Science 2.0

Universal Constants

To get the theory of relativity Einstein held the speed of light constant and let time and space vary.

These days cosmologists are holding the infinity of the universe as constant and letting its density and expansion/contraction rate vary.

In some sense quantum mechanics is about holding the observer constant and letting the physical interpretation vary (particle or wave; position or momentum; exist or not).

What would we get if we held consciousness constant and let the universe vary?…

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.…

Sunlight vs. Vitamin D

[This is part 3 of Epidemiology vs. Etiology]

You may have heard there is an epidemic of low vitamin D levels in the U.S.  An estimated 60% of Americans are at a level that has been correlated with increased risk of nearly all chronic diseases, including cancer, heart disease, diabetes, autoimmune diseases, and depression.  My personal belief is that the epidemiology is horribly flawed.  But perhaps not in the way you might think….

As most people know by now, we humans photosynthesize vitamin D in our skin when it is exposed to direct sunlight.  How fast depends on our ethnicity and amount of exposure.  Since I’m light skinned and get a lot of sun in my normal life, it came as a huge surprise when some routine bloodwork I had done about 9 months ago indicated I was “dangerously low.”

My doctor immediately prescribed large doses of vitamin D supplement, but I was convinced that the result was spurious.  Perhaps it was due to …

Medicine 2.0

Kim Scheinberg sent me a great article from The Atlantic that relates to my multi-thread rant on epidemiology.  Since the article speaks for itself, I’m just quoting points I think are salient.  The only words below that are not a direct quote are the headlines (i.e. “Did you know?”).  The emphasis is mine as well.

Did you know?

  • mammograms, colonoscopies, and PSA tests are far less useful cancer-detection tools than we had been told
  • Zoloft, and Paxil were revealed to be no more effective than a placebo for most cases of depression
  • staying out of the sun entirely can actually increase cancer risks
  • taking fish oil, exercising, and doing puzzles doesn’t really help fend off Alzheimer’s disease

Medicine has caught a plague

we think of the scientific process as being objective, rigorous, and even ruthless in separating out what is true from what we merely wish to be true, but in fact it’s easy to manipulate results, even unintentionally or unconsciously.

There is an

Epidemiology vs. Etiology

Over the last several years I’ve been digging into the science of cancer and systems biology, while at the same time looking at the epidemiology of disease and nutrition.  And the more I learn, the more I’m convinced that there’s a gap that our scientific tools and methodologies cannot account for.  While I’ve discussed this generally under the heading of Science 2.0 (also here), I’ve had a hard time putting into language the exact nature of the gap.

I’ve begun a series of posts that I hope will illustrate the gap, which I believe has to do with the fundamental difference between epidemiology (which is based on statistical observation) and etiology (which seeks to find causal mechanisms for observed phenomena):

Once I’ve completed these posts, I’ll attempt to explain the nature of the gap and what it means for the future of scientific inquiry.…

Will You Die From Cancer?

Use the arrows that appear if you hover over the bottom right of the Prezi.  You may want to expand to full screen first.

All feedback welcome.  If you like this, what subject would you like to see addressed next using Prezi?…

The Pattern

The wind was flapping a temple flag. Two monks were arguing about it. One said the flag was moving; the other said the wind was moving. Arguing back and forth they could come to no agreement.  The Sixth Patriarch said, “It is neither the wind nor the flag that is moving. It is your mind that is moving.” — Zen Koan

“The belief in an external world independent of the perceiving subject is the basis of all natural science.” — Albert Einstein

Does a whirlpool exist in the same way that a rock exists or that energy from the sun exists?  For something to exist it either has to have always existed, or there must have been a time prior to its existence.  Leaving for a moment the possibility that everything which exists today has always existed, let’s consider that it came into being at some point.

If something came into being, then not only must there have been a point in time prior to …


What fundamental truths exist in the universe?

This question, perhaps above all, is the basis for scientific inquiry.  Yet we rarely ask it in this way and we rarely step back to the very basic assumptions we hold about the possible form of answer we might expect.  For instance, is matter fundamental?  Meaning, if we could not talk about particles and mass, could we understand the universe as well (or better) than we currently do?

Einstein showed that there is an equivalence between matter and energy (E=mc^2), but what does that really mean?  Personally, I’m kinda stumped when it comes to understanding energy, and I suspect that many other people are too if they think about it.  Then there’s that pesky c^2 part of the equation, which seems even more nebulous.  Physics 101 tells us that c is the velocity at which light (a form of energy) travels, and that any velocity squared is acceleration.  Also we learn that velocity is distance over time


Daniel asks, Does the Mind Influence Physical Processes?

Proof: our mind sets out to modify our environment in particular ways (i.e. set goals); then we act in ways consistent with that intention; more often than chance, our environment changes in those intended ways (i.e. goals are achieved).

This is a form of entanglement — spooky action at a distance — between our minds and the environment (which includes other minds), but we usually dismiss this as trivial, not very spooky. On the other hand, we know that quantum entanglement exists and it seems spooky to us because we have no mechanism to explain it.

We also observe that there are quantum effects in the basic architecture of the brain (nanotubules) and wonder if these are somehow the “ghost in the machine” of consciousness. But this could be just a red herring. Perhaps quantum effects matter to consciousness, perhaps they don’t. Still quantum effects are part of the human experience in some sense — and so …

Troubling Statistics

In his eloquent article, Breaking the Galilean Spell (worth reading in its entirety), Stuart Kauffman has given me the words to finally be able to articulate the uneasiness I feel about statistical reasoning in an increasingly interconnected world:

…[Can] we make probability statements about the evolution of the biosphere? No. Consider flipping a coin 10,000 times. It will come up heads about 5,000 times with a binomial distribution. But, critically, note that we knew beforehand all the possible outcomes, all heads, all tails, all 2 to the 10,000 possibilities. Thus we knew what statisticians call “the sample space” of the process, so could construct a probability measure.

Can we construct a probability measure for the evolution of the biosphere into its Adjacent Possible? No. We do not know the sample space!

I won’t belabor the point except to say that I view the increasing irrelevance and danger of statistical reasoning as the essential argument of The Black Swan, the fundamental reason why the …

The Adjacent Possible

Stuart Kauffman has a concept called the Adjacent Possible which I find incredibly useful in understanding the world.  Simply put, if you think of the space of possibilities from the present moment forward and just concentrate on those that are achievable today — adjacent to the present moment — that’s the Adjacent Possible.

What’s interesting about possibility-space is that tomorrow’s Adjacent Possible depends on the actions and choices we make today; it’s not symmetric and it’s nonlinear.  Certain actions generate more future possibilities than others.  In my experience, those actions tend to be the cooperative ones, ones that produce network effects: financial, social and otherwise.

Due to our evolutionary heritage, having come from a resource-constrained world, we may be predisposed to see the more competitive actions which tend to shrink the Adjacent Possible.  Whether or not this is a bias or an actual state of affairs, much of our thinking is based on scarcity, so we are drawn to actions that become self-limiting.

Here’s …

Overcoming Bias

The title of this post is ironic.  What is science/truth/knowledge if not picking one story over another, in other words, the creation of bias?  Hopefully the bias we create is useful and allows us to predict and create a future that is better (in some agreed upon sense) than the past.

To get to “better” we have to be able to change our minds when we get stuck on locally maximal peaks.  That’s why I love this post on the Rationally Speaking blog called How to Want to Change Your Mind.  The techniques are simple, but profound, and harder to put into practice than they seem.  Here they are in summary:

  • Divorce your belief from your self
  • Think of disagreements as collaborative, not adversarial
  • Visualize being wrong
  • Take the long view
  • Congratulate yourself on being objective, not on being right
  • If you can’t overcome your competitive instinct, re-direct it

To these, I will add some of my own:

  • Truly Listen – I am

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

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 …

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?…

A Meditation on Biological Modeling

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

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.…