Pleiotropy, Natural Selection, and the Evolution of Senescence

PDF: Pleiotropy, Natural Selection, and the Evolution of Senescence

In 1978, at the age of 52, the great evolutionary theorist George C. Williams began to chronicle his own senescence, recording once a year how long it took to run 1,700 metres round a track in Stony Brook, New York. Williams presented the graph of his 12 years of slowing speed at his acceptance speech for the Crafoord Prize in Bioscience that he shared with Ernst Mayr and John Maynard Smith in 1999. He later published it in The Quarterly Review of Biology, with which he was involved for 32 years. The plot encapsulated his lifelong fascination: why do we decline with age?

The Breast Microbiome: Who Knew?

I had no idea. The following are some starting points for anyone interested in better understanding what it means to properly care for and feed your microbes…8)

We may not be able to see them with the naked eye. Occasionally we can see proof of their existence. Frequently we experience effects of their metabolism as an itch or skin that is warm to touch. Maybe a lump or an ulceration. A painful toothache or yucky old pink eye. Plain and simple we live with microbes. And the growing consensus among academia and nutritionists alike is that we depend on them as much as they depend on us.

The Breast Microbiome: A Role for Probiotics in Breast Cancer Prevention

Diet Affects the Breast Microbiome In Mammals

The Breast Has Its Own Microbiome–and the Mix of Bacteria Could Prevent or Encourage Cancer

Unhealthy gut promotes spread of breast cancer Disrupting gut bacteria had profound, sustained effects, making cancer more aggressive


This is something that has peeked my curiosity. I am seeing way too many correlations with the human colon, our skin, fermentation and its metabolite melanoidins not to document this. Apparently our skin has the ability to ferment sugars.

Many topical self-tanners contain the compound dihydroxyacetone (DHA)[sugar]. Topical DHA[sugar] formulations come in lotions, gels, mousses, sprays, and wipes. DHA is a sugar molecule derived from plants that reacts chemically with the amino acids[proteins] in the stratum corneum[skin] to produce pigment when applied to the skin. This reaction is known as the “Maillard reaction,” and it does not require UVR[sun] to produce a pigment change. The resulting pigments are called melanoidins, which are similar in pigment to melanin.

Once DHA[sugar] is applied to the skin, it takes approximately two to four hours to begin the tanning[fermentation] process and can continue for 24 to 72 hours. DHA is resistant to normal water, soap, and sweat exposure. The tan will begin to fade gradually three to seven days after application result of normal skin exfoliation.

Melanoidins are brown, high molecular weight heterogeneous polymers that are formed when sugars and amino acids combine (through the Maillard reaction) at high temperatures and low water activity. Melanoidins are commonly present in foods that have undergone some form of non-enzymatic browning, such as 1. Barley malts (Vienna and Munich), 2. Bread crust, 3. Bakery products and 4. Coffee. And humans too.

KEY -|- They are also present in the wastewater of sugar refineries, necessitating treatment in order to avoid contamination around the outflow of these refineries.

The polymers make the constituting dietary sugars and fats unavailable to the normal carbohydrate and fat metabolism. Dietary melanoidins themselves produce various effects in the organism: they decrease Phase I liver enzyme activity and promote glycation in vivo, which may contribute to diabetes, reduced vascular compliance and Alzheimer’s disease.

Some of the melanoidins are metabolized by the intestinal microflora.




Bacteroides: the Good, the Bad, and the Nitty-Gritty – PDF

By Hannah M. Wexler

By a variety of measures, the species Homo sapiens is more microbial than human. Microorganisms comprise only a small, albeit significant, percentage of the body weight (between 2 and 5 pounds of live bacteria). However, in terms of cell numbers, we are about 10% human and 90% bacterial! Further, the number of genes in our microbiome may exceed the number of human genes by two orders of magnitude, making us genetically 1% human and 99% bacterial! Consequently, bacteria play a major role in bodily functions, including immunity, digestion, and protection against disease. Colonization of the human body by microorganisms occurs at the very beginning of human life, and many of these organisms become truly indigenous to the host.

The human colon has the largest population of bacteria in the body (in excess of 1011 organisms per gram of wet weight), and the majority of these organisms are anaerobes; of these, 25% are species of Bacteroides, the bacterial genus that is focus of this review. This review will summarize the current state of knowledge about Bacteroides species, the most predominant anaerobes in the gut. The aspects of these organisms that will be covered will include their role as commensal organisms (The Good); their involvement in human disease (The Bad); and information about their physiology, metabolism, and resistance mechanisms as well as a brief overview of clinical characteristics (The Nitty-Gritty).

Bacteroidetes is one of the major lineages of bacteria and arose early during the evolutionary process. Bacteroides species are anaerobic, bile-resistant, non-spore-forming, gram-negative rods. The taxonomy of Bacteroides has undergone major revisions in the last few decades (see “Taxonomy” below), but the genus is now limited to species within the Bacteroides fragilis group, which now number 20. Names of species within the Bacteroides or Parabacteroides group to date are listed in Table 1. Many of these species were isolated as single strains from human feces. The percentages of anaerobic infections that involve particular species of Bacteroides are indicated in Fig. 1 and were calculated from the Wadsworth Anaerobe Collection database, including more than 3,000 clinical specimens from which a Bacteroides species was isolated. The proportions of the most important species for the most common sites of isolation are indicated in Table 2. The numbers of B. fragilis isolates are 10- to 100-fold lower than those of other intestinal Bacteroides species, yet B. fragilis is the most frequent isolate from clinical specimens and is regarded as the most virulent Bacteroides species.

Bacteroides may be passed from mother to child during vaginal birth and thus become part of the human flora in the earliest stages of life. The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, and their role as commensals has been extensively reviewed. A quote in a recent publication captured this attribute: “. . .with B. fragilis, as with real estate, it’s location, location, location”. When the Bacteroides organisms escape the gut, usually resulting from rupture of the genes. Third, both species exhibit multiple paralogous groups of genes, i.e., genes that seem to have derived from a common ancestral gene and have since diverged from the parent copy by mutation and selection or drift. The reasons for this seemingly inefficient use of genetic space are not completely clear, but it would seem that Bacteroides species are genetic “pack rats” that prefer to have all possibly needed versions of relevant proteins at hand and therefore will not need to rely on unpredictable mutations.

CONTINUE READING: Bacteroides: the Good, the Bad, and the Nitty-Gritty -PDF

Originally published in the American Society for Microbiology

Brain Dump – 2015.02.15 – Casein & Galactose

Lactose digestion in humansPDF

Lactose digestion in humans: intestinal lactase appears to be constitutive whereas the colonic microbiome is adaptable 

D-Galacturonic acid – Aldehydes are mainly used as solvents, perfumes, and flavoring agents or as intermediates in the manufacture of plastics, dyes, and pharmaceuticals.

The Effect of Pectin, Galacturonic Acid and Alpha Methyl Galacturonate upon the Growth of Enterobacteriaceae

Probiotic Saccharomyces cerevisiae strains as biotherapeutic tools: is there room for improvement?

Saccharomyces cerevisiae Fungemia: An Emerging Infectious Disease

Auto-Brewing Syndrome


Trehalose: current use and future applications.

A Sweet Potion to Put Embryonic Stem Cells to Sleep


Milk and A Short History of Nutritional Science – 4 Parts

Milk. It does no body good.

List of countries by milk consumption per capita

A Short History of Nutritional Science: Part 1 (1785–1885)PDF

A Short History of Nutritional Science: Part 2 (1885–1912)PDF

A Short History of Nutritional Science: Part 3 (1912–1944)PDF

A Short History of Nutritional Science: Part 4 (1945–1985)PDF

Stage of lactation – Content source

Human lactation stage can be divided into 3 major phases: colostrum, transitional milk, and mature milk. Colostrum is rich in immunologic components and contains relatively low concentrations of lactose but higher protein content, suggesting its important functions to be immunologic and trophic besides nutritional.

Transitional milk shares some of the characteristics of colostrum but represents a period of accelerated milk production to support the infant’s nutritional and developmental needs for rapid growth.

Mature milk is relatively similar to transitional milk, but the changes are not as remarkable as in the early weeks. The influence of lactation stage differs for different nutrients. For example, total protein and lipids show a gradual decrease during the first 6 mo of lactation. Whereas the lactose is initially low in colostrum and transitional milk, it then increases in mature milk and remains at the same levels for up to 6 mo. In addition to the alterations of total protein, protein composition also changes. Milks mainly contain 2 types of protein: caseins and whey proteins. The ratio of whey to casein in human milk can vary from ∼80:20 in early lactation to ∼50:50 in late lactation. Because the amino acid compositions differ between caseins and whey proteins, the type and content of the amino acids of human milk in turn vary during lactation.


What I Learned on Amazon

Little book, big cure starring niacin (vitamin B3)

If not a cure then very close to one. Briefly stated– The vitamin cure for alcoholism is niacin. The old fashioned kind that gives you a flush. 20 years ago this was the common form of niacin but has since been crowded out of the market by the no_flush, time release niacin which is not what you want to buy. Rugby makes this kind of flushing niacin. Swanson has their own brand of flushing niacin that is 500mg capsule x 250 capsules x $6.98 and as of December 2013. Swanson and Rugby niacin can be bought at Amazon. Buy the 500mg size and start with part of the tablet or capsule. Eat it at mealtime to reduce or eliminate the flush. Hoffer will say 1.5-3 grams is a good daily amount for you. You take niacin a few times a day and the daily total is 1.5-3 grams. Maybe some need more but start gradually. Don’t be scared of the niacin flush, it is your friend.

Everyone has a different niacin reaction. I started gradually….By now I am up to 1000mg first thing in the morning. Taken with 4oz hot or cold water. This produces more of a flush than when taken with food. The classic Abram Hoffer (niacin guru who lived to 91) advice is to take niacin after meals. I take a few more 500mg capsules during the day so I take about 2500mg daily. To get over the hump you need to spread out your niacin. You want to maintain high niacin levels in your body throughout the day. So divided doses of niacin.
I know that if I took zero niacin for a week then took 500mg with hot water, that I will get a strong flush. I have done this. This is what scares off niacin newbies. Once you start daily niacin and take it a few times during the course of a day, the flush gets diminished.

Niacin is the core but get this book for the full story. Such as take a good B-50 complex a few times a day. This is a common supplement and contains 50mg of all the B vitamins. Take Thiamin (B1) (preferably the benfotiamine variety of B1) for brain health and repair. Yes, the B50 complex contains niacin and thiamin but you need more of those two. Also take vitamin C. The easiest C to take for me is the magnesium ascorbate powder and I take a total of 3 half teaspoons each day in divided doses. This equals about 3 grams of C. Magnesium ascorbate is a buffered C.

Eating a more plant based diet will help you. Take chromium picolinate which helps glucose metabolism. Read the book- “Lifting Depression: The Chromium Connection”. He advocates 1000 mcg chromium picolinate daily. Many are in mild or severe depression caused by long term alcohol overuse. You might be a functional alcoholic who still does well at your job. Your life is not a mess but you have mild depression. Good for you! You have been strong so far. Intelligent use of niacin + B vitamins will lift this curtain of unhappiness.

Why all the B vitamins? Because high alcohol intake over years has put you into B vitamin deficiency. Why? Because alcohol functions much like sugar in your body and in the process of being metabolized it has been using up any store of B vitamins you have. When you start a high intake of niacin and the other B vitamins your sugar and glucose metabolism is returned to normal. So you will have reduced desire for alcohol due to hypoglycemic cravings. Cut it out totally perhaps.

You will find more information at co-author Andrew W Saul’s website. Getting on an exercise program will help your alcohol situation. Will give you a daily improvement you can feel good about, that will help lift you out of the alcohol pit. Last but not least, get God back into your life if you are so inclined. Prayer can help.


Hello realist, you know your stuff! Interesting that the lypo-spheric C produced by LivOn Labs has ETOH as an ingredient…supposed to make it encapsulate better. There is a good website: http://qualityliposomalc.com which claims to have the original recipe (mol)
that was created from a patent sold to LivOn by a Chinese gentleman. The author, Chris, lays out the research, ingredients and process to make this high quality product at home. I tried it twice, once with sodium ascorbate, which was completely disgusting 🙁
and then with ascorbic acid which made it pretty tart but more palatable. But the ETOH is a problem for me and it has a good amount of vodka in it.
Boy, the insulin and blood sugar connection is right on. I have more to say about that.
I am on board with vitamin D3 and have told so many people about it that when they see me coming they duck for cover! I have handouts and extra bottles to pass out and cannot believe that the FDA STILL advocates such a low dose, but it’s no different with C. I have been reading about the need to take Vitamin K with it…..bought some Thorne K2 drops (pricey) and not totally sure that’s the right thing. Also, I feel bad about the people I preached about D3 to but didn’t mention K. I guess we are all learning together. The best thing is to sit in the sun with lots of exposed skin :-)Thank you for your informative reply and willingness to share information.
I’ll read the Mark Sircus info and I would be so glad to correspond with you further via email.May God bless you.


Those optimum Vit C doses are for when you have a real problem. Lypo-spheric vitamin C is the most powerful and has gotten me out of a jam or two, If you have the funds then take two of these per day during initial period of a month or two. Magnesium is depleted in heavy drinkers. So lots of magnesium ascorbate kills two birds with one stone. Heavy drinking hurts liver functions which hurts the way the liver works with the fat soluble vitamins. So 5000 units Vit D and 20000 units Vit A for a while is good idea. My opinion quick release niacin (Swanson has it) dose of 500mg/3x daily is sufficient. I like NOW brand vitamins and buy my “stuff” at Swanson’s and Amazon.
Sodium ascorbate is good, Take it separate from mag-ascorbate. 6-10 grams total daily ascorbate intake is good to get over the hump. Once you are “good” then 3 grams is sufficient….much depends on how much you weigh. Obviously a man 6ft4inch tall and 280lbs needs more than a 5ft5inch guy.
Walk fast 30 minutes each day and do better every day. Faster or a bit longer every day. If your work situation allows an hour walk or more is good. Or walk a few hours each day off. Get those juices circulating.
_______post an emaill address if you want more.

Read what Mark Sircus has to say (on internet) about alkalinizing with baking soda aka sodium bicarbonate. Optimum way to do this is with Bob’s Red Mill brand of baking soda…also buy potassium bicarbonate which is a common brewer’s/winemaker’s item found at Amazon and ebay. Consume them together in a hot drink it goes through you quicker. In a 4 to 1 ratio of sodium bicarb to potassium bicarb.

My opinion is saying goodbye to heavy alcohol consumption is 75% bio-chemistry and 25% in your mind. Serious alcoholics have malnutrition problems and are pre-diabetic or have low level undiagnosed diabetes. They have insulin and blood sugar problems.


Hello realist, I want to thank you for an excellent review which enabled me to easily order these items from amazon. I do believe that correcting deficiencies of critical vitamins and minerals, plus adding healthy plant based foods to ones diet will improve many ills.
I do want to give you some information concerning your source and dose of vitamin C, if I may take the liberty. According to Thomas Levy, MD JD, an optimum dose of Vitamin C “would range between 6,000 and 12,000 mg daily, with most adults needing closer to 12,000”. This information is found in his 2002 book, Curing the Incurable, Vitamin C, Infectious diseases and Toxins. He also addresses the particulars of opti-dosing including the bowel tolerance issues.
It seems that magnesium ascorbate is acceptable in smaller amounts but as he words it “the dosage level of vitamin C that you would need to take on a daily basis would require an overdose of associated mineral forms (magnesium)”.
Calcium ascorbate should not be used at all and he recommends ascorbic acid or sodium ascorbate for a buffered version. The sodium is not a problem, per Dr. Levy.

More interesting reading is available at his website and now deceased Dr. Frederick Klenner, vitamin C pioneer, has his many clinical anecdotes available via Lendon H Smith’s “vitamin C conspiracy” at http://whale.to/a/smith_b.html
Thanks again, realist.


This book is SO helpful in understanding one of the causes of alcoholism and what you can do about it. If you know an alcoholic who has tried unsuccessfully to win his battle, this book could be the missing link. Both my parents were alcoholics. My father went through AA and detox centers over and over unsuccessfully until he died from cyrhhosis of the liver. I bought this book since addiction runs in our family and I have a family member who is struggling with dependency to prescription meds. When he takes the recommended dosages consistently, which is definitely the battle, he has noticed his need for anxiety meds reduce and his need for pain meds reduced. What this book has shown me is that all of our needs for nutrients are different because of genetics and lifestyle and some of us need thousands of times more than the recommended daily allowance. Niacin and B vitamin deficiency is at the top of the list for alcoholism and correcting the deficiency was the key to helping those in AA to success. Read this book, educate yourself and then find a good naturopath to help you with a plan to help you win this battle.