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Jun 30

I am always encouraging people to exercise and live an enriched life, so I figured I should post my weekend hike.

Had a great hike up La Luz trail that takes you up above 10,000 feet (3,048 meters) with an elevation gain of 3,775 feet (1,150 meters). This hike is in the Sandia mountains, which Albuquerque New Mexico is nestled up against. You pass through four different climate zones with changing flora and fauna (which I am sadly neglecting in knowledge). I was lucky enough to have met Dave a couple weeks ago at a coffee shop and he was my guide to this new playground that is only a few miles away from where I am currently living.

Sure this hike was no great adventure, but it was a very enjoyable long hike that additionally gave me a great multiple hour workout.

Jun 30

No matter what suggestions I make to try to improve your body and mental health (or the many other good sources of information and inspiration) it is nice to get some feedback on if your health is improving. You can use your subjective measurement of how you feel – which might be the most important, but it is also useful to have some concrete measurements than you can follow your progress.

All the hot buzz is personal health measurement centers around personal genomics, but in general your DNA does not change (mutations changes your genome and there are epigenetic changes (e.g. methylation). Therefore, you can’t use your genome as a measure of your changing health.

In a series of post I will discuss the many current cheaper and highly useful (predictive) measurements of your personal health you can use today. I will be concentrating on tests that are easy to implement and give a good bang for the buck.

Non-Invasive markers

Heart rate (self measurement or a heart rate monitor: low end $ 0.00, median $100, upper end $ 400)

Blood pressure ($ 50 – 100)

Physical aerobic ability

VO2 max (general fitness): done at exercise lab, but can do various approximate tests at home.

Body fat burning ability at different levels of exertion (approx $ 250 ? see Alan Couzens and his colleagues: Gordo Byrn, Matt Steinmetz )

Body fat

General body fat level not as good health predictor as visceral fat

(Tanita scales are the most popular: $100. )

Visceral body fat (DEXA scan: $125 -300 each scan)

Slightly invasive

Blood profile

Glucose (blood glucose meters: cheap or free but pay per test for strips)

Cholesterol: New home devices can measure cholesterol (approx $ 100)

Cholesterol, HDL/LDL (CardioChek PA: approx $ 550, might be new alternatives)

Inflammatory levels

C-reactive protein (CRP): no home test at this time.

IL-6: no home test at this time.

This is a first basic level of measurements that you can test and more importantly retest. Most of them you can do at home repeatedly (notable exception at this time is the inflammatory markers). The optimal test would be easy to perform, high reliability, and cheap so you can test many times. Additionally, no one test is the best measurement of ‘health’, so multiples test would give you a more accurate measurement of your health.

Tomorrow, hopefully I will concentrate on one of the simplest which is heart rate. There are multiple measurements that you take and get some predictive clinically tested health measurements.

Jun 27

New data released from CDC indicates that the number of cases of diabetes in USA has risen to 24 million (2007), up from 21 million 2 years ago (2005). Now, 8 % of the American population have diabetes. A further 57 million Americans are in the pre-diabetic stage, which makes this group prone to developing full blown diabetes. That would make a total of 81 million Americans being diabetic or pre-diabetic out of the 303 million population, a startling 25.7 % of the population.

The latest headlines about the obesity rate in America for teens claim great headlines about the rate leveling off. That is almost comical because all that means is that the rate is not rising as fast. The rate of obesity is still increasing, so not sure if people should be celebrating. 32 % of Americans kids still remained overweight or obese. With that high of a percentage of overweight children what do you think is going to happen to diabetes rate when these children hit adulthood or middle age?

As for American adults an article from 2007 indicates that 66% are overweight or obese (2003-4 data). According to the CDC website 33.3 % of men and 35.3% of women are obese. And remember these adults were not at the same level of obesity as the children of today, so again what will happen to these adult numbers when the current children become adults?

Gasoline, as we are all painfully aware of keep skyrocketing, with new record highs it seems almost everyday. On June 26th 2008 oil prices his just below $ 140 per barrel and speculation of $ 170 by the end of summer (update: today oil hit $ 142).

Obvious thought, why doesn’t America do a little less driving and a bit more walking. Lose weight, reduce the prevalence of diabetes, and save money and oil. Additionally, don’t you think carrying all those extra pounds add up to reduced gas mileage?

Not practical many would arguie, instead we are inventing more ways to make us lazy, such as power assisted luggage.

Funny how the models they used don’t represent the population of people that would really be using such a device. I thought the general idea of wheeled luggage and backpack devices was misguided to begin with. Carry the weight get some exercise.

What are the current trends: rising diabetes, obesity is not going away, rising oil prices, but we keep on wanting to reduce our bodies energy output. Does this compute ?

Well for you the betterment of your pocket book and health, why not this summer trying to increasing overall body energy output, for example by walking a bit more, and driving less.

What do you have to lose, other than some weight and more money in the bank. Even if you don’t need to lose weight (33 % of the population) I am sure getting in better shape would be good for your general health and you can still use the extra money.

Have a good weekend, get outdoors and enjoy the summer.

Jun 26

In previous posts (here, here, here, here) I have explained how the two simplest things you can do for better brain and body health is live in an enriched environment (new learning, novelty, etc), and exercise. But we all are limited by time. That is why I was quite excited by a post by Alvaro posted at SharpBrains who interviewed a leading neuroscientist, Dr Kraemer. Dr Kramer is widely published and wrote a very good review paper in nature reviews neuroscience, which examined the positive impact on the brain from aerobic exercise (a high impact review journal which you don’t get to write for unless you are highly published and respected).

The simple, but great idea, offered as practical advice in the interview was why not combine an enriched environment with exercise in the form of a walking book club. This would save you time and give you twice the impact (in theory). Why not combine intellectual engagement and exercise?

So head over to Alvaro’s interview of Dr. Kramer – very interesting and down to earth advice.

I was lucky enough to be involved in a book club back in Vancouver, Canada with some great friends, until I recently moved (temporary). The question I will have to ask my friends is how we are going to carry the wine (see resveratrol) during the walk and talk ?

I think once I go back to Vancouver we will have to implement the new and improved book club. Anyone reading this blog and living in Vancouver are welcome to join – I will keep everybody informed.

But beyond my own plans, the idea of an ‘active’ book club (walking is the easiest to implement I presume) could be started by any of you out there. How about it – this could be a whole new movement (well, if Oprah started one).

Jun 25

Here is a video of Chris Jordan (at TED conference) who is a photographer who wants to make visualization of data in our modern world easier to digest, easier to understand.

e.g. USA has the largest percentage of its population in prison compared to all the other countries in the world. He tries to make it easier for us to visualize the 2.3 million American imprisoned by showing us a picture of 2.3 million folded prison uniforms stacked up and across. 1 out of every 4 imprisoned people are Americans imprisoned in America.

384,000 women had elective breast augmentation last year in America. He mentions it is rapidly becoming the most popular high school graduation present. He visualize the number of these type of surgeries done each month by a collage of Barbie dolls.

He also points out he didn’t pick these examples as the most important issues in the world right now, but just as examples to make us think.


Keep your mind open, keep learning new things.

Jun 25

DNA contains the information, in a code, that enables an organism to become ‘alive’. Life is really all about information. That is why the previous post regarding Google getting into health is not far fetched since Google is all about information.

If you want to read a great series of articles about information and the coming petabyte age, including how this might change how we do science go to Wired magazine.

If life is all about information what happens when some information is lost – a decrease in life function and potentially death. A large part of aging is the loss of fidelity (integrity) of the system. There are many levels of information in the biological system: DNA, RNA, protein, signaling cascades, and system. At all of these levels the individual components can be modified (for the good and bad) and information can be lost. When information is lost the organism can suffer. A very simple example of this is through one or more mutations (one current theory) cancer can occur and the organism may die. Another example would a mutation of a gene, or modification along the way that reduces the amount and/or function of a protein. Now most biological systems are quite robust to alterations and can absorb the impact of many changes, but with enough loss the system no longer functions to the optimal level. Take the simple process of aging.

Just like you don’t want a corrupted hard drive of all the information you have collected – the picture of your graduation, the pictures of your family, etc, you don’t want to lose your biological information. With electronic data we can make backups, but we cannot do that with biological information (well you could store some of your DNA –but that does not represent the current you with all your memories etc).

Hence, for overall body and brain health you want to reduce the amount of lost information. You do not want mutations (skipping the importance of mutations for evolution), you do not want loss of normal RNA and protein expression under the appropriate environmental condition.

I could point you to a bunch of articles that is basically saying the same thing as I am (probably more elegantly) but I think the general idea is pretty easy to grasp and is really common sense. So I assume most of you are going to be thinking that what I have just pointed out above is obvious – a no brainer. The real question is what can you do to stop the loss of information?

How much would you pay to slow down your rate of information loss? Or would you argue that you really don’t care? Would you care if your hard drive slowly starts losing information – and you could not make a backup? Which do you care more about – the information on your hard drive, or your life?

Jun 24

So to jump from the big perspective of humanity (previous post on the Wade Davis video) now I am going to jump to the molecular level.


You can also go directly to Harvard website where you will find alternative versions of the video, including the ones that give a biological narrative to the videos (you have to click on the full version link). These versions of the video are obviously more interesting than the musical background one released on youtube – go watch and learn (click on full version link).

Some of us do our best learning via words and others by visualization (I can think of a few friends) – but in reality we probably all do the best by combining many modalities. I could not insert the biological narrative versions of the video or I would have.

I saw the video above previously, but then this weekend I saw a TED conference video from David Bolinsky, the person who made the incredible animation of molecular biology (above) and he talks about his goal to give us biological scientist, and everybody else, a better understanding of what I am calling: “The big picture of the small picture.”


He talks about how the video is part of a 5 year project, and therefore we can look forward to more videos.

To an enriched environment, from the global humanity perspective of Wade Davis, to the visualization of hard core molecular biology. If these types of videos (at a fairly continuous dose – take two and call me in the morning) do not lead to an enriched and healthier brain – then we will have to rethink this whole enriched environment idea.

Feed your brain.

Jun 24

One dilemma of blogging is on a day like today I want to blog three different things (with a limited amount of time); different perspectives, personal genomics, and simple measurements of health (including more measurements of the simple heart than you might think are possible). This also might be partially a product of my current living situation, which is far away from my scientific friends. Normally, at least once a day I would run into them in the hallway or my office, and at least once a week we would get together and I would spill out my knowledge of the day or week. It would be my release, now blogging has replaced these personal interaction. I might have too many things that I have come across that I want to share and no one to share it with – so I guess my blog viewers are forced (well they can click another channel) to listen to my ‘brain dumps’.

Back to perspectives. Exposing yourself to a great diversity of perspectives is part of living in an ‘enriched environment‘, which repeatedly has been shown to be good for your brain health.

I was fortunate enough this weekend to come across a wide diversity of videos from various great websites (eg fora.tv and TED conference), which I both highly recommend. As I have mentioned before there is no excuse for not exposing yourself to an enriched environment for the world of knowledge is at your fingertip (as long as you have an internet connection of some sort).

A big perspective (one example).

Wade Davis, an anthropologist gives a fascinating talk (TED video link). Or


If you have 18-19 minutes to spare watch this video. It is not science as many of us think about, but as a view of humans, culture, and humanity this is an enlighting perspective (take note (as one example) of the Polynesians ability to sense the distance of atolls by the waves against their boat) about the waves ). “Different visions of life, making for completely different possibilities for existence.”

Jun 23

I posted earlier today about the mountain of cancer data donated by GlaxoSmithKline. While scientist and big pharmaceuticals are constantly generating more biological data the bottle neck problem is mining this data to find useful information.

Over at PIMM, Attila in his blog discusses a feature article in Wired magazine and offers a potential solution to this data infoglut problem (which is only going to get larger) might be Google, whose mission statement is: “to organize the world’s information and make it universally accessible and useful”. Could Google with their infrastructure and high concentrations of very smart people make sense of the current, and coming, infloglut of scientific data sets? Very interesting question.


And an update on the personal genomic squabble between the California government, who sent ceased and desist orders, and the genetic testing companies is covered here.

Jun 23

Image via Wikipedia

Many scientist believe that in the near future there will be breakthroughs due to our ability to generate huge data bases, and more importantly our ability to mine them.

GlaxoSmithKline have done a huge and expensive study on cancer, and as of June 20 2008 released a mountain of data for free. They are not releasing all of the data, but the vast majority of it.

The data is mostly if the form of microarray results which the company has given to Cancer Biomedical Informatics Grid (caBIG), part of the National Cancer Institute to house.

Here is a link to where the data is located. It contains the genomic profile of 300 cancer cell lines. The genomic profiles include both the results of SNPs microarrays and microarrays to measure mRNA transcript expression.

Now this is potential a fantastic resource of information for the hundreds of thousands of cancer researchers. I am sure the data in this bank could be the start of hundreds of Phd degrees.

I really hope that the new generation of smart open source scientist can harness this data and make gold out of straw (one example would be Shirley Wu).

Taking a slightly cynical route, do you think GlaxoSmithKline, or their shareholders, would be happy with the company giving away information that contains ‘value’? Or is it more likely they have used massive computer power all their bioinformatic personnel to strip out all the gold before releasing this mountain of data freely to the public ? Yes, this move will build some ‘good will’ for GlaxoSmithKline with the public which is of some worth, especially with the current climate of the publics trust in big pharmaceuticals. However, it seems unlikely that big pharma is really in the habit of giving away valuable information. Could it be that even after shifting through this mountain of data on cancer cell lines that they only found a few nuggets, but overall the mountain was barren? That would be a scary thought regarding future cancer research.

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