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.  We might argue over the relative mix, but we agree that (a), (b) and (c) are all important.  Where we diverged came down to whether scientific utility was an absolute measure or a relative measure.  To quote Kevin:

EP(kev)=number of phenomena explained. Evidently, EP(rafe)=fraction of phenomena explained. I claim EP(kev) is more relevant to standard of living because if you can explain more phenomena, you can build more gizmos, means you can do more stuff with less effort, means a higher standard of living.

Here’s how I visualize the picture:

Kevin suggests that EP is a function of the curve labeled “Scientific Knowledge” whereas I feel it’s a function “the gap” in red.  My argument for why the gap is the relevant measure parallels the three components of EP:

a) “Explaining observed phenomena” means maximizing the quality and quantity of all observed phenomena.  It’s not enough to explain a subset of phenomena better and better if the number of new phenomena keeps increasing.  For instance, let’s say you came upon Earth in 1980 and did a scientific study to understand how personal computers worked.  You spend the next 20 years coming up with a theory that explains them perfectly, but this assumes they are being used in isolation.   How then do you explain the new behaviors they start exhibiting once they are connected up via the internet?  While your theory might have been perfectly useful in 1980, it becomes next to worthless by the year 2000.

b) Similarly, if you were looking to predict how a single computer were to behave, your theory that worked 100% of the time in 1980 would work only a small fraction of the time in 2000.

c) Technology is a bit tricker to understand from this perspective, but I believe it’s ultimately the same.  Kevin’s definition of “doing more stuff with less effort” is fine, but what it doesn’t address is how the “stuff that we want done” is a moving target.  In 1980 I wanted my computer to allow me to type words into it, remember them, print them out, etc.  By 2000 that function was subsumed: practically every computer program had this functionality built in, even games and email software (like the one I’m using to compose this blog entry now).  What I want out of my computer in 2000 includs word processing, but also involves a growing set of tasks on top of that.  More importantly, the category of “stuff that we want done” by technology is self-referentially — which is to say, exponentially — growing at all times.  In other words, technology’s utility depends on how well it bridges the gap on the chart above.

To be fair, Kevin might object that I have drawn the chart wrong because technology (being self-referential) always keeps the gap within bridgeable reach.  This is what we were arguing about in the comments of the first post regarding cardinalities and ordinalities.  So it could be that this whole argument hinges not on our definition of utility but rather whether the gap really is getting untenably bigger or not.

What do you think?  Is the gap getting bigger?  Do you buy either Kevin’s or my definition of utility?  Do you have another definition entirely?

Perhaps the most clarifying question of all (to my mind) is the following: Given your current understanding of what science is, how would you feel if your child said they were going to become a scientist?

Related posts:

1. The New Scientific Enlightenment
2. Why Falsifiability is Insufficient for Scientific Reasoning
3. Is Science Broken?

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 make my argument for why science is broken:

• Cancer’s Inconvenient Truths
• The New Scientific Enlightenment

Let the games begin!

Related posts:

1. Scientific Singularity?
2. Science 2.0
3. Shermer on Science

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 that our indifference to the pervasiveness of cognitive bias, combined with digital-age network effects has lead us to a crisis of truth; none of us, from Dittohead to Nobel Laureate, are able (practically speaking) to distinguish objective, scientific truth from carefully crafted stories.

What’s worse is that we continually craft these stories for ourselves as we go through life… it’s the basis for rational, conscious thought.

What’s even worse is how individual biases combine with scientific institutional biases (e.g. publication bias) to unintentionally corrupt the scientific process.  It’s gotten to the point where in 2010, headlines like these have seemingly little impact on the scientific community, and go unnoticed by policy makers and the general population alike:

• Million-dollar industry payments to doctors go undisclosed
• Science fails to face the shortcomings of statistics
• We’re so good at medical studies that most of them are wrong

“New Kinds” of Science

“[A]mong the great majority of active scientists… [reductionism] is accepted without question…. [T]he relationship between the system and its parts is intellectually a one-way street.” (Nobel Physicist, P.W. Anderson, 1972)

“if the stars in the universe were fractally distributed it would not be necessary to rely on the Big Bang theory” (new math applied to a cosmological paradox by Mandelbrot in 1974)

“The revolutionary new discoveries [complexity] researchers have made… could change the face of every science from biology to cosmology to economics.” (Waldrop, 1993)

“[U]nexpected results force a whole new way of looking at the operation of our universe…. [T]he ultimate scope and limitations of mathematics, the possibility of a truly fundamental theory of physics, the interplay between free will and determinism, and the character of intelligence in the universe.” (summary of A New Kind of Science, 2002).

“Reductionism is so rigid in its hopes to ‘entail’ everything in the unfolding of the universe…. I think reductionism is incomplete.” (Stuart Kauffman, 2009)

The “newness” that underlies each of these claims is not exactly new; it’s been discussed since at least the time of Aristotle.  The idea being that the whole is greater than the sum of the parts.

And that if scientific method focuses solely on reductionism — dividing the whole into easily-understandable parts — this will blind us to true understanding.

What’s new is the scientific approach to studying the bottom-up dynamic known as emergence.

The Nature of Scientific Proof

What counts as scientific evidence is always an evolving target, and an issue that can make or break careers.  But when human lives are on the line, scientific proof is not so important.  Inasmuch as science is more than self-indulgent theory, callings into question of scientific rules of evidence must be taken very seriously.

All proofs assume some specific form of consistent logic.

All logics are either incomplete or inconsistent.

Therefore, no proof is complete.

Ever since Karl Popper, scientists have been obsessed with syllogisms like this one (aka deductive reasoning)and its handmaiden, falsifiability.

This obsession has been at the expense of completeness though, as there are dozens of forms of logic which are equally consistent (like induction and abduction), but which rely on and promote creativity.

Statistical methods have played an increasing role in all of science since the advent of the computer.  Yet, their well-known limitations have been summarily ignored by science.  In the aforementioned excoriation of statistics it was observed that “The difference between ‘significant’ and ‘not significant’ is not itself statistically significant”.

In The Black Swan, the author (Taleb) pulls even fewer punches about what these shortcomings mean for scientific pursuit.  Ultimately he concludes that the combination of “unknown unknowns” with cognitive biases and increasing universal complexity means we are doomed to an eternally widening gap between what we know about the world and what we can know.  Even worse, we will become increasingly ignorant of or ignorance — by construction(!) — leading to dark times ahead.

Some scientists claim that the same epistemological conundrum is leading in the exact opposite direction: towards enlightenment.  Ironically(?) a modern convergence of science and spirituality is occurring, as epitomized by integral theory beginning in the late 1960s, but branching into related forms at an accelerated pace.  See, for example, a popular documentary, the rise of nonduality, and a new scientific conference.

Life, the Universe and Everything

For centuries, mathematicians and philosophers believed that everything true about the universe could — though not in practice, at least theoretically speaking — be written down and codified.  But then in 1931, Kurt Gödel proved an incompleteness theorem that dashed this hope even in principle.

It’s taken time for the gravity of Gödel’s discovery sink into the “grey matter” surrounding fundamental physics, but it’s finally starting to happen: “Some people will be very disappointed if there is not an ultimate theory…. I used to belong to that camp, but I have changed my mind.” (Stephen Hawking, Gödel and the end of physics, 2002)

The reticence of the scientific community to accept the incontrovertible could be seen as an example of science “advancing one funeral at a time” (an epithet wielded by Nobel physicist, Max Planck).  But it turns out the core issue is a paradox that is actually thousands of years old.

The issue is self-reference and it leads to many forms of paradox and uncertainty, including Heisenberg’s famous uncertainty principle.  The implications of self-reference for physics were summed up recently as follows: “After decades of debate, disputes over the mathematical rules governing reality remain unresolved” (ScienceNews, 2010)

Self-reference not only gives fits to quantum physicists, it calls into question one of the most basic premises of science, “the assumption that our world operates according to causal laws.” (Science’s First Mistake, 2010)

And it’s not just theoretical: one of the largest scientific industries in the world is desperately trying to fight the real-world effects of self-reference.

It should come as no surprise then that, in the void, theories that were once laughable to mainstream science are getting serious attention.

One such theory, biocentrism, challenges the primacy of physics in the pantheon of science, and replaces it with biology.  Moreover, it picks up the thread of observer-dependence laid down by quantum physics and weaves it into a narrative of a conscious universe, reminiscent of integral theory and its ilk.

If, as Einstein noted, “the belief in an external world independent of the perceiving subject is the basis of all natural science”; and if, as Popper proposed, falsifiability is the criterion demarcating science from non-science; then…

We must take biocentrism seriously. Because unlike every other “new age” theory accused of over-fitting the data, biocentrism makes falsifiable predictions which will likely be settled soon.

Plus, it may be the case that biocentrist theory explains phenomena that is often observed but not politically correct to talk about.  Says one noted scientist, “What Lanza says in this book is not new. Then why does Robert have to say it at all? It is because we, the physicists, do NOT say it––or if we do say it, we only whisper it, and in private––furiously blushing as we mouth the words.”

The Truth Wears Off

As if on cue, in December of 2010, The New Yorker published a tour de force of scientific journalism by Jonah Lehrer, subtitled, “Is there something wrong with the scientific method?”  Here are quotes from two well-respected scientists in the article:

“Whenever I start talking about this, scientists get very nervous” (Jonathan Schooler)

“[Michael] Jennions admits that his findings are troubling, but expresses a reluctance to talk about them publicly. ‘This is a very sensitive issue for scientists’”

What they are talking about is a mysterious phenomenon that resembles the bizarre observer-dependent causality of quantum mechanics, but at the scale of human population studies.  Referred to alternately as the “decline effect” and “cosmic habituation”, the effect has been shown to be both repeatable and predictable.  In a nutshell, the decline effect is as follows:

Many well-established, scientifically validated “facts” seem to decline in their validity over time as they are retested.

This is despite collective best efforts to recreate the exact conditions of initial experiments and account for red herrings like flawed statistical application, regression to the mean, publication bias, reporting bias, confirmation bias, survivorship bias, “significance chasing,” financial and other conflicts of interest, data collection issues, improper experimental controls, a priori faulty experimental design, and so on.

And yes, if you were paying attention, you would notice that the decline effect has a strong element of self-referentiality….

. . .

Not the Wind, Not the Flag

When reading about the decline effect, biocentrism and nonduality, it’s difficult for us scientifically trained folk to turn down our highly-attuned falsification mechanisms long enough to allow the synapses to connect the dots.  But the dots do seem to be connecting themselves lately.

The year after receiving a Masters of Science in Computer Science / Artificial Intelligence I read a book that I still recommend to people as the most important book I’ve read to date.  It begins with the following claims:

“[T]he mind is inherently embodied, reason is shaped by the body, and since most thought is unconscious, the mind cannot be known simply by self-reflection.”

“What universal aspects of reason there are arise from the commonalities of our bodies and brains and the environments we inhabit…. [R]eason is not entirely universal.”

“[W]e have no absolute freedom in Kant’s sense, no full autonomy.”

“The utilitarian person… does not exist…. People seldom engage in a form of economic reason that could maximize utility.”

“The phenomenological person, who through… introspection alone can discover everything there is to know about the mind and the nature of experience, is a fiction.”

“There is no poststructuralist person–no completely decentered subject for whom all meaning is arbitrary, totally relative, and purely historically contingent, unconstrained by body and brain.”

“[T]he classical correspondence theory of truth is false…. [T]hat statements are true or false objectively, depending on how they map directly onto the world….”

“There is no such thing as a computational person…. The neural structures of our brains produce conceptual systems and linguistic structures that cannot be adequately accounted for by formal systems that only manipulate symbols.”

“[T]here is no Chomskyan person, for whom language is pure syntax…. [C]entral aspects of language arise evolutionarily from sensory, motor, and other neural systems that are present in “lower” animals.”

At the time, these statements seemed scientifically blasphemous, but I suspect they would seem mundane and obvious to a recent MS graduate.  Though I sensed the inherent truth being spoken, it’s taken me a while to truly come to terms with the implications for my own understanding of the world.

As best as I can articulate, the questions being raised by “all of this” are as follows:

• Are there any universal truths at all?
• When we observe the world scientifically, are we studying the the universe as it truly is, or are we studying the nature of our minds, the structure of consciousness?
• Can scientific breakthrough occur without some form of completely irrational faith or spirituality?

These are questions that I still do not know the answer to, but I am getting more comfortable with the not knowing.

What I like best about the practice of embracing “I don’t know” is that it allows us to step back and get clarity on questions like, “Are there any universal truths?”  And when we do step back, we realize that the question is not about “truth” or “universal” but rather “are there”.

. . .

“Do numbers exist?”

Which brings us full circle to question of independence.

When ScienceNews ran the article chastising scientists for rampant misapplication of statistical methods, the word “independence” was used only once (in the context of replicating an observed finding).

This is a curious fact considering that the real elephant in the room, statistically speaking, is always whether correlated observations are independent of one another.  If they are not, then the statistical methods that scientists use violate the fundamental assumption required of them.

Of course, we all know that there is no such thing as true independence, don’t we?  The butterfly effect and so on.  But we use statistical theory and make probabilistic arguments all the time, both in science and in life.  Without it, we’d be paralyzed to the point of inaction.

As scientists though, we’ve got to admit, it bothers us (doesn’t it?) that one of the fundamental assumptions of our daily activity is false.  That we lie to ourselves every day so that we can get on with our work.

The biggest elephant of all though is the question of whether the world exist independent of our observing it.  You and Descartes may be sure that it does, but I still don’t know.

There’s a question that was posed to me in my freshman calculus class in college, that I thought I knew the answer to, but which has nagged at me ever since: “Do numbers exist, or are they constructs of the human mind?”

To this day, I ask the same question of luminaries at scientific gatherings, and I have yet to get a definitive answer.  Sometimes I ask it in a slightly different way: “Is math inherently part of the structure of the universe?”  I have yet to get a satisfying answer.

. . .

When the Levee Breaks

None of this existential teeth gnashing is new in science.  Thomas Kuhn coined the phrase paradigm shift to describe revolutions of thought such as the transition from Ptolemaic to Copernican cosmology in the 16th century, or the shift from classical to quantum mechanics last century.

But what is new is the accelerated number of paradigm shifts that are occurring during the span of a single human lifetime.   In other words, we are at a crossroads in history during which multiple pillars of the existing scientific method are cracking at once.

What exactly does this mean?

I don’t know.

But the levee is about to break.

And in the spirit of scientific progress I will give you my own falsifiable prediction (or is it resolution?) as the new year approaches:

Something big is happening.  Something positive.  We can all feel it, can’t we?  It is hard to define, but we will all recognize it in hindsight.  And when we do, historians will agree that the levee broke in 2012….

Related posts:

1. Why Falsifiability is Insufficient for Scientific Reasoning
2. Scientific Singularity?
3. The Process

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.

Related posts:

1. Physics.Cancer.GOV
2. Preventing Cancer Through DNA Replacement?
3. Approaching a Cure for Cancer

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?

Related posts:

1. Rafe Issues Challenge to Statin Industry
2. Epidemiology vs. Etiology
3. Crohn's Disease

This is by far the most constructive article on healthcare, because it clearly identifies the fundamental issue in healthcare – our internal conflict.  Here are the excerpts, but read the whole thing and forward it on.  I dare anyone to challenge this of course; that’s the whole point of discourse:

“Those following the long march to health-care reform know that one of the few things beyond argument is that the old approach is unsustainable and threatens to bankrupt the country. Perhaps a little belt tightening and bargain hunting of this sort might make our health-care dollars stretch farther”

“To help maximize the overall benefits in health care under a utilitarian framework and conditions of constrained resources, health economists use an analytic tool called cost-effectiveness analysis (CEA) that quantifies the added expenditure necessary to obtain a unit of health benefit (typically measured in quality-adjusted life years or QALYs, pronounced “kwallies”). The most common application of CEA is to examine the value of medical innovations compared to the standard of care routinely available, since new technologies are an important cause of the increase in health-care costs.

If the “unit cost” for a QALY of benefit (that is, the cost-effectiveness ratio) is less than some threshold (conventionally $50,000 or $100,000 per QALY), then adoption of the innovation is deemed “incrementally cost-effective,” since the benefit obtained compares favorably to that obtainable at similar cost using accepted medical technologies (such as dialysis, which has a cost-effectiveness ratio variously estimated at between $50,000 and $80,000 per QALY). Above the ratio, they are deemed not to be cost-effective. That is, the (relatively small) incremental benefits of the intervention do not justify the (relatively large) incremental costs.

“

“Of special interest is “Bernie’s kink” at the origin, which reveals how medical markets actually behave.  People prove to be unwilling to surrender quality using the same formula they would use to accept increased cost.”

“Of course, if all innovation in health care fell into this northeast quadrant, innovation could only increase the costs of care. That is, even so-called cost- effective health-care innovations would always cost more money than the alternatives they replaced. This is often a point of confusion, sometimes purposeful, as when our political leaders claim that “preventative medicine” is highly cost-effective and would therefore save money. In fact, while most recommended preventative services are cost-effective (meaning the value of their benefits in terms of QALYs gained justifies the costs in terms of dollars spent), only very rarely are preventative services actually cost-saving, even when all the “downstream” avoided medical expenses are folded into the analysis. Indeed, new “cost-effective” innovations are one of the principal reasons that health-care costs continue to soar.”

“the selling price (often referred to as willingness to accept, or WTA) and the buying price (willing to pay, WTP) of a QALY should be similar, and the societal threshold for accepting or rejecting a technology should be symmetric and pass through the origin of the cost-effectiveness plane as a straight line. However, as David Hume anticipated, a reproducible observation is that consumers’ willingness to accept monetary compensation to forgo something they have is typically greater, and often much greater, than their stated willingness to pay for the same benefit. Several explanations exist, including the so-called “endowment effect,” the psychological principle that people value items that they already have simply because they already have them.

A 2002 review of 20 studies by the late Bernie O’Brien and his colleagues at McMaster University found that the ratio of individuals’ WTA to WTP was always greater than 1 and ranged from 1.9 to 6.4 for two scenarios specifically related to health care. They suggested that rather than a symmetric accept-reject threshold on the cost-effectiveness plane, societal thresholds should reflect the WTA-WTP gap seen in individual preferences, which would be captured by a downward “kink” (subsequently known as “Bernie’s kink”) in the threshold as it passed through the origin, indicating that a QALY’s selling price in the southwest would always be higher than a QALY’s buying price in the northeast.

Thus, there may be an inherent cognitive bias against relinquishing the gains of health-care interventions that have already been accepted, and the cost savings from decrementally cost-effective innovation may need to be substantially greater than conventionally used thresholds suggest.“

“Indeed, fewer than 2 percent of all comparisons were classified in the cost- and quality-decreasing “southwest quadrant”, and only 9 (involving 8 innovations) were found to be decrementally cost-effective (0.4 percent of the total)—that is, they saved at least $100,000 for each QALY relinquished.”

 “That decrementally cost-effective innovations are so rarely described in the health-care literature suggests that medicine is distinct from most other markets, in which cost-decreasing, quality-reducing products are continuously being introduced—think IKEA, Walmart and the Tata car. Several reasons may explain this “medical exceptionalism.” First, there is fundamentally a lack of incentives both for physicians to control costs, especially under a fee-for-service regime, and for patients to demand less expensive treatment when insurance shields them from the direct costs of care. Second, medical “bargains” frequently come with health risks, and trading health for money strikes some as vulgar, regardless of ratio. The inherent ethical unease that decrementally cost-effective innovations can elicit poses a serious public relations and marketing challenge.”

 “But regardless of the mix, expanding coverage to the uninsured, caring for our aging baby boomers, and accommodating new, effective technologies—while still feeding, clothing, housing, and educating ourselves, and catching an occasional movie—will require our system of distribution of health services to be more cost- sensitive, and will almost certainly mean the adoption of some decrementally cost-effective strategies for saving money. For example, Canadian-style delays for expensive diagnostic or surgical procedures certainly pose real, albeit small, medical risks, and would fall into this southwest category. Getting insured Americans to accept such new risks may be difficult, but slightly quality-reducing (that is, risk-increasing) cost-saving strategies have already been widely adopted within the American system, even if not studied or widely acknowledged. The gradual increase in the “hassle factor” in accessing medical care is one covert way that the industry has found to limit the distribution of services. More overt examples of rationing already adopted include aggressively shortening hospital stays and limiting formulary options (which sometimes require patients to change from a medicine they have been tolerating well to another in the same class). Despite the fact that doctors regularly (although sometimes disingenuously) deploy patter informing patients that the hospital is a dangerous place to stay and that the formulary medication is “just as good” as the one they’ve been taking, these strategies are certainly associated with small but real risks. Even a preadolescent quickly learns the true meaning of “just as good”; perhaps a more mature citizenry can also come to appreciate some of the upside of having “just as good” alternatives.”

Related posts:

1. If Rafe Were In Charge: Major Medical Edition
2. Health Care Parallels Education
3. If I Were In Charge, Health Care Edition

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 hill-climbing techniques that incrementally achieve higher ground (logical deduction, reductionism) in order to deny that we are in new territory at all and “prove” every new claim as false.  But unless we eliminate most or all of our old assumptions and embrace the new ones, these techniques will always yield inconsistency.

Thus, it seems like a good idea to resist the urge to bring to in the heavy logical artillery until it’s clear we are on the upslope.  In practice what this means is adding more novelty — but not as much as last time.  This is the Boltzmann technique of simulated annealing: start with a high degree of heat/randomness and turn it down slowly, all the while pounding away with the tools of logic and reduction.

What I mean by Science 2.0 is an intentional (and methodological) injection of novelty into the scientific method.  This is the beginning of a series of posts on the hows and whys of such activity.  I hope you will join in constructively and creatively.

Related posts:

1. Non-Dualism
2. Why Falsifiability is Insufficient for Scientific Reasoning
3. The New Scientific Enlightenment

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 since it presupposes time (or at least well-ordered events).
3. I conjecture that the distribution of universes is unimportant, as long as all possible universes are represented in the multiverse (i.e. the distribution can be random).

It’s worth noting that this is a purely a metaphysical/logical argument and says nothing about specific physics or cosmologies.  One of the things that makes it hard to see why this is true from reading the Smolin/Susskind debate is that they bounce between the logical argument and various proposed, unimportant details (like whether black holes are the replication mechanism in question or not).

More importantly though, we hear scientists call one another “unscientific” whenever they propose an hypothesis that is unfalsifiable.  Here’s why I think that’s problematic:

• Ever since Popper, science has been obsessed with falsifiability, which is really about assuring consistency.
• Godel proved that there are true statements that cannot be proved.
• More specifically he unpacked “truth” into completeness + consistency and showed that we can’t have both simultaneously.
• Due to extant complexity (let alone potential infinity) completeness is out the window.
• If science is only concerned with consistency, then it’s a pointless endeavor; I can sit here all day and generate tautologies that are neither interesting nor useful.
• If science is about truth, then there needs to be a way of expanding the set of discovered tautologies along the completeness dimension as well.
• There are at least three formal logical systems which do that without sacrificing consistency: deduction, induction and abduction.
• Only deduction is formally falsifiable.
• But science relies on induction and many other forms of evidence too (statistical reasoning, clinical trials, simulation, storytelling, etc); this is the “democracy” Smolin himself referrs to in his TED talk.
• The structure of the Anthropic Principle is abduction.  So is the structure of Occam’s Razor.  And depending on who you believe Bayesian inference is either induction or abduction.
• Conjecture: Newton’s Calculus is a formalism based on abduction.
• Conjecture: strong emergence (aka novel emergence) is fundamentally abduction.  This may be why science has such a hard time with it.
• Conjecture: natural selection is fundamentally emergence/abduction.  This may be why Creationists have such a hard time with it.

There is no one true definition of what constitutes “Science.”  We hear reference to the so-called Scientific Method.  Ultimately, the holy Scientific Method is whatever scientists as a whole do; no more and no less.  To say otherwise is ad hominem.  Now I’m not claiming that ad hominem argument shouldn’t be counted as scientific evidence, but anyone who bows before Popper would.  The irony there is that ad hominem is a form of Bayesian inference.  And if you’re keeping score, that means that anyone who claims that you are being unscientific if you don’t forsake all unfalsifiable idols, is themselves committing the sin of inconsistency.  Which by their own logic means they are unscientific too.

To which I respectfully submit, their pants are on fire, hanging from a telephone wire.  And that’s a scientific fact.

Related posts:

1. The New Scientific Enlightenment
2. Scientific Singularity?
3. The Process

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 group” (all those that are picked) and an “out group” (all those that are not).  Of course, both sets are infinite and still have no structure.  But note that all the universes in one group or the other now stand in relation to one another.  That is, they share the property of “in-ness” or “out-ness”, and between the two groups there’s the relationship of “different”.

The Process further divides these sub-multiverses in unknown ways, and this sorting creates other relationships between universes.  You can visualize a network of universes with the connections representing these relationships.  The network is infinite, and if you consider any subset of the network, it’s also infinite.  But these subnetworks are no longer arbitrary, they are networks themselves and networks have structure.  And since a subnetwork by definition shares the same connection relationships as the original network it is a “sub” of, the subnetwork is structurally similar to the network itself.  That is, the network is self-similar, which in mathematical terms means it’s fractal.  Of course this fractal we are talking about is infinite, and so wherever you start, it’s turtles all the way down, and all the way up.

Notice that the process of identifying subnetworks does something interesting, it creates an asymmetry that wasn’t distinguishable before.  For any network N, if you choose a subnetwork, n, then N “contains” n but not vice versa.  This containment relationship can viewed as a network where the connections are arrows, meaning they have directionality, N –> n.  You may have noticed that we just went from talking about a network of universes to a network of networks (of universes), but that’s okay.  Remember the multiverse is infinitely infinite, and we’re just chatting about some arbitrary aspects of it.  There’s lots of other aspects we could talk about instead, but it’s starting to get interesting here, so let’s continue….

Somewhere in the fractal multiverse network of networks described by The Process there is a subnetwork (actually an infinite number of them) where the structure is like this: each universe is connected to by only one other universe but connects to an infinite number.  Let’s call this structure, Time, and note that there are an infinity of subnetworks of the network which have this Time structure.  Unless stated otherwise, I’ll be talking from now on about networks with Time structure.

Remember though, the multiverse itself has no structure; The Process overlays structure on top of it and thereby allows us to know about things like Time.

Now let’s start using the words network, system, particle, entity, agent and universe interchangeably, so we can say things like “time network”, “temporal system”, “particles over time”, and “A causes B” to refer to roughly the same thing.  I realize that by overloading these terms I’m jacking into (and hopefully hijacking) your intuition about what these words mean, but that’s my intent.  Hopefully you’ll continue playing along by my rules and try not to project what you already know onto this alternative cosmology.

When we use the words network, system, particle, entity and agent, you might wonder whether we are talking about a universe or a multiverse.  The answer is Yes.   Remember, the multiverse is infinitely infinite and self-similar, so in some sense we can say it contains itself.  We have a hard time with infinity so this concept is mind-boggling, but if you follow the logic, hopefully you’ll accept this paradox as true.  So lets just use the word universe from now on and forget about multiverses.  And to not get confused, let’s refer to what we used to think of as the Universe as the known universe instead.  The known universe is where you live (or more precisely where you think you live) along with everyone and everything you know about or can imagine.

The known universe is expanding the more you learn about it.  The known universe is temporal.  And as we know from Einstein, it must therefore also be spatial — remember it’s not space and time but rather the spacetime continuum.  The known universe consists of particles (i.e. matter) and therefore — also thanks to Einstein — it consists of energy.  Time, space, matter and energy here may or may not be totally in sync with our intuitions of them, but just suppose they are the same thing and that our intuition is slightly biased by our particular experiences in life and could use adjustment.

We haven’t really talked explicitly about laws of nature, fundamental constants, invariant equations or even mathematics.  And I kinda jumped the gun when bringing Einstein into the equation (so to speak).  But it’s really hard to follow a line of thought without some sort of logical paradigm, some structure of thought.  In the end it doesn’t really matter what I’m saying, what you’re hearing, or whether any of this is “true”.  I’m just telling you a story, and hopefully it’s amusing enough for you to finish reading.

Originally we talked about The Process, which is infinitely complex and which describes all sorts of possible realities.  The known universe is one of those possibilities, one in which we see structure and patterns, order and complexity all around us.  Somewhere “out there” there may be portions of the multiverse (whoops, I said I wasn’t going to use that term anymore, sorry) where it’s still appears, unstructured and thus unknowable.  But let’s come back to the known universe and the “knowable” universe.

Because of the fact that we are here in the known universe thinking and talking about it, and not in some unknown or unknowable part, the non-random patterns that we see may look to us like universal laws (E=mc^2, the second law of thermodynamics, etc.)  Well, we know that even these laws are not truly universal, they apply to only certain scopes.   For example, “relativistic but not classical or quantum realms”, or “closed systems but not open systems.”  String theorists are looking for universal laws, but so far none have been found.  But let’s just grant them that they will eventually find some (or one).  How would we be able to distinguish between a true Law and just a pattern that is very very persistent over all known scopes?

How about we stop using the word “law” and instead replace it with the word “principle” to suggest that it may really just be a pattern that we see in the known universe.  And as the known universe expands via our increase in knowledge/understanding/awareness, we might find exceptions to the pattern.  After all, that’s what’s happened to every “law” ever considered in the history of science so far, and why should that pattern stop?  (Sorry, my paradox detector just went off, let me reset it….)

Coming back to principles, there’s one that emerged from the last few paragraphs, did you notice it?  Cosmologists call it the Anthropic Principle, which is the notion that the universe appears ordered in the particular way that it does with these nifty laws and constants because of the very cosmic coincidence that we are here observing it!  In other words, we live (and can only live) in the known universe, by definition.  And we wouldn’t be “here” and able to “notice” anything if we were in some unknowable part.  That’s a pretty trippy concept, but one that many physicists take very seriously.  It’s the same kind of argument as for why we haven’t been contacted by aliens yet: there’s a decent chance we are the most advanced intelligence out there and we’ll have to wait for others to catch up so we can communicate.  It’s also the reason that your keys are always in the last place you look.

Remember the Anthropic Principle because it’s really useful.  It has the same logical structure as Darwinian evolution and other “emergent” phenomena.  Is this Generalized Anthropic Principal (GAP) a universal/fundamental one?  Who knows.  Probably not.  We anthropic agents are so self-absorbed.

Another principle that emerges from our cosmology is Coherence.  Because of The Process, birds of a feather flock together.  Actually, The Process defines which birds are of which feather, so this is a tautology, though it’s fun to think of it as “like attracts like”.  But we know that really it’s just co-incidence: the birds exist at the same Time.  Using the analogy of birds, we can ask whether these coincident birds are different birds or the same bird.  But it’s a silly question because the answer is Yes.  Think of quantum coherence, if you like.

Now let’s say we are talking about particles and not birds, and instead of Coherence we’ll say Gravity.  Isn’t it the same thing?  We talk about stars and planets and other astral bodies as if they were coherent entities, but If there were no gravity, would those entities exist?  Or let’s talk about the Cooperation of the cells in your body; without it, would you exist?  We’ve all heard about the “law of attraction” from The Secret, isn’t it the same thing?  You imagine the future you want, and that acts as a beacon guiding you in every decision you make, every micro-decision, every unconscious action until at some point you find yourself living in the future you imagined.  Coherence, cooperation, attraction, unity.  Same thing.

Here’s a secret: there is no Process.  Or if you prefer, The Process is completely random.  Yet that doesn’t change anything I’ve said above.  Think of it this way: in an infinite series of random numbers, all patterns appear eventually, right?  So “somewhere” in the infinite randomness, The Process “produces” the structure I’ve been talking about.  Or maybe the fact that we’re anthropically talking about it produces the structure.  We are The Process.  Or more generally, we humans are part of The Process.  The Process is the universe.

Related posts:

1. The New Scientific Enlightenment
2. Why Falsifiability is Insufficient for Scientific Reasoning
3. Notes from TED

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 using nanomagnets and still others siRNA. Glazier is in agreement with the target and kill approach and outines a number of such methods in his book, Cure, in which he also argues forcefully for the importance of taking somatic evolution seriously in our approaches to treating cancer.

One potential problem with target and kill, as Glazier points out, is that if you don’t get all cancer cells, you run a high risk of recurrence.  Which belies an even bigger problem: how do you detect which cells are cancerous and which are not?  Glazier calls for behavioral pattern recognition, i.e. looking for cells that are proliferating and also exhibiting invasive behavior at the same time.  But it remains to be seen whether such pattern recognition is possible in practice.  A possible way to keep tabs on cell behavior is to do continuous in situ monitoring or ultrasonic nanotech.

Enhance Immune Response

The immune system is really good at identifying and killing cells behaving badly (although the majority of the time the immune system’s targets are foreign invaders like viruses).  But what if we could boost the immune system so that it was better able to deal with cancer cells?  Essentially create a vaccine for cancer.

The difficulty with immunotherapies for cancer has always been that it’s not in the “charter” of the immune system to fight the body’s own cells; when it does we can get what are know as autoimmune diseases.

Reiter, et al are working on a clever hack of the a class of immune cells called tumor-infiltrating lymphocytes (TILs) wherin they extract TILs from a tumor, enhance their tumor-fighting potential and reinject the enhanced TILs back into the tumor.

The achilles heel of immune enhancement will always be comprehensiveness.  That is, if you don’t get everything, cancer can eventually evolves resistence by becoming too hard for the immune system to detect or by learning how to fight off the immune response.  And if you get overly aggressive, you risk harming the patient in other ways.  And cancer has proven to be extremely tricky in outwitting the immune system.

Genetic Modification Approaches

Modifying genes, either by enhancing tumor suppressors or reducing tumor promotors, has been a popular appoach in recent years.  Often the approach has been to focus on individually important genes or to try to find exhaustive sets of genes which, when modified appropriatly, stop cancer progression.

One problem is that genetic information is not organized into atomic functions or even sets of functions, but rather in complex, multi-scale functional networks with built-in redundancy.  In such networks, you can modify, add or delete many nodes and links without changing the overall network behavior significantly.  Still, recent advances do show promise, as with microRNA replacement.

Another confounding factor is genetic modification is that the genetic code seems to be organized a bit like a toolbox of mix-and-match parts that get shuffled around by evolution.   Thus if a trait or function is adaptive, it might emerge by more than one evolutionary path using different arrangements of genetic code and entirely different mechanisms (this is known as convergent evolution).  Theoretically the malignant behaviors that characterize cancer — unregulated proliferation and invasiveness — could re-evolve, just as happens in organismal evolution; after all, to the cancer cells malignant behaviors are are adaptive, it’s just us mulitcellular beings that view the behavior as bad.  What I mean by this is the following; vision has been achieved a number of different ways by organismal evolution with the genetic toolbox, so what’s to stop somatic evolution from achieving proliferation and invasiveness in different ways than is normally seen in human physiology?

Viewing the problem from a slightly different angle still, consider the following.  Cancer itself works by making massive numbers of changes to individual cells’ genetic networks.  This source of heterogeneity is what provides the grist for the evolutionary mill.  The vast majority of these mutations don’t work out and the cells die off or — more problematically — the mutations remain dormant in successive generations of the cell line.  But every once in a while you end up with a rearrangement of the network that is viable and which creates cells who don’t “play nice” with their neighbors (i.e. cancer).  Thus, if you have created a therapy targeted to a particular gene, there’s a good chance it won’t work anymore because the gene now sits in a different functional context; the original function you were targeting may now be served via different mechanisms.

A more harmonious variant of genetic modification is to replace entire cells with stem cells and allow them to differentiate into the appropriate cell type, effectively cleansing the genome.  This type of work is being done but is very preliminary and the stems cells themselves are prone to becoming cancerous, presumably due to their pluripotency and robust replicative potential.  Still, this line of inquiry seems promising to me, because it honors the body’s own developmental programming to replace badly acting cells with good ones, instead of just, say, killing bad cells and leaving a physical (and behavioral/ecological) void for surrounding cancer cells to exploit.  While currently solid tissue cell replacement requires surgery, down the road we can expect a veritable Cambrian explosion of nanobots that will be able to precisely navigate to targeted areas and do the work of cell replacement and genetic modification.

Prophylactic / Preventative Approaches

Aubrey de Grey works on the radical extension of the human lifespan and believes that there’s no theoretical limit to how long we can live if we hack our biological inheritance appropriately (BTW, many others agree, including Ray Kurzweil).  Organ replacement and regrowing failed body parts is a forgone conclusion (it’s happening already), and de Grey says that the only disease that presents a problem long-term is cancer, due to the relentlessness and “cleverness” of somatic evolution.  De Grey proposes therefore that the only real approach is one of indefinite prophylaxis, i.e. take specific steps to intervene on a regular basis so that somatic evolution stays in check and we don’t get the unregulated proliferation and invasiveness that is cancer.  His WILT approach argues we achieve this by regulating the length of telomeres which are critical to the proliferation process.

Carlo Maley says that the WILT approach should work, but the technology is a far way off and it’s hard work to go this route.  Maley believes that we may be closer on the prophylactic front with by boosting cancer-suppression genes, as in the super p53 approach.

Several months ago I started asking cancer researchers the following question: if we were somehow magically able to replace the DNA in every cell in your body with a clean copy at regular intervals, would that prevent cancer entirely?  While most who answered thought that in theory this would work, some startling research recently has me wondering whether it would.  The discovery of non-genetic forms of persistent heterogeneity (Brock, et al, Spencer et al, and Sigal et al), combined with the logic of somatic evolution and the genetic toolbox, leads me to be fearful that unregulated proliferation and invasiveness might re-emerge without genetic (or genomic) heterogeneity.  Even if non-genetic heterogeneity is not broad enough to provide an “escape hatch” from full DNA replacement, it might be broad enough to thwart a WILT or super p53 approach.

Other preventative approaches focus on detecting pre-cancerous cells — ones that are most likely to turn malignant at some point — and removing them either surgically or with more advanced technology like radio waves.

Hijacking Microorganisms

Then there’s the approach of co-opting existing viruses and bacteria (also here, here,and here) since these microorganisms have exquisitely evolved to be effective at targeting and dismantling individual cells and cell types in multicellular organisms like humans.  There are several issues with this approach though.  First is that in order to “repurpose” these critters to do our therapeutic bidding, we have to simultaneously help them outsmart our immune system while making sure they don’t harm normal cells; not such an easy task.  Second, there is a danger in messing with viruses and bacteria in that these are populations with the potential to evolve (despite whatever measures are taken to avoid this) and as such could get out of control.  Third, there are always unintended and unpredictable consequences when injecting a body with foreign substances, especially ones that are alive….

Fighting Evolution with Evolution

There are a number of ways to approach fighting cancer “with” evolution, one of which was mentioned already (the TIL approach).  Another is to use evolution as a mad tinkerer/designer to create sophisticated biological agents that empirically do the job well.

Maley and Pepper are looking at changing the microenvironment to shape somatic evolution so that there is less selective pressure for cells to compete with one another.  David Basanta and his colleagues at the Moffitt Research Center modeling various aspects of evolution in the hopes to be able to one day shape it’s direction.

David Rasnick suggests that if we are to really take somatic evolution seriously we need to recognize that normal human cells are vastly more robust than cancer cells and that most cancer cells die off with the smallest perturbation to their environment.  The problem is that they mutate and adapt very quickly.  Rasnick’s “perturbation theory” says we should look to induce stresses into the body that normal cells are equipped well to deal with and on a relative basis, cancer cells are not.  While one could think of chemo and radiation in this regard there are two problems: (1) they can damage DNA making the heterogeneity worse; (2) normal cells are not equipped to deal with these perturbations either.  Examples of perturbations normal cells are equipped to deal with include radical changes in various lifestyle dimensions (extreme exercise, extreme diet changes) or inducing natural stress reactions.  Rasnick notes that many cases of “spontaneous remission” occurred after prolonged periods of extremely high fever.  One thing that’s for sure, as technology advances we will have more and more ways to cleverly perturb cells.

Doing Less

In our “Just Do It” society we often forget that sometimes less is more:

• Surgery Not Necessary For Most Late-Stage Colorectal Cancers
• Chemo spurs some cancer cells
• To Survive Cancer, Live With It

Related posts:

1. Cancer as Evolution — 2008 Summary
2. Cancer as Evolution, part 2
3. The Conflict Between Complex Systems and Reductionism