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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The Apollo 11 launch close up and slow

Check out this a wonderful video and commentary regarding the launch of Apollo 11, the first lunar landing. All of this action is captured with a still video camera perched almost unimaginably close to the rocket exhaust. 500 frames per second turned 30 seconds into 8 minutes. This video reminds me about the many ordinary things that had to happen according to plan in order to allow the success of what has to be the one of the most spectacular journeys in the history of humankind. Keep in mind that the Saturn V Rocket was 363 feet tall, only one foot shorter than St. Paul's Cathedral in London. Each one of the F-1 engines (which are still the most powerful rocket engines ever built) were 12 feet in diameter at the nozzle, and there were five of these monsters powering the launch.

Apollo 11 Saturn V Launch (HD) Camera E-8 from Mark Gray on Vimeo.

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Dawkins’ Greatest Show on Earth

Richard Dawkins released The Greatest Show on Earth in November to really and truly assemble substantial amounts of understandable evidence in one place for those 40% of Americans who can't stand to follow the evidence where it leads and for those of us who want the hordes to quit making excuses and to follow that evidence. I haven't read Dawkins' new book yet (though I own it), but Jerry Coyne has read it, and he reviewed it at The Nation. Coyne begins his review by characterizing the absurdity of refusing to acknowledge evolution by natural selection. The situation is as bad as as this hypothetical:

Imagine for a moment that a large proportion of Americans--let's say half--rejected the "germ theory" of infectious disease. Maladies like swine flu, malaria and AIDS aren't caused by micro-organisms, they claim, but by the displeasure of gods, whom they propitiate by praying, consulting shamans and sacrificing goats. Now, you'd surely find this a national disgrace, for those people would be utterly, unequivocally wrong. Although it's called germ theory, the idea that infections are spread by small creatures is also a fact, supported by mountains of evidence.

Coyne also describes Dawkins' chapter setting forth powerful evidence illustrating that evolution is a tinkerer:

In a wonderful chapter called "History Written All Over Us," Dawkins shows that animal anatomy is like a medieval palimpsest, carrying traces of our evolutionary ancestry. Human goose bumps, for instance, serve no function: they're remnants of the muscles used by our mammalian ancestors--and our living relatives like cats--to erect their fur, making them warmer and giving enemies the illusion of greater size. Modern genome sequencing has also uncovered vestigial DNA: useless, broken genes that are functional in our relatives and presumably were too in our ancestors. Our own genome, for instance, harbors nonfunctional genes that, in our bird and reptile relatives, produce egg yolk. Embryology--the study of development--brings more proof to the table. The pharyngeal arches of the early, fishlike human embryo are derived directly from the gill arches of fish, though they go on to become, among other things, our larynx and eustachian tube.

Coyne has given us a well-written review. Now it's time for me to go read Dawkins' book itself, so I can speak first hand. BTW, Catch this excellent 3-minute video of Dawkins describing the purpose of writing The Greatest Show on Earth.

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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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