T. Ryan Gregory, of Genomicron, has put together a killer rescourse on Evolutionary theory for educators, students, and interested people.  It’s called Evolver Zone.  Right on!

Photo Credit: Stefan Kraft, courtesy of the Wikipedia Commons

Micheal White sets the record straight about what the platypus genome is and what it isn’t.

Is the platypus part bird, part reptile part mammal, an amalgam of very different groups of animals? Is it a primitive mammal that resembles the early ancestors of all mammals? Can we figure out just what this creature is by gazing at its genome?

Find out here.

This is a review of a recent article, cooperation in Defense against a predator,  in the Journal of Theoretical Biology by Jozsef Garay of the Research Group of Theoretical Biology and Ecology of Hungarian Academy of Sciences.  Here’s the abstract:

The origin and the evolutionary stability of cooperation between unrelated individuals is one of the key problems of evolutionary biology.  In this paper, a cooperative defense game against a predator is introduced which is based on Hamilton’s selfish herd theory and Eshel’s survival game models.  Cooperation is altruistic in the sense that the individual, which is not the target of the predator, helps the members of the group attacked by the predator and during defensive action the helper individual may also die in any attack.  In order to decrease the long term predation risk, this individual has to carry out a high risk action.  Here I show that this kind of cooperative behaviour can evolve in small groups.  The reason for the emergence of cooperation is that if the predator does not kill a mate of a cooperative individual, then the survival probability of the cooperative individual will increase in two cases.  If the mate is non-cooperative, the–according to the dilution effect, the predator cofusion effect and the higher predator vigilance–the survival probability of the cooperative individual increases.  The second case is when the mate is cooperative, because a cooperative individual has a further gain, the active help in defence during further predator attacks.  Thus, if an individual can increase the survival rate of its mates (no matter whether the mate is cooperative or not), then its own predation risk will decrease.

Hamilton’s “selfish herd” theory (1971) claims that predation risk is lowered when animals huddle in groups, and is lowest for those that are in the middle of the “herd”.  Buffalo are a good example.  We call them selfish since if one Buffalo is attacked, the others don’t generally help it, they just run.  But, as a group they are safer in large numbers.

The trouble with such a theory is it doesn’t explain how altruistic behavior (helping out a fellow group member at the risk to oneself) would develop.  Garay’s paper aims to help make sense of how this is possible.

His argument hinges on a Game Theoretic model that shows that although in the short term, a non-altruistic strategy confers a better survival rate, in the long term the altruistic strategy does.

If there are only 2 animals, A and B, and we assume that a predator can only realistically attack one at a time, then the probability of A being attacked is 1/2 in a single round of predation.  So, in a one-shot game, if B is attacked, A’s best strategy is to cut and run, since helping B may result in injury or death.

But, if the same game is played over and over (that is, if they run the risk of being attacked often, as is the case in real life), then A’s best strategy is to help out B.  This might seem incongruous, but it isn’t.

If B dies in the first attack, then A’s probability of being attacked in the next round is 100%!  If he has a less than 100% chance of dying by way of helping B in the first attack than he is better off helping B since on the next round he’ll still have only a 50% chance of being attacked.  50% is certainly better than 100%!

The above is true even if B NEVER helps out A.  That is, if A is the only Altruistic one in the (2 man) group, then it is still to his advantage to continue to be altruistic.  But, if B also is altruistic (helps A when A is attacked) then this is all the better for A.  Also, B would then enjoy the same benefits as A.

What is interesting to me is that this argument doesn’t hinge on kin selection at all.  Kin selection is the idea that an individual is far more likely to come to aid of another individual who shares a large portion of their genome (like children, siblings, ect) than they are to a total (genetic) stranger.  But, here, the two don’t need to be related at all.  The risk of predation is enough to “glue” them to one another.

References:

Garay, Jozsef.  2009.  “Cooperation in Defence against a predator.”  Journal of Theoretical Biology.  257 (2009) 45-51.

Hamilton, W.D., 1971. “Geometry for the selfish herd.” Journal of Theoretical Biology. 31, 295-311.

Wilson, E.D. 1975. Sociobiology.  The Belknap Press Harvard University Press, Boston.

John Hawks reviews an article in the NY times, by Gina Kolata, on Grants for Cancer Research.  Here’s an excerpt from the original article:

Yet the fight against cancer is going slower than most had hoped, with only small changes in the death rate in the almost 40 years since it began.

One major impediment, scientists agree, is the grant system itself. It has become a sort of jobs program, a way to keep research laboratories going year after year with the understanding that the focus will be on small projects unlikely to take significant steps toward curing cancer.

“These grants are not silly, but they are only likely to produce incremental progress,” said Dr. Robert C. Young, chancellor at Fox Chase Cancer Center in Philadelphia and chairman of the Board of Scientific Advisors, an independent group that makes recommendations to the cancer institute.

The institute’s reviewers choose such projects because, with too little money to finance most proposals, they are timid about taking chances on ones that might not succeed.

Hawks sees a few risks inherent in the approach taken by Kolata’s article in it’s portrayal of the research granting process:

This kind of story runs a risk: if you applied for grants and didn’t get them, are you just whining? I mean, ninety percent of grant applications are not funded, so if you’re even average good, you’ve got to submit 10 before you have any expectation of return.

The other risk of the story is that readers will draw that conclusion that there are so many deserving grants that go unfunded, all we need to do is raise the funding level. This overlooks the very high costs of the current review system — flying all those people around for panels, handling the paperwork, paying the grant agencies’ bureaucracies, plus the support staff at universities and other institutions to collect the grant money — “indirect” costs of grants that cover administration now amount to nearly half of federal grant budgets. There’s no question that this money could be better allocated.

More interestingly to me, he uses the metaphor of a “research-space”, that is a topological landscape in R3, where there are hills and valleys representing scientific breakthroughs at the high points.

Think of cancer research as a search space, where research advances are moving toward some (perhaps several) peaks. Now, the question is what kind of change will bring you closer to a peak?

Well, it depends how close to the peak you already are. If you’re already close to a peak, a very large change can do nothing but take you further from it. An incremental change will be roughly halfway likely to take you up a small amount; halfway likely to take you down. So if you think you’re already very close to an acceptable cure rate for cancer, you should focus on the very small incremental improvements.

On the other hand, if you’re far from a peak, a large change is not unlikely to take you closer to the top, and it will certainly get you there a lot faster.

But worse, what if you’re climbing some low peak, where the outcome — even if you do everything entirely right — is poor? A small incremental change will never do any better than the short peak you’re on. But a large change has some chance of finding some other peak — a radical shift in treatment that would bring much better outcomes. The likelihood of that for any particular change may be very low. But your coverage of the search space would be vastly larger — making progress much faster.

In other words, if we don’t know where we are in the research space, our best bets are often large jumps, since the probability of already being close to the top of a peak is low.  But, of course, that could take us farther away from the peak if we ARE close to one.

Having a navigator and a map would be more than handy.  But, that is a large task all its own, that also would require funding!

So, the new Darwin movie, Creation, staring Jeniffer Connelly and her husband Paul Bettany looks ridiculous:  Darwin is writing a book that is going to “Kill God!” and be the most “Explosive book of all time!”  (Apparently the book is filled with some kind of Metaphysical TNT.)   But, I don’t mean that in a bad way.

Supernatural explosives and Jeniffer Connelly, What’s not to love?

I got a funny chain email today:

Mmm ... I love bananas

My fiance is about to go back to school to get her masters in education so that she can become a middle school mathematics teacher.  She’s fairly confident that she’ll want to teach in the Portland public education system, but private schools have their draws.

Here, the Professor lists a number of benifits of teaching at a private institution.  Among them:

Our café serves healthy food using local and organic ingredients whenever possible. The food is fresh, varied, and nutritious.

As a fitness coach, I can’t stress enough how important healthy eating habits are to a students brain functioning and academic experience.  It’s an issue my fiance and I discuss a lot, but one she’ll have no control over as a teacher in a public school.

Not as strange as it sounds.  Here’s a blog by a teacher, a Libertarian, and a Buddhist, all of which is reflected in his blog.

Readers of this blog know that I’m not shy about my Libertarian tendencies.  But, what they might not know is that I was a practicing Buddhist for many years, also.   So, I find it very cool to see a new blog on two subjects I feel very close to.

(HAT TIP:  The Professor.)

I love this stuff:

The blue arrows represent the obvious route to RNA, going from prebiotic compounds (marked here by 7,8, and 10) to nucleobases (3) and ribose (4). And the big red X shows the point at which this route fails.

Sutherland and his colleagues started with the same ingredients, but cooked them in a different recipe, marked in green. Instead of trying to build the two parts independently, the scientists instead built a single molecule that had more and more components of the two parts already in place. They used just four reactions, all of which worked efficiently, to get one of the four ribonucleotides, known as cytidine. At the end of the process, the scientists zapped the mix with ultraviolet light (something that would be easy to come by on the early Earth, unprotected by an ozone layer). They eliminated some of the unwanted side products and turned some of the cytidine into another unit of RNA, known as uracil.

The Recipe of Life.  You think the food network would be interested in a show?

Why do we need them?

They make creationists sad:

Driving home from church recently, I spotted one of two new billboards sponsored by a local coalition of atheists. “Don’t believe in God? You are not alone” was their message, an attempt, the group declares, to let the city know that good people in Dallas, like atheists, don’t need God. I’m sad to see the ads go up in my city, but not really surprised. The drift away from conservatism in religion, and in politics, is much more obvious in our nation today.

(HAT TIP: Evolution Blog)