4 Responses to “The building blocks of life are nicely suited for a very crowded environment”

1. stunney Says:
   July 31st, 2007 at 12:22 am

   I wonder if there's something similar at work in this stuff:

   In Games, an Insight Into the Rules of Evolution

   ….In recent papers, Dr. Nowak has argued that cooperation is one of the three basic principles of evolution. The other two are mutation and selection. On their own, mutation and selection can transform a species, giving rise to new traits like limbs and eyes. But cooperation is essential for life to evolve to a new level of organization. Single-celled protozoa had to cooperate to give rise to the first multicellular animals. Humans had to cooperate for complex societies to emerge.

   "We see this principle everywhere in evolution where interesting things are happening," Dr. Nowak said.

   While cooperation may be central to evolution, however, it poses questions that are not easy to answer. How can competing individuals start to cooperate for the greater good? And how do they continue to cooperate in the face of exploitation? To answer these questions, Dr. Nowak plays games. His games are the intellectual descendants of a puzzle known as the Prisoner's Dilemma. Imagine two prisoners are separately offered the same deal: if one of them testifies and the other doesn't talk, the talker will go free and the holdout will go to jail for 10 years. If both refuse to talk, the prosecutor will only be able to put them in jail for six months. If each prisoner rats out the other, they will both get five-year sentences. Not knowing what the other prisoner will do, how should each one act?

   The way the Prisoner's Dilemma pits cooperation against defection distills an important feature of evolution. In any encounter between two members of the same species, each one may cooperate or defect. Certain species of bacteria, for example, spray out enzymes that break down food, which all the bacteria can then suck up. It costs energy to make these enzymes. If one of the microbes stops cooperating and does not make the enzymes, it can still enjoy the meal. It can gain a potential reproductive edge over bacteria that cooperate.

   The Prisoner's Dilemma may be abstract, but that's why Dr. Nowak likes it. It helps him understand fundamental rules of evolution, just as Isaac Newton discovered that objects in motion tend to stay in motion….

   ….To study cancer, however, Dr. Nowak had to give his models some structure. In the Prisoner's Dilemma, the players usually just bump into each other randomly. In the human body, on the other hand, cells only interact with cells in their neighborhood.

   A striking example of these neighborhoods can be found in the intestines, where the lining is organized into millions of tiny pockets. A single stem cell at the bottom of a pocket divides, and its daughter cells are pushed up the pocket walls. The cells that reach the top get stripped away.

   Dr. Nowak adapted a branch of mathematics known as graph theory, which makes it possible to study networks, to analyze how cancer arises in these local neighborhoods. "Our tissue is actually organized to delay the onset of cancer," he said.

   Pockets of intestinal cells, for example, can only hold a few cell generations. That lowers the chances that any one will turn cancerous. All the cells in each pocket are descended from a single stem cell, so that there's no competition between lineages to take over the pocket.

   As Dr. Nowak developed this neighborhood model, he realized it would help him study human cooperation. "The reality is that I'm much more likely to interact with my friends, and they're much more likely to interact with their friends," Dr. Nowak said. "So it's more like a network."

   Dr. Nowak and his colleagues found that when they put players into a network, the Prisoner's Dilemma played out differently. Tight clusters of cooperators emerge, and defectors elsewhere in the network are not able to undermine their altruism. "Even if outside our network there are cheaters, we still help each other a lot," Dr. Nowak said. That is not to say that cooperation always emerges. Dr. Nowak identified the conditions when it can arise with a simple equation: B/C>K. That is, cooperation will emerge if the benefit-to-cost (B/C) ratio of cooperation is greater than the average number of neighbors (K).

   "It's the simplest possible thing you could have expected, and it's completely amazing," he said….

   ….The subject of human cooperation is important not just to mathematical biologists like Dr. Nowak, but to many people involved in the current debate over religion and science. Some claim that it is unlikely that evolution could have produced humans' sense of morality, the altruism of heroes and saints. "Selfless altruism presents a major challenge for the evolutionist," Dr. Francis S. Collins, the director of the National Human Genome Research Institute, wrote in his 2006 book, "The Language of God."

   Dr. Nowak believes evolutionary biologists should study average behavior rather than a few extreme cases of altruism. "Saintly behavior is unfortunately not the norm," Dr. Nowak said. "The current theory can certainly explain a population where some people act extremely altruistically." That does not make Dr. Nowak an atheist, however. "Evolution describes the fundamental laws of nature according to which God chose to unfold life," he declared in March in a lecture titled "Evolution and Christianity" at the Harvard Divinity School. Dr. Nowak is collaborating with theologians there on a project called "The Evolution and Theology of Cooperation," to help theologians address evolutionary biology in their own work.

   Dr. Nowak sometimes finds his scientific colleagues astonished when he defends religion. But he believes the astonishment comes from a misunderstanding of the roles of science and religion. "Like mathematics, many theological statements do not need scientific confirmation. Once you have the proof of Fermat's Last Theorem, it's not like we have to wait for the scientists to tell us if it's right. This is it."

   ….

Comment by stunney — July 31, 2007 @ 12:22 am

2. Thought Provoker Says:
   July 31st, 2007 at 8:25 am

   Hi Mike,

   From your link…

   …a bit like finding a friend in a busy subway station during rush hour.

   I believe this gets into the evolutionary advantages of doing a "quantum database search". But instead of searching a virtual database, the DNA is searching a real-world database made up of "friends" in a very "busy subway station".

   From Patel's Quantum Algorithms and the Genetic Code

   Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever!) explanation of why living organisms have 4 nucleotide bases and 20 amino acids. It is amazing that these numbers arise as solutions to an optimisation problem.
   …
   (2Q + 1) sin−1(1/√N) = PI/2 .
   …
   The only exact integral solution is Q = 1, N = 4. Base-pairing during DNA replication can be looked upon as a yes/no query, either the pairing takes place through molecular bond formations or it does not, and its task is to distinguish between 4 possibilities. The other interesting solution is Q = 3, N = 20.2. The well-known triplet code of DNA has 3 consecutive nucleotide bases carrying 21 signals, 20 for the amino acids plus a STOP. 3 base-pairings between t-RNA
   and m-RNA transfer this code to the amino acid chain.

   Humans are directly using DNA to build quantum computers. The DNA structure appears tailor made to amplify quantum effects (very long string of quantum sized components). Now, it turns out the DNA language itself is optimized to take advantage of a computer-like algorithm.

Comment by Thought Provoker — July 31, 2007 @ 8:25 am

3. stunney Says:
   July 31st, 2007 at 4:43 pm

   Thought Provoker wrote:

   Now, it turns out the DNA language itself is optimized to take advantage of a computer-like algorithm.

   Isn't optimization a design-theoretic concept?

   Kinda like the inverse-square form taken by the law of gravity being optimized for star-formation and stable planetary orbits, which apparently it is.

Comment by stunney — July 31, 2007 @ 4:43 pm

4. Thought Provoker Says:
   July 31st, 2007 at 6:36 pm

   Hi Stunny,

   Isn't optimization a design-theoretic concept?

   It is one of the reasons I feel it is appropriate to call the Third Choice an ID hypothesis.

   I feel life on Earth started with Quantum Mechanics "front loaded" in it and QM has guided the life process ever since.

   I suggest there is no such thing as natural randomness, just the ultimate complexity of a completely interconnected spacetime universe.

   Since it is most likely the basis behind the interconnected quantum effects will remain unknown (non-deterministic) it is, FAPP, metaphysical.

   In short, it doesn't bother me to have people from either or both sides of the Culture War presume the Third Choice is consistent with their philosophical/religious opinions.

Comment by Thought Provoker — July 31, 2007 @ 6:36 pm

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