Something Fishy About Mercury

Here is a fascinating discussion on NPR’s Forum from earlier this year on the subject of mercury and fish:

If you’ve listened to this the whole way through (which you should), I’m curious as to how it will affect your habits, if at all.  And why?

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A Meditation on Biological Modeling

This is not my meditation, it was created by Cellucidate:

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Cancer as a Complex Adaptive System

Heng, et al recently published a review paper that brings together and touches on many different aspects of cancer complexity.  I thought this an opportunity to selectively quote the paper and organize the quotes loosely around various complex systems concepts they relate to.  I’m curious whether this makes sense to readers of this blog, or whether there’s too much unexplained jargon and too many large conceptual leaps.  Please ask questions or make comments freely below.

One preface I think will help is to understand that genome, karyotype and chromosome refer roughly to the same thing.  Here are several schematics that I will present without explanation that together illustrate how genes relate to genome/karyotype/chromosome structure, and how that in turn relates to the so-called genetic network (loosely equivalent to the “proteome”).  Of course “gene” is an outdated and inaccurate concept, so don’t get too hung up looking for genes here, just understand that they are sub-structural elements of the genome.

From MSU website

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Prediction Markets for Valuing Private Companies

Everyone seems to have an opinion on the future prospects of Facebook and Twitter. Some of us even feel strongly enough to want to bet on it. Unfortunately, the companies are privately held, and unavailable to be bet on in the traditional way, via the stock market. It is not just household names like Facebook and Twitter that people might want to bet on, but also smaller companies like Weebly, or the Universal Record Database (URDB.)

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Will The Real AGW Skeptic Please Stand Up?

Normally, I don’t debate random bloggers on Anthropogenic Global Warming (AGW).  However, I made an exception for Robin Hanson.  For those who don’t already know of him, he was both an early proponent of decision markets and has a reasonably well known journal article on why two Bayesian rationalists can’t agree to disagree. I’m a fan of his work and have been reading his blog for years.

Yesterday, he put up a post titled CO2 Warming Looks Real.  He’s not an expert. Like me, he has an economics background and did some detailed research.  Yet from the title and body of the post, I though he must have reached a very different conclusion than I did. So I thought I’d try to engage him to find out where we differ. The results were interesting.

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World’s Most Ambitious Crowdsource

Everyone has heard about the Large Hadron Collider, arguably the most ambitious and complex engineering project ever undertaken, anywhere.  The purpose, no less ambitious, is to answer all sorts of burning questions about the nature of the universe, including whether the Standard Model of particle physics is valid.  Given such ambition and high stakes, it would surprise most people that the LHC is managed in a collaborative manner with very little hierarchy.  Essentially it’s a giant, crowdsourced science experiment.

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Foldit

Has anyone played Foldit, the protein-folding game that is designed to advance the science?  This Wired article makes it sound like Ender’s Game meets biochemistry!  Sounds like the Poehlman kid is the protein-folding equivalent of Stephen Wiltshire.  I love the crowdsourcing, the meta-evolutionary algorithm of it (to find the savants), and the implications for science.

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Five Things You Can Do Right Now to Improve Your Life

1. Smile.

2. Spend time with friends, or even try and make a new one.

3. Help another person. Donate a small amount of money, that has nominal value to you, but significant value to someone else. (Kiva, Vittana Foundation.)

4. Quit Smoking. It might be even worse for you today.

5. Stop worrying about tomorrow.

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Peer-Review vs. Info Prizes and Markets

I have been having a 140 character discussion with Ciarán Brewster (@macbruski) via twitter.  And while it’s kind of interesting to force complex subject matter into very few characters, it is limiting the discussion, so I will summarize it so far here and hopefully others can weigh in too.

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Game Theory and Military Planning

In “Game Theory: Can a Round of Poker Solve Afghanistan’s Problems?” Major Richard J.H. Gash creates a simple two player game to show how game theory can be used to influence military planning. Gash’s game involves two villages in Afghanistan with the choice to either support the “Coalition” or support the “Taliban.” The scoring of the game generates a payoff matrix that is similar to that of the Prisoner’s Dilemma with a non Pareto-optimal Nash equilibrium. Unfortunately, Gash oversimplifies the game to just one round. In reality, Afghan villages participate in multiple rounds of decision making, with the actual number of rounds unknown, leading to differing strategies and outcomes than those proposed by Gash.

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Cancer “Progress” Report

Despite hundreds of billions of dollars appropriated for cancer research, as well as the efforts of thousands of the world’s best minds, progress in preventing or curing cancer has been almost non-existent. I find this unacceptable. We should be doing better. We need to be doing better. So what’s the problem? and more importantly, how can we fix it?

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Placebo Effects: Marijuana and the “Contact High”

Many users, and friends of users of marijuana report experiencing a “contact high.” That is, they purport to experience some of the effects of marijuana simply by being in contact with or around those using marijuana. Virtually all users wrongly attribute this experience to the inhalation of second hand smoke. This is unlikely for a number of reasons. Since exhaled smoke is virtually devoid of psychoactive substances and is widely dispersed in the surrounding air, it is not possible for one to inhale even a small fraction of a working dose. Additionally, many, including noted pharmacologist and psychedelic researcher Alexander Shulgin, report similar experiences involving drugs that are not inhaled, indicating that these effects are due to different biological processes.

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Physics.Cancer.GOV

Yesterday, from the Director of the National Cancer Institute, addressing one of the two largest cancer research conferences of the year:

NCI commenced a series of workshops that began to bring aspects of the physical sciences to the problem of cancer. We discussed how physical laws governing short-range and other forces, energy flows, gradients, mechanics, and thermodynamics affect cancer, and how the theories of Darwinian and somatic evolution can better help us understand and control cancer.

Read more on my Cancer Complexity Forum post.

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Cold Fusion

I remember reading this Wired article in 1998 suggesting that the “debunking” of cold fusion may have been way premature.  Last night, 60 Minutes did a pretty convincing piece claiming that more than 20 labs around the world have reported “excess heat” from cold fusion experiments:

Vodpod videos no longer available.

Click here for the full story.

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A Serious Solution to Carbon Emissions

As I’ve made clear before, I remain skeptical that carbon emissions pose a significant marginal threat of climate change. The likely climate sensitivity to CO2 is substantially less than the natural variability over human timescales.  Seeing as how temperature trends over geologic time scales are currently downward, I don’t think it’s worth wasting much effort on CO2 reductions.

However, let’s assume for a moment that I’m wrong.  What should we do? I don’t think we can actually decrease our energy usage very much and support our civilization. So we have to find non-petroleum energy sources.  Biofuel technology doesn’t look very good at the moment.  Scaling will require major land use changes that I contend are probably a net negative environmental impact. The cost-benefit for solar does look better, especially in certain geographic areas. But it seems to me the only massively scalable solution at our current level of technology is nuclear fission.

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The Vanguard of Science: Bonnie Bassler

The import of this talk goes way beyond the specific and stunning work that Bassler and her team have done on quorum sensing.  In my mind, this is the prototype for good biological science:

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Approaching the Singularity from Two Points

I happened to come across two interesting posts with Singularity implications that I thought you might be interested in.  First, the Singularity Hub reports that Osiris has a promising phase II trial underway for a treatment that uses foreign stem cells to repair the muscle damage from heart attacks.  If you’re about 40 like Rafe and I, this means your chances of dying from heart disease could go way down.  Now if we can just make some progress on cancer, we’ll be centenarians.

Second, via Prometheus, Wired reports on a robot-software combination that was able to generate, test, and refine it’s own hypotheses to identify coding for orphan enzymes in yeast. Obviously, this is a very special purpose kind of science.  But the fact they got a closed loop is very impressive.  I also like the fact that it’s in the biological sciences. Hey, maybe some descendant of this program can solve the aformentioned cancer problem.

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The Nature of Innovation

One of my favorite talks of all time is Ken Robinson’s on how children are born naturally innovative and the process of schooling and growing up in our society beats it out of them by the time they are adults.  More recently, Elizabeth Gilbert (of Eat Pray Love fame) opened some eyes with this talk on how we think of individual creativity and where it comes from.

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Two Books On Cognitive Science You Should Read

As I mentioned in this post, one of the three primary planks of my worldview is that, “…the human brain is a woefully inadequate decision making substrate.” I started adopting this posture in graduate school and have refined it with constant input from the cognitive psychology and neurobiology literature over the years.  Luckily, you don’t have to put in that kind of time. Simply go out and read Rational Choice in an Uncertain Worlds by Hastie and Dawes and The Accidental Mind by Linden.

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Climate Shifts as a Complex Systems Property

Via a post at the always terrific Watts Up with That, a pre publication version of this paper examines the non-linear coupling dynamics of the climate. Its hypothesis is based on the mathematics of synchronized chaos (sorry, no good introductory link available).

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Crohn’s Disease

Debbie Maier asks us on the Upcoming Topics page to address Crohn’s Disease.

I don’t know too much about it except that it’s an autoimmune disease and has a complex, multi-causal etiology and pathology.  In my reading on autoimmune diseases in general there seems to be a direct link between latitude an incidence.   Specifically, the farther from the equator you live the more likely you are to get Crohn’s, Type 1 diabetes, rheumatoid arthritis, and so on.

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Health and Fitness Q&A with Kevin

Whenever I have a question about health matters that is too complex for an MD or academic researcher to get right, I ask Kevin.  Nobody I know has a better combination of broad-based current knowledge of the primary literature, plus a whole-system view and understanding of compex dynamics, plus the practical will and experience in living by (and updating) his conclusions.

Here are some questions I had for Kevin recently and his answers.

Rafe: Do the BPA results (such as they are) cause you concern?  Do you still use your Nalgene bottle?  Would you let your infant or child drink from a plastic bottle or sippy-cup?

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Teaching Metacognition to 7th Graders

Gary Marcus says he’d like for there to be a course on metacognition for kids:

Call it “The Human Mind: A User’s Guide,” aimed at, say, seventh-graders.  Instead of emphasizing facts, I’d expose students to the architecture of the mind, what it does well, and what it doesn’t.  And most important, how to cope with its limitations, to consider evidence in a more balanced way, to be sensitive to biases in our reasoning, to make choices in ways that better suit our long-term goals.

What a brilliant and practical idea.

Anyone want to take a stab at a syllabus?

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But I Was Probably Right About Climate Models

I try not to practice false modesty (those of you who know me well probably just did a spit take at that understatement).  So while I try to stand up and admit when I’m wrong, I also like to stand up and point out where I’m right.

It shouldn’t be a surprise to any of you that I came to the conclusion that climate models are pretty much total bullshit. My problem with them is that they are incomplete, overfitted, and unproven.  It turns out that one of the foremost experts on forecasting in general also thinks that these models have no predictive value. In fact, items (6) and (7) of their statement shows that you can predict the future temperature really well simply by saying it will be the same as the current temperature.

You can read their more formal indictment of climate forecasting methods here.

Oh snap!

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Particle Physics Follow Up

In the comments to this post, Rafe and Daniel asked me to tell them the punch line of Lightness of Being.  I’ll do my best.  Spoilers ahead.

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Good Particle Physics Book

I apologize for the posting lull.  I’ve had a bad cold and been struggling to add Monte Carlo simulation to my discrete stochastic model of the startup lifecycle (if anyone is planning on using Oracle’s Crystal Ball, I can tell you the good and bad). But I’m almost finished with my next substantial post.

In the meantime, I finished a really good physics book: Lightness of Being by Nobel prize winner Frank Wilczek. It requires a basic knowledge of quantum mechanics (I suggest Al-Khalili’s Quantum) and particle physics (any recent popular book that spends more than one chapter on the Standard Model).

Given that, it does an awesome job of explaining three things that have always bothered me. First, how the strong force can possibly get more powerful the farther away you get. Second, why we can’t break protons and neutrons into their component quarks.  Third, where the heck a proton’s mass really comes from. It turns out all three things are related and the explanation is quite elegant.  I don’t know why the dozen other physics books I’ve read in the last five years ommitted an explanation (or at least an explanation that stuck with me).

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Early Detection: better late than never

Here is the scariest image in all of cancer:

Graph from Fortune Magazine article.

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Cancer as Evolution — 2008 Summary

Click here to read part 4 in this series.

As 2008 closes, it appears that momentum is picking up for the somatic evolution view of cancer.  Here are three recently published papers of note:

• The Evolution of Cancer (Goymer, et al, Aug 2008, Nature)
• Cancer Research Meets Evolutionary Biology (Pepper, et al, in press, 2008 Evolutionary Applications; Santa Fe Institute working paper)
• Genome Based Cell Population Heterogeneity Promotes Tumorigenicity: The Evolutionary Mechanism of Cancer (Ye, et al, Dec 2008, Journal of Cellular Physiology)

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Best Talk of Pop!Tech ’08

Vodpod videos no longer available.

The reason I like this talk so much (besides that it’s well-presented) is that it introduces us to the idea of invisible etiology.  Such a powerful concept, one that I feel has the power to help us solve so many mysteries, once we take it seriously.

Something that I’ve been thinking about lately: does homelessness have an invisible etiology (or etiologies), and if so, what is it?

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Group Selection Meme on the Rise

This is from a recent Seed Magazine article.  Click on the image to enlarge it.

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The Conflict Between Complex Systems and Reductionism

The following is a recent paper by Henry Heng published in JAMA.  I’ve linked concepts mentioned in the paper to corresponding explications from this blog.

JAMA. 2008;300(13):1580-1581.
The Conflict Between Complex Systems and Reductionism
Henry H. Q. Heng, PhD
Author Affiliations: Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan.

Descartes’ reductionist principle has had a profound influence on medicine. Similar to repairing a clock in which each broken part is fixed in order, investigators have attempted to discover causal relationships among key components of an individual and to treat those components accordingly.

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What is Cancer?

[ I’m asking for your help in answering this question, read past the fold to see how ]

In my post on invisible etiology, I challenged us all to be as open-minded as possible when dealing with our most complex problems, for this is the only way to make the invisible become visible.  Here’s where I attempt to practice what I preach.

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Invisible Etiology

One of the most poignant moments of this year’s Pop!Tech for me — which, BTW had many — was Gary Slutkin’s talk on the idea of violence being a virus.  You may have heard about his work in stopping violence in Chicago in a NY Times Magazine cover article earlier this year.  The premise is simple: if you throw out what you think you know about violence and just look at the etiology of how it manifests in the world, you find incredible similarities to the etiology of microbial viruses.  This includes not only how it spreads from person to person, but also the larger epidemiological patterns, and importantly, how it can be stopped via interventions which logically follow from the hypothesis that violence is a virus.  Not that violence is caused by those invisible critters we call viruses, but rather that violence itself is a virus.

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Go Forth and Reify

reify |ˈrēəˌfī|
verb ( –fies, –fied) [ trans. ] formal
make (something abstract) more concrete or real

Imagine if an alien landed on Earth to study modern society and you were assigned the task of being its local guide.  You get to the subject of money and the alien is perplexed.  What is money?  Is it paper currency?  Clearly not, since you can exchange that paper for other forms of currency, such as coins, foreign bank notes, electronic funds, treasury bills, and all sorts of derivatives, assets (both tangible and intangible, liquid and illiquid), services, promises, and so on.  After hearing all of the various aspects of money, the alien tells you that money doesn’t really exist.

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Don’t Cop Out on Knightian Uncertainty

I apologize for the posting lull. I actually spotted an issue than I wanted to address a few weeks ago, but I’ve been pondering how to approach it.  It’s pretty complicated and subtle.  I even ran a couple of drafts by Rafe to refine my thinking.  So please bear with me.

As I’ve mentioned before, I am a fan of Dave Zetland. When I saw him propagate what I think is a fundamentally false dichotomy in this post, I knew I had to take on the concept of Knightian uncertainty. It crops up rather often in discussions of forecasting complex systems and I think a lot of people use it as a cop out.

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Beyond the Gene

In an earlier post, I argued that the gene concept is in bad need of a makeover.  It turns out that Evelyn Fox Keller and David Harel feel the same way and have made an actual start of it in a paper titled Beyond the Gene.  In the paper they propose a new lexicon:

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