Extra sensory perplexion?

Science and belief systems
Science is interested in understanding the world as it really is....but, surprisingly, only up to a point! You have to play by the inferential rules, like how to design experiments, evaluate data, and so on.  But you also usually have to stay within bounds.  That means, you have to stay within the limits of what is considered legitimacy at any given time.  And if you don't, you'll get a critique like this one,

“It’s craziness, pure craziness. I can’t believe a major journal is allowing this work in.  I think it’s just an embarrassment for the entire field.”

We're not talking about cheating here.  We're talking culture, and that means within the tribally accepted belief system.  Currently, the science tribe doesn't accept supernatural explanations, so we don't accept hypotheses based on divine intervention in experiments.  Thus most scientists say that religion is outside the realm of science, and at present so is consciousness.  Subjective experience is also not viewed as objective science!

Of course, what is 'supernatural' is what we don't know how to understand.  But if  we discover some new factor or force--as happened with the use of telescopes and microscopes, or electromagnetism, the new things are melded in with the known, and hence natural world.  No longer supernatural.

At any given time, people tend to believe that all fundamental forces of that sort are known, even if we  don't know the details of how they work in various cases (such as predicting traits from genes?  future climate? electron orbits?).   But if current theory is correct, isn't the world made entirely by molecules and energy and don't they follow universal rules that intertwine them with each other (like gravity, filling space and time)?  If that's the case, then nothing is truly independent of anything else, and things we observe could be causally connected in ways we didn't expect.

Heresy?
A paper soon to be published in a highly respected psychology journal, after standard peer review, that claims that something of this order occurs to explain extra sensory perception (ESP, or psi as it's called these days).  For example, physics routinely invokes 'entanglement' by which particles in different places can affect each other in ways such that one particle 'knows' the status of the other.  So why can't information be transmitted and hence received and interpreted elsewhere, such as by one person perceiving such things without any standard physical evidence of information transfer?

This paper, described today in the NYTimes, and freely accessible online -- and the subject of discussion for some weeks already in the blogosphere -- is a report of 9 different trials of psi.  A thousand Cornell undergrads were asked to perform different tasks -- guessing which screen would show an erotic picture before the computer had randomly selected it, for example -- and the results interpreted by the investigator as showing that 'precognition' exists.

The rationale for this decade of experimentation seems to be that what we know about physics makes it possible

The development in quantum mechanics that has created the most excitement and discussion among physicists, philosophers, and psi researchers is the empirical confirmation of Bell’s theorem [see the paper for citations], which implies that any realist model of physical reality that is compatible with quantum mechanics must be nonlocal: It must allow for the possibility that particles that have once interacted can become entangled so that even when they are later separated by arbitrarily large distances, an observation made on one of the particles will simultaneously affect what will be observed on its entangled partners in ways that are incompatible with any physically permissible causal mechanism (such as a signal transmitted between them).  

and evolutionary theory makes it plausible.

If psi exists, then it is not unreasonable to suppose that it might have been acquired through evolution by conferring survival and reproductive advantage on the species. For example, the ability to anticipate and thereby to avoid danger confers an obvious evolutionary advantage that would be greatly enhanced by the ability to anticipate danger precognitively.

Well, of course, if this were so it would also not be unreasonable to suppose that most species in addition to humans would have this ability, and that a trait with the huge selective advantage that psi would surely have would not be as difficult to detect -- or as intermittently useful and reliable -- as it's proving to be.

And, the paper is getting just the kind of broadside critique any heretical challenge to accepted wisdom will get.  The quote above, for example, about these results being just crazy is taken from the story in the Times, is from a Ray Hyman, emeritus professor of psychology at the University of Oregon and described as a 'longtime critic of ESP research'.  Of course, maybe he's a reflex, superannuated critic.  Because there are also those who are applauding the results -- finally mainstream science shows psi exists.  But, as is generally the case, reactions to this paper tend to be based on people's preconceived notions about ESP rather than the science.  Reactions as predictable as, well, as psi!

Or just bad science?
A rebuttal of the methodology is already available online, presenting a number of explanations for the apparent positive results of this work, including that it's a confusion of exploratory and confirmatory data (that is, the investigator refines his testing based on previous findings and doesn't correct for this), and that a Bayesian analysis that evaluates the plausibility of new results based on what has been found or assumed before, shows that none of the results are significant after all.

Indeed, the idea that psi even exists, much less what it is, is has been thoroughly controversial, or rather, rather thoroughly dismissed by scientists (in our current tribe).  Mostly, it's been for good reason.  Claims of the phenomenon have largely been unsupported by adequate evidence.  Frauds and trickster showmen have been deeply implicated in ESP shows, seances, and the like.  Tarot card readers are clever at making educated guesses and safe predictions.  So why should we believe any such claims?  Is invoking 'entanglement' to explain psi any different than other after-the-fact true-sounding WAGs (wild ass guesses)?  Or is it the right kind of explanation, but simply far ahead of what we actually know about what we call 'entanglement'?

History shows that some such things, like alchemy and phrenology, have presaged what became legitimate science, even if their initial premises were guesses based on poorly observed aspects of Nature.  Many accepted ideas, like earth-centered astronomy or the four humours theory of medicine, have clung on for centuries even though clearly wrong (we now know).  If someone actually shows that psi is 'real' that will mean showing the nature of the mechanism or that it can be systematically repeated, or something of that kind.  Then, it will become part of the normally accepted world.  The skeptics will be laughed off as having been conservative Luddites impeding progress.

Or both?
On the other hand, hucksters and legitimate scientists alike have offered countless explanations and theories that went absolutely nowhere.  And the claims of studies of psi find only slight statistical supporting evidence (making the big assumption of no kinds of bias or misapplication of significance tests, such as how truly multiply blinded participants and observer were, whether multiple testing was corrected for, and what 'significance' level--p value--should be used).  Why should the evidence be so weak?   In this context, the author's totally Kiplingesque 'evolutionary' Just-So explanation supports  suspicion more than it supports the hypothesis, because it's so egregiously trying too hard, far too hard, for something that involves a participant and a computer (of course some day we may find a million year old computer fossil).  If humans evolved for anything, perhaps it was to be gullible!

Nonetheless, pseudo psi-ence aside, there remains the legitimately serious question of how we could ever tell psi from sound, and how can we decide the limits of acceptable claims, of what constitutes scientific understand of the real world?  This has been an issue, often unstated, throughout the history of science.  In a way, it's what keeps science so conventional and incremental in daily practice, but in the long run what makes science interesting.

Old dirt, new dirt, old water, new water and Laws of Nature

Thomas Malthus

There is an ongoing battle between the Malthusians and their opponents about whether we can sustain our population agriculturally or whether we inevitably outgrow our means of sustenance.  David Montgomery's book Dirt, about soil erosion and the history of human civilizations, to which we referred in yesterday's post, has some pithy things to think about.

This book says that way before Malthus (who you can friend here), even the classic Romans "exuded confidence that human ingenuity would solve any problems.  Cicero crisply summarized the goal of Roman agriculture as to create 'a second world within the world of nature.' " That's exactly the way technophiles, representatives of science, industry, capitalism, and the status quo argue today:  not to worry, technology will solve all problems!

But like every aspect of complexity in Nature, how right would Malthus have to be to be basically right, and if he's 'mainly right' or 'right in the long run', is his principle a basic principle of Nature?  What kind of evidence would one need to determine if he was 'right' or not? Let's think about this briefly.

There are about 7 billion people alive today, uncountably more than in Malthus' time, much less the time of the ancient civilizations whose dirty habits may have led to their collapse.  Agricultural yield may have petered out here and there due to erosion, salt deposits, and the like.  But worldwide there's far more crop acreage than back then and far more yield per acre.  Instead of dealing always with new dirt from recent growth and new water from rain, we're now living on old dirt (vegetable matter called 'oil') and old water (pumped up from wells).  But we're doing fine, so Malthus must have been not slightly but massively wrong!

Dust bowl, Keota, Colorado
1939

Yes, there are patches of disaster here and there--in northern Africa for example, and our dust bowl last century.  And more people, even if a small percentage of the human species, are starving than ever before, according to statistics we've seen.  But, so? There will always be some areas where things screw up or rapid climate change outpaces people's ability to adapt.  In earlier days, local drought may have meant death, but today there can be airdropped relief packages.  So, yes, some people do outgrow their  land but no, it's not that our whole species is overpopulating.  Technology has, with some bumps in the road, served us well.  Malthus was wrong!

Wait a doggone dirty minute!  If many aspects of science are right, climate change, erosion, and our dependency on fossil-fuel for fertilizer to replace lost topsoil, and on big machines to grow and transport food, will lead us predictably into horrendous Malthusian collapse!  That's why so many are concerned with humans' degradation of the earth, clearing of tropical rainforest (whose soil, thin already, will quickly disappear), and why so many are saying to Eat Local.  And, of course, many are saying as they have been for a while, that there are just too many humans.

Malthus himself was aware of technical advances, but his view was that if technology improved yield, population would grow to catch up and eventually to pass the new capacity.  Montgomery's book basically argues that latter point, and that most civilizations have fallen into decay because of their dirty habits.

Whatever one might say about Malthus, his 'law' was certainly not unexceptionable like the law of gravity, or the ideal gas law, or Ohm's law about electricity.  But then what was it?  Is it a law of Nature at all?  Do such laws have exceptions?  Is it a kind-of-maybe generalization about Nature, beneath which there might be some law(s) acting that we don't know about?

Now, Darwinian evolution that we all love and invoke so much and so often so literally, was largely premised on the Malthusian principle that populations always outgrow their resources.  So, if Malthusian population pressure isn't a Law of Nature, where does that leave natural selection, the cornerstone of Darwinian worldviews and the force that drove it in his mind---and that is so often so blithely invoked?  The reason there was natural selection and only the best in life made it through life was that there was competition for limited resources.  If that weren't so, why, the stumblebums of the living world could do just fine.

Where complexity reins, and observations we make are incomplete on the scale of the events we're trying to understand, what are the criteria we should maintain for understanding, for developing theory, without which science would not be science?

These issues are not just down and dirty, or digging the gossipy society dirt. They also apply to other sciences in which slow non-steady change has to be interpreted if we are to understand both the nature of Nature and the future we and our descendants will face.

Yes or no, take your pick: the implications of uncertainty

From Flickr via
Wikimedia Commons

It's holiday book-reading time, the best part of a holiday.  One isn't usually given a dirty book on these occasions, but a very interesting book under my tree this year was Dirt, by geologist David Montgomery.  This discusses a topic vital to survival: the soil.  The subtitle gives away the author's point:  "The Erosion of Civilization."

Dirt is about the repeated way that agriculture and other uses of the land by large human populations, such as cover much of the earth these days, erodes or degrades soil much faster than it can be replaced by natural processes.  Montgomery points out that soil buildup is slow, and erosion, too, may be so slow that we hardly notice it. In our current scientific, data-laden age, with huge populations and rapid growth, we seem more able to notice the changes than our ancestors may have been able to do.

Although we have only sparse data on relative rates of soil production vs soil erosion, the data do indicate that loss is greater than gain.  But in a pithy sentence the author notes that

This leaves the issue in a position not unlike global warming--while academics argue over the details, vested interests stake out positions to defend behind smokescreens of uncertainty.

And it's not just global warming.  We see the very same posturing in regard to biomedical genomics in which convenient self-serving positions are taken in regard to the effectiveness of genomic predictions of health and disease susceptibility.  Some argue that genetic causation is complex and that there are better ways to spend health resources (both in terms of research and application), while others promise near immortality from 'personalized genomic medicine'.

MT readers know where we stand on that particular issue.  But a more important and deeper point is the pervasiveness of the same kind of issues in our society.  We purport to be a fact-driven 'evidence based' society, that relies on science for important decisions.  But from foreign policy, economics, and many other fields, to genetics we face masses of data on phenomena that clearly involve many different contributing factors.  Often, we don't even know what all the factors are, much less being able to measure them accurately.

Normal science, the scientific method we pretend to follow so rigorously, is designed to answer very focused questions.  We do this by isolating one variable at a time under controlled conditions, so we can determine what that variable does.  But with complex causation this is difficult to do, if not impossible in practice, and single causes may not have much explanatory power even if we could estimate it accurately.  Often we deal with processes too slow to be accurately predicted by extrapolation from what we can confidently estimate from science.  We know that's true about evolution, but it applies also to soil abundance and climate change among others.

As 2011 starts out, dealing with such complexities is perhaps the most important general challenge to science today.  In many areas, it doesn't much matter how a question is approached or answered, and much of the perhaps properly ridiculed attention of academic research is rooted in trivia taken far too seriously (when professors should be teaching instead).  Who cares whether a hangnail led Shakespeare to write Othello, or how an ostrich leg-bone evolved?  Only a few professors struggling for dominance in their journals!

But a lot of major questions that science is being asked to answer do have major implications for our society, lifestyles, and behavior.  When that is the case, since those of us who are haves like to have more, more, more (or, at least, not to have to change from comfortable ways of living), it is only natural to see vested-interest posturing.  Each side thinks it's right, and resents the benighted opposition, and each side will tend to slant the facts or color their interpretations in their own self-interest.  Literature going back to the beginning of literature shows the natural resistance to change in human society, especially among the established generation at any given time.

There is no easy way out of this when facts are incomplete and phenomena too slow or complex, so that we need to extrapolate beyond direct observation.  Sometimes, the process is really slow in this sense.  In other times, things can change very rapidly, but we just don't understand them enough (or care to).  Major economic collapses or political dominoes leading to military disasters are clear examples.

Our lives, or those of our children, depend on acting on knowledge.  The history of dirt shows how entire civilizations can go under if they fail to act soon or definitively enough.  In the past, perhaps they had no knowledge or choice.  But we do have at least the archeological record, and some choice.  But we rarely seem to act before tragedy strikes.  We are each of us too rooted in the vested interests of our own lives to be as free to act as might be best, and uncertainty provides a handy excuse for inaction.

Can science adapt to the new landscape of complexity?

Mendel's thinking, current thinking, superficial objections and metaphors

Our friend and ex-student, Jen Wagner who is both a knowledgeable geneticist and a practicing lawyer interested in human rights law as it applies to genetics, sent us a link to a blog post that is worth thinking about....carefully. The topic is the often confused nature of the 'gene' or inheritance.  Many people, including many professionals, hold and express strongly causally determining views of what a gene is: they refer to genes 'for' some trait, or implicitly imply that is what they have in mind.  The blog post argues that we've been influenced too much by Mendel's single-gene work (though he didn't have a specific gene concept), whereas the truth is that traits are affected by many different genes whose variation tinkers with the trait's details in each individual.  The blog argues against the widespread metaphoric treatment of genomes as the computer-like information 'program for' the organism, fitting in well with our electronic information age.

We are indeed prisoners of the kind of thinking Mendel was doing in the mid-1800s.  He was looking for integral (that is, whole-number) effects.  That's what is meant by 'gene for' rhetoric: a given gene causes something, or not, depending on the variant in that gene in an individual.  Mendel designed his experiments with peas very explicitly to deal with such simple situations, and he was looking for integral relationships (for example 3 dominant to 1 recessive offspring from certain matings).  He was trained in part by scientists developing the atomic theory of matter, and ideas such as that every element was a multiple of the carbon atom.  Naturally, he sought (and found) such numbers.  His work was so elegant that others later on, in the early 20th century, used it to build what became the theory of the gene, as a single, discrete causal unit of life.

This didn't seem to gibe with complex or quantitative traits (like stature, mentioned as an example in the blog post), but several investigators, including most notably including our friend RA Fisher in 1918, pointed out that if many 'Mendelian' factors contributed to a trait it could appear quantitative, like how tall you are or your blood pressure, even though each factor was a discrete thing (as Mendel's Elements causing green or yellow, smooth or wrinkled peas were).

We now recognize that genomes are concatenations of many different sorts of causal effects, sometimes overlapping along a chromosome, and with complex combinations and interactions.  In that sense, no one gene is 'for' a given trait.  It's an important point, but there's a caution: it's somewhat wrong to diss this view as if it's naive, and as if today we have a theoretically different view, because we really haven't.

Genetic elements are not just protein codes, but do many things.  But they are discrete, and discretely varying, sequence elements in DNA, and they vary in discrete ways.  That they act in combinations is true, and that can bring about complex traits.  But there is nothing conceptually different about this.  And in evolutionary terms, each genetic element evolves as standard theory would have it: by changing frequency of its varied states in populations.

The authors who point out the faults in our 'gene for' models are making valid points, but if they are arguing that there is something fundamentally wrong, they themselves are being misleading.  To speak of the genome as the program for the organism, in computer metaphors is misleading because there are many differences between computer code and genetic code.  But it is clear that the genome is a source of information on which much of the development and life of organisms rest.

What is new, and needs better professional and scientific understanding, are the implications of causation due to hundreds of contributing elements.  It is not a new theory that is needed, though there are many newly known kinds of interactions and causal relationships.  What is needed is a titering of the idea that single genes are dominant in the production of traits, and that evolution usually works by affecting single key genes.  Instead, genetic action in aggregate is more important than is generally recognized and when that is the case, the individual element's contribution is generally very small.  It's a complicated subject, but this takes the focus of biological causation away from individual genome elements on to the action of aggregate variation.

So, while we do seem to be trapped by a history of Mendelian single-gene thinking, because single-gene thinking was incredibly powerful as a research tool, what we need is not new theory or an abandonment of Mendel's ideas, but a recognition of the implications of basic ideas we have had for nearly a century.

Does the hook hurt? What about the experiment?

Do fish feel pain?  Unequivocally yes, according to Victoria Braithwaite, a fish biologist here at Penn State.  She described how she knows this on The Forum, a radio program on the BBC World Service on 12/18.  It's very odd that this wasn't understood until her work -- a paper that garnered much attention by Braithwaite and co-authors was published in 2003 (but has been selectively forgotten or ignored by many) -- but very nice that she's cleared that up.  Amazingly, people have long labored under the belief that fish are insensate creatures.

The reasoning behind such views is difficult to understand.  Fish certainly avoid danger, but they don't have facial expressions we can read, and they are cold, slimy, primitive creatures (well, relative to us humans, we like to think!).  They reproduce like, well, like fish so with such numbers what's the advantage of pain receptions?  They have primitive brains (relative to ours).  

Or is it more than just the arrogance that goes with the angler's realization that we're in charge?  Not so long ago, lobbying was done among life scientists to write to Congress to oppose legislation that might regulate the kinds of experiments that could be done on fish.  Our noble peers in biology wanted to be left alone, not constrained, after all!  It was even said that pain in lab animals was good for them--yes, it was said!--because it made them resilient to the conditions under which they lived.  We're not enamored of bureaucrats who feel they can meddle in our daily research life, but this wholly self-interested campaign-of-convenience by scientists was gross.

Anyway, the idea of piscal pain experience would be more convincing if they had what we would at least recognize as neural pain receptors.  In fact, pain wiring was long ago worked out in birds and mammals, perhaps, according to Briathwaite, because it's easier to feel empathy with these creatures.  But, even the question of whether fish have the neural wiring that transmits the  stimulus to the brain wasn't known until Briathwaite et al.'s work.

And yes, fish do have them!  (Sorry, anglers and zebrafish torturers!).  Transmitting pain information is done in two stages, by two different types of nerve fibers, the A-delta and C fibers.  A-delta fibers transmit information about damaging or noxious stimuli instantaneously and the second transmits it more slowly.  Fish have both of these nerve types, though in a different ratio from birds and mammals (fish have more of the C type, relative to other vertebrates).

But, says Braithwaite, "finding the fibers themselves doesn't necessarily tell us that the second stage of pain is going on", that when the signal passes up the spinal cord to the brain, the fish becomes aware that it has been damaged.  To test this, Braithwaite et al. provided fish with a painful stimulus, either vinegar or bee venom, injecting small amounts into the snout of rainbow trout.  They injected saline solution into the snouts of a control group of fish, and found the two groups had very different responses.  The respiration rate of those injected with the pain stimulus quickly accelerated and stayed high, and these fish went off their feed, while the control group responded to being handled and injected with increased respiratory rate and not eating, but their respiration quickly went back down and their feeding behavior returned to normal.  Which Braithwaite et al. interpreted as clear evidence that they feel pain.

But does it matter?  Is it enough to modify their behavior?  That is, do the fish respond to pain?  Fish have a low tolerance for novelty, so the researchers put Lego objects into the tanks, treated them with pain injections, and observed their behavior.  Would they avoid the Legos, as normal? In fact, when treated with pain stimulus, they did approach the novel object, which the researchers interpreted as showing that the fish were distracted from their normal behavior by pain.  But, they were able to reverse this with pain relief.  They gave the fish some morphine and observed that they again avoided the Legos, as normal.  (Are you nauseous yet, given that they knew by now that fish feel pain?)

Braithwaite says that responding to something that is damaging is important evolutionarily, and only vertebrates can have the experience of learning from pain, and learning to avoid it.  But, do fish suffer when they feel pain?  Is that an odd question?  Isn't perceiving pain by definition suffering? Is it more than self-centered for us to couch this in terms that relate to our, human, kind of experience?  Braithwaite explained that they've found an area in the fish brain that's devoted to processing emotional information, as in other vertebrate brains.  It's more rudimentary in fish, but if it's damaged or lesioned, the fish's ability to respond to emotional information is impaired, she said.

And further, do fish have consciousness?  Ascribing consciousness to a non-human animal is a tricky area, Braithwaite said.  She takes her model of consciousness from Gerald Edelmann, who says that consciousness is modular.  She didn't expect to find all the modules we have in fish, but says there is evidence for two of them; 'primary consciousness' and 'phenomenal consciousness'.

Primary consciousness is the ability to create a mental representation of something, and Braithwaite says that fish can do that.   That is, they can do spatial mapping.  Phenomenal consciousness is how we experience and understand the world.  Braithwaite's view is that the fact that fish can learn from experience is evidence that they have phenomenal consciousness, too.  And, the evidence of fish consciousness is, to Braithwaite, both evidence that fish can suffer, and that they are deserving of welfare rights, as are birds and mammals -- equivalent to humans.  Sport fishermen, especially those who enjoy catch and release fishing, need to consider that fish feel pain, as do fish farmers.

This is all well and good, and it's good to see the old conceit that fish don't feel pain put to rest, but we think there are also lessons here about academic hubris that should, but probably won't be learned. The anthropocentric conceit isn't new, but we're supposed to be scientists, to deal with the real world, not the one we wish were out there!  We have bestialized the world except for ourselves.  In the west, at least, this might be a consequence of long-standing (convenient) biblical views that God, in His wisdom and compassion, gave us dominion over the fish of the sea, and over the fowl of the air, and over every living thing that moveth upon the earth (does that include bacteria and hookworms?).

Whatever the source, we want to be able to have our will with these beasts and will not welcome the latest piscine bulletin.  It's bad enough that after having our experimental will with chimps we have to let them live out their natural life (but not monkeys), and we are not supposed to subject lab mice to torture (as we and our IRBs define it, which turns out to be pretty lenient).  But fish?!

Carnival of evolution

Check out this carnival of evolution-related blogs.  A monthly collection -- motley perhaps, but good!

The New Year

With the dawning of a new year, we would just like to take this moment to express our thanks to those who have taken a look, or more, at Mermaid's Tale during the past year.  We try to produce a flow of commentaries on the passing science scene, and on the nature of life as we see it.

But this would not be worth it, and would not work, were it not for the many thoughtful comments that you have left for us and others to see.  The blogosphere is crowded, and we know that you don't have to be here, and you don't have to stay.  We especially thank our regular readers, who know a lot more than we do about a lot of things, and don't let us get too far out of line!  We hope we can continue to provide a thoughtful forum in the coming year, with your help.

And we wish anyone who may alight on this page, by chance or by design, a Happy New Year!