Where There's Data There's Hope

Larry Smarr-Where there's data there's hope

So thanks a lot. I never thought I was going to get into this business. I’m a scientist, a physicist, and computer scientist professor. But when I came from Illinoi to La Jolla in 2000 I started getting into learning more about nutrition and my weight was one variable I was starting to monitor.

But I quickly went up and these are powers of 10 to 100 variables with blood variables, up to a million with my SNPs and genetics. And now I’m up to somewhere in 25 billion with my microbial data.

And the first part of this journey was about improving my body and getting back in shape; I was really out of shape and just you know, getting healthier. And I never really expected that what this was going to lead to is in the second part as I got more and more data deeper inside of me that I was going to discover I have a chronic incurable disease; Crones disease, which I never had any idea.

So as long as we are going to be exhibiting the data, this was me when I left CSA running the super computer Center, came to Illinoi. I hadn’t been exercising for about 20 years. I was eating like most Americans do because as you notice in the obese epidemic this is what Americans look like.

And when I got to this much more health conscious fitness environment in La Jolla started using all of the sorts of things, you know I’ve got a Fitbit on, I had a Body Media for 24/7 for a year. I do Zeo; I’ve done 400 nights of Zeo.

So I use all the sorts of things you’ve been talking about and I did a lot of learning of the biochemistry of my body and then adapting what I put in my body to be appropriate to what a human is instead of the crap that we normally put in our bodies.

I discovered I was pretty diabetic infact, and so I was very keen to reduce the inflammation in my body and I learned of course from things that the ratio of omega-6 to omega-3 fatty acids are really critical and as you see most people with diabetes or heart disease are up in the something like 20-1 omega-6 like corn oil to omega-3 which is like olive oil, fish and so forth. And the average American isn’t far from being chronically ill that’s what the obesity epidemic is telling us.

You can see where the ideal range is and down there is my range. So I got there by you know taking six fish oil pills a day and so forth, and I should be at this point (and this was about 2005) really in a state of low inflammation. Now to find this data out, this is a blood test and I wanted to make that change in my body. You know don’t trust the diet books, actually measure.

And so I went to the doctor and said I wanted to do this and he say, well there’s no insurance code for that because it’s preventative.

So I found out you could go online to yourfurturehealth.com and I could get this test and go down to Quest Diagnostics and they draw my blood, and off to the web and I came back and found this out. So I realized and we now know it’s something like 25% of all blood test in the US are not associated with hospitals or doctors. So I said, wow this is cool. What else can I learn?

So I realised that I could actually do all of these different sub systems in my body, and I’ve just done a paper if you’re interested in biotechnology take you through a sort of a how to guide to measure all these things using blood. And I did it over time because I really wanted to understand you know more about how the biochemistry in the body was working, and the amazingly enough only one of these was far out of range and the slides are better than this, but they put them on a Mac so what do you expect.

CRP is a complex Reactive Protein was the only one far out of range, and how far. Well this is basically seven years of me taking CRP. This is a general measure of inflammation in your blood. It should be less than one in that blue band at the bottom, and you can see the shock when I had got my inflammation down by being very omega-3 conscious that i was five times, 500% over the upper limit. And then to my horror it went up to like 15 times and then by January of this year it was up to 27 times. Now put that in perspective, four times higher – a CRP of four is enough to quintuple your future chance of heart attack because inflammation is what drives plaque to the formation of coronary arteries.

I had two episodes of antibiotics to try and bring this down, but you can see because I measure the data points, the 27 down to six happened before because I took the measurement the day before I started the antibiotics and the day after; I was quantifying things mostly with my internal immune system.

So for seven years I’ve been trying to figure out what in the world could be causing this inflammation inside of me and particularly these large episodic things. so because I had got out of the doctor thinking and hospital thinking and into the web thinking, while I was at yourfuturehealth.com, what other tests could I do. And they had this comprehensive stool test and I said, huh stool, who would have thought.

And so I’ve started doing that. I’ve done like 20 of these so far. And everybody talks about blood being this window into the body, but your largest immune organ is your large intestine. That’s where 85% of your neurotransmitters are like serotonin and dopamine you think are in your brain; they’re in your colon.

And this gives you an enormous window into the immune system and inflammation, and this is one thing, lactoferrin I had no idea what lactoferrin was. I had to self-teach myself by going to scientific literature and using you know what Wikipedia say lactoferrin is.

Anyway, it’s a protein that comes off of the neutrophils that are the white blood cells when they’re attacking things and it should be less than seven which is that green line. And mine peaked last year at 124 times the upper limit, so at 900. You look that up in the medical literature and you find out that the test that they use to find out do you have inflammatory bowel disease, which is a chronic disease or IBS which is not a chronic disease. And at these levels 900/1000 it has to be IBD.

Now my doctor who had done the colonoscopy had said you don’t have IBD I’d notice it. You know I’ve done your colonoscopy, I’ve been inside and you don’t have it. And I said, like you must be doing these all day long. He said, yeah I do, I do dozens of these a day. I said, so that’s why you don’t have time to read the scientific literature.

So I started getting more articles and how can I have a chronic disease. I feel you know, do I look like I have chronic disease. I mean this idea that you can feel what’s going on inside of you that is just so epistemologically false; you just can’t do it.

And so as you’ll see, there are things that are completely out of whack inside me and I would never know that by ‘feeling’, which is the first thing your doctor asks you when you come in the office.

So, when you read about this you find out that how is it that you come to have something like this. Well they say it’s a complex interphase between post genetics, that’s human genetics, your immune dysfunction and microbial factors.

Cool! Let’s go measure them. Turns out you can’t.

So in particular I was one of the early 23andme users, and you can just go to 23andme and you type in Crohn’s and up comes these are points along your DNA out of the 1 million that they have on 23andme, which have been shown to be associated with people who have IBD or Crohn’s.

And on some of them I’m green and I’m less likely to have it, but this one is Interluken-23 Receptor, now who knew what that was. It’s a pro-inflammatory chemical that basically I make more than the average person.

So does that have anything to do with Crohn’s? So I look up the Intreluken-23 Receptor, and sure enough here it is, Interluken-23 is the master regulator in Crohn’s disease. So I’m self-teaching myself this as I’m taking the data. The data is telling me what to look up and then I get these scientific articles.

So then I say what about the immune system, how do you measure your immune system response?

Well, this wonderful stool test, stool is such a lovely way to learn about your data, your body has so much data in it, it’s just people don’t have respect.

And so Lysozyme is very easy to measure, and lysozyme is an enzyme that is created by the wall of your colon; it’s your point defense against bacteria. It’s like the Gatling gun you know the last step, I’m going to kill them with the Gatling gun – that’s what this this does and you can see it’s supposed to be below the green line of 600.

And in this time I’m in this war, this episodic war between my innate immune system in trying to kill a bunch of bacteria that are not supposed to be there. Now how am I going to figure out bacteria?

Well it turns out as part of the stool test it cultures the good and bad bacteria, and they have a way of measuring it; 1, 2, 3, and 4 and 4 is like normal. And if you can see my blue, which is E.coli, are always there. But things like lactobacillus, which is in yoghurt and kefir and things like that if these were all four high you would have four stacked up and you’d be at that black line of 16.

So if there’s white in there it means I’m suppressed in those good bacteria. So evidently I have got this period of wipe out and this escalating coming back and forth. Well that’s great except that you can only culture about 15% of the species of bacteria that are in you. so I wouldn’t say that you want to ty this at home yet, but this idea that the microbes are critical to your health, this is the cover of the Economist from August, and so the gut microbes have tremendous things to do with all kinds of diseases and in your health.

So what it is that I sent off some stool to Craig Venters lab in Maryland. They sequenced it with sequencers and I got back a disc drive literally a 2 terabyte disc drive that had a 35 gig file on it which was like okay, now what. and fortunately I’m a scientist and had a grant from the Moore Foundation to build a global center for microbial metagenomics, and I had staff that knew how to take this stuff and actually figure out who the microbes were. It takes about a half a CPU year per person to turn that 35 gigabytes into a set of who’s there.

And what I had found that – and I had downloaded 50 more people and sent them through the things, so that’s 25 CPU years, but we have a super computer center at San Diego so that worked.

I called the director and said I need a discretionary account…

So anyway what I found to like 20 healthy people who had been done through the National Institutes of Health in Human Microbiome Program that has been spending millions of dollars in the last five years figuring this stuff out, all of my healthy ones that should be there are like down by 10 or 20 or 30 times from what they should be. And in the vacuum of what this eco-niche is all these bad bugs that come in particularly like 60 times E.coli and (misinygines?) that were in this, anyway they took over.

So now what I’m going to do is of course a good quantifier wants to do it in time, so I’m going to repeat this and I just happen to have my doctor who is expert in this gave me some antibiotics for a month. And I just happened to go back to my refrigerator and my freezer at home and found I had a sample that I had taken from the day after I had stopped taking the antibiotics and froze it in case I might need it in the future.

So I quickly put that in dry ice and sent it off to the Institute, plus four month later to see how my body might have rebound. And what this means is that I can begin to really quantify the state of the microbial ecology. Now why that matters is your human cells that you’re spending so much time quantifying are 10% of the cells in your body, 90% are in these microbes. And in terms of 23andme and all that or even full human genome, that’s 1% of the genes; 99% of the genes of your body are in the microbes. So if you don’t quantify those you’re not really quantifying the super organism that you are.

So what I’ve learned by this experience over 10 to 12 years is you know when you go into the doctor’s office and he says how do you feel, this is next to useless. What you want to say is what are your numbers, what do they look like over time, how do they compare with the population. And if that’s what the doctor looks at then talks to you then you can have a useful conversation.

So my endpoint where I’ve come to is where there’s data, where you can actually quantify your body and get a sense of knowledge and a sense of if not control and an ability to at least understand what’s happening to you there’s hope.