The inner life of your cells

I don't claim to understand most of this Harvard video regarding the inner life of cells, but I'm fascinated by the visuals. This 2006 video by Alain Viel, Robert A. Lue and John Liebler, functions as a biography about you (and me) and brings to mind the following passages from Harold M. Franklin's poetic/scientific book, The Way of the Cell, Page x (2001):

One response to the question, What Is Life?, is simply, Look around! Note the birds and butterflies, zebras and ammonites, the intricate web of life present and past, and joined the unending struggle to ensure its continuance in the face of human arrogance and mindlessness. This has been eloquently said by others, far better than I could, and it is not what I have in mind here. For the past 40 years, I’ve been immersed in research on the biochemistry and physiology of microorganisms, with emphasis on the fundamental aspects such as bioergetics and morphogenesis. In consequence, the central problems of life present themselves to me at the interface of chemistry and biology. How do lifeless chemicals come together to produce those exquisitely ordered structures that we call organisms? How can molecular interactions account for their behavior, growth, reproduction? How did organisms and their constituents arise on an Earth that had neither, and then diversify into the cornucopia of creatures that can live in each drop of pond water? My purpose is not to “reduce” biology to chemistry and physics, but to gain some insight into the nature of biological order. Inevitably, then, this is a personal book–one scientist’s attempt to wring understanding from the tide of knowledge. It grew out of the experience of a lifetime devoted to research, scholarship and instruction; but since my purpose is to make sense of the facts of life rather than to expound the facts themselves, this inquiry walks the edge of science proper. The arguments and conclusions presented here seem to me sound, but they are certainly not the last word on the subject. The most valuable lessons that the discipline of science teaches are to play the game of conjecture and reputation, to appreciate the provisional nature of our knowledge, and to prize doubt! If what I have written here encourages a few readers to look up from their gels and genes to peer at the far horizon, I shall be well content. Of my shortcomings as an investigator, scholar, philosopher and expository I am keenly aware . . .
Every month it seems that I hear yet another sad story about someone who has been stricken by a terrible disease or who has recently died. When they hear of these things, most people wonder, "How could this have happened?" Though I also mourn these events, I inevitably find myself wondering how bodies work at all. They seem far too complicated to work for even a second, much less for a lifetime. I know that they work, because I sitting here breathing and writing, but how is it possible that the extensive mechanical-seeming processes taking place within each of my cells successfully scale up to the organism level? Every breath is miraculous and every act of conscious generosity is beyond explanation (including religious "explanation"), at least to those of us who are honest.

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Talking monkeys

Robert Seyfarth describes how monkey calls used by Vervet Monkeys might be precursors to language. Vervets give different types of calls in reaction to different kinds of approaching predators. These calls are simple. They are not language, though Seyfarth suggests that these types of calls are precursors to language.

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Why Can’t They Just Stop the Leak?

I've been watching the Gulf Oil leak reports with a technical eye. They report that citizens have sent in over 100,000 suggestions on how to stop the leak, and more on how to clean it up. It's so simple: Just plug it. But I'd wager that the bulk of the suggestions are innumerate; they have no comprehension of the scale of the problem. As though the oil leak is like oil dripping from a car. This is a column of oil at least 2 feet wide and thousands of feet long already moving fast and under pressure. Stopping it is like stopping a freight train with the engines running. And doing it in one of the the harshest environments man has ever tried to work in on this planet. Many of the clean up suggestions, even the ones based on home testing, neglect to consider the scale. What might work in a sink is not practical to do to an ocean. BP has already consumed most of the world's available dispersant Corexit™ in an attempt to keep much of the oil suspended in the water. Sawdust? Hay? Hair? There isn't enough on all the heads in America. People, please do basic arithmetic before sending in suggestions. I heard one fairly clever suggestion from a brother-in-law: Freeze it with liquid nitrogen. My instincts first boggled at the immense cost of doing it. But then I considered and replied with a more convincing argument: Consider wrapping a fire hose in dry ice. All you get is a hole in the dry ice because any cooled material is moved down the pipe before it can slow the flow. I looked up some more details when I got home: Nitrogen won't even evaporate at the the pressure down by the wellhead. I think it's great that people are thinking. But it also shows the world how distinct thinking is from reasoning.

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So tempting to anthropomorphize . . .

This National Geographic video on cockroaches is fascinating by its own rights, but the quote at the 30 second mark sounded like information that might apply to more than a few of the annoying people in the news: "The cockroach doesn't really have a brain per se, but it has instinct and a ferocious desire to survive and reproduce."

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Your Neandertal Ancestors

Scientific convention used to be that modern humans came out of Africa and completely replaced Neandertals (also spelled "Neanderthals") without interbreeding (for example, see here). New evidence suggests that this hypothesis is incorrect, according to an article by Ann Gibbons called "Close Encounters of the Prehistoric Kind." The article appears in the May 7, 2010 edition of Science (available online only to subscribers). An international team has now completed the draft sequence of the Neandertal genome, which includes more than 3 billion nucleotides collected from the bones of three female Neandertals who lived in Croatia more than 38,000 years ago." The analysis described was astoundingly complex, and the consequences of this analysis are startling:

By comparing this composite Neandertal genome with the complete genomes of five living humans from different parts of the world, researchers found that both Europeans and Asians share 1% to 4% of their nuclear DNA with Neandertals. But Africans do not. This suggests that early modern humans interbred with Neandertals after moderns left Africa, but before they spread into Asia and Europe. The evidence showing interbreeding is "incontrovertible," says paleoanthropologist John Hawks of the University of Wisconsin, Madison, who was not involved in the work. "There's no other way you can explain this."

Therefore, many people living outside of Africa carry "a small but significant amount of DNA from these extinct humans." The consequences of this amazing finding are not lost on anyone:

In a sense, the Neandertals are then not altogether extinct, says lead author Svante Paabo, a paleogeneticist at the Max Planck Institute for evolutionary anthropology in Leipzig Germany, who is surprised to find out he was part Neanderthal. "They live on in some of us."

The Science article presents the following list of things we now know about Neanderthals:
  • The genomes of modern humans and Neanderthals are 99.84% identical.
  • The scientific data don't support interbreeding when scientists had most expected it (between 45,000 and 30,000 years ago in Europe).
  • Neanderthals coexisted with modern humans in Europe from 30,000 to 45,000 years ago, and perhaps in the Middle East as early as 80,000 years ago.
  • The amount of admixture is tiny, even among Europeans and Asians, but Neanderthals "are significantly more closely related to non-Africans than Africans on average.
  • The new data fits with the discovery of fossils and stone tools from Israel caves about 80,000 years ago (modern humans and Neanderthals both used these caves and had much in common--they used similar tool-kits and under the same animals). One Neandertal skeleton from the Middle East looked "less robust than Neanderthals in Asia and Europe.
  • Despite the ability to sequence some Neanderthal DNA, there is no possibility of cloning a Neanderthal.
  • "The isolated DNA was in pieces typically about 50 bases long, and there were many missing stretches. Further, despite the story one often hears in the mass media, DNA is not completely responsible for the appearance of an animal. "Chemical modifications to the genome, the way chromosomes arrange in the nucleus, and maternal components in the egg all play a role in translating a genetic blueprint into a viable individual." None of these are available with regard to Neanderthals. As soon as you substitute another oocyte (e.g., that of a modern human) for that of a Neandertal, you would change the resulting organism.
Despite the fact that there was some interbreeding, it did not happen much. This article quotes evolutionary geneticist Sarah Tishkoff, who asked "Was it a cultural barrier?" We are cousins with every living thing on planet Earth (including trees and see here), but many of us are both cousins and descendants of Neandertals. Therefore, for those of you who have had ancestors from anywhere outside of Africa (keeping in mind that all of us have ancestors from Africa), you are African and you are Neandertal. I'm planning on having a bit of fun the next time a bureaucratic form requires me to designate my "race."

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