Biology is drowning in data and complexity

In the April 2010 edition of Nature (available only to subscribers online), you can read a counter-intuitive story of illustrating that more information is sometimes add confusion, rather than making things simpler. Maybe another way of putting it is that the path to understanding can often take one through phases of disorientation resulting from new influx of accurate data. This particular story, by Erika Check Hayden, titled "Life Is Complicated," considers what has happened in the field of biology subsequent to the Human Genome Project. Prior to the Project, many biologists guessed that the human genome contained about 100,000 genes that coded for proteins. At the conclusion of the project, however, we found out that only about 21,000 human genes code for proteins. One might think that this would simplify the field of biology, especially since biologists now know what many of these genes are. Many people thought that we were going to have for ourselves a clearly understandable "blueprint," of the human species. The opposite is happening, however: "It opened the door to a vast labyrinth of new questions." What kinds of questions? This article really surprised me with the vast scope of new territory opened up by the Human Genome Project. It can be summed up by Hayden's quote from biochemist Jennifer Doudna: "The more we know, the more we realize there is to know." Hayden explains that sequencing the genome undermined "the primacy of genes by unveiling a whole new classes of elements--sequences that make RNA or have a regulatory role without coding for proteins." It turns out that "much non-coding DNA has a regulatory role "that we are just beginning to understand." To illustrate how complex things have gotten, Hayden discusses what we've now learned about a single protein, "p53," which for many years was simply known as a tumor suppressor protein. Consider what we know now: In 1990, several labs found that p53 binds strictly to DNA to control transcription, supporting the traditional Jacob-Monod model of gene regulation. But as researchers broadened their understanding of gene regulation, they found more facets to p53 . . . [R]esearchers now know that p53 binds to thousands of sites in DNA, and some of the sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein-protein interactions can be tuned by the addition of chemical modifiers such as phosphates and methyl groups to create through a process known as alternative splicing. P53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems willfully ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions. Hayden reminds us that the p53 story is one of many similar stories in post genomic-era biology. She explains that we now know that many of the signaling pathways that we thought we were close to understanding are not simple and linear but organized in vast complex networks that sometimes appear fractal. She quotes James Collins, a bio-engineer: "Kevin made the mistake of equating the gathering of information with a corresponding increase in insight and understanding." Here's another counter-intuitive result of this new dilution of information: many of our models have gotten too complex to be useful. In many cases the models themselves quickly become so complex that they are unlikely to reveal insights about the system, degenerating instead into mazes of interactions that are simply exercises in cataloging. The genome project has made biologists into kids in a big candy store: a candy store with unending aisles and endlessly deep bins of dazzling, disorienting candy, much of which is currently out of our reach. Such is the horizon of new knowledge, equal parts frustrating and tantalizing.

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Complexity as a curtain for fraud

“Whoever knows he is deep, strives for clarity; whoever would like to appear deep to the crowd, strives for obscurity. For the crowd considers anything deep if only it cannot see to the bottom: the crowd is so timid and afraid of going into the water.”

Friedrich Wilhelm Nietzsche, The Gay Science (1882).

“. . . using financial complexity allegedly to deceive and then using so-called independent experts to validate the deception (lawyers, accountants, credit rating agencies, "portfolio selection agents," etc etc ) . . .”

"Now we know the truth. The financial meltdown wasn't a mistake – it was a con"

Why are many human systems complex? If we’ve learned anything over the past few years, it’s that there are two reasons—there are two kinds of complexity. Sometimes, complexity is required to get the job done. I think of this as “parsimonious complexity.” For instance, the Mars Rovers are extremely complex robots, but every part of these magnificent robots has a specific function that furthers a clearly and publicly defined mission. There are also instances where complexity is purposely injected into a system. I think of these as instances of “gratuitous complexity.” It’s important to keep in mind that all forms of complexity serve as entry barriers to activities, due to the limited attentional capabilities of humans. Very few of us have the stamina or intellect to thoroughly understand all of the artificial systems people create; many of us don't have the stamina to thoroughly understand even simple systems. When an activity is more complex, it is more difficult to understand and more daunting to those wishing to participate. Activities that are more complex are thus accessible to fewer people. For instance, chess is more complex than checkers, in that the state space of possible moves is larger in chess than in checkers. Checkers is easy to learn and play. But many checkers players don’t graduate to chess due to the increased complexity. Some systems are so incredibly complex that only the chosen few are able to participate.

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The body is not a machine

Pyschiatrist Randolf Nesse is a gifted writer who I have followed for many years. I first learned of Nesse's work when I read Why We Get Sick: The New Science of Darwinian Medicine. Nesse is one of the many respondents to this year's annual question by Edge.org: "What will change everything?" Nesse's answer: RECOGNIZING THAT THE BODY IS NOT A MACHINE As we improve our knowledge of bodies, they don't fit very well within our venerable metaphor of the body as a "machine." One of his points is that we can describe machines, whereas a satisfying description of bodies seems so elusive. The complexity of the body is, indeed, humbling:

We have yet to acknowledge that some evolved systems may be indescribably complex. Indescribable complexity implies nothing supernatural. Bodies and their origins are purely physical. It also has nothing to do with so-called irreducible complexity, that last bastion of creationists desperate to avoid the reality of unintelligent design. Indescribable complexity does, however, confront us with the inadequacy of models built to suit our human preferences for discrete categories, specific functions, and one directional causal arrows. Worse than merely inadequate, attempts to describe the body as a machine foster inaccurate oversimplifications. Some bodily systems cannot be described in terms simple enough to be satisfying; others may not be described adequately even by the most complex models we can imagine.

[Related DI post: The Brain is not a Computer]

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The language of science is always so amazingly precise . . . except when it isn’t

The language of science is always so amazingly precise . . . except when it isn't. Consider, for example, the word "life." Scientists have long struggled to determine exactly what qualifies as "life." For instance, are viruses “alive?” In the October 23, 2008 edition of Nature (available only to subscribers online), an article titled "Disputed Definitions" considers other often-used disputed terms. The article is divided into sections written by specialists from the relevant disciplines. The subtitle of the article is "Nature goes in search of the terms that get scientists most worked up." Consider how often you encounter the following disputed terms. Consider "paradigm shift," made popular by Thomas Kuhn in his often-cited 1962 book, The Structure of Scientific Revolutions. Kuhn argued against the then-popular view that science marched incrementally toward the truth. Sometimes, "normal science" doesn't explain all of the phenomenon, straining a prevailing scientific theory. If the strain of accommodating evidence is great enough "eventually some new science comes along and overturns the previous consensus. Voila, a ‘paradigm shift.’" The often-used term "paradigm shift" is used in at least two ways, however. In its broad sense it encompasses the "entire constellation of beliefs, values, techniques and so on shared by the members of a given community." In the narrow sense, it refers to "concrete puzzle-solutions." Another often-debated (and currently fashionable) term is "epigenetic."

Continue ReadingThe language of science is always so amazingly precise . . . except when it isn’t

To deal with “arrogant” scientists we need to move beyond reductionism and break the “Galilean Spell.”

I don't want no god on my lawn Just a flower I can help along 'Cause the soul of no body knows how a flower grows... Oh how a flower grows . . .

“Longer Boats,” by Cat Stevens (now known as Yusuf Islam).

Why are so many religious people uncomfortable with so many scientists? I can think of several reasons. According to many Believers, scientists are arrogant know-it-alls. Believers see scientists as emotionally sterile lab-dwellers who flaunt their white coats and their fancy lab equipment. Scientists exacerbate the situation by speaking and writing using esoteric language that makes science-phobes feel ignorant. By using such difficult concepts and language, scientists have raised the bar, which excludes many folks from joining scientific discussions. It’s not like the “good old days,” where people were generally informed enough to join many conversations regarding science (or social science). Things are different now.

Continue ReadingTo deal with “arrogant” scientists we need to move beyond reductionism and break the “Galilean Spell.”