Fixing Science

Thoughts on what's wrong with the enterprise of science, from the viewpoint of someone who wants to improve it, not kill it. Why "science" appears increasingly irrelevant to many Americans and is losing ground.

Wednesday, October 19, 2005

New Scientist coverage of Fundamentalism

The magazine NewScientist has a feature section on fundamentalism in the October 8-14, 2005 issue. They really still don't get it.

To hear them talk, Science, capital S, is responsible for everything in life which is good, and for none of the bad - and the reverse is true for Religion. "If only everyone was a scientist, war would vanish, poverty would disappear, injustice would be gone, life would be a utopia" seems to be implicit. They working hypothesis is that Science brings progress, and Religion brings decay.

They confound technical knowledge with wisdom, and the implicit argument is that Science has a monopoly on both, while Religion has neither.

Meanwhile, although coverage of nuclear winter has become passe, the magazine discusses how the 1918 flu virus has been recreated by scientists, and how out technological utopia has created global warming and environmental destruction on unprecedented scales. Are we to believe that global warming and environmental pollution are due to religious zealotry, not applied technology?

Above all, in the dimension of humility versus hubris, it is not clear that scientists grasp that most of what they believe will be overthrown, not in a small way, but in a large way, within 100 years, if we extrapolate the only data set we have - the historical record. If asked, they will state that science is provisional, but the rest of the statements of many reveals the opposite belief, that not only is Science immortal, but that the particular world view held today by science is at last, almost perfect, and correct in all essential features.

So, when William Dembski asks whether we should investigate whether evolution on earth is being manipulated by outside forces, it seems to me that the response of Science is inappropriate. Yes, Dembski has another agenda, but by the rules of science the person asking and the reason someone asks a question is irrelevant to whether it's a good question.

It is certainly possible that many local or national governments are under the sway of secret powers, and the stuff of good novels. Given a few billion year head start, there's no reason to confidently assert that some intergalactic farming and mining consortium isn't growing the Earth for its own purposes; I mean, we would do that sort of thing, if we could.

Of Science and Religion, only one group is constructing huge population surveillance systems, biological warfare devices, ever "better" nuclear bombs. The credulous argument that these are "neutral activities" by "good people" simply being misused by "bad people" needs scrutiny.

The more important axis of battle may be whether man is arrogant or humble, and there are those with each trait in each camp.

I never thought of myself as a Luddite, but, if asked if we want another 100 years of "progess" like the last 100, or not, I do have to pause and consider where that would take us.

What I do not hear, is scientists saying "We hear your pain." What we do hear is "Well, they restored the 1918 flu - oh, those scientists, just out of control." Hmmm. Maybe, for all the hypermagnified downside, control is not such a bad thing.

When scientific "freedom" intersects global survival, someone has to ask these questions. Attacking the loonies in fundamentalist religion doesn't address those questions.

There may be some hope, with the upsurge in web-publishing, that a forum for freely discussing these issues that is not under the control of big government or big science is emerging. Whether evolution has occured in the past is not our key issue. Whether science can be brought under some sort of self or externally imposed control, before it kills us all, is the issue.

Thursday, October 06, 2005

Blogs as a life form

If there are evolutionary shaping forces, one place they might be seen is during the very rapid set of changes corresponding to fetal development. For example, in the womb, by classical wisdom, the only interaction pathway between the woman and her fetus is that she's providing food, shelter, and some antibiotics. This is one interesting place to wonder whether there's not a lot more going on, which is why in-utero development beats, say, laying eggs and letting the fetus develop independently. We can ask what tools science has to test whether there's more going on than housing, and, if so, how to detect it. (the same tools might apply after birth, as some households may effectively only supply food and housing, while others supply a far more interactive, nurturing, morphogenic field for directed development of a child.)

Anyway, that's hard to study, but an analog in the world around us that might be way easier to study is the rapid and exponentially accelerating evolutionary growth of the electronically-supported collaboration systems on the planet.

It's not just that there's a "world-wide web" that has "changed everything." There are sub-niches that are rapidly filling in an ecological fashion. Email and web home-pages evolved fairly slowly, with interactions measured in days or weeks. Then we got instant messenger, with interactions measured in seconds, and list-servers with interactions also in days or weeks.

Now there is an astounding growth in a new life form called "blogs" or weblogs.

One can ask, "why is there any niche space left? Why don't web-pages, email, list-servers, and Instant Messenger" already fill the available space, crowding out any nice for blogs at the table?

One reason is that blogs aren't competing. In fact, the other information forms of "ground cover" spread rapidly, but are like a base level, and blogs are coming in ABOVE that level, as a second story addition, in a whole new space that the first level opened up for them.

So blogs deal with the information overload problem by successive filtering of data. They also deal with the recontextualizing problem, that is a living problem that has to be redone each day, not done once forever. So blogs help answer - but what facts are IMPORTANT for me to be aware of RIGHT NOW? And WHY are those the important facts?

But no single blog can do this. The power is in connectionist links, and a huge, globe-spanning array of value-adding sensors that, collectively, create a dynamic image of what's important right now and bring it to your doorstep.

This is, in that sense, a global BRAIN model, evolving neurons, some locally concentrated, some globally spanning, and focused, so far on INPUT processing, that is, they are largely SENSOR arrays. But, we would expect, shortly, the rest of the equation to be revealed, namely, EFFECTOR neuron arrays.

IF we have to pick an analog in point in time to a human fetus, we're still in utero,
pre-birth, but getting to that extremely clumsy period of rapid convergence of the SENSES on making sense of all the noise, but a fairly longer period of time on figuring out what is connected to what in terms of MUSCLES, characterized by pretty spastic or ineffective attempts at motion.

So, we have a very active canvas, with very active painting going on in an evolutionary
nature. If there are design rules in this local part of the univers, or design assistance,
or morphogenic fields, or resonances, or outside influences to be applied, NOW is certainly the time of maximum leverage, so we'd expect to see them come into action, be up-regulated right about now.

Do we? Where do we look, and how? Is the growth of, say blogs,
a) FASTER than we'd expect?
b) DIFFERENT than what we'd expect?
c) Does it, like an incoming flying saucer in the movies, make a number of
different trajectory changes in it's path, instead of just falling in a straight line,
giving away that there's someone at the controls with an INTENT?
(well, someone besides Google, Microsoft, Yahoo, etc.?)

Is the growth of blogs not just LIKE the growth of a fetus, but SURPRISINGLY like it?
Is is SO LIKE it that there must be some sort of resonance, or template, or solution to equations that is effectively FORCING a certain line of development?

Can we see any LEAPS over obstacles? Any place where the linear, incremental growth suddenly turns into a TRANSITION, like piston power to turbines,that was UNPREDICTED?

Wednesday, October 05, 2005

Avian flu - slithagadee?

From today's New York Times:

Two teams of federal and university scientists announced today that they
had resurrected the 1918 influenza virus, the cause of one of history's most deadly epidemics, and had found that unlike the viruses that caused more recent flu pandemics of 1957 and 1968, the 1918 virus was actually a bird flu that jumped directly to humans.
The work, being published in the journals Nature and Science, involved getting the complete genetic sequence of the 1918 virus, using techniques of molecular biology to synthesize it, and then using it to infect mice and human lung cells in a specially equipped, secure lab at the Centers for Disease Control and Prevention in Atlanta.


But the research, and its publication, also raised concerns about whether scientists should publish the genetic sequence of the 1918 virus. And should they actually resurrect a killer that vanished from the earth nearly a century ago?

"It is something we take seriously," said Dr. Fauci of the National Institute of Allergy and Infectious Diseases, which helped pay for the work. The work was extensively reviewed, he added, and the National Scientific Advisory Board for Biosecurity was asked to decide whether the results should be made public. The board "voted unanimously that the benefits outweighed the risk that it would be used in a nefarious manner," Dr. Fauci said.
Others are not sanguine.

Richard H. Ebright, a molecular biologist at Rutgers University, deplored the publication of the viral gene sequence and the reconstruction of the virus. "There is a risk verging on inevitability of accidental release of the virus and a risk verging on inevitability of deliberate release," he said. And the 1918 flu virus, Dr. Ebright added, "is perhaps the most effective bioweapons agent ever known."

============== Perhaps this from Shel Siverstein is appropriate now...

Here you can read Silverstein's "The Slitheree-Dee" in its entirety:Banned Width: THE SLITHEREE-DEE

Moral infrastructure?

One generic religious belief that might have scientifically observable consequences is that there is a moral infrastructure on earth, at least for people. This has some set of absolute rules, and provides at least negative feedback (or possible also positive feedback) beyond that you'd expect to get from (a) other people and (b) your self as pathways.

And there is some sort of accumulator (sin, karma,...) that keeps track of a sort of score of how you're doing.

It stops being scientifically testable if the note is added that the rewards or punishments only arrive after you die.

It's pretty well established that belief is such a universal system of personal accountability has a substantial effect on social functioning: people tend to be more honest and less corrupt if they think they're likely or certain to get caught. Sometimes this is viewed as part of "social capital."
( The World Bank's readable "Social Funds and Social Capital"; "Investigating the roots of civic morality: Trust, Social Capital, and Institutional Performance"; "Social capital in a global information age".) In any case it's widely accepted, even by the World Bank, that belief systems around morality have a dramatic impact on social functioning, ability of a country to evolve and develop economically, etc.

In other words, this is not purely an academic question - it has very real social, political, economic and personal consequences. If sources diverse as the Bible and the World Bank agree that personal moral systems have a dramatic or even determining role in the survival of nations, this argues that there is more than the imagination at work here and there is some real phenomenon at work.

It's also pretty obvious that denial of such a system has observable consequences in behavior in people and organizations, although, in literature and movies, bold statements of "See, I am invincible!" are often followed a short time later by total collapse. "Pride goeth before a fall."

The US government, for example, appears to believe that it can spend a trillion dollars a year more than it takes in forever without the debt ever becoming due - a larger scale exhibition of this belief taken to extreme.

So, life and literature are full of examples of people (and kingdoms) that didn't "get away with murder"; but life around us appears to have blatant examples of some who are getting away with it, so the observational data is mixed.

It is, however, potentially subject to scientific study and has not, that I know of, been studied. One of the questions of course would be, if there are universal justice norms, what are they?

Maybe there are, but they're not what we think. For example, some people become very rich and powerful through extremely bad behavior. So, is what we call "bad" actually considered "good" by this universal metric? If we were to measure it, we'd have to be careful about what we assumed the rules were that were being enforced, and solve for those as well.

Even within each religion there are substantial disagreements as to what the rules are and which ones are more important. The Christian Bible details the destruction of the city Sodom for sin, for example, but few people note in Ezekiel 16:49 which sin was their downfall:
"Behold, this was the guilt of your sister Sodom: she and her daughters had arrogance, abundant food, and careless ease, but she did not help the poor and needy." (NIV 1970)
So we can't assume that "general knowledge" correctly represents the putative rules.

And, do the rules, if there are rules, apply just to people, or do they apply to bacteria, cells, organ systems, animals, plants, teams, companies, countries, cultures, movements, swarms, water, rocks, chemical reactions, etc.? Generally, scientific laws are widely applicable.

Still, it's amenable to study by scientists by scientific observations.
Is there a behavioral-response feedback system (in THIS lifetime) in place here beyond that we'd expect from just ourselves and other people's delayed responses?

In that sense, is the evolution of society being shaped by the continuous or continual on-going application of some rules that science hasn't revealed or realized or elucidated yet?

I side with the field-study group on this and believe that such questions can be studied without requiring a model or a mechanism to be defined beforehand. First, empirically, is there some surprising phenomenon that cries out for explanation?

If yes, then we can get to work on possible explanations.
If not, we don't need to waste mental energy on explanations.

People interested in exploring the impact of social capital might be interested in the Templeton Foundation's research on this and one project on whether the concept "spiritual capital" means something. The Templeton Foundation describes itself this way:

The mission of the John Templeton Foundation is to pursue new insights at the boundary between theology and science through a rigorous, open-minded and empirically focused methodology, drawing together talented representatives from a wide spectrum of fields of expertise. Using "the humble approach," the Foundation typically seeks to focus the methods and resources of scientific inquiry on topical areas which have spiritual and theological significance ranging across the disciplines from cosmology to healthcare. In the human sciences, the foundation supports programs, competitions, publications, and studies that promote character education and the exploration of positive values and purpose across the lifespan.

Tuesday, October 04, 2005

Design - who cares? Most of us!

The question of whether the universe is designed or accidental is different than the question of whether life on Earth, the biosphere, is proceeding free of outside intervention or not.

People, corporations, and countries have a really hard time distinguishing "coincidence" from "enemy action", and it's not for lack of trying.

The question becomes a legitmate scientfic question when it has detectable and testable implications for how things, or people, or events behave. One significant and open question is to what extent actions (by people, or teams, or companies, or countries) have inexorable consequences. Is there some sort of global accountability, or can we get away with pretty much anything if we're clever? Is there some sort of conservation law that we'd be wise to wise up to,
when determining personal or national strategy? Is the playing field flat or not?

And these are different questions than those of organized, instituionalized religion, and to what extent morality should be decided, decreed, and enforced by one bunch of people on another.

Anyway, science, at least implicity, having so far detected on its current instrument dials no God or underlying morphic field or agent in the vicinity of Earth, effectively asserts that no such field or agent exists. One presumes that the "intelligent design" crowd, after discussion, would take the opposite position. Curiously, the two quests overlap: science has always been interested in finding order underneath apparent chaos, laws and rules behind confusing actions.

Business theorists in the US have always been big fans of invisible forces, in their case the "invisible hand" of Adam Smith and free-market capitalism with putative emergent optimization of resource allocation. The US administration spends much time and energy observing the "invisible hand" of enemy action in Iraq and other spots around the globe. The "Moral Majority" sees connections that others don't between destruction of "moral fiber" in point A and bad things happening subsequently at point B.

Probably, in fact, a case could be made that most moral codes through the ages have been attempts to consolidated and simplify rules based on the fact that certain behaviors and good or bad outcomes are related in ways that are not instantly obvious to the actors in question.

So it is certainly true that intellectual machinery to detect and assess both outside intervention and a built-in consequence-enforcement system are of great social interest. One might wonder, in fact, if consequence are automatically enforced why we need to have any additional man-made laws, another question for another posting.

So, these are some questions that seem to be valid, scientifically determinable questions:

1) Is there currently on-going outside intervention in biosphere evolution on Earth?
Or, in more detail, who is messing with whom, where and why?

2) Are there built in rules or laws, (whether natural or imposed by some agent), pertaining to consequence of actions, beyond those detected so far by science, and beyond those imposed by man via laws and mores?

3) If there are such rules (#2), do they apply as well to teams, departments, companies, races, and nations as they do to individuals? Do they apply downward to body systems, organs, cells, bacterial swarms, organelles like mitochondria, etc?

And finally, the key question - if there were such rules, why haven't they been seen yet by science and where should science be looking instead to see them? This isn't intended to be
a hostile, rhetorical question but a legitimate request for information. What experiment will reveal outcomes that are inexplicable given current theory, but are predictable given a different theory and model?

I wish there were a better dialog over that question, and less shouting and name-calling and rock-throwing among those who should be helping each other with this common question.

If one hypothesizes that there are remaining hidden forces (natural or otherwise) that significantly impact our lives, and if Science hasn't found them to date, what would that mean?
Some options are:

1) science has been looking in the wrong place or at the wrong time.
[ aka "the car never makes that noise when it's in the shop." ]

2) science has been looking with the wrong detection or analysis tools.
[ such as, it's a low-level feedback loop that is mapped to "negligible terms" by linear regression techniques. (see also#3) ]

3) The detection tools used by science have a blind spot, and the
phenomenon of interest is precisely in that blind spot.
[ such as, pulsars ]

4) The event was seen, but disbelieved, discounted, ignored, or misperceived.
[ most Nobel prizes seem to be for such detection of phenomena
that "fly in the face of reason" and are therefore very hard to
"see" because they hide in plain sight, so this is not an uncommon
"feature" / "bug" of the Scientific Method as practiced today. ]

5) The phenomenon requires changing MANY assumptions of current understanding simultaneously, and the scientific method only really deals with changing ONE assumption at a time in a sequence.

[ Interestingly, this is the sort of question Intelligent Design people raise about evolution - how one gets across "gaps" and comes up with, say, ball and socket joints, or eyeballs with lenses, etc., when there is no apparent sequence of small-steps that climbs that hill. ]

All of these issues are ones that architects of "the scientific method" should honestly
be concerned about. Improving the performance of science on all of these fronts is my question in getting from "science101" to "science201".

Monday, October 03, 2005

Nobel Prize and hiding in public

A discovery that maybe in the "pulsar" category (hiding in plain sight) was the Nobel Prize announced yesterday. What makes this so interesting is the tremendous resistance, skepticism, and derision the winners got when they originally presented this idea to scientists who already knew without actual testing that ulcers were caused by stress and life-style.

Moral: Once your mind is made up, for better or worse, you become effectively blind to contrary evidence, and even actively hostile to those who present it.


The Nobel Prize in Physiology or Medicine 2005 goes to Barry J. Marshall and J. Robin Warren "for their discovery of the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease".

God, Intelligent Design, Science,and Evolution

I'm working my way around to making a comment on "Intelligent Design"and whether "it" should be taught in high school Biology classrooms. This posting isn't there yet.

To my knowledge, no scientist has yet proven the existence of God, or "God" if you prefer, or the non-existence of God. Definitions vary so much the whole discussion keeps shifting. Some say this is not a legitimate question to ask, although it has, in fact, preoccupied most of the last 20-50 centuries of scientific inquiry. Can we bring this around to a question that even scientists would have to, perhaps grudgingly, agree is a legitimate question of models that has testable implications?

How persuasive should it be that Science has not yet found God, despite all that looking?
My own sense here is to investigate several questions that do have answers, or at least about which we can say something or test something. So, my question is, what are the right questions we should be asking.

Here's some candidate questions:

1) what fraction of the core, indisputable, vast-majority-held views of Science have, over the last 5000 years, survived the test of time over 100 years? Take any point in time, over 100 years ago, look at what was "obvious to everyone", go forward 100 years, look at whether the same thing was still "obvious to everyone." Rough answer, less than 10%. Maybe way less.

2) Same question about "medical science" and specifically biology. Same answer.

3) What fraction of the known universe has been observed in detail and well-modeled?
Fact: over 98% of the visible universe is in the plasma state, for which our intituition based on "liquids, solids, and gases" is not applicable.
Fact: The universe has been, by scientists estimates, around for 15 or so billion years.
It has been carefully observed for, oh , 10,000 years at the outside, mabye more like
100 years. Whatever it is, it's a pretty tiny window.

So, over space, less than 1% of the universe has been sampled. Over time, less than 1%.
Over states of matter that we know about, less than 2%. Multiply those together and we
can put an upper limit on what we've observed at less than 0.0002% of the universe.

This is somewhat like looking at a set of data points that cover a page of paper, and extrapolating a curve to where it hits the Andromeda galaxy. An honest assessment
would be that (a) we cannot be highly confident of our conclusions based on the sample size, and (b) we cannot be highly confident of our conclusions based on prior historical track record of science.

This isn't to say that "religion" or non-science has a BETTER track record, only to say that I believe reasonable men and women would have to agree that, after calibration, "science" is not a 100% persuasive body of knowledge and processes.

That's "in general". What about "in specific"? How good are scientific tools at detecting conscious interventions versus random happenings, on historical data sets for which we HAVE ground truth?

Again, I'd say that the track record is pretty dismal there too.
More later.

Sunday, October 02, 2005

Crumpled paper theorem

Any discussion of seeking common ground and overcoming problems due to participants having different reference frames should mention the "crumpled paper theorem." (also known as the Brouwer Fixed Point Theorem - and this link has a nice picture.)

What it says boils down to this. If you run off two copies of a photo on the copier, take and crumple it up into a ball and set it on top of the uncrumpled one, there has to be at least one point of the image in the flat sheet that has exactly the same point of the crumpled image directly above it.

The simplest case of "crumpling" is just rotating. If you rotate the top flat sheet, the center of rotation remains fixed in the right location directly above the same point in the lower sheet.

However, my application of this theorem to universal understanding and the issues of science and society is that, if two people have representations of the same universe in their heads, regardless how "crumpled" they are, the two of them should always still be able to find at least one point of common agreement to work from.

Or, rephrased, there is no one on the planet that you disagree with on absolutely everything.
We all have something in common, at least pairwise.

Interestingly as well, if the top sheet is simply displaced and rotated somewhat, you only need to find two points of agreement, align those, and the two sheets will be entirely matched up or "registered." This implies to me in social communication settings that it is really worth the effort to find at least two points in common between two communicators, and reactivate those on both sides, share the joy of shared beliefs, before proceeding with the rest of the discussion.

The impossible dream

There are two impossibly high standards kicking around the core of the sciences that really need to be changed: clinical trials and computational models (Turing machines).

George Bernard Shaw, "No question is so difficult to answer as
that to which the answer is obvious."

In the same way that a company or country shouldn't have rules or laws on the books that they don't plan to enforce, my pragmatic side says that science shouldn't have standards that cannot possibly be met. The illusion of a standard damages practice. "The perfect is enemy of the good."

On clinical trials, "everyone knows" that the "gold standard" is a double-blinded, placebo-controlled trial in humans of representative ages and sexes. Aside from all the other problems with these, one show stopper is simply that this "standard" fails to scale up appropriately. I don't know the exact number, but probably the US could afford to do something under 10,000 of these, maybe under 1,000 of these at any one time - at probably over a million dollars apiece. And there aren't enough subjects. And we really don't want to test on pregnant women. On the other hand, and again I don't have the numbers, there are probably easily 1000 times that many new foods, products, cosmetics that hit the market in a given year. This gap will only widen. And, there are very few old people who only take one drug. In fact, by picking such persons, the sample has already become unrepresentative.
And even if it didn't widen, there is little in the way of post-approval testing of the drugs in vivo, in social settings as actually used, so there are all these changed-context issues.

In computation and communication, the core model is the Turing Machine - which models all computation on the basis of a theoretical paper tape that is infinitely long, never decays, doesn't have noise, and we have infinite time to do the calculation. In all realistic situations however, we have finite and even short time, we have finite space, there is substantial noise, and the data is flawed. The right model for computation and communication using serial symbol strings should make those limits explicit. Then again we have the problem that the meaning of data depends on context, which was left out by Turing. Probably the minimal correct model would at least be the level of image-processing primitives, where 2-D images have redundant parallel information and much higher bandwidth (One picture is worth 1000 words.). The proofs of these being equivalent all assume infinite time and space and energy, which don't hold in the world I live in. Given finite and small time, space, and energy we have to ramp up.

By ramping up, I mean two things. First, communcation has to be massively parallel to even get near the bandwidth necessary to communicate a message before the message has become irrelevant, along with context. Second, almost everything has to be either in shorthand or totally unspoken (implicit) or, again , the mssage won't fit. The problems of people having differing implicit worlds is well known.

This is not an occasional problem - this is the shape of the keyhole through which our entire understanding of the universe must be pushed. And like the impact that shoving waves or light through a slot has on the resulting output pattern, this is NOT a neutal impact. In mathematical terms, we're convolving the signal with the fourier transform of the keyhole, or some such thing.

In practical terms, no one can write a 135 page paper any more. No one will read it.
The window is getting even smaller, not larger, as time goes on. Probably the largest paper
that scientists will read is down to 12 pages, and anything much longer than 6 is at risk of being ignored.

Not just scientists are hitting this distortion-creating limit. TV messages have to fit in 8 minutes or less. Student attention span is well under 55 minutes. Blogs (unlike this one) should really have thoughts that fit on less than one screenful, which can be read in 4 minutes or less.

Someone needs to compute the system transfer function of this keyhole effect, and hypothesize what thoughts simply cannot be discussed any more because of it. Anyone notice a loss of ability to discuss long-range planning or complex subjects with policy makers?

Everyone sees all these problems but mistakes them for local issues, local symptoms, and doesn't see the fact that they are so deeply embedded in our system of "science" and social discourse that the output of that system has become throttled, distorted, and missing entire octaves of harmonics.

I thank John Gall, author of Systemantics - How things Fail, for the insights into finding system problems in what look like collections of misattributed local problems.


What seas what shores what grey rocks and what islands
what water lapping the bow
And scent of pine and the woodthrush singing through the
What images return
O my daughter
T. S .Eliot

Blogosphere as connectionist engine

Maybe one of the surprising strengths of the blogosphere is that it creates a planetary-scale neural net, a connectionist engine that keeps reshuffling and resorting new information into context.

It combines a massively-parallel associative memory with value-adding resurfacing features that keep the most interesting items bubbling up to the surface and highlighted. "Facts" get recontextualized with value-added discussions of their immediate relevance or lack of it, which changes from moment to monent.

This is so neat! This is way more powerful than a "storage-and-retrieval system" or a "Google search-engine".

A few links on connectionism and the wikipedia's article on connectionism with great links - as it says "connectionism is an approach in the fields of cognitive science, neuroscience, psychology and philosophy of mind. Connectionism models mental or behavioral phenomena as the emergent processes of interconnected networks of simple units."

Now you see it, now you don't...

"Did you ever notice, that if you think about something at 2 AM, and then again at noon the next day, you get two different answers?"

That pithy quote, which Charles Schultz had his cartoon character Snoopy observe one day, is worth a great deal of pondering.

Everything is context-sensitive, as we are just starting to realize.

The vast majority of communication problems, between people, or different teams, or cultures, or nations, are due to the fact that we each live in a different world of overlapping contexts, and that the meaning of something changes as the something is moved from one context to another.

This problem is recognized one of the core problems in Einstein's Theory of General Relativity, where the issue is described as one of "parallel transfer". Relativity is definitely on to some basic truth, because in Relativity, there is no ultimate difference between content and context - content causes context and context causes content and both are two sides of the same coin, two equally valid representations of the same underlying universe. Failing to account for differences in "reference frames" is why so many of us who actually observe the same thing and think the same thing mistakenly believe we are seeing different, and conflicting things.

I came across the term "context-processor" a few days ago, and realized how perfectly that described a major need right now. We've been building computing structures that were great as "content-processsing" engines, but only if context was static. Now, what we need is "context-processing" engines as well, and formal computer-assistance at "keeping things in context" while transferring them from one of us to another through a data-and-context repository in the middle.

That term is in Capturing and Supporting Contexts for Scientific Data Sharing via the Biological Sciences Collaboratory, by George Chin Jr. and Carina S. Lansing at the Pacific Northwest National Laboratory. (CSCW '04, November 6-10, 2004, Chicago Illinois, USA)
(Available in the ACM Digital Library). The research area of Computer-Supported Cooperative Work is increasingly revealing how collaboration depends on understanding shared contexts.

And, the most pivotal problem in biological sciences, evolution, and probably ultimate human life and meaning is the nature and operation of multicellularism, in the larger sense. How is it that the "many" form "one"? Why do they do it? How is this functioning related to the wholistic concept of "health" and "unity"? How does this fit the activity of "getting organized" that preoccupies so much of our days? Why isn't in vivo the same as in vitro, and what should we do about Science to account for that more easily? Where are our studies and observations and analyses wrong because we didn't account for it?

Saturday, October 01, 2005

Fascinating loop-based thingies

Besides the well-known coil of wire that has such a place in scientific history, there are some other loop-based thingies of note. Tornados and hurricanes, that form a loop and then take on a "life of their own", drawing energy out of the thin air, literally, in order to self-organize.

There are two particularly fascinating objects that basically have no moving parts, yet produce an intentionally crafted output - probably something the "intelligent design" people should note in passing.

One is the Vortex Tube, with a nice animation
and the other is the Cavity Magnetron

In the vortex tube - a block of metal with shaped groves and holes and no moving parts, compressed air is injected and separated into hot air, which comes out one end, and cold air that comes out the other. These are commercially sold for industrial cooling and actually work.

The cavity magnetron (key to microwave ovens, radar, etc.) is hard to find a good diagram. It consists of a block of copper with various holes (cavities) cut into it. It has a fixed electric field between a central element and the rest of it, and a fixed magnetic field aligned crosswise to that. Electrons leave the central filament, and interact with each other in such as way as to generate microwaves of a pre-designed frequency. There are no moving parts, no amplifiers, and the electrons only interact with each other and fixed walls.

These are, to me, fascinating. Air interacts with air, separating hot from cold. Electrons interact with electrons, generating desired microwaves. The only "control" exerted on these processes is the fixed shape of the context in which the rest of the events occur.

While on the loop, one has to reference M.C. Escher and strange loops, as described in Godel, Escher, & Bach by Douglas Hofstadter.

An example that neatly demonstrates how bad our own intuition is is Martin Gardner's "non-transitive dice". These are 6-sided dice that have the following unusual numbers on them: die A: (3,3,3,3,3,3) (that's one die with all threes), B:(4,4,4,4,0,0) (four fours and two zeros), C:(5,5,5,1,1,1) (three fives, three ones), and finally a die "D" with (6,6,2,2,2,2) (two sixes and four twos.)

If you pick them in pairs, here's the deal. B beats A, 2/3 of the time.
(if you say the higher number wins.) C beats B 2/3 of the time. D beats C
2/3 of the time. And, A beats D 2/3 of the time, to close the loop.

There is no "best" die. If I let you go first and pick any of the four you like, I can find one of the remaining 3 that will beat the one you just picked 2/3 of the time. Like M.C. Escher painting's staircases, you go up, up, up, and find yourself on the fourth "up" right back where you started, arriving from below.

Science's blind spots

I'm not science-bashing, just science-improving. I'm interested in hearing from others what they think are the main blind-spots of the institution of "Science" as currently practiced.

A few examples might help. Pulsars, cosmic objects somewhat like giant strobe lights, are the third-brightest objects in the radio-frequency-sky, right after the sun and the center of our own galaxy. (Hear a pulsar here!) However, they were not detected for many years after adequate radio telescopes were built and sky-surveys conducted, because everyone "knew" that all the high-frequency spikes were just "noise", so they were all filtered out, looking for the "real" signal. Pulsars, like strobe lights, have a very low AVERAGE brightness, being "off" most of the time, so they were being filtered out. Only when a brash female grad student decided one day to remove the filter were they suddenly seen again.

Science in the USA today probably has many blind spots, but especially anything that takes more than 8 years to collect data before a preliminary report can be produced would be close to invisible, because no one would get funding to investigate it.

My own thought is that almost anything that is dominated by feedback loops will be missed or ignored, becuase almost all our statistical penetration software is designed around linear causal models, of the type R. A. Fischer developed in Statistical Methods for Research Workers (1925), primarily for different fertilizer treatments for populations (fields) of plants. All by itself, this makes most interesting systems ineligible including the economy (do prices drive wages or do wages drive prices?), evolution ("do chickens preceed eggs or vice versa?), most human and political relationships, love, personal and social opinion formation, etc.

This is true in spades if the feedback is very low order (under 0.1 percent per loop), and there is high noise. So, for example, how long would it take Science, in a thought experiment, studying a cubic foot of air, to come up with the idea that a tornado might be the result of lots of air interacting with itself in a feedback loop? In fact, while vortices are fascinating, they are seldom studied in basic science class because "the math is too hard." (to quote an earlier post - "bad bolt!" )

Also, from general human behavior, anything that causes a lot of pain and frustration tends to become rapidly invisible. This would include intractable poverty, lower-back-pain, etc.

I learned from a visit once to a get-toghether at Abbott's Magic in Wisconsin that there is a very strong "audience effect." Even if one person in the audience sees you do some slight of hand, if everyone around them didn't see it and acts indifferent, the one person will actually forget that they ever saw it. It's erased, post-hoc.

That effect is much stronger if someone is spending billions of dollars pushing the position that the effect doesn't exist or matter. An example of this is the "placebo effect", which is just about the most fascinating thing on the planet, except for the fact that no one sees how to make a buck off it, and it threatens the interests of the pharmaceutical companies, so we hear a great deal of the message ("Feel bad? Ingest our molecule!") and very little of the opposite view.

In fact, there's a huge amount in the human visual stream that's pre-processed away, especially things that are not expected, not wanted, painful, or stereotyped into such a category so strongly that they evaporate - the way a ninja can become as invisible as the waiter who must have come and refilled your water glass, but you can't recall the event occuring at all.

Dorothy Nelkin remembrance

I was going to contact Professor Dorothy Nelkin yesterday to discuss the fact that I'd finally gotten around to getting this blog going on this topic, and was saddened to discover that she had passed away in 2003. (NYU online) I've been way too busy to notice.

I took her grad seminar at Cornell in "The Sociology of Science" a few decades ago, and, coming from an engineering and science background, it was a transformative event for me - maybe the most life-changing course I've ever taken.

Well, I'll dedicate this site to her then, and see if I can help carry on that line of work. Probably I should go read the rest of her books!

Friday, September 30, 2005

Public Health as prototype of Science201

These ideas are shared by others. A great example is the textbook Health program Planning - An Educational and Ecological Approach (4th edition), by Lawrence Green and Marshall Kreuter - McGraw Hill, (c) 2005, a textbook used at Johns Hopkins Bloomberg School of Public Health.

On page 3, the authors quote Rene Dubos, in his book Mirage of health: Utopias, Progess, and Biological Change: "Modern man believes that he has achieved almost complete mastery over the natural forces which molded his evolution in the past and that he can now control his own biological destiny. But this may be an illusion. Like all other things, he is part of an immensely complex ecological system and is bound to all its components by innumerable links."

The authors then comment: "Dubos' comment rings true for those grappling with the complex health problems that dominate the contemporary landscape. Ecological approaches, however, have proven difficult to evaluate because the units of analysis do not lend themselves to the random assignment, experimental control, and manipulation characteristic of preferred scientific approaches to establishing causation. Although linear, isolatable, cause-effect model of scientific problem solving remains as the point of departure for the training of health professionals, practitioners find that the ecological perspectives insinuate themselves into their consciousness; .. They cannot ignore the contextual reality that health status is unquestionably influenced by an immensely complex ecological system. ... By definition ecological sub-systems do not operate in isolation from one another."

So, it's not really that we're using the tool wrong, but that it's the wrong tool.

Using science101 to tackle such problems is like trying to use a screwdriver to remove a bolt - one is likely to only end up frustrated and injured. The response to date by scientists has been "stupid bolt!" when the better response should be "stupid screwdriver!"

Please note the distinction - I am not recommending that the toolbox of science be thrown out, only that it be respected for its strenghs and extended to also include a nice set of ratchet driver wrenches as well. We need the "science201" version of the toolkit, that makes us all gasp and go "Wow, when did that come out?? It's great!" . That's where this blog is heading - for those who want to help with the journey, welcome aboard!

The scientific method

An overview in the wikipedia of the scientific method describes 4 basic steps:

Wikipedia continues: "The above includes observation in steps one and four. Each step is subject to peer review for possible mistakes. These activities do not describe all that scientists do (see below) but apply mostly to experimental sciences (e.g., physics, chemistry). The steps above are often taught in education1."

Note the caveat about experimental sciences. The method above was designed and tuned to work well for studying a certain class of things - namely, those that can be separated from their context, uprooted, brought into the lab for study, and for which experiments can be designed that can be repeated, both in this lab and, after publication, in other people's labs as well to see if they can be reproduced. It works as well for things that seem to have no necessary context, such as chemistry.

The subjects of study for which this approach works well are called, fascinatingly "the hard sciences", possibly because they're so easy to study with such tools. (Like using the metric system, what's perceived as hard by outsiders is really the easy way to do things.) For "hard sciences", this works really well, and brings us electricity and refrigerators and TV.

But, when you get to looking at "life", or sociology or psychology or the economy or government or religion, this easy approach bogs down. Things are not easily separated from their context, or, like dead deep-sea fish, can be separted but lose a lot in the process. Experiments are not easily repeatable. These are known as "soft sciences", but could almost be known as failures of science.

The accepted mantra in science is that, if classical science (science101) doesn't work well, what we need is more training, more of it, more mathematics, better people, obviously the people are doing something wrong, using science101 wrong.

It's our hypothesis instead that science101 is itself the problem here, and we need science201 that, in the limit of easy problems, reduces to science101.

Thursday, September 29, 2005

What is this blog about?

This is my first blog. I'm setting it up in response to the on-going debate between religion and science, brought home this week in the Intelligent Design lawsuit in Dover, Pennsylvania, USA.
(Pew Forum review of the case)

My thesis is that, ironically, the institution of "Science" has itself failed to evolve sufficiently rapidly to meet social needs. Additionally, in the middle of a heated confrontation with "Religion", some would say "Now is not the time to discuss that -- it only gives comfort to the enemy."

I disagree - now is exactly the time to discuss it. Scientists have no idea how close they are to being simply thrown out, to their utter amazement. The flaws of creationists and intelligent designers loom huge, but the flaws in their own system are minimized to the vanishing point.

It is not my point to destroy Science - it's my goal to push Science, like any other system, to become reflexive, to ask what features 'version 2" should include, and how to transition the legacy users from version 1 to version 2. It's my goal to hold Science up to its own standards, identify some very real gaps, and discuss how those can be addressed to preserve the best features and values of science, while adding flexibility to deal more graciously with the types of open, irretrievably context-embedded problems that plague our country and planet.

There has been way too much focus down into the microscope, as if the solution to pressing world problems can be found in DNA, or subatomic theory. It's time to figure out how to get similarly strong traction on the problems that are still there, untouched by science, outside the window.