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good news from the abyssal plain

I saw something the other day about life on Earth that gave me a lift. Science Now reported that the Census of Marine Life, after a decade of surveying marine organisms all over the world, has documented that 90% of the ocean’s biomass consists of microbes, larvae, and plankton. The total mass of these little critters is equivalent to 240 billion elephants! Elephant-equivalents. The researchers pulled the creatures from the sea itself, from the mud, from the deep-sea vents, and from the bottom of the abyssal plain. (The phrase “abyssal plain” gives me the chills!)

Using new generation sequences researchers identified 18 million DNA sequences. Mich Sogan, a Woods Hole scientist, says “there could be as many as a billion bacteria and archaea, another group of single-cell organisms like bacteria.” A couple of interesting findings are: 1) the microbial diversity increased the deeper they looked in the water column, 2) but sometimes a microbe’s environment  is simply one other organism.

A bonus interest for me is to learn that the richest marine organism environment is the plateau off the Pacific Northwest Coast where 25,000 to 35,000 different microorganisms live in each litre of sea water. I’m writing this post from Beaverton, Oregon, where my wife and I are planning to move next month. So I can just drive to the coast and wade in the rich microbial soup.

All this lifts me because I relish the thought that here on Earth, whether or not we humans commit to being responsible stewards to the one life-perfect planet we know of, the richness of life code on the planet is ineradicable. Human affairs often discourage me, but life is indomitable. The Earth has occupied a sweet-spot for life for billions of years and will continue to for many more.


playing doctor with the iphone

Below is a video from Nature Medicine. It’s intended to introduce the journal’s readers — I imagine MDs and PhDs — to iPhone apps from the iTunes Medical category. Not a bad idea. When I posted a couple of weeks ago my take on whether or not the public needs doctor navigators when getting health info from the internet (Not!) I said at the end the docs ought to check-out the iPhone apps if they want an eye-opening experience. Here’s the Nature Medicine’s video.
Vodpod videos no longer available.
more about “Mobile Medicine”, posted with vodpod
I suppose some people will feel there is something forbidden about a non-physician looking at the Medical apps and will avoid them, but there’s nothing that prohibits them from downloading and using them. You don’t need a license or degree to download, say, the Drugs and Medications app, or the Instant ECG: An Electrocardiogram Rhythms Guide, or the Stethoscope Expert app. Anybody can download any of them. I’ve got the University of Maryland Medical Center Medical Reference on my iPhone right now. I’ve had others.
My point is just this: some doctors are freaked-out that their patients are getting access to health information over the net. It troubles them and I suspect the medical profession wishes the internet would just go away. The truth is, not only is the internet not going away, direct access to information and information tools formerly available to doctors exclusively is more readily available to the public with each passing day. Millions of people are already walking around with health and medical information tools in their pockets or purses. This availability is on the verge of explosive expansion because many entrepreneurs see a golden opportunity in the public’s well-documented desire for health and medical information. My recommendation to the medical community is to get with it and start participating in projects to help make this development as constructive as possible for all concerned.

books that changed my life

My wife and I are moving out of state next month, so we’re unloading stuff we don’t want to transport. I’ve had to look at my book collection and cull the ones I can live without. In the process I realized there’s a small set of books that have framed my way of looking at the world and kindled passions that will continue the rest of my life. They’re the books that have old yellow stickies sprouting from between the pages, yellow highlights and scribbles in the margins. I donated about 60 books to the local library, but these I’ll keep to the end.

Eric Jantsch, The Self-Organizing Universe: Scientific and human implications of the emerging paradigm of evolution, 1979.

Actually, I found this book after reading James Gleick’s, Chaos. Chaos was an unusual best-seller in ~1987 I guess because we all experience “chaos” (in the colloquial sense) in our lives, and people evidently were looking for some insight. A lot of readers never finished the book because it explored the physics and mathematics of chaos, not necessarily the common term. Nevertheless, Chaos made the term “butterfly effect” part of our vernacular. It was a good introduction to chaos theory, but by the end of the book I was wondering: “With chaos being so pervasive in nature, how is it we see order and organization?” Jantsch’s book tackled that conundrum.

Basically, Jantsch presented a framework for how the world organizes via hierarchical systems from the fundamental dynamics of the micro (atomic forces, molecules and basic physical properties) through simple living entities, complex organisms, ecosystems, and social systems. It is a set of concepts that are a theory of organization from basic dynamics up through the most complex things we know, living systems and our own societies. Here’s how Jantsch defines systems:

The notion of system itself is not longer tied to a specific spatial or spatio-temporal structure nor to a changing configuration of particular components, nor to  sets of internal or external relations. Rather, a system now appears as a set of coherent, evolving interactive processes which temporarily manifest in globally stable structures that have nothing to do with the equilibrium and solidity of technological structures.

The mind-blowing idea that came through in this work is that there are processes that, when fed by external energy flows, can become so stable that we think of them as things. Especially in living systems, a lot of things are really just processes that persist as long as the right conditions exist and only that long. They’re called “process structures.” It looks like an oxymoron, but you can perceive some persistent processes as structures. When you get that, it tends to alter your notions of permanence and change. Some complex systems such as living organisms persist during what we call life, but when the sustaining conditions end the processes collapse and it’s all over.

Humberto Maturana and Francisco Varela, The Tree of Knowledge: The biological roots of human understanding, 1987.

The authors of this book set out to show that cognition is not simply our eyeballs and brain somehow internalizing what’s “out there” but is absolutely contingent on our biological structure and processes. Moreover, cognition is a result of our experience and interaction with other people through language. Their notions are pretty trippy. The book’s cover art is a Salvador Dali painting. But the key for me is that they build their argument for how “knowledge” works from the ground up, starting with processes of self-organization at the molecular level. From there they describe how living things come about through a process of  “learning” clear up through humans with our shared knowledge and shared cognition.

Maturana and Varela’s key idea here is autopoiesis, self-organizing systems similar to Jantsch’s ideas.

Our proposition is that living beings are characterized in that, literally, they are continually self-producing. We indicate this process when call the organization that defines them an autopoietic organization. […] The most striking feature of an autopoietic system is that it pulls itself up by its own bootstraps and becomes distinct from its environment through its own dynamics, in such a way that both things are inseparable.

Werner Loewenstein, The Touchstone of Life: Molecular information, cell communication, and the foundations of  life, 1999.

Backing up all the way, Loewenstein goes about explaining the organization that enables the complexity of living things by starting with entropy and information theory. You can’t get more basic than the laws of thermodynamics!

Neither Jantsch’s or Maturana and Varela’s books deal in detail with how information in chemistry figure into their notions of self-organization, but it’s there. Loewenstein makes the idea of information the theme of his book and caries it through from the idea of macromolecules clear up through cells, intracellular information exchanges, inter-cellular communication, and special information structures like neurons. But what I took away from this treatise is that the molecular structures at the cellular level are information devices as surely as the laptop I’m using to write this post. We’re so used to thinking of information in terms of human language and symbols that it seems strange to think that the conformations of proteins, DNA chains, “messenger” RNA and the intricate interactions among them are just as informational. But the robust and growing science of bioinformatics is based on just such ideas.

Dennis Bray, Wetware: A computer in every cell, 2009.

Actually, I’m just finishing this one. It’s a very interesting look at the internal informational working of cells that give these basic units of living things a capability of awareness and appropriate responsiveness that deserves more attention and respect. Cells aren’t just bricks in the wall; they’re participants in some astute biology. Wetware brings together in the cell Loewenstein’s molecular informational processes and Maturana and Varela’s philosophical views of life processes as forms of cognition and learning.

What runs through all these books is the idea that the universe’s fundamental properties and rules allow the emergence of processes of great complexity; complexity sufficient to reach the level of life and at least one organism — us — with the capacity for self-awareness and splendidly subtle thought. That’s a truly amazing range of possibilities based on some very foundational laws. How this is possible is a chain of events that we can only partially explain at this point. The rest of the story requires details we’re only getting a glimpse of right now. It’s certainly a set of riddles that will keep me fascinated the rest of my days.


A lot of computer security wastes a huge amount of time and isn’t worth it

Have you ever wondered, as I have, when trying to get around the “password not recognized” messages from some innocuous web site, how much time people spend simply trying to get something done with their computer but are messed up because they’re locked out by some snafu? Answer: a lot! An article says that all the messing around with passwords that is forced on us costs us a lot of wasted time while not really protecting things of value. As an old friend of mine from Mississippi used to say, “The juice ain’t worth the squeezin”.”


Keep the expectations real

“The promise of a revolution in human health remains quite real,” wrote Francis Collins, director of the National Institutes of Health, in an essay published March 31 in Nature. “Those who somehow expected dramatic results overnight may be disappointed.” (From Wired Science)

Collins–writing about progress in genomics over the past ten years since the human genome’s first draft–sounds like Barack Obama talking about the health insurance reform package.

One of the things I’ve mentioned here a number of times is that the whole question of figuring out how genes and other life processes put us together and what’s happening when disease strikes has turned out to be a lot more complicated than scientists thought ten years ago. Collins’ explanation has an air of defensiveness.

I happen to be reading Dennis Bray’s Wetware: A computer in every living cell. Bray is a systems biologist and the book is an excellent tour not only of the intricacies of genomics but of other informational systems of the cell that play a role in how a cell works. It’s mind-blowing how intricate and nuanced the many, many molecular processes of even a single cell are. Just one cell is perhaps the universe’s most elaborate Rube Goldberg device. Everything that happens is a frenetic, dynamic interplay of molecules banging together with stochastic–not certain–outcomes. It’s a wonder it works at all!

But work it does, and truly it’s a wonder worthy of deep contemplation. We only know a portion of the details about cellular systems, so it’s going to be a long time until many of the very pragmatic results people want,  like curing complex diseases, are reached.

We humans have been doing science in a rigorous way for only a few hundred years. And only in recent decades have we begun to tackle the really complex systems in our world: the cell, the brain, ecosystems, our climate. You’ve got to step back and take satisfaction in what’s been done so far and enjoy the eager anticipation of what’s to come.


DIY primary care

During all the hubbub about President Obama’s signing the insurance reform bill yesterday I saw CNN’s Dr. Sanjay Gupta say that a recent report on new medical school graduates in the US shows that only 2%! intend to be primary care docs. Uh-oh! That’s a problem because, according to the traditional model, that’s not nearly enough to serve as entry points for all the specialties in the system.

So I’ll return to the proposal I made in my post about establishing a new 21st  century health paradigm:

Develop an actionable plan for the goal of enabling each individual to become his or her own primary care authority for 90%-95% of health incidents.

If the docs don’t want to do it then let’s build a system to support every person becoming their own primary care person. Doctors coming out of medical school evidently don’t want to do primary care because the pay isn’t good.  Maybe it’s because the skill and knowledge is of lower value than, say, brain surgery. We lay people already handle about 80% of the physical problems we have. Just go to any drugstore and walk through the OTC products for flu, aches and pains, cuts and sprains, sleep aids, hemorrhoids, eye and ear care, constipation and on and on. Add to that the ~$100 billion “nutraceutical” (foods that have a health benefit like vitamins, herbs, fish oil, etc.) business and you see we citizens are already doing a lot. But we still have the paternalistic doctor culture that makes expanded DIY unthinkable to most people, and we have only poorly developed systems of support. We’ve got organizations advocating “participation” in medicine, but I’m advocating going further over the next decades.

Actually I think the paradigm shift is already underway. We’ve got health 2.0, mobile health, e-health, the quantified self, whole-family genomes under discussion, personal health records, and self-organizing support in social media. But these things are pieces of a bigger puzzle. What we need is a total system putting these components into a synergistic whole that is of much greater utility and impact for the average person. We need to develop information and educational resources using the power of the digital, connected environment to empower folks. This will take time — perhaps a couple of generations — and the investment of goal-directed resources.

I think the internet is about to do for health care what it has done for communication and other professions formerly centered on experts: allow ordinary people to have access to information and powerful tools for the first time. But to put it together we need to hold a new vision and to work toward its achievement in a concerted way.


a couple stories about global growth

A couple of articles from today.

China Drawing High-Tech Research From U.S.

Looking Beyond the Staggering Mobile Stats in the BRIC Countries


playing by the rules

Last week I read something disappointing. An article (that I didn’t bookmark) said that in some survey Americans don’t see climate change as as much of concern as a year or two ago. That amazes me. I know it was a horrendous winter on the East Coast, and some hanky-panky dug up about some scientists involved in climate research exposed the all-too-human backside of science; but how can people with bigger stakes in the future than I have become complacent about something with such far-reaching consequences?

I’m 64 so I won’t personally experience the full consequences of climate change; I’ll have  been recycled by the worms well before the whole thing plays out. I don’t have any children, but I do have a couple of young-adult grandchildren by way of marriage who I care about. They call me “Uncle Dave.” But I don’t see how people with responsibility for tomorrow’s children can get blase about what’s going to happen 30 to 100 years from now. As I pointed out in one of my first posts to this blog, the children being born today have a 50/50 chance of living to 100. When I see a tyke being wheeled down the sidewalk in one of those strollers that looks like a spaceship escape pod I feel a pang of sadness to think that he or she might have to live in a badly degraded world with perhaps unprecedented human turmoil.

Then I read an opinion piece from the LA Times that expressed my perception of the situation very well. In a column titled “The Earth has its own set of rules,” B.E. Mahall and F.H. Bormann said the following:

The Earth has its own set of rules, solidly grounded in laws of physics and chemistry and emergent principles of geology and biology. Unlike our economic model, these are not artificial constructs. They are real, and they govern. Earthquakes, tsunamis, volcanic eruptions, hurricanes, tornadoes, 100-year floods, massive wildfires and disease epidemics are dramatic examples of parts of nature, neither all service nor all harm, creating and destroying, and governed by rules that are indifferent to humans. Our anthropocentric economic model for interacting with the world ignores and is proving to be incompatible with Earth’s rules, and is therefore on a direct collision course with them.

To achieve a more accurate model of our relation to nature, we need to see ourselves as part of nature, governed by nature (not economics), beholden to nature for ecosystem services and subject to nature’s disturbances.

Precisely! The Earth is a platform that has occupied a sweet-spot around the sun for several billion years that has permitted the most complex things in the universe we know of to evolve. Humans are at the apex of this process having evolved a capacity to comprehend the workings of Earth’s rules, to have some degree of insight and foresight about what might happen down the road, and a capacity to make choices and decisions that affect the whole. But, overall, a lot of people seem content to continue with business as uaual and just wait to see how it all ends up.

Earth is a unique place for a prolonged, open-ended experiment with life. The outcome is not determined. The universe is neither for us or against us: it’s indifferent to our welfare. It’s up to us to actively make it work out well…or not.


Article: Remember the Tamagotchi?

In Wired News last week Thomas Goetz wrote an article about how — in the rapidly emerging world of sensors and self-monitoring — we may become something like the Tamagotchis kids wore a decade or so ago. The Tamagotchi (in case you’ve forgotten) was a little character on a watch face that you had to pay attention to during the day or it got sick and even died from neglect.

The new thing is to use the medical sensors that are being developed to get real-time information from your body and use it to give you a reading on how you’re doing. This could be constructive information for a variety of health situations. I referred in my post last week on things that need to be done for a new health paradigm as an avatar system. It could live on your smartphone, pick up sensor information from your body, compare it with your on-phone health profile, and tell you how you’re keeping up with health goals like exercise. It could feed you — or nag you — with appropriate health information. I agree with Goetz that a game interface may be the most interesting way to interface with some health informaiton.

This evening I’m attending the VLAB meeting at Stanford called “The Internet of Things: Sensors Everywhere.” I hope to get a better fix on where body sensor tech is and what we can expect in the near future.

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Mechanics effects gene expression too

I’ve been posting a lot about the complications of genetics, largely as a response to recent criticism about the perceived failure of private and government research investments in genetics to return treatments for disease. My attitude is that there’s been a failure to have realistic expectations about just how complex genetic processes are. I’ve already pointed to articles about “RNA editing” and “epigenetics” and how they affect gene expression.

Now add another factor: gene expression affected by mechanical forces around DNA. Epigenetics and RNA editing are about chemical reactions with DNA or RNA that play a role in determining which genes get turned on or off. But research by U Michigan that’s going to be published in Physical Review Letters has shown that mechanical forces like stretching play a role too.

Scientists understand the chemistry involved in gene expression, but they know little about the physics. The U-M group is believed to be the first to actually demonstrate a mechanical effect at work in this process…

“We have shown that small forces can control the machinery that turns genes on and off. There’s more to gene regulation than biochemistry. We have to look at mechanics too,” said Jens-Christian Meiners, associate professor in the Department of Physics and director of the biophysics program.

We’re all pretty familiar with the idea that DNA forms long helical chains of molecules that resemble a twisted ladder. But this twisted ladder also coils into loops. Proteins acting like buckles connect distant parts of the DNA chain and attach the loops at specific points. These loops and contact points are part of gene expression.

The researchers used “optical tweezers” to stretch out the DNA so that it couldn’t loop back on itself naturally. That threw the normal genetic expression process off. The inside of a cell is an extremely active place with molecules furiously banging into each other all the time. So that brings up a question:

While this experiment was performed on free DNA, the scientists say forces as much as 100 times stronger are regularly created inside cells as contents shift and buffet each other. “If we can basically shut this process down with the tiniest force, how could all these larger forces not have an impact on gene expression?” Milstein said.

Good question; one the researchers are trying to figure out. And it’s one more factor that needs to be taken into account for an in-depth understanding of the how our genes work to make us who we are or to make us sick when they malfunction.

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