Wednesday, July 23, 2014

Legumes and Potatoes are Certainly P-A-L-E-O

Tubers are as Ancient as Bipedalism

The Paleolithic Age started ~2.6 mya and extended to only 12,000 years ago. The last Homo neanderthalensis existed up to ~25,000 years ago, and in fact their DNA exists in nearly all of us. One of our ancient human ancestors, Australopithecine boisei (formerly known as Paranthropus boisei), did not eat the stiff and hard textured nuts that their tough jaws and mean bite alluded to, but instead appeared to consume a diet rich in soft sedge tubers (including tigernuts) that grew buried in the soft land near waterways and shorelines. He had nickname, Nutcracker man. And lived with great longevity from 2.4 mya to 1.4 mya, impressively longer (that I'm aware of) than any other hominin ancestor that humans have had. Nutcracker man indeed started our human evolution with increasingly larger brain sizes during his 1 million year reign and likely planted the seeds for yet even larger brain sizes in 'subsequent prototypes' in Homo.

The moors, peatlands, and marshlands of Scotland and northern Europe were very similiar to the Paleo 'nutriscape' and terrain during the transition from Ice Ages to mega C4 sedge and grasslands. I suspect our ancestors consumed a pretty heady diet of plant fiber and starch because sedge tubers/corms/rhizomes (including tiger nuts), cattail bulbs, water chestnuts, wild carrots, yams, and other starchy roots were common underground storage organs (USOs).  Tubers like tigernuts and other underground sedge roots had a different, more evolved form of photosynthesis that required less molecules of water and selected during the shift in weather from moist and aquatic to dry grasslands. The final electron donor switched from water which had become intermittently scarce to sugar/starch molecules. During intermittent freezing and warm periods, sugar and starch additionally served another role as a buffer from cold trauma and frost.

Tigernuts and sedges were offspring of the new C4 photosynthetic plants and grew plentifully. Papyrus is also an example of a sedge. C4 plants and roots produced a radiation signal that was found in great amounts in C13/C14 isotope density studies from enamel and Nutcracker remains from 1-2 mya. Being sweet, starchy and high in protein, it was no wonder that our ancient ancestor found sedge tubers and tigernuts so delightful to exploit.

In the Paleolithic Age, both Homo and Australopithecine fed themselves well enough to not only survive the Ice Ages, predators, pathogens and newly discovered bipedalism, but also to grow a higher capacity cranium. One of the leading theories for this is digestible carbohydrates. Without complex carbohydrates and high fiber starches from USOs it is unlikely that fruit and honey alone would have exploded the process of encephalization. For tens of millions of years our primate cousins had failed to forge larger brains as frugivores. What changed? Researchers Brown et al reviewed the diet of our primal forefathers and noted they likely consumed "high carbohydrate sources including plants particularly those with underground storage organs (USOs) such as reed mace (Typha), common reed (Phragmites), water chestnut (Trapa natans) and yellow water lily (Nuphar lutea). USOs have repeatedly been implicated in hominin evolution and particularly encephalisation and bipedalism in the Africa [83], [72], [84]–[85] although this has been challenged [86]."

USOs provide valuable nutrients for brain fuel: zinc, magnesium, carbohydrates, sucrose, vitamin C (one serving, almost 50% of RDA), and protein. In terms of the brain-gut evolution, digging for tubers also tied our ancestors to the ground in more ways than the descent from the arboreal heavens to terra firma living and bipedalism. SBO probiotics (soil-based organisms) clung to every new bite of dirt-covered tubers. For tree hugging primates, the new terrain brought not only fresh and novel food, but also broad exposures to a whole new world of micro-organisms. Remember, diet (dirt lol) is the biggest driver of the microbiota and evolution of the gut. Transformation of gut and brain occurred simultaneously I believe. Our herbivore colon shrunk as our brains exponentially expanded... or even doubled: gut and cranium.

AG Brown et al, 2013
Site Distribution at the Edge of the Palaeolithic World: A Nutritional Niche Approach

This paper presents data from the English Channel area of Britain and Northern France on the spatial distribution of Lower to early Middle Palaeolithic pre-MIS5 interglacial sites which are used to test the contention that the pattern of the richest sites is a real archaeological distribution and not of taphonomic origin. These sites show a marked concentration in the middle-lower reaches of river valleys with most being upstream of, but close to, estimated interglacial tidal limits. A plant and animal database derived from Middle-Late Pleistocene sites in the region is used to estimate the potentially edible foods and their distribution in the typically undulating landscape of the region. This is then converted into the potential availability of macronutrients (proteins, carbohydrates, fats) and selected micronutrients. The floodplain is shown to be the optimum location in the nutritional landscape (nutriscape). In addition to both absolute and seasonal macronutrient advantages the floodplains could have provided foods rich in key micronutrients, which are linked to better health, the maintenance of fertility and minimization of infant mortality. Such places may have been seen as ‘good (or healthy) places’ explaining the high number of artefacts accumulated by repeated visitation over long periods of time and possible occupation. The distribution of these sites reflects the richest aquatic and wetland successional habitats along valley floors. Such locations would have provided foods rich in a wide range of nutrients, importantly including those in short supply at these latitudes. When combined with other benefits, the high nutrient diversity made these locations the optimal niche in northwest European mixed temperate woodland environments. It is argued here that the use of these nutritionally advantageous locations as nodal or central points facilitated a healthy variant of the Palaeolithic diet which permitted habitation at the edge of these hominins’ range.



Paleo People Loved Legumes

Neanderthals probably didn't do a fantastic job with legumes and small grain grasses because now they are extinct. It took a few dozen thousands of years...a slow demise, if that one of the reasons for their demise. During the latter portion of the Paleolithic, smarter hominids came along and figured out how to soak and cook legumes and SGGs. Food processing easily removes toxins and transforms them toxic, hard bumps of plant seeds into edible and delicious sources of starch, fiber, fat and protein.

Wrangtham et al in 'The Evolution of Hominin Diets' (2009) discusses the use of legumes in the end of Paleolithic Age, before the advent of agriculture. Plant evidence doesn't survive time well. What was unearthed was corroborated at a variety of sites widely distributed throughout Europe and Eurasia.

Legumes may be questionably Paleo® but they are unquestionably bionic for the gut microbiota and fuels the most important populations throughout the entire length of gut. The special fibers in legumes are unequaled when it comes to the combination of both RS3 and non-starch polysaccharides. Instead of raising blood sugars, legumes are low glycemic index meaning they impact insulin minimally or in fact lower it. Legumes have no dearth of clinical human trials that demonstrate its value for significantly lowering cancer, inflammation, insulin resistance, blood sugars, and gastrointestinal disorders.

Wrangtham et al in 'The Evolution of Hominin Diets' (2009)
"The richest food plant assemblage of Mousterian date, at

Kebara Cave in Israel, is dominated by a legume seeds of a
range of species, the form of some of which might suggest
collection while underripe (Lev et al., 2005). Towards the endof the Paleolithic, legume finds are scattered across Europe,
for example the pea and bitter vetch at Öküzini, Turkey; lentil
at Konispol cave, Albania; and vetches and other legumes at
Santa Maira, Alacant, Spain (Baales et al., 2002). Another
rich example of pre-agricultural legume foragers comes from
Hallam Cemi in Turkish Anatolia (Savard et al., 2006).



New Environments and New Plant
Strategies

Monocot stems and legume pods may have provided a significant mass of plant foods during the expansion into thel ower latitudes of Eurasia, where a vast array of yams and
legumes have emerged in the modern human food web as
domesticated plants. Moving further northwards still, these
kinds of resources diminish significantly, both in diversity
and in biomass availability. The quest for plant foods will
have presented an increasing challenge.
The cooler northern vegetation stands would have been
characterised by a range of open biomes including “arctic
steppe” (Cwynar and Ritchie, 1980; Zazula et al., 2003)
and closed vegetations characterised by woody dicots and
coniferous trees. Woody dicots are reasonably rich in edible
nuts, kernels, and fruits and, in certain families, edible roots
and tubers. As mentioned above, the lower the biological
productivity, the greater evolutionary pressure to protects eeds and storage organs from predation, and so it is generally
true that, especially as they move northwards, human
feeders are presented with a more complex “landscape of
toxicity” by dicots than tends to be the case with monocots,
particularly in the context of the seeds and tubers upon whicht he plant itself relies to cross the non-growing season. The  kind of transferable ecological 
knowledge that allowed feedersto move from one monocot to another in more southerly
biomes is not directly transferable to the dicots in northerly
biomes. 

Read: "Gory Details -- Here’s the poop on getting your gut microbiome analyzed"

Interesting read:

https://www.sciencenews.org/blog/gory-details/here%E2%80%99s-poop-getting-your-gut-microbiome-analyzed


"Here’s the poop on getting your gut microbiome analyzed"


I asked two different companies to analyze my gut microbiome. American Gut (left) gave nearly opposite results to those from uBiome (right) with respect to the major phyla of bacteria in a duplicate sample.




For more gut stool analysis consider the following functional medicine labs:

Stool -- Genova Diagnostics, Biohealth, Great Plains, Doctor's Data, etc
Urine -- Genova Diagnostics (ONE, Nutri Eval, Organix, etc)


The stool testing gives a partial view of what's inside that the Am Gut and uBiome lack -- protozoa, helminths, parasites, pathogenic yeasts, fungi, and the pathogenic bacterial overgrowths compared with symbiotic, beneficial commensal populations (E coli, Bifido, Enterococcus, Lacto, SBOs, etc)

Urine testing gives a partial view of what's going out of the gut


Caveat: all the current testing is imperfect including functional medicine testing, but what they can reveal are the (more stable) pathobionts and yeasts, which usually survive and thrive once colonization resistance and gut barriers are no longer functioning well or at all.  Recently 16S pyrosequencing was done as part of the Ribosomal Database Project (RDP) on a sample of healthy Korean gut microbiota. Geographical differences were seen compared to other Asian and American countries however between Korean guts, there was homology and core phylogenetic similarities.

In 8 Koreans (below), their guts were tracked monthly for 3 time points. Temporally, great shifts are notable on nearly every gut. I think it indicates clearly that our gut is like a playground. Kids, toddlers, nannies and teenagers all vie for spots and it's constantly shifting over time. Studies show even between meals, the microbiota show significant shifts. A diet protocol can shift populations in only day.

Temporal Month-to-Month Microbiota Shifts
Korean RDP, 2011
Source


Tuesday, July 22, 2014

AHS and Gut Microbiota Robustness, Diversity and Meandering

Robust, Meandering Gut
Source: van den Abbeele, 2013


The Ancestral Health Symposium is less than one month away, August 7 to 9th at UC Berkeley campus!

Several gut talks will be available (in addition to mine) which I am highly excited about:

The Gut; Diet, Flora, Health and Disease: Research and Recommendations
The environment of westernized societies is vastly different than that seen in non-westernized societies or during our developmental history. Differing lines of data show that exposure to dirt and bugs cause disease while other data show exposure prevents disease. How do we account for this discordance? More importantly how do we use this data to become healthier? While there is still very much we do not know about this field, this talk will attempt to critically examine trends in the data so as to extract practical applications for the attendees.
Speaker: Michael Ruscio, D.C., B.S.

Lifestyle and Autoimmune Disease: It's Still About Your Gut, but Not All About What You Eat
A variety of factors contribute to the development of autoimmune disease, among them genetics, leaky gut, and nutritional deficiencies. Although the power of therapeutic diets in the management of autoimmune disease is becoming increasingly recognized, an underemphasis on lifestyle contributors to immune dysfunction and gut health jeopardizes the efficacy of nutritional intervention. Chronic stress, inadequate sleep, inactivity and overtraining each negatively impact the health of the gut by interfering with digestion, damaging the gut barrier, or altering the gut microbiome. Understanding why and how to address lifestyle factors will enable the autoimmune disease patient to fully benefit from diet modifications.
Speaker: Sarah Ballantyne, H.B.Sc., Ph.D.

Bone Broth and Health: A Look at the Science
A South American proverb claims "Good broth will resurrect the dead." While that's clearly an exaggeration, chicken soup has enjoyed a reputation as "Jewish penicillin" and bone broths are served to convalescents all over the world. In this presentation, Dr. Daniel will review the science that supports consuming bone broth for healthy bones, joints, skin, digestion, immunity and emotional stability. She will discuss 19th and early 20th century studies on gelatin, as well as recent investigations into the "conditionally essential" amino acids proline, glycine and glutamine and "the essential sugars" N-Acetylglucosamine and N-Acetylgalactosamine. Finally, she will report on Dr. John F. Prudden's clinical trials healing osteoarthritis, rheumatoid arthritis, Crohn's, and even cancer with cartilage. In short, much science supports the ancestral wisdom of consuming bone broth.
Speaker: Kaayla Daniel, Ph.D., CCN



Cry Me a River: Robustness and Diversity in the Gut

Van den Abbeele and his colleagues in Belgium recently published on probiotics (eg microbial network units) and fiber/prebiotics. They establish that a meandering-river-like gut has optimal function because it has freedom and power to be flexible and adapt to shifting environmental factors analogous to a meandering river ecosystem. I like the vision that these researchers create. By following the energy flow of water that starts with low energy potential (like plant fiber v. pack of Oreo cookies), higher ecological niches and higher microbial diversity are created. Studies support that the higher the diversity and abundance, the more stable and robust the gut environment to changes. With less legs to stand on, the gut ecosystem collapses far more easily under small pressure or stressors. The factors they list as modern stressors include C sections, formula diet, antibiotics and high digestible, refined, Western diets. Antibiotics can originate may originate from both livestock/dairy/egg sources and healthcare.

Complex Cross-feeding in the Anti-Fragile,
Robust Ecosystem
Le Chatelier et al, 2013

In our gut different currencies exist; this works much like in a thriving village, various services and goods are exchanged depending on the talents and gifts of the inhabitants. Gut microbes exchange carbon (CO2, SCFA, lactate, etc and methane, CH4) and gasses (H2, sulfur) and extensively cross-feed each other. A healthy colon has biochemical pathways similar to a compost heap for degradation. Intimate cross-feeding of by-products of plant fiber breakdown (carbs --> shorter carbs --> oligosaccharides --> glucose, fructose, etc) feeds groups with different specialties in breaking down a broad variety of fiber. A productive community will have higher diversity and skilled enzymes for cutting a variety of plant fiber and resistant starches.

Studies are far back as ~20 yrs have shown that resistant starch is not broken down in the guts of ~25% of healthy controls (Cummings 1996; Hylla et al 1998). The same is true for inulin prebiotics. The keystone or 'star players' were extinct. How do you play if the star players are missing? Game over?

Obese rodent models have broken guts. What about RS digestion? Impaired? Quite. No weight loss was seen when obese mice models failed to ferment resistant starch (RS2) in an RS feeding study (Zhou, 2009).



Absent Allies in Obesity and Insulin Resistance

Le Chatelier et al recently reported that "Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population ['low gene count', LGC]) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals ['high gene count', HGC]. The obese individuals among the lower bacterial richness group also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese participants."

The bacteria-poor with low diversity and microbial abundance (LGC) had the following observations:
  1. decreased butyrate producers: Clostridiales (Anaerotruncus colihominis, Butyrivibrio crossotus, anti-inflammatory F prausnitzii), M smithii
  2. increased mucus degradation potential (more R gnavus, torques; extinct Akkermansia)
  3. decreased methane and hydrogen production potential combined with higher hydrogen sulfide creation potential
  4. increase in Shigella, Campylobacter, and Staph overgrowths
  5. increased indicators of oxidative stress (peroxidase)
  6. inflammatory phenotypes -- high leptin, low adiponectin, insulin resistance, elevated FIAF (ANGPLT4), high insulin, high BG, adiposity, high TG, low HDL, high hsCRP

In lean, bacteria-rich folks, the below following species were potently higher in abundance. These are part of the hallmark of optimal gut health, our ancestral core microbiota.
* F. prausnitzii
* Bifidobacteria
*  Lactobacillus
* Butyrovibrio
* Alistipes
* Coprococcus
* Akkermansia
* M. smithii


'Richness of human gut microbiome correlates with metabolic markers', Le Chatelier et al, 2013, PDF and REVIEW.
Species of bacteria limit weight gain 
Researchers also observed that obese people in the bacteria-deficient group gained more weight over time than individuals in the other group. In bacteria-poor individuals, eight specific species of bacteria were present in low numbers, or were even absent altogether. These species may have a protective role in preventing weight gain and in the long run their detection will open the way to the development of new probiotics that will help to combat weight gain. 

With identifying and quantifying only a few species, researchers can fingerprint and differentiate the lean versus the sick/insulin resistant individuals harboring the less robust, non-meandering gut microbiotas.

Again, show me your gut microbiota, and I'll show you missing allies.

7 Steps to a More Robust, Meandering-River Gut



Synergy

The 7 Steps works for many because it combines healthy environmental organisms (grit/SBO probiotics/plant organisms/mud/manure) with the optimal fuel for the gut microbiota...evolutionary plant fiber from ancestral tubers, whole seeds/grains, and legumes. Synbiotics are probiotics + prebiotics and our most ancestral foods combined these because before 50-70 years ago, most places in the world still did not have running water, household toilets or ubiquitous triclosan, hand sanitizers or soap! Prior to refrigeration, unspoiled food was fresh, fermented or semi-fermented.
"More recently, another plausible mechanism has surfaced in the synbiotic combination of resistant starch, Lactobacillus acidophilus and Bifidobacterium lactis [34]. These investigations identified enhanced apoptosis of carcinogen-damaged cells in rat colon by the combination treatment [34]. In contrast, the probiotics provided no protection when a low resistant starch diet was fed and the resistant starch had no protective response in the absence of the probiotic [35]. (Davis, Milner 2009)"

Tuesday, July 15, 2014

REBIOSIS with Probiotics: Enterococcus faecalis


Erotic Bar Chill Out Lounge

Rebiosis

In healing the gut, rebiosis needs to occur -- reintroduction of lost life to a dysbiotic terrain. Nearly all health conditions being studied are now emerging with correlations to intestinal dysbiosis. And as we know by fixing dysbiosis, we can resolve many health conditions from allergies to autism spectrum to hypertension.

The loss of our microbial 'limbs' in the gut can likely be attributed to 4 main factors:
(1) altered birth: mothers that lacked commensals, C-section birth, use of formula
(2) widespread use of antibiotics in healthcare
(3) sanitation (food, processed pickles, hands, water/soil, fecal contaminated drinking water, etc)
(4) pollution and toxins -- mercury, arsenic, xenoestrogens (do you have moobies?), etc

Enterococcus wiped out by Amoxicillin
Petersen, Round, 2014



Probiotics

From the last post, the lost of several flora strains occurs with common antibiotics such as amoxicillin, cephalexin, and ciprofloxacin. In some people these are easily replenished by consuming a fiber and RS rich diet but on a strict Paleo or VLC diet, the fuel for our probiotics are severely lacking. I think further degradation of the microbiota and health can occur. This is not measurable in modern terms unless we look to functional medicine to assess gut function using tests from Genova Diagnostics, Biohealth or Doctor's Data. Thank you to gentle readers who have sent me their results! I'll get to them and appreciate your patience.

A couple of probiotic strains, Enterococcus faecium and E. faecalis, help to fill in where antibiotic damage has occurred to the gut. In Germany, we got to try to Symbioflor (red) which contains E. faecalis. My daughter had a smidgen of eczema on a cheek after stress from finals. This probiotic helped to rebalance the gut-skin axis and helped the eczema disappear completely (and being a teen, it wasn't overnight or fast lol).

The studies for E. faecalis are great. Europe is always more progressive for this type of research and development. The studies showed clinically significant improvement across the board in immunomodulatory function in tonsillitis, upper respiratory tract infections, immune status, bronchitis, sinusitis, and irritable colon.
Source (p.164)


In short....

Re-biosis = re-establishment of healthy balance and harmony to microbial ecosystem 
--WEED
--FEED
--SEED mutualists, commensal microbial populations


WEED
--botanicals, probiotics/prebiotics
--exercise doubles butyrate

FEED
--gluten-free, dairy-free, allergen free (GMO soy, corn, egg whites, omega-6 oil) for 3-6 months
--bone broth (glycine, minerals), glutamine, poached egg yolks (vitamin A, PC, choline, folates, B12)
--glucomannan, inulin, cooked resistant starch (RS3 preferred over RS2), psyllium, pectin, etc

Fiber rich diet

Lotus root
Water chestnut
Purple potatoes
Carrots
White mountain yam (3-4 kinds in Asia)
Burdock
Konjac
Yacon
Kudzu
Yam
Purple sweet potatoes
Pumpkin
Heirloom potatoes

Whole GF grains (croix, purple/red/black/brown rice, amaranth, millet, buckwheat, sorghum, oats)
Legumes (purple speckled, red, adzuki, white, fava, pea, mung,etc)
Lentils
Heirloom maize
Seeds, nuts: lotus seed, almond, etc

Cellophane mung bean and sweet potato (jap chae) noodles and sheets



SEED
--minimally washed, trusted vegs
--Lactobacillus, SBOsfermented items: kraut, kimchee, natto, kombucha, kefir
--probiotics




Friday, June 6, 2014

AHS 2014: August 7-9th U.C.Berkeley... GET YOUR ANCESTRAL ON

Only two months away~!!

The venue has returned to my old haunting grounds, UCB campus, where I did my undergrad in Nutrition and Food Science and worked for two years in Plant Biology as a lab technician. Hope to see and meet many ancestral health fans! My family and I are re-patriating back to California from Shanghai, so it is a homecoming on many fronts.



AHS 2014: Aug 7-9th

Location: U. C. Berkeley Campus
Theme: WOODSTOCK lol

Registration is open

AHS11 Rockstar edition ~ AHS11 was the inaugural Woodstock. Nothing is like the first time but hopefully some of magic and mystery will be re-created this year with an amazing collection of events, topics, speakers, and eye-opening panels this year. I hope for lots of casual hanging out as well.

Ode to Seth Roberts ~ We will be missing and honoring our friend and AHS co-founder. His contributions to our community, his fairness and attention to science will never be forgotten.

PROGRAM





Topics I'm Attending For Certain

Since this blog is called Animal Pharm, the opening speaker has got my undivided attention.

Zoobiquity: Species-Spanning Medicine
Speaker: Barbara Natterson-Horowitz, M.D., M.A., B.A.
Scheduled at: August 7, 2014, 10:10 am
Animals and humans get the same diseases, yet physicians and veterinarians do not often consult one another. Spontaneously-occurring diseases such as cancer, heart disease, obesity, and infection as well as psychiatric conditions including self-injury, compulsive grooming, sexual dysfunction and substance-seeking affect not only people but a broad range of animal species. An integrated, interdisciplinary approach using the latest in medical and veterinary science to understand physical and behavioral health can lead to novel insights, hypotheses, and innovative therapies. This species-spanning approach challenges academic institutions, clinical practitioners, pharmaceutical companies, and biotech firms to recognize comparative medicine as a translational science, bringing knowledge from the veterinary medicine to the human hospital bedside.



My talk is @11:50

Re-Savaging the Gut: Solution to the Identity Crisis of the Ancestral Gut
Scheduled at: August 7, 2014, 11:50 am
The gut microbiota has undergone radical changes. Human gut anatomy are unaltered but the microbial ecosystems have degraded. Health may mirror these changes and how we acquire our microbiota including the ways we procure our food -- shifting at the neolithic from tedious hand foraging to village crops to (now) massive, post-industrial farming operations and livestock production. Our distance from the dirt is immeasurable. New technology allows characterization of the ancestral gut. Comparatively, species in ancestral and non-industrialized guts are robust in diversity and less fragile in balance. Ways to resolve this 'gut identity' crisis involve re-wilding and revisiting the ancestral, soil-connected gut.



My brilliant co-speaker from AHS11. Ancestral genetic polymorphisms determine many things. My family and I did 23andme (fyi, they're still open and analyzing ancestry). We don't have the main MTHFR SNP but we own one of the COMT variants that affect carbon methylation; it explains why the ancestral diet suits us and our DNA very well. We have also 2 of the main FUT2 variants for non-secretors in the Asian population which might explain a few of our gut vulnerabilities to MTHFR, COMT and the gut toxins which are related to methylation. FUT2 secretion is related to the capacity the mucosa membranes to secrete fucose on the surface, which feeds the grazing beneficial gut symbionts like a grassy lawn. The absence of fucose affects both pathogen adherence (non-secretion confers protection against norovirus, HIV and campylobacter infections) and susceptibilities to gut conditions (T1D, celiac, ulcerative colitis, Crohn's, autoimmunity, etc). Lack of beneficial gut flora when fiber/fuel is missing or due to antibiotics are strong factors affecting gut health depending on individuality. Check out Tim's solutions.

It's Your Parents Fault! Methylation: How 1 Carbon Affects Your Brain, Your DNA and Everything in Between
Speaker: Tim Gerstmar, N.D.
Scheduled at: August 9, 2014, 3:35 pm
Why is it that some people don't get better in spite of a good diet and lifestyle? One recently identified issue is defects in methylation, the epigenetic process by which the body turns on and off almost every process in the body. While normally methylation works seamlessly and without any need for conscious control, mutations in the methylation genes can 'gum up the works' and lead to chronic health issues. Our ability to identify genes has recently allowed us to peer inside this process, identify dysfunctional methylation genes, and provide help for suffering people.



Researcher and professor, Blaisdell bridges technical brain science and research for advocating the role of play. Only the smartest animals evolved to 'play'. My playground is this blog, lol. Often I try tell my kids don't fear screwing up because it's an awesome way to explore, learn and play.

Functional Frivolity: Human Brain Evolution and Play as an Adaptation for Childhood Learning and Education
Speaker: Aaron Blaisdell, Ph.D.
Scheduled at: August 7, 2014, 11:00 am
Despite appearing frivolous, play is a special adaptation for normal human brain development. I review human brain evolution, and describe how play is an adaptation to teach children how to be a successful hunter gatherer. The modern educational system, by contrast, arose during industrial period and is maladapted for brain and cognitive development. The result is an epidemic of developmental and mood disorders. Recent movements in developmental and educational psychology advocate a return to the natural conditions that foster development of a child into an intelligent, creative, and happy individual.



Stanton is one of my favorite mountain men and authors (The Gnoll Credo). “We are born and we die.
No one cares, no one remembers, and it doesn’t matter. This is why we laugh.”

How We Got Fat (and Sick): Mitochondrial Dysfunction, Leptin Dynamics, and the Ratchet Effect
Speaker: J. Stanton, B.A.
Scheduled at: August 8, 2014, 2:45 pm
The question "Why are we gaining weight?" neglects an equally important question: "Why can't we lose the weight we gain?" The multiplicity of competing hypotheses, and the overwhelming failure rate of current interventions, suggests that current top-down paradigms, in which the brain controls fat mass, are incorrect. Based on current peer-reviewed research, a new, bottom-up paradigm is proposed, in which the energy requirements of individual cells both cause and predict fat gain, metabolic dysfunction, and the failure of fat loss. It will be shown that this bottom-up paradigm has both explanatory and predictive power lacking in current top-down models.


Keith and his gorgeous wife live and breathe health and ancestral fitness. He's the modern LaLanne minus the juicer.

From Teflon to Tang - Proposed Effective Training Methods for In-Mission Astronauts, with Take-Aways for the Earthbound Mortal
Speaker: Keith Norris, B.A.
Scheduled at: August 8, 2014, 11:00 am
Contrary to popular belief, neither Tang nor Teflon were created for or by NASA. Rather, these technologies existed previously, and were co opted by space agency to satisfy mission-specific needs. The success of Tang and Teflon's association with the space program then propelled their representative "brands" in the public's consciousness. In much the same way, the technology and know-how now exists to prevent one of the most limiting obstacles to prolonged spaceflight -- muscle-wasting and bone deterioration (sarcopenia and osteoporosis). What can be done to curtail in-flight muscle-wasting and bone loss, and how might this knowledge transform training protocols on earth?



Unfortunately HPA deficits are widespread for both men and women. Good news is that it's all fixable. Grrrrrrls, this is very important. Multitasking and being wanna-be-perfect-Martha's are just a few parts of the problem. Truly it's a cortisol conundrum. And VLC and IF just make it worse. Thank you Stacy for highlighting this at AHS. If you want long telomeres, keep the adrenals and HPA strong and resilient. Adrenals are the vital foundation of health, even bigger than the gut.

Ancestral Health for Women in the Modern World: the HPA Axis Meets the HPT and the HPG Axes
Speaker: Stacy Toth, B.A.
Scheduled at: August 8, 2014, 11:25 am
The evolutionary biology perspective has proven to be an invaluable tool in creating dietary guidelines for the optimal human diet. However, we are learning that there may be stark differences between optimal nutrition for women versus men. In particular, the female body responds differently to changes in macronutrient ratio as well as meal timing due to links between the hypothalamic-pituitary-adrenal axis and both the hypothalamic-pituitary-gonadal and the hypothalamic-pituitary-thyroid axes, in part due to the combined roles of leptin and cortisol. Women may experience adverse health effects, including hypothyroidism and hypothalamic amenorrhea, in response to low carbohydrate diets and intermittent fasting.



I can't wait to hear about why breastmilk is alive (!!probiotics!!) and secures a mammal's future.

The First Paleo Food: It's Breastmilk and It's Alive!
Speaker: Philip Goscienski, M.D., F.A.A.P.
Scheduled at:
August 9, 2014, 2:40 pm
Before the Agricultural Revolution a human's first culinary experience consisted of breastmilk. A biological system that evolved from a modification of sweat glands took more than five million years to become an extremely complex form of sustenance for newborn mammals. The most obvious benefit of breastfeeding is that it provides a complete nutritional system that will sustain an individual until it can forage for food. That is only part of the story. Breastfeeding has a major influence on immunity, brain development, future chronic diseases and the health of the breastfeeding mother.



I didn't know myopia was reversible and am eager to learn some tricks and science. Obviously paleo is not enuf, both my children have this.

Myopia: A Modern Yet Reversible Disease
Speaker: Todd Becker, M.S.
Scheduled at: August 9, 2014, 10:30 am
Myopia, or near-sightedness, is generally assumed to be an irreversible, genetically determined condition that can only be ameliorated with corrective lenses or surgery. Its prevalence is 30-40% in the U.S. and Europe, and more than 50% in some Asian countries, but it is rare in Africa and in pre-industrial cultures. The incidence of myopia correlates with IQ, school achievement, and industrialization, suggesting that an environmental factor is at work—namely, near-work. This talk will review the biology and epidemiology of myopia and present experimental evidence that myopia can be reversed naturally by specific focusing techniques and practices.



The Naughty Nutritionist, I love this lady~!!

Bone Broth and Health: A Look at the Science
Speaker: Kaayla Daniel, Ph.D., CCN
Scheduled at: August 9, 2014, 1:50 pm
A South American proverb claims "Good broth will resurrect the dead." While that's clearly an exaggeration, chicken soup has enjoyed a reputation as "Jewish penicillin" and bone broths are served to convalescents all over the world. In this presentation, Dr. Daniel will review the science that supports consuming bone broth for healthy bones, joints, skin, digestion, immunity and emotional stability. She will discuss 19th and early 20th century studies on gelatin, as well as recent investigations into the "conditionally essential" amino acids proline, glycine and glutamine and "the essential sugars" N-Acetylglucosamine and N-Acetylgalactosamine. Finally, she will report on Dr. John F. Prudden's clinical trials healing osteoarthritis, rheumatoid arthritis, Crohn's, and even cancer with cartilage. In short, much science supports the ancestral wisdom of consuming bone broth.



Telomeres are amazing. I hope he bridges the latest info on the gut microbiota's influence on telomere's and longevity. The Three Genetics (Nuclear DNA, Mitochondrial DNA, and Gut Microbiome) of Longevity in Humans Considered as Metaorganisms (hat tip, Gemma).

Approaching Immortality - Maintaining Youthful Physiology as We Age
Speaker: Daniel Stickler, M.D.
Scheduled at: August 9, 2014, 11:50 am
Aging is a disease that kills over 100,000 people each day. We age because;1.) We gradually build up byproducts of metabolism in our cells that will outpace our ability to get rid of them,
2.) We have a biologic hourglass called telomeres, and3.) We accumulate toxic and damaging waste products in our extracellular compartments.
We can alter these responses through many lifestyle mechanisms; nutrition, exercise, stress, and environmental exposures and if we stave off frailty long enough, we may be alive long enough to take advantage of major life extension technology.

Wednesday, June 4, 2014

Update - RS2 and RS3 are Not Exactly the Same Thing

Update ~ RS2 and RS3 are Not Exactly the Same Thing


(Hat tip: M. McEwen) Feeding raw potato (RS2) in this ancestral diet study (human v. Theropithecus gelada) appeared to overfeed and increase the RS2-chomping gut populations—Bacteroides and E. rectale—in the human simulated gut. Populations that do not eat RS2 at all or proficiently—lactobacilli and bifidobacteria—were decreased with raw potato. These sub-colonies prefer dining on oligosaccharides (beans, inulin, endive, banana), RS3 and other fiber.


However, with simulated gelada baboon gut, minimal changes were observed and this is consistent with animals without salivary amylase. Only Old World primates known as ceropithecines have evolved AMY1 (salivary alpha-amylase) to consume starches from fruit seeds that they carry in their cheek pouches.




RS2 Alone Burns FAST&FURIOUSLY in Proximal Colon; But, No Change in Stool pH
RS2 is butyrogenic, (mildly) bifidogenic and burns with smoking hawwt intensity at the caecum. However, to flood the entire colon with health promoting butyrate, other plant fibers (including RS3) are needed to add bulk and carry the beneficial granules distally toward the rectum. In human RS2 alone trials, stool pH failed to improve compared with controls indicating that little fermentation occurred toward the end of the colon (here, here, here). One experiment was 4 weeks and low fiber. These experimental diets used RS2 alone + NSP ~10 g/day, similar to that typically observed in low fiber S.A.D., Paleo, VLC or Atkins induction diets (e.g. 1 fruit + 100 g/day vegetable + little legumes or whole grains). Conventional fiber is also known as NSP, non-starch polysaccharide.

Two cups of romaine lettuce is ~ 2 g NSP fiber; one 7.5 inch carrot, 2.3 g.


High stool pH indicates a lack of both colon fermentation and butyrate flooding the colon. More and more studies are showing that stool pH can be a reliable marker for colorectal cancer (Walker et al 1986; Newmark, Lupton 1990).


Granular RS2 particles are covered with a brilliant number of constellations for bacterial amylases to adhere and attack. On the other hand, crystalline RS3 matrices are gradually, slowly degraded with quite a lot of endearing and sustained fermentation to the distal colon, unlike granular RS2 starch (hat tip: Gemma).


“The starch granule size seemingly presents
a very favourable target for attack by
amylase with many potential sites for binding of the
enzyme. In spite of this apparent binding advantage, the
complete breakdown of starch within an intact granule is a
fairly slow process. Crystalline areas tend to be unfavourable
for enzyme attack and, in addition, the granules may
contain small but variable amounts of proteins and lipids
that can also hinder starch–amylase interaction. Most of
the starch consumed by humans will have been cooked
and/or subjected to various processes during food production
that disrupts the granules to a greater or lesser
extent, but raw starch is consumed in many animal feeds.
Processing that disrupts general granule integrity and
reduces the degree of crystallinity, increases the susceptibility
to amylase.”


We like RS a lot. It’s an unconventional fiber, and synergistic with other gut fuel. Together, they are bionic nourishment that our intestinal cohabitants are intimately familiar with for tens of millenia, if not hundreds.


While technically correct that raw potato starch is a valid form of RS2, using it as a sole source of RS for your gut microbes is probably not the best plan of action.  Looking back at studies that used just RS2, we see that RS2 is somewhat unique in that in ‘burns fiery hot’ once it exits the small intestines.  This means that the RS2 granules are converted to short chain fatty acids SCFA, mostly butyrate, in the cecum. SCFA and butyrate are mildly acidic and lower pH. In many ways RS2 ‘behaves’ physiologically and biologically like soluble fiber. Like pectin or gums, it does not bulk stools significantly compared with non-soluble fibers or retrograded RS3.





RS3 Burns Perfectly Prolonged All the Way to the Distal End of the Colon
Cooked-cooled, retrograded RS3 starch is a insoluble, large matrix of crystalline structures, and on the other hand, ‘burns slowly.’ It is insoluble and behaves like insoluble fiber and architecture to soft stools and providing bulk by increasing water holding capacity. I believe it provides a solid scaffolding for microbial ecosystems to colonize and flourish.


Ever notice how hardly anyone complains of flatulence when eating RS3 rich foods such as cooked and cooled potatoes and rice?  This is probably due to the fact that it is slowly fermented and the gasses produced are dealt with by gas-degrading microbes in a timely fashion. We had originally taken the lack of gas to indicate lack of performance, but this is wholly unfounded. The older ileostomy studies prove conclusively that the RS3, formed from cooked and cooled starches, arrives intact in the large intestine and modern microbe studies using 16s rRNA sampling prove that RS3 has profound effects on the gut microbiota leading to all of the positive changes we desire.


Epidemiological studies on consumption of RS3 rich foods like beans and lentils show protection against diabetes, obesity, prostate disease as well as colon cancer. In moderate fiber human studies (here, here), the combination of RS3, RS2, RS1 (total 38 g/day) + NSP 20 g/day (including raw green banana flour) was associated with significant improvements of every marker of gut health, including the largest drop in stool pH recorded in human studies. The lower and improved pH mark how microbiota fermentation and butyrate very likely and consistently flooded the entire length of the colon to the distal end. Also, dilution of ammonia and lower concentrations of fecal carcinogens (p-cresol, phenols) were noted. The authors concluded:


“In a typical Western diet (usually low in NSPs and starch) most
fermentation occurs in the proximal colon with limited effect
on the distal colonic environment (14)...


Fecal pH can be lowered by a variety of changes in the diet
(46, 47). Acid fecal pH has been linked with protection
against bowel cancer (48, 49). Epidemiological evidence
suggests that a drop in pH by 0.5 units is associated with
reduced risk (48, 49). During this study we were able to
reduce fecal pH by 0.6 units. To our knowledge, this is one
of the largest diet-induced changes in human fecal pH
reported. Studies using lactulose (SO) and oat bran have
recorded decreases of 0.4 units. The results obtained here
are most likely due to the higher amounts of [mixed] RS used
because there was a significant inverse correlation between
RS intake and pH, and between fecal starch and pH.
In humans the majority of colon tumors occur in the distal
colon (51). Thus, the measurement of fermentation-dependent
events in feces may reflect the environment in the distal
colon (52), and provide useful predictors of the antineoplastic
properties of certain diets.”


The mix of cooked RS3 and fiber produced outcomes that vastly contrast with the human study where RS2 did not dilute ammonia, but retrograded RS3 did.


Therefore, we feel it prudent to not seek total intake of prebiotic, fermentable fiber from isolated RS2 sources.  A diet supplying very little fiber, regardless of total carb count, and supplemented only with a refined RS2 (such as Bob’s Red Mill potato starch or Hi-Maize corn starch) will not be nearly as healthful as it could be if the RS2 was augmented with an array of other fibers. 

Both insoluble fiber and RS3 are enriched in low GI starchy foods -- lentils, peas, legumes, whole GF grains. Other roots/vegs and tubers are also abundant in either RS3 (sago, cassava, taro, heirloom potatoes) or insoluble fuel (turnips, okra).




RS and Total Dietary Fiber
From the ancestral evidence and modern studies, just getting the USDA recommended 25g/day of fiber is not enough.  More likely 40-80g/day would be optimal.  “Fiber” is such a fickle word...the fiber listed on nutrition labels is considered Total Dietary Fiber which includes every type of fiber that resists digestion.  Googling for the information you can get ‘conventional fiber’ charts.


From experience, 20-30g of ‘USDA-approved’ fiber is not that hard to achieve, nor is 20-40g of RS from real foods. For example, these 3 meals provide a nice blend of RS and fiber:
  • ½ cup soaked buckwheat porridge, ham, 1 Tbs raw potato starch BRM or green banana flour (WeDo's or Mt. Uncle's)
  • 1 cup cooked broccoli, 1 cup of pre-cooked lentils, ¼ cup kraut, ½ cup walnuts
  • chicken kale salad with raw carrots and 1/2 cup wild rice, five (small) roasted red potatoes


If you are concerned about the effect on blood glucoses (BG) and the glycemic load on the above foods, be assured that all the above have low GIs (glycemic indices) of ~20-50. Each meal contains 1 to 2 servings of carbs (15 net carbs) and need to be adjusted and personalized based on individual insulin sensitivity, exercise, diet, relaxation, stress, sleep, hormone status and health goals. PHD is 150 g/day high GI ‘white’ carbs, in other words, ~10 servings carbs.


Fermenting (soaking) lentils and legumes completely changes the structure of the beans and unlocks many nutrients, cooking then enriches insoluble fiber in addition to creating more resistant starch—besides making them edible. Cooling them crystallizes further resistant starch. Expanding on raw and cooked tubers and root vegetables, consuming a diverse and variety of plant fiber (green banana/plantains, lentils, legumes, gluten-free grains, nuts) secures phytochemicals which are anti-aging and cancer-protective antioxidants.


3 Posts Written By: Tim Steele, Grace Liu




NSP = non-starch polysaccharide (conventional fiber)
RS = resistant starch


See prior Animal pharm:

Feeding the Microbiota: Non-Starch Polysaccharides (NSP), Resistant Starch (RS) and Mucous