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.”