Scientific Singularity?

A couple of weeks ago Kevin and I went around on the topic of whether or not science is “broken”.  We came to the point of agreeing that we have different basic assumptions of what constitutes “utility”.  And because of this, while we could agree that each of our arguments made sense logically, we ultimately end up with opposite conclusions.  After all, for something to be broken it means that it once served a purpose that it no longer is able to serve due to mechanical/structural failure.  And to have a purpose means that it has value (i.e. utility) to someone.

So whether science is broken or still works depends your definition of utility.  Kevin and I agreed on a measurement for scientific utility, based on (a) how well it explains observed phenomena, (b) how well it predicts new phenomena, and (c) how directly it leads to creation of technologies that improve human lives.  We can call it “explanatory power” or EP for short.  …

Is Science Broken?

By this I mean just what you think I mean.

Is science dysfunctional (i.e. functioning against its stated purpose) and could it be fixed?  I will leave it to you to determine what science’s stated purpose is, though by any standardly accepted definition, I claim that science is broken.  I’d like to run an experiment here to try to either change my belief or solidify it.

In the comments below, I invite you use the Like buttons to vote on what you believe.  You have only three boxes to choose from: Broken, Not Broken, and Undecided.  I respectfully ask you to first use the appropriate Like button and only then add your arguments/comments/questions if you have them.  Also, please categorize your arguments/comments/questions by making them replies to of one of the three top-level boxes (if you “think outside the boxes” I will delete your comment; sorry it’s my experiment :-)

In order to begin the debate, I will refer you to two blog entries which …

The New Scientific Enlightenment

There is a massive paradigm shift occurring: beliefs about the nature of scientific inquiry that have held for hundreds of years are being questioned.

As laypeople, we see the symptoms all around us: climatology, economics, medicine, even fundamental physics; these domains (and more) have all become battlegrounds with mounting armies of Ph.D.s and Nobel Prize winners entrenching in opposing camps.  Here’s what’s at stake:

. . .

Scientific Objectivity

In 1972 Kahneman and Tversky launched the study into human cognitive bias, which later won Kahneman the Nobel.  Even a cursory reading of this now vast literature should make each and every logically-minded scientist very skeptical of their own work.

A few scientists do take bias seriously (c.f. Overcoming Bias and Less Wrong).  Yet, nearly 40 years later, it might be fair to say that its impact on science as a whole has been limited to improving clinical trials and spawning behavioral economics.

In 2008, Farhad Manjoo poignantly illustrates …

A New Cancer Mentality

This interview was done as part of the New Cancer Mentality initiative:

New Cancer Mentality is a grassroots organization focused on giving cancer patients a virual townhall to ask their questions to leading oncologists and researchers about their work. Furthermore, New Cancer Mentality focuses on bringing about collaboration between researchers as well as giving researchers an online forum to share their views and what needs to be done to cure this disease.

If you’d like to learn more or join the movement, check out blog and contact David.…

A1 vs. A2 Milk

Large scale epidemiological studies have linked casein (a cow’s milk protein) to autoimmune disease and heart disease (see The China Study).  I just ran across the following twist on this theme which purports to explain a mechanism: a genetic mutation many years ago in domesticated cows transformed the original, safe casein (“A2”) into a toxic form (“A1”).  Most cow’s milk available today has both.

What do people think of this?  Has anyone tried personally to ingest milk products that are exclusively A2?

Given the dubious connection between cholesterol and heart disease, could the bad rap on cheeses, cream and ice cream have more to do with A1 and sugar than the animal fat and cholesterol?…

Science 2.0

I liken cognition to a hill-climbing search on the landscape of theories/models/maps that explain/predict reality.  It’s easy to get stuck on peaks of local maximality.  Injecting randomness creates a sort of Boltzmann machine of the mind and increases my chances of finding higher peaks.

But I have to be prepared to be more confused — and question more assumptions than I intended to — because chances are my new random placement on the landscape is initially lower than the local maximum I was on prior.  This part is scary.  People around me don’t understand what I’m saying initially because I necessarily need new words, new language, to describe the new landscape.

And rather than start totally afresh with a new lexicon, I notice it’s more productive (personally and in communication) to overload old terms and let them slowly blend into their new meanings.  We all resist the strain, especially those who did not sign up for the jump through hyperspace.  They use the …

Why Falsifiability is Insufficient for Scientific Reasoning

In my post about The Process it turns out that I stepped on a pedagogical minefield when using describing the Anthropic Principle (AP).  Two preeminent physicists had a very public argument a while ago in which one called the AP unscientific because it’s unfalsifiable.  I will return to that in a moment since it’s the crux of what’s wrong with Science right now, but I need to get the terminology issue out of the way first.

Lee Smolin claims that AP is bad and favors a Cosmological Natural Selection view instead (on grounds of falsifiability).  I believe this is a false dichotomy and that they are really one and the same.  Here’s why:

  1. Normally natural selection requires some form of “replication” or it’s not actually natural selection.   But replication is not needed if you start with an infinity of heterogeneous universes.  In other words replication is simulated via the anthropic lens over the life-supporting subset of all possible universes.
  2. Replication is a red herring anyway

The Process

Imagine a multiverse, infinitely infinite.  There’s just infinity.  Or if you prefer, nothing.   There’s no space, no time, no matter, no energy.  There’s no structure whatsoever, and nothing “in” any of the universes that make up the multiverse.  it’s not even clear whether these individual universes are separate from one another or the same.  But since our minds seem finite and we have to start somewhere, let’s imagine them as separate: an infinite collection of universes with nothing in them, no dimension, and no relationship between them.

Now lets assume there is some process for picking out universes from the multiverse.  Since there’s no time in the multiverse, the process has no beginning and no end.  It’s like a computer program, but it’s infinitely complex.  Let’s call it The Process.

If The Process is infinitely complex and has no beginning and no end, what can we know about it?  We know that it picks some universes but not others, which effectively creates an “in …

Approaching a Cure for Cancer

James Watson, co-discoverer of DNA’s double-helix structure recently called for a back to basics approach in dealing with cancer.  In previous post threads I’ve discussed cancer’s complexity and in particular the confounding and scary implications of somatic evolution, which underscores some of the reasons we are not winning the “war on cancer.”  Here I will discuss some cutting edge approaches to treating and preventing cancer and how they might pan out in light of the complexities of the disease.  The categories below are not mutually exclusive, and the examples cited are nowhere near exhaustive, but this should give you some food for thought.  If you have ideas, questions or know of approaches that should be highlighted, please comment.

Target & Kill Approaches

Biris and Zharov are making some exciting progress in using nanotubes to tag and then track cancer cells inside the body as they move around.  They propose to kill the cancer cells by heating up the nanotubes using lasers, while others are


How do we know what we know?

If you grew up like me you were brought up in a culture based on a dualist metaphysics, one that asserts that there is an objective reality outside of ourselves (whatever “we” are) and that we know about it indirectly through our senses and conscious reasoning.  This is the basis of the Western traditions of science, liberal arts and symbolic systems (such as mathematics and human language).  Essentially anything that can be studied is part of this metaphysics.  Gödel showed us that this metaphysics will never lead to complete knowing, though everyone agrees we can continually refine our knowledge and thereby at least asymptotically approach enlightenment.

Descartes proved to us that each of us individually do indeed exist, and he tried to argue further that the universe as we perceive it — however imperfectly — does indeed exist too.  But before you drink too deeply from the Cartesian well, keep in mind that his argument for an external

Egyptian Mummies Yield Ancient Secrets of Good Journalism

This is based on an LA Times article here

What strikes me most is how athlerosclerotic the science itself is.  Or perhaps it’s just the reportage?

The opening line of the article is “CT scans of Egyptian mummies… show evidence of… hardening of the arteries, which is normally thought of as a disease caused by modern lifestyles….”  One of the researching cardiologist draws this conclusion: “Perhaps atherosclerosis is part of being human.”

The LA Times reporter covering the story (Thomas Maugh) rightly points out at the end, “The high-status Egyptians ate a diet high in meat from cattle, ducks and geese, all fatty.”  Which of course entirely negates the hypothesis of heart disease being part of the natural human condition.

It’s clear why the researchers — both cardiologists — would want ancient evidence to support the notion that heart disease is normal.  But the fact is that the preponderance of evidence around the world in epidemiology as well as cardiology indicates that …

Daniel Nocera’s Gift

I just saw the most important talk I have seen in 300+ TED, Pop!Tech, etc talks that I’ve watched.  And at the risk of hyperbole, I will say that the worst case scenario is that Daniel Nocera simply wins a Nobel Prize (and yes, I’m willing to bet at even odds that it happens in under 10 years from today).  But if the system is able to scale through replication, it will be at least as important as penicillin in terms of ending human suffering and will have a bigger impact on the world as a whole.  Here’s why:

  • Input: Water (clean, saltwater or dirty water)
  • Outputs: Electricity + Pure drinkable water
  • By products: nothing (other than what was in the water)
  • Resources required to assemble: all abundant and most have substitutes
  • Knowledge required to assemble: simple
  • Cost to assemble: relatively cheap

Essentially what Nocera has done is reverse engineered and re-created a super-simplified photosynthesis process.  It’s a closed loop (i.e. autocatalytic) so …

Rafe Issues Challenge to Statin Industry

I have been trying to get the straight scoop on whether statins actually decrease mortality and morbidity in a significant way and I haven’t been able to find any real evidence that they do.

If you ask a cardiologist it’s clear that they believe unequivocally that statins work, mostly because they see what statins to do blood cholesterol levels.  But remember, cholesterol numbers in and of themselves do not matter.  They are a proxy variable for cardiovascular health.  Plaque buildup matters.  At one time blood cholesterol numbers were the only non-invasive indicator we had of plaque buildup, but that’s not true anymore.  However, drug companies are highly incentivized to prove that statins improve health.  So they fund lots of studies.

Notwithstanding the systemic bias when there are profit motives and publication motives, we can turn to these studies and see if statins actually work.  The best way to remove bias is to look at large-scale meta-analyses, like this one.  If you simply read the …

Complex Systems Symposium

Should be of interest to everyone who reads this blog.  Here’s the program, here’s the website, and here’s some more info that you can’t get from either yet:

Dear all:

Just wanted to share with you all a couple of updates for our Fall Symposium.  We’re very pleased to have two invited speakers so far: John Christiansen of Argonne National Laboratory (ANL) and Mitchell Waldrop of Nature magazine.

John is the director of the Advanced Simulation Technologies Center at ANL, and has over 30 years of modeling and simulation experience across many fields, including: meteorology, ecology, botany, anthropology, archeology, healthcare, and more.  He will present some of his work on a recent NSF Grand Challenge in Biocomplexity, which created an agent-based model to study the rise and fall of Ancient Mesopotamia.  He will also use this work to illustrate different hardware and software platforms, with a particular focus on the challenges on going from the desktop to HPC.

Mitch is currently the editorial

Should You Use Sunscreen?

This is a very complex topic, as the following talk suggests:

The main takeaways from this that I got are:

  1. Cancers for which sunlight deficit is a risk factor are orders of magnitude more prevalent than the few for which overexposure is a risk factor.
  2. People who are using sunscreen regularly are precisely the ones who shouldn’t be.
  3. We should be very careful and sparing about recommending sunscreen usage or sun avoidance, and always temper such advice with the tradeoffs of not getting enough sunlight.

As someone who wonders on a regular basis whether the public has the right information to make informed decisions about health-related tradeoffs, I am curious… does the above strike you as surprising?  What do you currently do regarding sun exposure, and are you likely to change anything based on the above?  What do you think the overall message that reaches the masses is regarding sun exposure?…

Something Fishy About Mercury

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

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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?…

A Meditation on Biological Modeling

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

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

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.…


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.…

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.…


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.…

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:

Click here for the full story. Watch here.

It’s interesting to me that the best skeptic they could find on the subject (Richard Garwin) was thoroughly unconvincing, simply asserting that there must be a measurement problem, without he himself daring to go measure.  You’d think it would be worth a looksy.  More interesting still was the independent expert in measuring energy (Rob Duncan) who came in as a total skeptic and came out as a believer.

But my favorite part of the story is near the end when Fleischmann (co-discoverer of cold fusion) appears to be having both a literal and figurative last laugh.  Man, what a bad beat he and Pons got.

Besides Garwin, who are the …

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.…

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:…