People only see what they are prepared to see
-- Ralph Waldo Emerson

“If I had an hour to solve a problem I'd spend 55 minutes thinking about the problem and 5 minutes thinking about solutions.” -- Albert Einstein

“Student: Dr. Einstein, Aren't these the same questions as last year's [physics] final exam? Dr. Einstein: Yes; But this year the answers are different.”

Have you ever noticed how when you are prepared to buy a car, suddenly, there are car commercials everywhere? I’ve noticed the same phenomena when I ask a question in science—now that I am attuned to a particular topic, I see articles and discussions everywhere. It may be that I’m becoming aware of a topic just as the rest of the scientific community is also starting to wrestle with a subject, perhaps because of a recently published experiment that shifts the paradigm and forces us to consider new possibilities. The danger in this, I guess, is the trap that one of my colleagues describes as “group think.” My colleague believes that conferences are NOT good for innovative thinking because the conference group moves toward consensus on a topic as the talks progress. The individuals in the group reach closure on a particular topic rather than keeping the questions open.
The Gestalt Theory of Closure is about how we fill in incomplete information based on the common templates we carry in our minds. The human mind wants—maybe needs—to complete open questions. In Joseph P. Hallinan’s book, “Why We Make Mistakes”, he refers to framework errors, where based on previous information, experiences, or backgrounds we assume a framework for making the decision when the particular situation is not analogous. I see the framework error all the time on the program I like to watch with my kids called “Mystery Diagnosis.” Almost all of the missed diagnoses result from physicians assuming the symptoms they are seeing are familiar, and if the patient does not improve, then the doctor’s answer is often “It’s in your head.” It makes me wonder if the computer Watson would NOT make these misdiagnoses because Watson does not need to make the framework assumptions but can sift through all possibilities.
The topics of questions, and closure, are even more important to me because they offer the only solution to the problem that I have wrestled with for a good portion of my life, which is “How can I get this person to see what I’m seeing?” The Zen masters have it right: The best way to achieve a new perspective--to achieve enlightenment—is to ponder a question that does not have an easy answer --that the framework required to answer the question lies outside the framework of a solution.
In science, the biggest discoveries can arise from pondering paradoxes. The answer to a paradox is often found by a profound shift of paradigm. In biology, I can think on many examples, from a re-casting of the Central Dogma to the acceptance of prions. Questions? Please.
Next Blog: Question Authority

Truth and Beauty

Beauty is truth, truth beauty, that is all
Ye know on earth, and all ye need to know.
John Keats's "Ode on a Grecian Urn"
Beauty itself is but the sensible image of the Infinite.
Francis Bacon
The search for differences or fundamental contrasts between the phenomena of organic and inorganic, of animate and inanimate things, has occupied many men’s minds, while the search for community of principles or essential similitudes has been pursued by few; and the contrasts are apt to loom too large, great though they may be.
D’arcy Thompson, from On Growth and Form

Scientists throughout the ages have wrestled with the concept of beauty. In physics and mathematics an ugly theorem or proof is looked upon with skepticism. I ran across a book review of Ian Stewart’s “Why Beauty is Truth: A History of Symmetry” written by Martin Gardener (Scientific American, April 2007). Stewart concludes that 1) "In physics, beauty does not automatically ensure truth, but it helps.”; and 2) “ In mathematics beauty must be true--because anything false is ugly." Gardener’s review is a good discussion and gives examples of beautiful proofs that are not true, and some ugly solutions that are.
The concept of symmetry as beauty in physics or mathematics requires a group-- a relationship of the elements to each other so that as the group is manipulated or rotated the relationship is maintained. Symmetry arises out of the connections and relationships of the group. Symmetry is beautiful, not because symmetry in itself is beautiful, but because it allows us to make sense—to see—the connections of the elements. Therefore, it is NOT symmetry that is beautiful, but that we see the connections or the underlying relationships that give rise to the symmetry.
In biology, the symmetry we see is a physical manifestation of the physical principles that give rise to the form. One needs only to look at the spirals of a cone shell, or the intricate patterns in an animal’s coat to see Beauty. D’arcy Thompson’s mathematical treatments of these forms give us a deeper appreciation, and a deeper sense of wonder-- as Bacon describes-“making sense of the Infinite.” Mandelbrot’s fractal, a repetition of a geometric pattern at different scales, really just extends the work started by Thomson. The insight from fractal’s that many of the forms (all?) we see in nature can be replicated by a repeated pattern at different scales really doesn’t inform much of the underlying principles.
Thompson’s reductionist approach “essential similitudes” that all biology may ultimately be explained by mathematics and physics, is something that Thompson acknowledges may not be adequate to explain the complexity of systems seen in biology. How can physics explain self-awareness? Stuart A. Kauffman, in his excellent book “Re-inventing the Sacred: A New View of Science, Reason, and Religion” , takes the reductionist approach head-on and offers an alternative view that is worth reading.
We see symmetry in biology, and this physical manifestation of the underlying principles is beautiful in that we are able to connect disparate organisms, and even see the similar patterns in inanimate objects, because the same principles are working to generate these patterns. But there is a deeper Beauty. My previous Blog talked about the awe that I felt at seeing the evolutionary connections between micro-organisms. There was no symmetry in the recognition of the relationship of convergent and divergent nucleotides. There is great Beauty in recognizing the connections—making sense of the Infinite. And there is great Truth in this Beauty.

NEXT BLOG: What Has Been Seen Cannot Be Unseen.

Awesome Biology

Awesome Biology

“The most beautiful thing we can experience is the mysterious. It is the source of all true art and science. He to whom this emotion is a stranger, who can no longer pause to wonder and stand rapt in awe, is as good as dead: his eyes are closed.”
Albert Einstein
In my last blog, I wrote about the sense of awe and wonder that scientist’s feel in the course of their work, and how over time we sometimes lose or forget this motivation that caused many of us to choose a science career. I think it’s easier for cosmologists or astrophysicists, than for biologists, to be in touch with these emotions as they go about their work. How could you gaze upon the vastness and complexity of the Universe and not feel a sense of awe and wonder?
But biologists have their own universe that is no less awe inspiring. I marvel at the beauty and complexity of even the simplest forms of life, and more important, the connections and interplay between organisms. One of the great stories of modern biology—a story that is currently being written-- is the interaction of the biome with our human bodies. There is accumulating evidence that our human immune systems are heavily influenced by the commensal bacteria and parasites living in our gut. There is at least one reported instance of parasitic pig worms, Trichuris suis, ameliorating the effects of autism1. There is a good review on a possible link between gut bacteria and cancer that concludes “Gut microbes are increasingly being linked to medical conditions including obesity, inflammatory bowel disease, diabetes, and cancer.” 2
What is even more remarkable is that our cells may be influenced by miRNA’s carried in exosomes from fetuses, from cell–to-cell, and even from the plants we eat.3
How is it than when we look at the boundaries of life on a fine scale that the boundaries become blurred and indistinct? This is not dissimilar to what is seen in the wacky world of quantum physics where connectivity, action-at-a-distance, and the ability of matter and energy to pop in and out of existence blur the boundaries of even the most fundamental relationships in the physical world.
I once had a physics professor ask me, as a biology major, to define life. I gave what I thought was a pretty good answer, until he began to ask questions like “Is a virus alive?” He concluded by saying that if I could not define clearly what I was studying, then I was wasting my time. Perhaps one of the goals of the modern biologist is to create that definition of life.
Next Blog: Truth and Beauty
1. http://the-scientist.com/2011/02/01/opening-a-can-of-worms/
2. http://the-scientist.com/2011/08/01/sharing-the-bounty/
3. Zhang, L., et al., Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res. 2011