, but that is just a simple correlation.

Based on an experimental study on a comparable "Westernized" (?) population, the Japan Lipid Intervention Trial found optimal ranges to be:

Total Cholesterol:180-260 (anything above or below has significant p>0.001 increase risk of all-cause mortality)

LDL: 80-200 (anything above or below has significant p>0.01 increase risk of all-cause mortality)

Triglycerides: N/A - no significant relationship.

HDL: anything above 50 has significant p>0.01 decrease risk of all-cause mortality.

Interestingly, LDL values are usually not measured directly, but only calculated using the Friedewald equation, which has been shown to be inaccurate, especially at low triglyceride values. If you really want to drill down on your blood lipids, your doctor should know that the standard total/LDL/HDL panel is outdated and that newer tests are more accurate.... like the NMR LipoProfile test or a VAP test.

These new tests are important, because not all LDL particles seem to cause heart disease. VLDL particles are smaller than average and are more likely to embed in arterial walls, given predisposing conditions like inflammation (C-reactive protein (CRP) is a good marker of inflammation). If your fasting triglycerides are low you probably have normal healthy LDL, but if they are high you may have much more VLDL. If you also have out!

Saturday, December 20, 2014

Chemical Use and Abuse in Agriculture: What's the Problem?

Peter Lehner's recent blog post on ACOEL was inspiring, but also puzzling, because he mentions three problems with agriculture, but only 2 are real problems.

While I agree with the need for a renewed emphasis on environmental contaminants in farming, the issue of 2,4-D seems out of place in his discussion.  Certainly the role of unregulated chemicals in our food supply needs to be brought up to international standards (*cough* Europe).  And certainly the disastrous role of factory farming in harming the environment and, through the over use of antibiotics, breeding new antibiotic-resistant diseases urgently needs to be addressed.

But 2,4-D and glyphosphate are some of the least toxic herbicides available, having been subjected to more scrutiny than any other compound in agriculture. They have been used for decades in both agricultural and turf and domestic garden applications, and the licensing of genetically engineered (GE) crops resistant to these herbicides really doesn't change anything.  2,4-D is already used as a pre-emergence and post-harvest weed control, and the new GE crop gives farmers the option of using it once or twice during the growing season.

These common weedkillers have been used, are currently being used, and will be used, whether or not our country goes down the GE crop road.  What's more, EPA has used the licensing of Dow's Enlist Duo GE soybeans to significantly increase regulation of herbicide use, with the option to review in 6 years.  It should be pointed out that the outcome of GE crops resistant to 2,4-D will likely be the same as it as for glyphosphate: industry will shoot itself in the foot by overusing single-chemical herbicides to the point that weeds evolve resistance.

While other areas of environmental regulation are woefully lacking (antibiotic overuse and GRAS chemicals), the use of herbicides is well-regulated and not a major risk to human or environmental health. NRDC would be well to focus on the important agricultural issues and let settled issues alone.

Thursday, December 18, 2014

Important Nutrients in the Methionine Cycle

Graphic from the inimitable  GSH is glutathione.
Studies suggest that betaine, along with vitamins B6 and B12 and folic acid, helps reduce higher levels of homocysteine. (This article has lots of citations.)  I think there is now good evidence that the problem with methionine  is really a problem with homocysteine.  Having high levels of homocysteine is related to a higher risk of heart disease and stroke.  Food sources of betaine include beets, broccoli, grains, shellfish, and spinach.  More info on betaine.


Also note the importance of amino acids like cysteine, glycine, and serine: Cysteine and glycine are converted to glutathione (an important water-soluble antioxidant) with the addition of selenium.  Pea protein and collagen are good sources of glycine, but neither contains much cysteine.  Serine can reduce homocysteine levels, and pea protein is also a good source.

Paleo Diet Reading List

Reading about human origins can be fascinating, and informative.  It has been said that nothing in biology makes sense except in light of evolution, and the same could be applied to diet. I originally wanted to understand the physiological biochemistry of digestion, but several textbooks later I had lots of facts but very little understanding.  While strolling at the zoo, I realized I needed textbooks that described the differences between animal digestion -- a comparative physiology textbook, perhaps.  But again, after reading all of the most popular titles, I had only scattered facts and no theory of the differences between human and animal digestion, or even between carnivore, omnivore, and vegetarian modes of sustenance.

Luckily, two Harvard professors have written books on human evolution with particular emphasis on how dietary changes made us human.  In the process, they provide the best, although somewhat contradictory, source of information on comparative dietary physiology.  Daniel Lieberman's The Story of the Human Body (2013) is a more traditional telling of human evolution, but it is written in an attempt to answer the question of how our paleo bodies have adapted (or not) to modern lifestyles.  Richard Wrangham's Catching Fire: How Cooking Made Us Human (2009), is an extended argument concerning the importance of cooking to human evolution, but he does deal extensively with the comparative behavior and anatomy of humans, proto-humans, chimps, and other primates.  Only at the end of his book does he tackle the problem of modern dietary choices for humans, and then only as a parting shot.  John Hawkes, at the University of Wisconsin, is often mentioned as an authority on human evolution, and I would include his Great Courses lecture (2011) in this triumvirate of human evolutionary tales.

The above works often reference modern accounts of extant hunter-gatherer tribes to understand what life might have been like during the Paleolithic era.  The most notable of these books are Lee's account of the !Kung San, and I would also suggest Weston A. Price's classic Nutrition and Physical Degeneration: A Comparison of Primitive and Modern Diet and their Effects.  A modern synthesis and review of the same subject matter can be found in Lindeberg (2009).

It is interesting to compare the literature on human evolution with the diet book literature making use of ideas in human evolution.  The originator of the "Paleo Diet", Loren Cordain has several books specifying his interpretation of the evidence.  While his 2002 book specifies a diet that seems more restrictive than what I've read in Lieberman and Wrangham, I haven't had a chance to read his 2012 book yet.

1. Lieberman D. The Story of the Human Body: Evolution, Health, and Disease. Knopf Doubleday Publishing Group; 2013.
2. Wrangham R. Catching Fire: How Cooking Made Us Human. Profile Books; 2009.
3. Price W. Nutrition and Physical Degeneration: A Comparison of Primitive and Modern Diets and Their Effects (Hardback). Benediction Classics; 2010.
4. Lindeberg S. Food and Western Disease: Health and Nutrition from an Evolutionary Perspective. Wiley; 2009.
5. Lee RB. The !Kung San: Men, Women and Work in a Foraging Society. Cambridge University Press; 1979.
6. Cordain L, Friel J. The Paleo Diet for Athletes: The Ancient Nutritional Formula for Peak Athletic Performance. Rodale; 2012.
7. Cordain L. The Paleo Diet: Lose Weight and Get Healthy by Eating the Food You Were Designed to Eat. J. Wiley; 2002.

Wednesday, December 17, 2014

Tuesday, December 16, 2014

Paleolithic Nutrition compared to Modern American Diet

From: Lieberman D. The Story of the Human Body: Evolution, Health, and Disease. Knopf Doubleday Publishing Group; 2013.

Sunday, December 14, 2014

New Innate GMO Potatoes and the Consumer

“When will these scientists stop playing God and just let food give us cancer?” 
- The's response to new low-acrylamide potato.

A new Genetically Engineered (GE) potato has gained regulatory approval for planting in U.S. Ironies and contradictions abound with Conagra's Innate Potato, which may pose more problems for both producers and consumers than it solves.

The new potatoes harbor low levels of acrylamide-generating amino acids.  Acrylamide is categorized as a probable human carcinogen, and the problem of acrylamide in potatoes was first identified in 2002.  Since then, a large-scale effort to reduce acrylamide in potatoes has examined everything from fertilizer applications, to soil quality and planting date, and has finally resulted in a GE potato.

But this new potato presents a problem to McDonalds, etc.  How to promote a potato that fixes a problem most people didn't know was a problem?  Mother Jones points out the conundrum: "The only potential sales pitch would involve the lower dose of acrylamides. But saying "Our new fries might be less carcinogenic than the ones we've been selling you for 50 years" doesn't have much of a ring to it. "

The GMO debate is often between proponents of growers -- GMO is good for farmers -- and proponents of consumers -- GMOs are unnecessary and maybe bad. Up to now, almost all GMO crops have been designed to benefit growers. But this new potato shifts the dynamic. It offers a positive benefit to consumers. Especially, to health-conscious consumers!  But Mother Jones points out what a problematic product this must be to market, as it appears to be tailed specifically for a group of consumers who are already leery of genetic engineering...

Excess or Insufficient Micronutrients?

Some authors have argued that excess micronutrients, specifically zinc, iron, and copper are a cause of a number of diseases, from atherosclerosis to Alzheimer's. (1) But other writers argue that most Americans are micro nutrient-deficient (very few Americans are macronutrient deficient!). (2)

Micronutrients are critical for human health, but many have relatively narrow ranges associated with optimal health.  Assuming that U.S. dietary guidelines are valid (debatable, but a good starting point), how many people really are receiving inadequate or overabundant micronutrients?

I searched journal articles featuring contemporary data from the U.S. NHANES which surveys a representative sample of the U.S. population.  

Large portions of the population had total usual intakes (food and supplement use) below the estimated average requirement for vitamins A (35%), C (31%), D (74%), and E (67%) as well as calcium (39%) and magnesium (46%). Only 0%, 8%, and 33% of the population had total usual intakes of potassium, choline, and vitamin K above the adequate intake when food and multivitamin use was considered. The percentage of the population with total intakes greater than the tolerable upper intake level (UL) was very low for all nutrients; excess intakes of zinc were the highest (3.5%) across the population of all of the nutrients assessed in NHANES.(3)

Population-based studies indicate that vegetarians have lower mean intakes of vitamin B-12 and zinc and higher intakes of fiber, magnesium, and vitamins A, C, and E than do nonvegetarians. Usual intake data suggest a similar prevalence of inadequacy between vegetarians and nonvegetarians for magnesium and vitamins A, C, and E, with both groups at high risk of inadequate intakes of these nutrients. These same data report that vegetarians have a higher prevalence of inadequacy for iron, vitamin B-12, protein, and zinc than do nonvegetarians. Vegetarians should optimize intakes of vitamin B-12, zinc, and protein; and both vegetarians and nonvegetarians need to increase intakes of calcium, magnesium, fiber, and vitamins A, C, and E. (4)

But these studies only analyze reported food intake, which is notoriously unreliable, even, possibly, in NHANES. Interestingly, NHANES also does actual blood tests, and the results from that research found very few physiologyical (as opposed to dietary) deficiencies.  CDC's National Report on Nutritional Indicators (2012, valid for the period 2003-2006,  only found deficiencies in B6 (11%), Iron (women: 10%), Vitamin D (8%), Vitamin C (6%).   This same report indicates that folate supplementation is responsible for lowering deficiency to less than 1% of the U.S. population.  They also note that many women have iodine levels "bordering on insufficiency".  They did not note any micronutrient excesses. (5)


(1) Power Foods for the Brain.  Barnard, Neil.  2013

(2) see, for example, and

(3) J Am Coll Nutr. 2014;33(2):94-102. doi: 10.1080/07315724.2013.846806.
Multivitamin/mineral supplement contribution to micronutrient intakes in the United States, 2007-2010.
Wallace TC1, McBurney M, Fulgoni VL 3rd. (Affiliation: Council for Responsible Nutrition)

(4) Am J Clin Nutr. 2014 May 28;100(Supplement 1):365S-368S.
Nutritional adequacy of plant-based diets for weight management: observations from the NHANES.
Farmer B.PlantWise Nutrition Consulting LLC

(5) Second National Report on Biochemical Indicators of DIet and Nutrition in the U.S. Population. 2012

“A Safe and Affordable Food Supply”: New GMOs Battle Resistant Superweeds

Stacked-trait GMOs
Herbicide-resistant weeds have more than doubled since 2009 to infest approximately 70 million acres of American farmland –an area larger than the states of Ohio and Illinois combined.  20 years after the introduction of genetically engineered (GE) Roundup Ready corn and soybeans, more tools are needed to maintain productivity.  

 GE crops were hailed as a major advance precisely because they did away with the need for more toxic herbicides like 2,4-D: Robert Fraley, executive vice president and chief technology officer at Monsanto, recently affirmed that "herbicide tolerant crops have been a great enabler. They've enabled farmers to use safer and more environmentally friendly chemicals and replace the products that were previously used...The benefits have been so real and so clear. As I said, it's reduced pesticide use."

However, use of Roundup (glyphosate) steadily increased, even as more and more weeds became resistant.  In 2007, as much as 185 million pounds of glyphosate was used by U.S. farmers, double the amount used six years ago, according to Environmental Protection Agency (EPA) data.

2,4-D and Dicambra are herbicides that are already used to “burn down” the weeds in the autumn, and as pre-emergent herbicides as a prophylactic in the spring, before planting.  But up until now these more-toxic herbicides could not be used during the growing season, as glyphosate can on GE corn and soybeans.  More tools were needed to maintain yields.

Enter Dow's Enlist Duo
Dow recently secured regulatory approval to roll out Enlist Duo in 2015, a stacked-trait GE for corn and soybean cultivars.  Stacked traits have already been used to enhance herbicide-resistant Roundup Ready soybeans with Bt, a natural pesticide.  There are also stacked trait soybeans that contain transgenes to produce oils that are less susceptible to rancidity, and commands a premium price on the market. 

The new GE crops will be resistant to both glyphosate and 2,4-D, allowing farmers to kill glyphosate-resistant weeds during the growing season. 

2,4-D is a plant hormone that kills broadleaf plants (but not grasses like corn, or wheat) by overstimulating growth.  In contrast, glyphosate works by inhibiting a crucial plant enzyme that is not present in animals.  Both are widely used in both residential (lawns and gardening) and commercial (farm) settings. 

Resistance Will Develop
Agronomists predict  that resistance to 2,4-D will develop as rapidly as resistance to glyphosate, because farmers will spur evolution by using the same herbicide on the plants in the same fields, successively selecting for anything with resistance.  USDA and EPA have vowed to better manage the technology, but compliance with integrated pest management strategies is voluntary.

2,4D has been known to drift off fields and kill nearby woodlots, fruit trees, and organic crops, so Dow has changed the chemical to reduce volatility and designed special nozzles to better control application.  EPA is “imposing first-time ever restrictions to manage injury to sensitive crops.  The EPA has put in place restrictions to avoid pesticide drift, including a 30-foot in-field “no spray” buffer zone around the application area, no pesticide application when the wind speed is over 15 miles per hour, and only ground applications (with the special nozzles) are permited. 

Another first for the GE crops is that the EPA is also imposing requirements to reduce potential for developing resistant weeds, such as mandating extensive surveying and reporting to EPA and grower education and remediation plans.  EPA will reevaluate after 6 years, and may impose new restrictions at that point. 

Resistant Superweeds
Some of the most common resistant weeds are: Marestail, Giant Ragweed, Volunteer Corn, Common Ragweed, Lambs quarter,  Agronomists idenitify resistant weeds based on the fact “that most... soybeans are RoundupReady, and that if weeds are still in the soybean field at the end of the season, then there must have been a failure of the system (i.e. spraying herbicides didn’t control them)."

"Experience with the Enlist system indicates that even without a fall herbicide treatment, multiple in season application of 2,4D seem to control marestail well.  Doing so will probably result in the development of resistance to 2,4-D in marestail, though, since this is the type of approach that led to glyphosate resistance – multiple applications of the same herbicide for control of the same weed." -Mark Loux, OSU Extension Herbicide Specialist

Resolution Mine gets Go-Ahead

The Resolution mine has been proposed on land between the small towns of Superior and Globe, Arizona, in an area already famous for its Grand Canyon-esque copper mines.  Unfortunately for the Rio Tinto-owned Resolution mining company, the proposed mine was directly underneath a popular campground on National Forest land.  Fortunately for the company, the U.S. Congress has just passed a spending bill with provision to transfer the land from the National Forest to the company, so it looks like the mine will move ahead.

A placemark shows the location of the Oak Flat Campground, the approximate location of the proposed Resolution Mine.

Watch this surreal video highlighting how Resolution plans to mine the ore deposit more than a mile and half below the ground.

 The video reminds me, somehow, of the giant alien mine in Total Recall:

Wednesday, December 03, 2014

Antinutrient Resources

In general, plant secondary metabolites can have positive and negative effects (Weston A. Price). The reason I don't try to categorically avoid them, but treat them with caution, is that these effects are multiplicitious and biological: very hard to predict what they will do, good or bad...

However, unless we know about the problems with antinutrients, we won't know why eating raw flour or dough is dangerous, why green potatoes are toxic, or how many raw red kidney beans it takes to kill a man (not very many).

But on the whole, unless you are allergic, most antinutrients will be digested, and some are actually good for you. For example, this article mentions that inositol hexaphosphate is a break-down product of phytic acid. Most phytic acid is broken down by digestion, and there is evidence that it can have beneficial effects as well as deleterious effects.

This article points out that most sweet potato antinutrients are destroyed by baking, as opposed to boiling. This FAO article on all the major food crops and their antinutrients specifies that " Heating to 90°C for several minutes inactivates trypsin inhibitors", which explains why baked sweet potatoes are nontoxic. (But the article also points out that diseased or moldy sweet potatoes may have toxins that are not completely deactivated by cooking ....moldy vegetables should not be consumed. Apparently, toxins in normal potatoes are also not destroyed by normal cooking methods. Furthermore, sweet potatoes do not have lectins, but normal potatoes do. These compounds can have some antidigestive effects, but most should be destroyed by cooking.

Antinutrients are important, but I think methionine and nutrient density / glycemic index considerations are more important overall. A few potatoes or slices of bread shouldn't hurt most people, but if you have the luxury of chooses less toxic plant products, sweet potatoes and especially squash and pumpkins are some of the best sources of nutrients, with the least amount of antinutrients.

Soylent Formula and Macronutrient Ratios

I'm designing the perfect foodstuff. Inspired by Soylent (video), but they don't understand the basic truth that endurance exercise (and oh-so-much of life is endurance exercise) (or you can watch a video of Peter Attia's self experimentation) is powered by fats, not carbohydrates and sugars.

Just look at these hunter-gatherer-runners (video). In The Story of the Human Body, Dr. Daniel Lieberman concludes that “Like it or not, we are slightly fat, furless, bipedal primates who crave sugar, salt, fat, and

starch,” he writes, “but we are still adapted to eating a diverse diet of fibrous fruits and vegetables, nuts, seeds, tubers, and lean meat. We enjoy rest and relaxation, but our bodies are still those of endurance athletes evolved to walk many miles a day, often run, as well as dig, climb, and carry.”

Soylent Nutrition:
(Carbohydrate/Fat/Protein ratio of 50/30/20):
Ingredients                                                                  Quantity
Soylent Blend                                                                                                      166.2g 
oat flour  36.67
Sweetener, maltodextrin  55.0
rice protein 80% ultra  40.0
vitamin and mineral premix  9.3
Oil, soybean lecithin 2.0
gum acacia rosa 3.5
Salt, sea 0.7
artificial vanilla flavor 0.6
Sweetener, sucralose, Splenda 0.2
Gum, xanthan, Ticaxan, pwd 0.2
Oil, canola 16
Oil, fish, sardine 2.2

Monday, December 01, 2014

Don't Spike Your Blood Sugar

There have been a number of scientific papers in the last couple years, and now a number of high-profile articles (like last week's Time Magazine article "Ending the War on Fat") that have found no correlation between fat -- even saturated fat -- and Alzheimer's, diabetes, cancer, or heart disease. The idea that cholesterol and saturated fat are the cause of heart disease is no longer supported by the best available science.

However, there is still broad consensus among health professionals that we need to avoid processed, sugary, and high-glycemic foods. High-glycemic foods are energizing for an hour or two but then cause sleepiness and craving for more (usually high-glycemic) snack foods. These foods are dangerous because they raise blood sugar, leading to a crash afterwards, a "roller-coaster" blood sugar dynamic that promotes over-eating and a variety of diseases.

Gary Taubes, in Good Caloreis Bad Calories, explains how sugar metabolism makes you fat:

"Glycerol phosphate is produced from glucose when it is used for fuel in the fat calls and the liver, and it, too, can be burned as fuel in the cells. But glycerol phosphate is also an essential component of the process that binds three fatty acids into a triglyceride. It provides the glycerol molecule that links the fatty acids together. In other words, a product of carbohydrate metabolism --i.e. burning glucose for fuel-- is an essential component in the regulation of fat metabolism: storing fat in the fat tissue. In fact, the rate at which fatty acids are assembled into triglycerides, and so the rate at which fat accumulates in the fat tissue, depend primarily on the availability of glycerol phosphate. The more glucose that is transported into the fat cells and used to generate energy, the more glycerol phosphate will be produced. The the more glycerol phosphate produced, the more fatty acids will be assembled into triglycerides. Thus, anything that works to transport more glucose in the fat cells -- insulin, for example or rising blood sugar, will lead to the conversion of more fatty acids into triglycerides, and the storage of more calories as fat."

"So yes, dietary fat is responsible for fat accumulation, but it is carbohydrates that mediate the accumulation, and the energy balance of the body as a whole. Don't spike your blood sugar, and your body will continue burning fat, not storing it."

Sunday, November 23, 2014

"Fewer than 5,000 remain"

The U.S. Fish and Wildlife Service recently listed the Gunnison Sage Grouse as "Threatened" under the Endangered Species, act, one step shy of being actually "Endangered".  The ESA specifically prohibits killing a species listed as Threatened or Endangered.

The outcry has been significant, to the point that the Colorado Governor (a Democrat) is preparing a lawsuit in opposition. (Durango Herald)

Only a few scattered subpopulations currently remain out of the historic vast swath of occupied habitat.  Source: WildEarth Guardians Species Fact Sheet

The largest population, in the Gunnisun Basin, appears to be stable and not at risk, but many of the subpopulations continue to shrink.  Source:  USFWS Fact Sheet.

A chart of the small subpopulations showing overall decline since the late 1990's.  Since 2011 there appears to be a promising increase.

However, because the Gunnison population has increased since the 1990's and makes up the largest share of the total population, the total population has increased since 1996.

Saturday, November 22, 2014

What Do Carnivores Dream About?

Anyone with a house cat already knows the simple truth of a new study on the comparative physiology of sleep across mammals. Carnivores sleep much more than would be expected compared to herbivores and omnivores:

Of course, these data don't answer the original question, but only raise more questions.

This website uses the data to conclude that humans should eat a vegetarian diet, because human sleep requirements match those on the Herbivore sleep regression, and we don't get as much sleep as other omnivores of the same body weight.  But based on discussion in The Story of the Human Body: Evolution, Health, and Disease by Daniel E. Lieberman humans in their modern form -- i.e. that would be recognizable as human today -- cooked their food, which consisted of vegetables and meat and fish.  None of the other animals in this study cook their food.  Perhaps our higher quality diet allows us to spend less time digesting and more time alert?

But herbivores spend very little time asleep!  In fact, from this data, one might conclude that a limit on the size of herbivores is the number of hours in a day.... the largest herbivores spend almost the entire day (and much of the night) awake and, probably, eating.  In contrast, carnivores sleep the most, presumably because they can satisfy their nutritional requirements with less time and effort.

Why don't humans sleep more?

Wednesday, November 19, 2014

Threatened and Endangered Species around Albuquerque, New Mexico

Threatened and Endangered Species from Bernalillo County, New Mexico:
Mexican spotted owl (Strix occidentalis lucida) USFWS T State S The owl inhabits canyon and forest habitats across a range that extends from southern Utah and Colorado, through Arizona, New Mexico, and west Texas, to the mountains of central Mexico. They require mature, old-growth forests of white pine (Pinus strobus), Douglas-fir (Pseudotsuga menziesii), and ponderosa pine (Pinus ponderosa); steep slopes and canyons with rocky cliffs for their habitat.
Southwestern willow flycatcher (Empidonax traillii extimus) USFWS E
State E The southwestern willow flycatcher breeds in relatively dense riparian tree and shrub communities associated with rivers, swamps, and other wetlands including lakes and reservoirs. Historically the southwestern willow flycatcher nested in native vegetation including willows (Salix sp.), seepwillow (Baccharis salicifolia), boxelder (Acer negundo), buttonbush (Cephalanthusoccidentalis), and cottonwood (Populus sp.). Following modern changes to riparian communities, this subspecies still nests in native vegetation, but also uses thickets dominated by non-native tamarisk (Tamarix sp.) and Russian olive (Elaeagnus angustifolia), or in mixed native non-native stands

Yellow-billed Cuckoo (Coccyzuz americanus) USFWS T
State S Status applies only to western population beyond the Pecos River Drainage; breeds in riparian habitat and associated drainages; springs, developed wells, and earthen ponds supporting mesic vegetation; deciduous woodlands with cottonwoods and willows; dense understory foliage is important for nest site selection; nests in willow, mesquite, cottonwood, and hackberry; forages in similar riparian woodlands;

Rio Grande Silvery minnow (Hybognathus amarus) USFWS E
State E The Rio Grande silvery minnow extirpated; historically Rio Grande and Pecos River systems and canals; reintroduced in Big Bend area; pools and backwaters of medium to large streams with low or moderate gradient in mud, sand, or gravel bottom; ingests mud and bottom ooze for algae and other organic matter; probably spawns on silt substrates of quiet coves.

New Mexico meadow jumping mouse (Zapus hudsonius luteus) USFWS E
State E
The New Mexico meadow jumping mouse (jumping mouse) is endemic to New Mexico, Arizona, and a small area of southern Colorado (Hafner et al. 1981, pp. 501-502; Jones 1999, p. 1). The jumping mouse appears to only utilize two riparian community types: 1) persistent emergent herbaceous wetlands (i.e., beaked sedge and reed canarygrass alliances); and 2) scrub-shrub wetlands (i.e., riparian areas along perennial streams that are composed of willows and alders) (Frey 2005, p. 53).

Other Special-Status Species in Bernalillo County, New Mexico:

Obsolete Viceroy Butterfly (Limenitis archippus obsoleta)                       USFWS SOC
Slate Millipede (Comanchelus chihuanus)                                               USFWS SOC

Burrowing owl (Athene cunicularia) USFWS SOC Associated with prairie dog (Cynomys sp.) towns in dry, open, short-grass, treeless plains.

Common black-hawk (Buteogallus anthracinus)
State NM T
Southwestern U.S. is the northern extent of this species’ range. Occurs in New Mexico almost exclusively during the breeding season and in migration. Breeding populations known chiefly from the Gila River Valley in the southwestern portion of the state and from along the Mimbres River and the Rio Hondo watershed. Strongly tied to cottonwood gallery forests. In Texas breeds in or near the Trans-Pecos Region, with breeding documented in particular in the Davis Mountains and possible breeding along the Rio Grande. In New Mexico, uncommon summer resident, generally, restricted to the mountainous riparian habitats of the San Francisco, Gila, and Mimbres river drainages. 

Neotropic Cormorant (Phalacrocorax brasilianus)
State NM T
The Neotropic Cormant reaches its northern distribution in southern New Mexico. It feeds in lakes and wetlands.

Bald eagle (Haliaeetus leucocephalus alascanus)
State NM T
Occurs in New Mexico year-round. Breeding is restricted to a few areas mainly in the northern part of the state along or near lakes. In migration and during winter months the species is found chiefly along or near rivers and streams and in grasslands associated with large prairie dog colonies. Typically perches in trees.

Northern aplomado falcon (Falco femoralis septentrionalis)
State E
Associated with semi-desert grasslands with scattered yuccas, mesquite, and cactus.The species has also been reintroduced on the Armendaris Ranch in Socorro and Sierra Counties and on lands administered by the BLM, White Sands Missile Range, and the SLO beginning in 2006.

Peregrine falcon (Falco peregrinus)
State T
A year-round resident and local breeder throughout NM, nests in tall cliff eyries; also, migrant across state from more northern breeding areas in US and Canada, winters along coast and farther south; occupies wide range of habitats during migration, including urban, concentrations along coast and barrier islands; low-altitude migrant, stopovers at leading landscape edges such as lake shores, coastlines, and barrier islands.

Arctic peregrine falcon (Falco peregrinus tundrius)
State NM T
Winters along coast and farther south; occupies wide range of habitats during migration, including urban, concentrations along coast and barrier islands; low-altitude migrant, stopovers at leading landscape edges such as lake shores, coastlines, and barrier islands.

Southwestern Willow flycatcher (Empidonax trailli extimus)
State NM E
The flycatcher is a summer breeder within its range in the United States. It is gone to wintering areas in Central America by the end of September. For nesting, requires dense riparian habitats (cottonwood/willow and tamarisk vegetation) with microclimatic conditions dictated by the local surroundings

Northern goshawk (Accipiter gentilis)
State NM S
Breeds in coniferous forests; winters in farmlands, woodland edges, and open country. Breeds from Alaska east through Mackenzie and northern Quebec to Newfoundland, and south to New Mexico, Great Lakes, and New England; also southward to northern Appalachians. Winters south to Virginia and Southwest.
Unlikely to occur in project area due to lack of coniferous forest habitat.

Broad-billed hummingbird
State NM T
Reaches extreme northern range in desert canyons of southern New Mexico with dense mesquite thickets.
Unlikely to occur due to lack of canyon habitat.

White-eared hummingbird (Hylocharis leucotis)
State NM T
Irregular summer visitor to extreme southeastern Arizona; rare in New Mexico and Texas. Found in Mountain woodlands.

Brown Pelican (Pelecanus occidentalis)
State NM E
Generally found in warm marine waters, rarely occurring inland.  Only individuals seen in New Mexico, near water. May be storm-driven birds that moved inland during duress.

Baird's sparrow (Ammodramus bairdii)
State NM T
A winter resident in New Mexico and Texas. Generally prefers dense, extensive grasslands with few shrubs. Avoids heavily grazed areas.

Bell’s Vireo
State NM T
A small insectivorus bird, prefers dense vegetation of scrubby woodlands, old fields, or mesquite brushlands.

Gray Vireo (Vireo vicinio)
State NM T
Species strongly associated with piƱon-juniper and scrub oak habitats. Distributed mainly across the western two-thirds of the state. Prefers gently sloped canyons, rock outcrops, ridge tops, and moderate scrub cover. 


Spotted Bat (Euderma maculatum)
State T
Found in open habitats, Ponderosa Pine forests, and marshlands. Suitable roosting sites limits distribution to areas within flying distance of cliffs and stony outcrops. (Adams, 2003)

Pale Townsend’s Big-eared Bat (Corynorhinus townsendii)
State S
Habitat includes montane forests and arid habitats with limited desert scrub vegetation.  Roosting sites include caves, cliffs, and rock ledges but have been found in abandoned mines and other man-made structures. (Adams, 2003)

E = Endangered. Any species considered by the USFWS as being in danger of extinction throughout all or a significant portion of its range. The ESA specifically prohibits the take of a species listed as endangered. Take is defined by the ESA as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to engage in any such conduct.
T = Threatened. Any species that is likely to become an endangered species within the foreseeable future throughout all or a significant portion of its range. The ESA specifically prohibits the take (see definition above) of a species listed as threatened. 

Wednesday, November 12, 2014

Comparative Physiology: Maximum Lifespan

A conundrum if the amino acid methionine is a determinant of maximum lifespan: Why do carnivores and vegetarians live the same? Perhaps it could be for different reasons.... antinutrients for the latter and methionine for the former. These are universal rules that apply even between disparate physiologies. I haven't been able to find any papers that examine methionine diet content versus longevity.
SourceEcology and mode-of-life explain lifespan variation in birds and mammals, Proceedings of the Royal Society BDOI: 10.1098/rspb.2014.0298

This is a valuable resource on important "carninutrients" lacking in vegetarian diets.  

Monday, November 10, 2014

Wendell Berry on the Problem of Private Land Ownership

"We share a common health....

....If we have the "right to life" as we have always supposed, then that right must stand upon the further right to air, water, food, clothing, and shelter.

It follows that every person exercising the right to hold private property has an obligation to secure to the rest of us the right to live from that obligation to use it in such a way as to not impair or diminish our rightful interest in it.

 But --and here is the catch-- that obligation on the part of the landowner implies a concurrent obligation on the part of society as a whole. If we give our proxy to the landowner to use-- and as is always implied, to take care of -- the land on our behalf, then we are obliged to make the landowner able to afford not only to use the land but also to care properly for it.

This is where the grossest error of our civilization shows itself. In giving a few farmers our proxies to produce food in the public behalf for very little economic return we have also given them our proxies to care for the land in the public behalf for no economic return at all. This is our so-called cheap-food policy, which is in fact an antifarming policy, an antifarmer policy, and an antiland policy.

We hold the land under a doctrine of private property that in practice acknowledges no common health."

---from Another Turn of the Crank.  Essays by Wendell Berry.

Saturday, November 08, 2014

Problems with Wheat

Discoveries in the last 15 years have implicated wheat in a range of autoimmune diseases.  Celiac disease affects a small (but increasing) segment of the population.  This disease is triggered by an allergy to gluten, a specific protein in wheat.  But there are at least two other important antinutrients in wheat that affect everyone, whether or not they are gluten-intollerant. 

The first, and possibly more benign, is WGA (Wheat Germ Agglutenin), a toxic component of wheat that is usually destroyed by cooking.  Importantly, it is much more sensitive to wet heat than dry heat(i.e. baking), which may not be 100% effective in denaturing WGA. This agluttinin, (a type of lectin) can bind to receptors in the small intestine, effectively "gumming them up" and preventing complete absorption of nutrients.  In addition to limiting the nutritional value of meals containing WGA, lectins can also cause gastrointestinal distress or dysbiosis by passing more undigested food to the large intestine, where it is fermented by the microbiota.

The second, and more worrisome component of wheat, is gliadin.  Sometimes referred to as a type of or component of gluten, in 2000 gliadin was found to mimic the ability of cholera toxin to open the tight junctions between intestinal epithelial cells.  By activating the "zonulin" receptor, gliadin (and cholera toxin) make the gut permeable to large particles of food, which enter the body undigested.  Until the early 1980's it was believed that the human digestive system was impermeable to larger particles of food and that only food that was completely broken down into its amino acid, sugar, and lipid components could be absorbed by the body.  This is mostly true, but gliadin can short-circuit the natural process.

Source: Fasano A. Zonulin and Its Regulation of Intestinal Barrier Function: The Biological Door to Inflammation, Autoimmunity, and Cancer. Physiological Reviews. 2011

The outcome of increased intestinal permeability is immune exposure to the entire gamut of ingested substances.  The resulting inflammatory response binds and removes the transgressive food particles, but not before 1) increasing systemic inflammation, and 2) teaching the immune system to recognize and react to a very large array of compounds ... some of which may look like compounds in the human body. 

Therefore, ingestion of wheat sets up the necessary and sufficient conditions for the generation of autoimmunity.


Pusztai A, Ewen SWB, Grant G, Brown DS, Stewart JC, Peumans WJ, Van Damme EJM, Bardocz S. Antinutritive effects of wheat-germ agglutinin and other N-acetylglucosamine-specific lectins. British Journal of Nutrition. 1993 July;70(01):313–321.
Fasano A. Leaky Gut and Autoimmune Diseases. Clinical Reviews in Allergy & Immunology. 2012 February 1;42(1):71–78.

Fasano A. Zonulin and Its Regulation of Intestinal Barrier Function: The Biological Door to Inflammation, Autoimmunity, and Cancer. Physiological Reviews. 2011 January 1;91(1):151–175.

Drago S, El Asmar R, Di Pierro M, Grazia Clemente M, Tripathi A, Sapone A, Thakar M, Iacono G, Carroccio A, D’Agate C, et al. Gliadin, zonulin and gut permeability: Effects on celiac and non-celiac intestinal mucosa and intestinal cell lines. Scandinavian Journal of Gastroenterology. 2006 April;41(4):408–419.

Further Reading:

Gluten Freedom: The Nation's Leading Expert Offers the Essential Guide to a Healthy, Gluten-Free Lifestyle Hardcover – April 29, 2014
by Alessio Fasano and Susie Flaherty

Wheat Belly: Lose the Wheat, Lose the Weight, and Find Your Path Back to Health Paperback – June 3, 2014
by William Davis

The Wahls Protocol: How I Beat Progressive MS Using Paleo Principles and Functional Medicine Hardcover – March 13, 2014
by Terry Wahls M.D. and Eve Adamson 

Tuesday, November 04, 2014

Paleo Diet

Over the last million years a group of primates began walking upright. This genus, Homo, (our species, Homo sapiens sapiens, evolved about 200,000 years ago) is distinguished by a number of physiological and morphological adaptations to their environment.   Importantly, a change in diet from our primate relatives appears to have been the key change that drove our recent evolution.

What was the paleo diet of the genus Homo?

Stephan Guyunet provides this analysis:

"All we know is that they ate some meat. Although humans eventually became top-level predators, we also don't know whether these early humans were actively hunting, or simply scavenging what other predators left behind-- perhaps using their tools to access gristle, brain, and marrow inaccessible to other animals.

At the same time as tool-marked bones appear in the archaeological record, early humans began undergoing a remarkable physical transformation, which represented (in large part) a progressive genetic adaptation to a new subsistence strategy. Our brain doubled in volume, our gut became smaller, and the proportion of small intestine to large intestine increased. Our teeth and jaws became smaller and less robust (Daniel Lieberman. The Story of the Human Body. 2013).

What does this signify? The consensus is that these changes occurred in response to a shift toward a so-called "high-quality" diet. This means a diet that has a higher calorie density and contains less fiber, relative to the typical primate diet of leaves and low-calorie fruit (the latter is not at all suitable for a modern human). The small intestine is what breaks down and absorbs protein, carbohydrate, and fat, while the large intestine ferments fiber to extract calories from it. The shift from a large-intestine-dominant gut to a small-intestine-dominant gut signifies a shift from getting most calories from intestinal fiber fermentation, to getting most calories from direct absorption of protein, carbohydrate, and fat."

Sunday, November 02, 2014

Another Ecosystem Analogy

"....The idea [is] that fewer excess carbs in the gut leads to more competition which favors indigenous gut microbes over bad or pathogenic bacteria. A good example in this paper likens friendly gut microbes to your lawn. “It is thought that our commensal, or friendly, bacteria serve as a kind of lawn that, in commandeering the rich fertilizer (carbs) that courses through our gut, out-competes the less-well-behaved pathogenic “weeds.” The more healthy grass you have, the fewer weeds will be able to become established.” But if you were to spray your lawn with roundup (like antibiotics) and continue to add fertilizer, soon you will have a weed-filled yard. According to the authors: “Resident microbes hold pathogens at bay by competing for nutrients.”


Tuesday, October 28, 2014

How Long Does Food Stay in the Stomach?

I started wondering how long food stays in the stomach. They say fruit moves through quickly, but can you feel food exiting your stomach, passing through the pylorus to the small intestine?  How does it happen? Bit by bit or in one semi-continuous emptying?  

According to the best website on the topic, "when the peristaltic contraction reaches the pylorus, its lumen is effectively obliterated - chyme is thus delivered to the small intestine in spurts....Liquids readily pass through the pylorus in spurts, but solids must be reduced to a diameter of less than 1-2 mm before passing the pyloric gatekeeper. Larger solids are propelled by peristalsis toward the pylorus, but then refluxed backwards when they fail to pass through the pylorus - this continues until they are reduced in size sufficiently to flow through the pylorus."

If you eat after a meal (i.e. snacking), before the stomach has emptied, what happens? Any liquids or very small bits would almost immediately begin passing the pylorus, but large chunks would swirl in the grinder until they're small enough. But can the stomach segregate new snack bits from older meal bits? Or does adding snacks on top of still-digesting meals slow exit of all food while the stomach continues grinding?  Interestingly, I found out that one of the functions of the stomach is to coagulate colloids (e.g. milk) with acid and protease so that they don't immediately enter the small intestine.

Has does the stomach know when to empty? What controls it? The small intestine can exert negative feedback control on the stomach, slowing down peristalsic emptying if the small intestine is full. In other words, the stomach is a holding tank until the small intestine is ready, and it slows down or speeds up peristalsis to small intestine.

I think even the feeling of intense hunger, which feels like it emanates from the lower stomach, is not the stomach at all but the small intestine communicating, "I'm ready for more!". It is the body speaking to the mind....that raw pang of yearning and focus is the voice of the body.

This website is a great resource!

Wednesday, October 22, 2014

New Paper Continues Confirmation of Age-Defying Diet

In the last 15 years a number of research groups around the world have converged on an explanation for how dietary restrictions can lead to lifespan extension. These teams have narrowed the search to a handful of compounds.*  The central candidate, by far, is an essential amino acid called methionine, found in high amounts in meat and fish, but in very low amounts in most plant foods.

Reducing consumption of this single amino acid extends lifespan by 15-44% in every laboratory animal tested to date. This effect is sufficient to completely explain previous results that found dietary restriction of total calories led to lifespan extension. Turns out it wasn't the calories -- it was the methionine.

Methionine restriction reduces visceral fat with concomitant decreases in basal insulin, glucose, and leptin, and increased adiponectin and triiodothyronine. Methionine restriction also prevents age-associated increases in serum lipids.(source)

A new paper published this month by Koziel et al confirms previous methionine restriction results in human cell culture, mice, ratsfruit flies, and yeast. Koziel et al used human cell culture to specifically examine mitochondrial function and showed that oxidative stress is reduced by this dietary intervention.  This work supports the traditional free radical theory of aging-by-oxidative stress.

Methionine is an interesting amino acid because it promotes growth, including muscle and bone development. It is essential, and that is the point: restriction appears to promote a healthy stress-response that can confer adaptive resilience to senescence.  Other researchers have postulated that methionine restriction causes an increase in autophagy, the process whereby cells break down and recycle unused or damaged cell components. Instead of the free radical theory of aging, this theory would postulate that Methionine restriction induces a starvation-type response where cells begin to recycle their constituents at an increased pace. In this theory, "stress" is a good state to be in, because it puts cells in an active phase of self-repair. Cite: 1 and 2.

* The two other most promising age-defying compounds are rapamyacin (an antibiotic with a plethora of strange and powerful effects throughout the body) and resveratrol.  

Farewell to a good pair of Army Boots

Fresh out of the box, I took my Magnum Boots Desert Spider 8.1 HPi "Moon Boots" for a test in my backwoods.  I walked on rain-slick logs over the creek and ran up and down thick pine duff hills.  They were a good pair of boots with some pretty serious flaws, but also lots of good design ideas.  And they actually fit my feet, which is the most important thing a pair of boots can do.  That's the reason I wore them for two full field seasons even after the "rope gripping" tore out after the first couple months.

Tear on cheaply-stiched "rope gripping" patch tore out after the first couple of months.  Also note the Aqua-sealed drain holes on the fore foot, definitely the worst place to put holes in a boot!

They never did break in, though -- up to the day I finally trashed them they still felt stiff where the material has to flex around the ankles.  And the "drain holes"  were a big mistake: they let every puddle, no matter how small, splash in, plus all the dust and dirt on the trail.  I eventually plugged them with Aquaseal. 

Boot linings are usually the first to tear out, and these boots were no exception. 
Synthetic boots are on par or better than leather boots now, and the weight and cost savings of foregoing Vibram rubber is a fair tradeoff.  I just bought another pair of synthetic boots but decided to go with Irish Setter hunting boots.  The fit isn't as good for my toes, but they are lighter and seem to be of higher quality construction.  Time will tell.  
Note wear on the non-vibram soles.

(Note: my Desert Spider boots were size 9 wide)