Many common folk also have a decidedly deterministic, perhaps fatalistic opinion of genetics. “It’s in the genes. There’s not much that you can do about it.” Nothing could be further from the truth; and although I can easily genuflect at the altar of genetics, I do not worship there. Your genes are just a reasonable plan for a particular way things can happen. Genes are just cogs in the wheel of life. They’re not here to cause disease; they are part of the structure of life.

For something so important to life, it’s quite surprising that there are so few of them; we humans have somewhere in the vicinity of 35,000 genes. Indeed when the human genome was first published scientists were incredulous to find that the number was so low (prior estimates were that there were at least 100,000.) And as if to prove that numbers aren’t everything, we humans don’t even measure up in this department as well; the average rice plant has around 40,000 genes. But then again, it’s not what you’ve got; it’s what you do with it.

It’s true, you can’t change your genes, but we are beginning to discover that Nature and Nurture do need each other. You can affect the way that your genes function. Matter of fact you do it all the time. For example, it may turn out that that dirty door knob your mother touched while she was pregnant with you may have had more influence in certain areas than all your DNA and RNA combined. As we move further into the meat and bones of this book, you will see how and why.

Genetics is typically thought of as being very complicated and difficult for the average person to understand, and this may well be true. However, the goal of this book is not to turn you into a geneticist, but rather give the advantages of conducting your life in such a way as to benefit from the knowledge of genetics.

Car showrooms can cast an interesting light on human behavior. While waiting my turn in a local dealership to buy a car, I had the chance to observe the interaction between the salesman and the young couple that he was attending to. Diligently he spouted out facts and details about the engine torque and horsepower, the suspension, and steering as the husband stood by obviously not understanding an iota of it all, but duly shaking his head and feigning great interest.

At the end of the soliloquy, our salesman of course asks if there are any questions. Not wanting to be seen as unintelligent, the young husband say no, he doesn’t have any. The young wife, on the other hand, had a burning question:

Where were the cup holders?

This simple interaction not only changed the way that I chose to write books, but changed my way of communicating in my medical practice. Most people who buy cars don’t want to repair them; they want to drive them. Yes, there is probably a very nice motor under the hood, but most intelligent people do not need convincing that there is a squirrel on a treadmill instead. For them the car is a means to an end; a way to get someplace. So, if you are willing sometimes to suspend disbelief that I am making this all up, I will repay the favor by spending the majority of our short time together teaching you how to get someplace with The Genotype Diet, rather than bludgeoning you with details that you could have easily gotten someplace else.

However, facts do make for the best stories, and I fancy myself a bit of a storyteller. However I do promise to try and keep the terminology down to a reasonable minimum, while keeping the nomenclature at the level where the names of things could at least serve as an interesting name for a pet.

“Here, Allele! Sit! Good doggy! That’s a good Allele!”

Gillian Roberts sent along this link to an interesting article about how the human genome changes with age. Sound like it is right out of The GenoType Diet if you ask me.

As I've been tinkering with this new blog software, I've become acutely aware of the importance of skins and themes. For the uninitiated, a theme (the more 'proper' wording) or skin (what everyone calls them) are a set of variables that a programmer often adds into a program that allows people to change the appearance of the program in ways that make it more personalized. For example this blog uses a variation of a skin called 'Nautica', which give it a rather pleasing blue palette. To get a better idea, you can browse the various skins for the blogging program Wordpress.

As I went along I began to see the GenoType characterizations as skins of a sort. If blood groups, secretor status an whatnot are the body, then the GenoTypes would be the choice of wardrobe.

For example, look at this graphic:

If we compare the basic type A characterizations and diet, we would see that type A has problems from a mostly tolerant immune system, a greater risk of heart and artery problems, and a greater risk of cancer. Reasonable enough, since that is what the research literature suggests. Type A's have less p53 tumor suppressor activity and their arteries are more prone to inflammation.

However, under simple blood type association, there is really no prioritization of this information.

If we look at the GT3 Teacher program we would see that the diet is skewed more towards cancer protection. It is in the GT3 Teacher that the p53 tumor suppression susceptibility winds up. GT5 Warrior on the other hand, seems to carry the arterial risk; probably because of the two, they are the more thrifty type. Thus if you GenoType as a blood group A Teacher, you will be wearing the 'cancer prevention skin.'

Technically if you are type A you could wear several skins, however if you GenoType as a Teacher, the Teacher skin will be the most therapeutic for you. Same with type O: You might need the 'metabolic syndrome' skin (GT2 Gatherer) more than the 'catabolic inflammatory' skin (GT1 Hunter).

Ditto for the B's and AB's.

Hopefully this will help folks see how values can change when one migrates from the BTD values to the GTD system. Somewhere in the allowable GenoTypes for people with type A blood, there will be that old BTD avoid, however, if it is not in your new GenoType values (or if it flipped to being actually beneficial!) it is because its BTD avoid status was less relevant than the benefits it provides under your new GTD skin.

One of the features that can be of most use when GenoTyping someone is actually one of the hardest to come by: Getting the ABO blood groups of your parents.

Its importance should come as no surprise, since epigenetic changes are largely influenced by the patterns of gene activation and silencing that occur as part of

• The heritable epigenetic component (you start off with the patterns of gene expression that your parents give you)
• The prenatal environment (there are two major bursts of methylation activity in the fetus: at about 8-12 weeks, then again in the last trimester)
• The immediate postnatal environment (these are mostly related to gene expression due to hormones such as growth factors)

In fact one of the studies that got me interested in the largely unrecognized effects of blood groups as a modulator of the epigenetic environment was a study that looked at childhood ear infections and blood groups. However, unlike most epidemiologic correlation type studies, this one looked at the blood group of the child’s mother.

Maternal blood group A gave a relative risk (RR) for intervention of 2.82. The noted occurrence of an attack of acute otitis media (AOM) before the first birthday gave a RR of 6.13. When these two factors were used together, the RR climbed steeply to 26.77.

Now to understand just how strong this association is we should look at exactly what a RR (relative risk) is. Basically it is just the odds (over 1) that something will occur over it being random. An RR of 2 (about the RR of elevated cholesterol causing a heart attack) means that people with elevated cholesterol are twice as likely to get a heart attack as people whose cholesterol levels are more desirable. Thus the study is saying that if you are a kid with an ear infection in the first year of life, and you mother is blood group A, you are 26 times more likely to have a recurrence.

Here is a chart I made which compares relative risks for several common problems and factors associated with that risk. Obviously, this is a very strong association.

Are the effects of having a blood group A mother and getting ear infections the result of some sort of fetal programming? We know that some studies have linked the ABO antigens to cellular differentiation (the process where developing cells move from general embryonic 'germ' types to cells with more specific functions, like a pancreatic or epidermis cell.)

ABH antigen expression was considered as suggestive evidence for the assumption that blood group antigens could serve as early immunomorphologic markers of endothelial differentiation of mesenchymal cells, thus specifying the location of future blood vessels. Extending the conceptual framework of blood group antigens' significance we consider them as being possibly involved in the process of fetal morphogenesis.

In epigenetic terms, we may wind up being more interested in your parent's blood types are that perhaps we need be with yours.

Every once in a while, amid the junk mail, bills and catalogs, I receive a letter which surpasses all prior. In a wonderfully sycophantic endeavor this gentleman writes to ask me for a complete set of my works so he can continue on his mission to educate the Indian public about healthy living. Apparently the gentleman does it free of charge.

Sir, your books are on their way.

1.

What does The GenoType Diet, Sudoku, and musical harmonics have in common? They are all based on matrix relationships; tables (really arrays) in which the constituents relate to each other in particular ways.

Many years ago, I took a summer course in computer music composition with Charles Dodge. Dodge, primarily known for a piece he created out of the Earth's magnetic field, was a gifted and supportive teacher, who in no short time clued me into the fact that I was no composer, but rather something that he termed a 'musical systems pre-programmer.' In short, the guy who wrote the programs that composers used to make music.

One of the things he was working on that I found especially fascinating was a concept that he called 'harmonic foldover', the idea that at certain points the sonorities ('resonance') of certain base frequencies could be manipulated to produce new harmonics, which would be created a precise intervals.

One of the most striking things that you hear when people talk about foods and diets, is who often they express their preference in musical terms.

"I try to eat in harmony with my local agriculture."

"I'm really in tune with this diet."

"A high protein diet really resonates with me. I can feel more balanced."

Working on the GTD food choices, I often reminisced about Dodge's theories. Although I've long forgotten his exact modus operandi I suspected that one could do this by using a series of mathematical tools called linear transformations, especially what are called Fourier transformations. Any example of a Fourier transformation would be to split up a radio frequency into its more basic fundamentals. Most of these functions work on matrices, not terribly different than those found in any Sudoku puzzle.

Here is a Latin Square, a matrix where each number occurs exactly once in each row and exactly once in each column.

The early Chinese mathematicians also had something called "Magic Square' which did something similar.

Again, art mimics life.

Fast Fourier transformations of matrix data are useful for many things, from the symmetry analysis of numbers and determining trajectories of comets. Because matrix data falls into the realm of linear algebra, transformations of the data always leave behind parts which have not been changed, the direction of the change, and how much change has occurred. These are called the Eigenvalues and Eigenvectors of the transformation. I love Eigenvalues, because they so easily plug into the multivariate characterizations that comprise the GenoTypes.

Now for the mimic part: 'Matrix' is derived from the Latin word matrices for 'womb'. Embryos are interested in symmetry, since it is an index of stability in their developmental environment and subsequent fitness. And, it would not be unkind to describe your journey through life from birth on as a type of epigenetic trajectory.

'All that openeth the matrix is mine.' --Ex. xxxiv. 19.

With this type of analysis, I can see that the future development of The GenoType Diet system will occur by way of food relationships, not individual foods. Put a live food, a piece of fish and a carbohydrate into that Latin Square and you will see what I mean*.

I described it at a recent working lunch for the NAP folks as 'visiting a deep cavern, having a normal conversation and soon realizing that all the words, their tones and inflections were blending into a constant drone of overtones as echoes and reverberations of each prior word are added to the base sound ---but a drone that is as identifiable as the voices of the people speaking. Now imagine that by being able to hear that sound, you could add more words and noises to make the overtone more pleasing and enjoyable.

That would be Geno Harmony.

* And maybe also see why the GTD products have names like 'Activator' and "Catalyst'.

2. A recent blog entry features this statement:

Frankly, I'm finding that naturopathic education is still leaving a lot to be desired (amazingly, they don't teach nutrigenomics; have one class each in genetics and immunology; and do not learn any statistics or bioinformantics). I know that there are the ‘nuts and bolts' to teach, such as the anatomy and physiology, but it is surprising just how little space these students have for the real aspects of naturopathic practice, since they are so busy learning and memorizing a lot of things which will allow them to pass a board exam, but could more easily be simply looked up while in practice.

Which caused some upset with one of the clinic interns, who felt that this might give the impression that the education that they are receiving is not up to standard. I know my tone was a bit harsh, and I do apologize for that.

But like Laurie Anderson once said, "It is not the bullet that kills you; it's the hole."

I don't think naturopathic education is sub-standard. Far from it. NDs graduating from CNME approved schools are very highly trained medical professionals. My gripe (and it is only my opinion) is that the education is insufficiently non-standard, and perhaps unnecessarily formalized. But one should not take these things too far. Decrying and dissecting your education is the official national pastime of naturopathic medicine.

The John Bastyr College of Naturopathic Medicine, graduating class of 1982.

A possible reason why the long headed GT5 Warriors are often taller than GT3 Teachers and GT4 Explorers:

In the article the development of skull measurements and head measurements (length and breadth) and of the cephalic index, calculated from these measurements, since the Neolithic period are presented. The results obtained from the historical material are compared with those of living persons. The measurements as well of the skull as of the head show secular changes. The following general trend was found: an increase of body height is connected with a debrachycephalisation* and a decrease of body height is connected with a brachycephalisation. It can be emphasized that brachycephalisation/debrachycephalisation are part of the secular trend. Therefore environmental factors are responsible for the described changes of measurements of the skull and the head in a broadest sense.

* Debrachycephalisation: the tendency for head shapes to become less 'square-like' and more elongated over succeeding generations. Brachycephalisation is the opposite.

Is head size modified by environmental factors? Z Morphol Anthropol. 1998;82(1):59-66.

A hypothesis is framed about which any influences of the nutrition may cause variations of the cranium, but concerning physiological data, kinds of nutrition and special victuals' ingredients cannot still be mentioned. If such connexions are proved, at last the well known brachycephalization among European populations since the Middle Ages and the beginning debrachycephalization in the present time could partially be interpreted.

The brachycephalisation problem, a nutrition constitutional problem? Gegenbaurs Morphol Jahrb. 1989;135(5):689-96.

Probably why GT4 Explorers usually are thicker boned than GT1 Hunters:

A growing body of archeological evidence suggests that the dramatic climatic events of the Last Glacial Maximum in Europe triggered important changes in foraging behavior, involving a significant decrease in mobility. In general, changes in mobility alter patterns of bending of the midshaft femur and tibia, resulting in changes in diaphyseal robusticity and shape. This relationship between levels of mobility and lower limb diaphyseal structure was used to test the hypothesized decrease in mobility. Cross-sectional geometric data were obtained for 81 Upper Paleolithic and Mesolithic European femora and tibiae. The sample was divided into three time periods: Early Upper Paleolithic (EUP), Late Upper Paleolithic (LUP), and Mesolithic (Meso). In addition, because decreased mobility often results in changes in sex roles, males and females were analyzed separately. All indicators of bending strength decrease steadily through time, although few of the changes reach statistical significance. There is, however, a highly significant change in midshaft femur shape, with LUP and Meso groups more circular in cross-section than the EUP sample, supporting archeologically based predictions of decreased mobility. Sexual dimorphism levels in diaphyseal strength remain low throughout the three time periods, suggesting a departure in Upper Paleolithic and Mesolithic foragers away from the pattern of division of labor by sex observed in modern hunter-gatherers. Results confirm that the onset of the Last Glacial Maximum represents a crucial stage in Late Pleistocene human evolution, and signals the appearance of some of the behavioral adaptations that are usually associated with the Neolithic, such as sedentism.

Mobility in Upper Paleolithic and Mesolithic Europe: evidence from the lower limb. Am J Phys Anthropol. 2003 Nov;122(3):200-15.

However marauding GT1 Hunters are on average, taller than glacial refugee GT4 Explorers:

Long bone lengths of all available European Upper Paleolithic (41 males, 25 females) and Mesolithic (171 males, 118 females) remains have been transformed into stature estimates by means of new regression equations derived from Early Holocene skeletal samples using "Fully's anatomical stature" and the major axis regression technique (Formicola & Franceschi, 1996). Statistical analysis of the data, with reference both to time and space parameters, indicates that: (1) Early Upper Paleolithic samples (pre-Glacial Maximum) are very tall; (2) Late Upper Paleolithic groups (post-Glacial Maximum) from Western Europe, compared to their ancestors, show a marked decrease in height; (3) a further, although not significant, reduction of stature affects Western Mesolithics. Evaluation of possible causes for the great stature of the Early Upper Paleolithic samples points to high nutritional standards as the most important factor. Results obtained on later groups clearly indicate that the Last Glacial Maximum, rather than the Mesolithic transition, is the critical phase in the negative trend affecting Western European populations. While changes in the quality of the diet, and in particular decreased protein intake, provide a likely explanation for that trend, variations in levels of gene flow probably also played a role. Reasons for the West-East Mesolithic dichotomy remain unclear and lack of information for the Late Upper Paleolithic of Eastern Europe prevents insight into the remote origins of this phenomenon. Analysis of regional differentiation of stature, particularly well supported by data from Mesolithic sites, points to the absence of today's latitudinal gradients and suggests a relative homogeneity in dietary, cultural and biodemographic patterns for the last hunter-gatherer populations of Western Europe.

Evolutionary trends of stature in upper Paleolithic and Mesolithic Europe. J Hum Evol. 1999 Mar;36(3):319-33.

Not because of shorter upper legs, but rather shorter lower ones..

Among recent humans brachial and crural indices* are positively correlated with mean annual temperature, such that high indices are found in tropical groups. However, despite inhabiting glacial Europe, the Upper Paleolithic Europeans possessed high indices, prompting Trinkaus (1981) to argue for gene flow from warmer regions associated with modern human emergence in Europe. In contrast, Frayer et al. (1993) point out that Late Upper Paleolithic and Mesolithic Europeans should not exhibit tropically-adapted limb proportions, since, even assuming replacement, their ancestors had experienced cold stress in glacial Europe for at least 12 millennia. This study investigates three questions tied to the brachial and crural indices among Late Pleistocene and recent humans. First, which limb segments (either proximal or distal) are primarily responsible for variation in brachial and crural indices? Second, are these indices reflective of overall limb elongation? And finally, do the Late Upper Paleolithic and Mesolithic Europeans retain relatively and/or absolutely long limbs? Results indicate that in the lower limb, the distal limb segment contributes most of the variability to intralimb proportions, while in the upper limb the proximal and distal limb segments appear to be equally variable. Additionally, brachial and crural indices do not appear to be a good measure of overall limb length, and thus, while the Late Upper Paleolithic and Mesolithic humans have significantly higher (i.e., tropically-adapted) brachial and crural indices than do recent Europeans, they also have shorter (i.e., cold-adapted) limbs. The somewhat paradoxical retention of "tropical" indices in the context of more "cold-adapted" limb length is best explained as evidence for Replacement in the European Late Pleistocene, followed by gradual cold adaptation in glacial Europe.

* Crural index is the result of multiplying the length of the lower leg (tibia) by 100 and dividing it by the length of the upper leg (femur).

Brachial and crural indices of European late Upper Paleolithic and Mesolithic humans. J Hum Evol. 1999 May;36(5):549-66.