Category: Computer Programming
I'm almost done with the clinician implementation of the SWAMI GenoType package. I think it is very good.
I'm sure that there will be some debugging ahead, but we've been using it in the clinic and so far it appears to be quite stable. Beyond that, I just have to write the User Manual and the Admin Guide. If you are using nutrition in you clinical practice, you may want to incorporate this software. For more information, you can click here.
Now, I like writing computer code, but even I'm getting a bit burned out on the thing. I'm looking forward to getting some cycling time in, though the weather has not been all that cooperative.
Dr. Natalie and I just did up a new clinic newsletter. You can read it here.
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 â€˜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.
I've come back from paradise... or at least Saint Martin.
It was good to get some time out in the sun and swim in the beautiful blue Caribbean. I also rediscovered the pleasure of reading from books, versus all the reading that I do from computer monitors. With proper lighting it is just so much easier on the eyes. Everyone at the hotel was reading different books... except that they were all written by someone named Gresham.
I've never cultivated much of a taste for fiction, since you have to work so hard at populating a mental space to hold all the necessary components; the setting, theme, characters. I find that many people who do like fiction seem to have a type of RAM memory in a certain part of their brains that they can fill with all the plot details, then erase for use with the next novel. I feel sometimes that if I did too much of that it might push some of the other stuff out, so in the midst of all those murder mysteries, there I was with Paul Kennedy's â€˜Freedom From Fear' (a 900 page thriller on US history during the 1930's depression) and Larry Wall's â€˜Programming Perl' (made especially interesting by the fact that none of us took our computers with us).
I'm in the process of completing the SWAMI GenoType software (which is mostly written in Perl) and in a blitz of activity since my return it is now at the point where we can beta test it in the clinic. Pretty cool, if I do say so myself. It takes between 90 and 230 individual client parameters (blood groups, asymmetries, etc) and analyzes 700 individual foods according to 200 nutrient parameters (antioxidants, propensity to foster microbial overgrowth, acetylcholine content, etc.) For all those 12,600,000 individual calculations, the program is quite fast, though I do admit to a perverse pleasure sitting there for about 30 seconds watching it groan under the strain.
One of the mottos of Perl is that â€˜There is more than one way to do it' (TIMTOWTDI, usually pronounced "Tim Toady"). The more that I think about it, there is a lot of Tim Toady in my nutrition research as well.
Probably because at heart I am fundamentally a post-modernist.
Post modernists believe in AND more than OR, whereas modernists tend to give OR precedence in their lives and thoughts. The folks who get all bent out of shape about â€˜the GTD versus the BTD' are probably modernists and think that there is only one path to the truth. There is certainly one truth (or fact, or whatever) but that is not the same as saying that there is only one way to find it.
We've been rearranging the clinic this past weekend. My office is being converted into a more general-use, conference-type room. While this sounds perhaps like a demotion, it is actually being done at my request. With the addition of Dr. Colicci to the D'Adamo Clinic staff, we are doing more of a team approach to the patients, and this did not work with an office devoted to just one physician.
Probably the best thing we're adding to the room is a 4' by 8' white dry erase board. This will allow us to 'teach' the patient about the particulars of how we plan to structure their approach. I normally do a lot of this, most often drawing on the examination table paper (which many people take home as a souvenir). I love to explain stuff, but I'm a very 'visual' type person (love to draw, etc.) and if truth be told have always been a bit nonplussed by the whole 'performance' component of doctor consultations, i.e me behind the desk, across from the patient.
It is amazing what this small change in visit structure has done to my perspective. Whereas I used to think 'I've got six patients today,' I'm now finding that I'm thinking 'Hey, I've got six classes to teach today.'
This will also be helpful with regard to the practitioner training that we do at the Clinic, since I can't think of the last time I've seen a patient when there was not an extern or preceptor in as well. 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.
SWAMI is coming along nicely. I've written another 1,000 lines of code; mostly the 'calculation' subroutines. A bit more of that and I'll more onto the 'search and sort' and 'report' modules. I'm thinking of licensing a consumer version (SWAMI-lite) of the program that will allow anyone for a small fee to input their own data and run a single version of the SWAMI program. I'll just have to see how practical it is.
Final plug for the lecture that I will be giving at the New York Open Center, February 15th at 7:30 PM. It is only $30, and they give you a free hardcover copy of The GenoType Diet which I would be most happy to personally inscribe for you. Click here for more info.
This late breaking bit of news: I've just received an email that the supplement facts boxes are now online for all The GenoType Diet products. Hopefully this will provide folks with the information that they need to decide whether they want to include these products in their supplement plans. A big thanks to my friends Jon Humberstone and Keith McBride for working over the weekend to make this happen.
Video of the Month:
Michael Moore is a guy it is not hard to have an opinion on, and I actually have a few. However his film 'Sicko' does cast aside the curtain on the con-job that Americans are fed about just how 'great' our health care system is. In the meantime in this video clip he also shows just how flaccid and conformist the US major media is:
Perhaps you are a long time Blood Type Dieter and you're thinking of moving onto The GenoType Diet. Perhaps you've just heard about The GenoType Diet, but did not know about my New York Times bestseller, Eat Right For Your Type, the book about eating according to your blood type.
So.. which one is right for you?
Although they have very great similarities, the Blood Type Diet series of books and the new GenoType Diet book are actually two distinct dietary systems, which complement each other but work through different mechanisms.
Well, I've made it easy! Just complete the little quiz below and press the 'Find Out' Button. I'll tell you which book I think will be best suited for your needs.