Been looking at the Kindle book reader from Amazon, and I think they may well have produced the 'killer app' for the reading public; much like what the 'iPod' for music listeners.

It's not perfect; formatting is somewhat of a bear. For example, tables --a basic formatting tool of HTML-- are not supported, which makes me think that this is not going to go over big in academic circles (though many publishers will probably just convert their table data into a graphic images; not a solution for me, since most of my tables are generated dynamically by the programs that I write).

However, once you get the hang of things, publishing eBooks is pretty straightforward. Which is great, since I see my own future as an author veering ultimately into the realm of self-publishing, with its lack of editorial constraints. I also like the idea of a small gadget that can hold two hundred books means to the vertebrae of my two daughters, who seem to look more and more like a special forces team with their huge backpacks filled with very heavy paper books.

So... here is little gift for you all who either have a Kindle or a Blackberry or whatever. It is the Recipe Index from the www.dadamo.com website. Now you can shop by using your PDA or Blackberry or Kindle.

Just Download This File

Save it to your hard drive and upload it to your Kindle. If you have a Blackberry you need mobipocket to be able to read this file on a blackberry. You can download it free from here* just follow the simple directions. For other gadgets, just google you gadget with the keywords 'mobipocket' and 'prc file.' Most PDA and phone have some way of reading these files.

Enjoy, and let me know what you think of this first effort if you get it to work

* Thanks to C-sharp and Dr. Natalie, who let me know that the earlier link was no longer working.

Although I’m probably only one of five people on the planet who have not read it, the blockbuster success The DaVinci Code is just another indication that we humans have an innate curiosity about codes and their relationships and meanings. This blog will take us into the ultimate code of them all: The Code of Life.

By general agreement, a code is a rule for converting a piece of information into another form or representation, not necessarily of the same type. For example, I often write computer programs, most often to do some particular job or another on my website. Most programmers refer to this a “writing code.” Computer programming code appears to the non-programmer as a series of arcane jottings and numbers, but to both the programmer and computer, this code is in reality a series of highly specific instructions, executed step by step, that result in the computer performing some real world action; perhaps posting a message to an internet bulletin board or sending along an email.

Since computer programs are often rather large affairs with many loops and computations, writing good computer code is a daunting -if at other times stimulating- pursuit. It can be reassuring to remember that at any moment in time only very simple, rather dumb things are happening. What makes the computer program so powerful is that all these simple dumb things are happening extremely fast with a tremendous degree of accuracy.

Very few computer programmers can ever claim to have written a perfect program straight off. There are too many places that things can go wrong, computers being the terribly literal creatures that they are. For example, a command that tells a computer to print Hello World! to the screen might look like this:

23. PRINT “Hello World!”;

Simple enough, eh? Like the way we humans typically read books (from front to back and top to bottom) computers execute code from the top down. Thus, our line of computer code is numbered 23, so we can assume that there are twenty odd lines of computer code in front that will be executed before our screen lights up with the words “Hello World!” Perhaps line 22 tells the computer to make the screen font red, in which case our “Hello World!” would be rendered in red colored type. If we remove that line and run the program again, our font color goes back to black.

Look at our line 23 again and you will notice that the phrase you see -- Hello World! -- is in quotes, because in our simple computer language putting a phrase in quotes tells the computer where is the beginning and end of what you want sent to the screen is located. Without this type of instruction, computers are actually quite dumb, and have to rely on us to tell them where the beginning and end of various human things lie. Also notice that at the end of the line is a semi-colon, which in our little computer language tells the computer that this is the end of that particular line of code, so move down one line and execute that command next.

Computers are so literal that a mistake of even one character can cause a program to malfunction. For example, if you saw this line:

23. PRIINT “Hello World!”;

You’d probably guess that something is supposed to be printed. However the computer does not see PRIINT as the equivalent of PRINT. On the other hand if your code looked like this:

23. PRINT “Hello Wurld!”;

The program would probably still execute, since as far as the computer is concerned the command is correct and it’s in quotes, so it assumes that this is probably what you wanted. Once the command is correct, the computer doesn’t care if you tell it to write “Hello Wurld” or “Kick Me”. As long as its own language is correct, the computer will chug happily along, performing its assigned tasks.

Like computers, first impressions, and that light switch on the bathroom wall, genetics is remarkably digit business: On-Off; Yes-No; Love-Hate. So even if it looks complicated at times, don’t be fooled: It’s not. Just remember, like computers, genetics is simply a lot of small things happening in a clear-cut manner and if you get perplexed or lost, just take a step or two backwards and start again.

The mechanism of the genome is surprisingly similar to our simple line of computer code; so simple in fact that I will provide you with an “executive summary” of the whole affair in just two paragraphs.

A molecule called DNA periodically assembles copies of various parts of itself that are called RNA. RNA then travels to other parts of the cell where it is read as an instruction template, assembling chains of amino acids into something very useful: protein molecules of delightfully complex three dimensional shapes that are most often a class of proteins called enzymes.

Enzymes are special speed-up molecules that greatly foster the production and metabolism of the body’s tissues and secretions. Without them many biochemical reactions would occur so slowly as effectively negate their value. Just think about the difference between soaking a dirt stain in plain water for four days, versus soaking it for four minutes in a solution of water and laundry detergent and you’ll get an appreciation for the action of enzymes.

Enzymes catalyze many of the reactions involving proteins, fats, carbohydrates and minerals. Hormones, mucus, neurotransmitters, you name it; they are all made from enzymes.

Bingo. Life.

It sobering and a bit humbling, to ponder the fact that when we eat any kind of protein, we’re actually consuming the results of something’s DNA and some of their DNA as well. However we usually break down dietary proteins to their amino acid building blocks and start all over again.

Occasionally, wild molecular gyrations occur as the incredibly DNA long molecule prepares to replicate by winding itself up tighter and tighter on a tubular scaffold of its own creation. Splitting from the ends much like an old Manila hemp rope would, each of the two unraveling single strands then begins to assemble a copy of its missing partner, producing two unique strands of DNA and creating two daughter replicas from one original.

What happens is surprisingly simple. Good things are like that; a strong underpinning of fact and analysis, and a veneer of simplicity and common sense. Now why, on the other hand, is quite a different story.

I'm almost done with the clinician implementation of the SWAMI GenoType package. I think it is very good.

Happy SWAMI.

Here is a typical printout of the diet report.

Here is a typical printout of the chart report.

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.

Sad SWAMI.

Dr. Natalie and I just did up a new clinic newsletter. You can read it here.

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.

1.

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.

2.

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.

3.

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.

4.

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.

5.

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: