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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Another Musing on Our Evolving Ability to Perceive

I have occasionally ruminated our improved ability to see and understand the universe around us. On this blog, it usually is in terms of comparing the Young Earth view with what we've learned in the last few hundred years. Posts such as The Universe is not Specified to Human Scale and My limited vision make the point. But I've started another blog that focuses less on politics and culture, yet found that one of my first posts again addresses the issue of how we've improved our vision of the world around us in the last few dozen generations. Please peruse The Object At Hand: Light Lens a Hand, to Help us Understand and see if I am off the beam.

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Climate: OJ and the Haystack

Why Climate Change Denial Is Like the O.J. Trial is an interesting article. The essence is that the climate denialists are using the same techniques as the OJ defense team: Find anything resembling a needle in a vast haystack of data, then claim that the presence of the needle casts doubt on the character of the haystack itself. Because there is an overwhelming pile of evidence in support of anthropogenic global warming, there are bound to be occasional pieces of data that can appear to contradict the mass of affirmative information. The pile is overwhelming, especially to non-scientists. Therefore few have the patience to understand the whole thing. Those who want to spin the counter argument claim that, because the two sides are both represented, therefore the issue is in doubt. And, as in the OJ trial, if there is cause for doubt, then no action is to be taken.

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And now it’s Kirk Cameron’s turn . . .

Jenny McCarthy, a famous non-scientist who has toured the country warning that vaccines caused her son's autism, now says that her son doesn't actually have autism and that vaccines might not actually cause autism. You see, real science doesn't make things up. Real science is a self-critical activity . . . Now it's time for Kirk Cameron to see the light.

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How Good Need Medical Evidence Be to Prevent Quackery?

Here is an interesting observation posted in a medical journal. It concludes:

Advocates of evidence based medicine have criticized the adoption of interventions evaluated by using only observational data. We think that everyone might benefit if the most radical protagonists of evidence based medicine organised and participated in a double blind, randomised, placebo controlled, crossover trial of the parachute.

So, do we really know if parachutes are better than a placebo for surviving skydiving? Alt-Med advocates are all over this one.

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