Thursday, August 16, 2018

Proposed Changes to Regulations Implementing the Endangered Species Act


Regulations for Listing Species and Designating Critical Habitat

Economic Impacts: "the Services will continue to make determinations based solely on biological considerations. However, there may be circumstances where referencing economic, or other impacts may be informative to the public"

Foreseeable Future: use definition set forth in 2009, where foreseeable "extends only so far into the future as theServices can reasonably determine that the conditions potentially posing a danger of extinction ... are probable."

Delisting species: clarifies that the standard for listing or delisting is the same. Important because FWS does not have to "demonstrate that all of the recovery plan criteria had been met before" delisting. Because: Section 4(a)(1) of the Act provides the Secretary `shall' consider the five statutory factors when determining whether a species is endangered, and section 4(c) makes clear that a decision to delist `shall be made in accordance' with the same five factors.”

Not Prudent Determinations: FWS may decide not to designate critical habitat when it is “not prudent”. Currently this can only occur under two circumstances, but the change would allow the Service more discretion. "We anticipate that not-prudent determinations would continue to be rare." This is an effort to avoid lawsuits.

Designating Unoccupied Areas: clarify that the service can do so "When a critical habitat designation limited to geographical areas occupied would (1) be inadequate to ensure the conservation of the species, or (2) result in less-efficient conservation for the species." Further, "In order for an unoccupied area to be considered essential, the Secretary must determine that there is a reasonable likelihood that the area will contribute to the conservation of the species....Because the only regulatory effect of a designation of critical habitat is the requirement that federal agencies avoid authorizing, funding, or undertaking actions that may destroy or adversely modify such habitat, the likelihood that an area will contribute to conservation is, in most cases, greater for public lands and lands for which such federal actions can be reasonably anticipated than for other types of land."

Regulations for Prohibitions to Threatened Wildlife and Plants

(This proposed revision has received the most comments on

Summary: for newly listed species, there would be no legal penalty for “take” of threatened species. Section 7 consultation would still be required. This change would reduce the potential legal liability of APS, while not lessoning our consultation requirements.

“Currently, there are species-specific protective regulations for threatened wildlife in subpart D of part 17, but the Service has not adopted any species-specific protective regulations for plants. The proposed regulations would not affect the consultation obligations of Federal agencies pursuant to section 7 of the Act. Species listed or reclassified as a threatened species after the effective date of this rule would have protective regulations only if the Service promulgates a species-specific rule (also referred to as a special rule).”

This proposed change brings the USFWS regulations in line with the NMFS.

Section 7 Interagency Cooperation

“Nothing in these proposed revisions to the regulations is intended to require that any previous consultations under section 7(a)(2) of the Act be reevaluated….The Services anticipate that the proposed changes, if finalized, will improve and clarify interagency consultation, and make it more efficient and consistent, without compromising conservation of listed species.”

Destruction or Adverse Modification of Critical Habitat: This is a determination that is similar to a determination of Jeopardy for the species as a whole. For clarity, USFWS proposes adding the phrase “as a whole” to the current definition of Destruction or Adverse Modification: “`Destruction or adverse modification' means a direct or indirect alteration that appreciably diminishes the conservation value of critical habitat for the conservation of a listed species.”

The intent is that, “while an action may result in adverse effects to critical habitat within the action area, those effects may not necessarily rise to the level of destruction or adverse modification to the designated critical habitat. In adding the phrase “as a whole” to the proposed revised definition, we intend to clearly indicate that the final destruction or adverse modification determination is made at the scale of the entire critical habitat designation…..Just as the determination of jeopardy under section 7(a)(2) of the Act is made at the scale of the entire listed entity, a determination of destruction or adverse modification is made at the scale of the entire critical habitat designation.”

In each biological opinion, the determination regarding destruction or adverse modification is made by evaluating the effects of the proposed action on the species in light of the overall status of the species, the baseline conditions within the action area and any cumulative effects occurring within the action area.

Effects of the Action: “Confusion regarding application of terms has resulted in time being spent determining how to categorize an effect, rather than simply determining what the effects are regardless of category…. We collapsed the various concepts of direct and indirect effects, and the effects of interrelated and interdependent actions, into the new definition that the effects of the action include all effects caused by the proposed action.”

“The revised definition notes that these effects include “the effects of other activities that are caused by the proposed action.” It includes a distinction between the word “action” which refers to the action proposed to be authorized, funded, or carried out, in whole or in part, by the Federal agency and brought in for consultation with the Services, and “activity” or “activities,” which refer to those activities that are caused by the proposed action but are not included in the proposed action. Under the current definition, these activities would have been considered under either “indirect effects” or “interrelated” or “interdependent” activities. An effect or activity is caused by the proposed action when two tests are satisfied: First, the effect or activity would not occur but for the proposed action, and second, the effect or activity is reasonably certain to occur. “

“Under the first of these two tests, if an effect or activity would occur regardless of whether the proposed action goes forward, then that effect or activity would not satisfy the “but for” test and would not be considered an effect of the action.”

“As a practical matter, application of the “reasonable certainty” standard is done in the following sequential manner in light of the best available scientific and commercial data to determine if incidental take is anticipated: (1) A determination is made regarding whether a listed species is present within the area affected by the proposed Federal action; (2) if so, then a determination is made regarding whether the listed species would be exposed to stressors caused by the proposed action (e.g., noise, light, ground disturbance); and (3) if so, a determination is made regarding whether the listed species' biological response to that exposure corresponds to the statutory and regulatory definitions of take (i.e., kill, wound, capture, harm, etc.). Applied in this way, the “reasonable certainty” standard does not require a guarantee that a take will result, rather, only that the Services establish a rational basis for a finding of take.”

Environmental Baseline: The Services propose a stand-alone definition for “environmental baseline” as referenced in the discussion above in the proposed revised definition for “effects of the action.” The definition for environmental baseline retains its current wording. Moving it to a stand-alone definition clarifies that the environmental baseline is a separate consideration that sets the stage for analyzing the effects of the proposed action on the listed species and critical habitat within the action area by providing the foundation upon which to build the analysis of the effects of the action under consultation.

“It has sometimes been challenging for the Services and Federal agencies to determine the appropriate baseline for those consultations involving ongoing agency actions. The complexities presented in these consultations include issues such as: What constitutes an “ongoing” action; if an ongoing action is changed, is the incremental change in the ongoing action the only focus of the consultation or is the entire action or some other subset reviewed; is the effects analysis different if the ongoing action has never been the subject of consultation as compared to if there is a current biological opinion for the ongoing action; if a change is made to an ongoing action that lessens, but does not eliminate, the harmful impact to listed species or critical habitat, is that by definition a “beneficial action”; and can a “beneficial action” ever jeopardize listed species or destroy or adversely modify critical habitat. Further, the Services request comments as to whether the following language would address these issues: “Environmental baseline is the state of the world absent the action under review and includes the past, present and ongoing impacts of all past and ongoing Federal, State, or private actions and other human activities in the action area, the anticipated impacts of all proposed Federal projects in the action area that have already undergone formal or early section 7 consultation, and the impact of State or private actions in the action area which are contemporaneous with the consultation in process. Ongoing means impacts or actions that would continue in the absence of the action under review.””

Programmatic Consultation: “used to evaluate the effects of multiple actions anticipated within a particular geographic area; or to evaluate Federal agency programs that guide implementation of the agency's future actions by establishing standards, guidelines, or governing criteria to which future actions will adhere.”

Applicability: USFWS proposes to add language clarifying that consultation is not required when a proposed action will not negatively affect listed species or critical habitat in any real, or measurable, significant way; or that are beyond the jurisdictional control of the consulting agencies.

Biological Opinions: “USFWS proposes that the Service may adopt all or part of a Federal agency's initiation package or the Services' analyses and findings that are required to issue a permit under section 10(a) of the Act in its biological opinion. This provision would allow the Services to utilize portions of these documents in the development of our biological opinion to improve efficiency in the consultation process and reduce duplicative efforts. Adoption or incorporation by reference is typically done during consultations, and this provision codifies that approach.”

Expedited Consultation: “ Informal consultation has been an available optional process for 30 years and is most often utilized to address proposed actions that are not likely to adversely affect listed species or critical habitat. In contrast, expedited consultations are a new process and likely involve proposed actions that would otherwise go through the regular formal consultation process and require an incidental take statement. This consultation process is proposed to provide an efficient means to complete formal consultation on projects ranging from those that have a minimal impact, to those projects with a potentially broad range of effects that are known and predictable, but that are unlikely to cause jeopardy or destruction or adverse modification. “

Reinitiation of Consultation: “We propose to clarify that the duty to reinitiate does not apply to an existing programmatic land management plan prepared pursuant to the Federal Land Policy Management Act (FLPMA) or the National Forest Management Act (NFMA). when a new species is listed or new critical habitat is designated. In contrast, specific on-the-ground actions that implement the plan are subject to their own section 7 consultations if those actions may affect listed species or critical habitat.”

Monday, March 05, 2018

Economics Charts

Median Household Income in the 21st Century: Nominal and Real Estimates, January 2000 to January 2018

Forecasts for S&P 500 Trailing Twelve Month Earnings per Share, 2014-2019, Snapshot on 2 February 2018


Wednesday, September 28, 2016

Albuquerque 2016 Monsoon Season

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

Monday, June 20, 2016


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

The Problem with Nutrigenomics

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


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

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

What do genetic testing services measure?

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

Examples: MTHFR – metabolic pathways and nutrigenomics

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

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

Complexities interpreting SNPs

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

Mistakes in genomics data

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

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

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

Tuesday, April 05, 2016

Portable Real-Time Measurement of Air Quality

I recently purchased a Uni-Trend Air Quality Meter.

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

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

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

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

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

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

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

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

Monday, March 28, 2016

Metabolic Pathways

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

The Mayo Clinic - not as many supplements covered.

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

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

SigmaAldrich offers a searchable poster:

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

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

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

A long list of other resources.

Friday, March 25, 2016

Testing a Relevant SNP?

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

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

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

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

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

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

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

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

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

Thursday, March 24, 2016

Tama Hills and Environmental Consciousness in Japanese Anime Films

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

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

Development of Tama Hills, as depicted in Pom Poko.

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

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

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

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

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

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

(both laugh)"

(transcribed by

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

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

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

More information about locations that inspired Japanese animated films.

Wednesday, March 23, 2016

Food4me study tested Nutrigenomics...and found no benefits

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

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

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

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