Friday, May 30, 2008

Links of Interest

Nothing today. Here's some fun links.

Rot in the Phylogenetic Tree
New Species' Top Ten Chart and here.
Elephant Scientist Killed
Biblical Literalism vs. IQ And here. And here.
Side Stabbing Snakes
Tracking Life via Geology
The Rockefeller Lectures
Darwin's Tomatoes
Psychoneuropharmacological Mental Medicine Show

TED Talks
Objects that tell stories

Wednesday, May 28, 2008

Origin of Life

Evolution, as we know it, happens after the fact of life. We have no direct observation into how life was initially created. Whatever happened, happened long before fossils.

However, modern understanding of biochemistry suggests that the same competitive mechanisms that we observe in the biological competition between organisms also happens in the biochemical mechanisms that underly those organisms. In fact, chemical competition and success seems completely independent of life at all. This gives rise to the idea that whatever biochemical phenomenon that preceded life may well have followed the same rules of competition and selection of modern life.

Living organisms are complex; staggeringly, mind-bendingly complex. Heinlein said in one of his novels*, "Biochemistry makes atomic physics look simple. But presently it begins to make sense." One of the big problems of determining the origin of life is how to explain how such a complex system could have arisen from simple components.

The followings links explore these things in depth.

First, let's look at cosmology. Nobel Intent discusses the fundamental physics of the universe in this link on is our place in the universe special?

The Origin of Metabolism must be explained and that's the goal of this article.

DNA is a preposterously fragile molecule and the chances that it was basis of inheritance initially is hard to swallow. RNA, however, has some fewer limitations. Consider the Chemistry of RNA.

The Chemistry of a pre-biotic world is massively different from the modern world. Once life intervenes, the nature of geologic chemistry is itself altered. So, whatever environment life arose in it wasn't this environment.

One theory is early RNA organisms. This is the evidence of an RNA World.

Cells aren't merely naked hunks of biochemistry floating in the water. They are enclosed hunks of biochemistry floating in the water. Without encapsulating the chemistry, life can't get going. Here's an article on the the First Proto Cells.

If we started with an RNA world, how did it change. This article considers transitioning from an RNA world.

Once we have cells like bacteria, we have to consider the origin of eucaryotes-- those cells that compose animals, plants and fungi. There's some evidence that viruses are implicated in the Origin of Eucaryotes. We also have to wonder at the origin of DNA Life.

We're animals. We want to know where we came from. Like anything else biological, when we look at our origin things get complicated. This article looks at The Scrambled Origin of Animals.

Things also got interesting when Plants Invaded the Land.

Skipping ahead to human speculations. One of the problems we have is determining the commonality of genes. A gene, for example, might generate a given protein in a stem group of animals. The animals multiply and mutate, spread around, hybridize and mutate again. In the resulting population, how do we determine the history of that gene? We do not have the original sample-- that's dead and gone. Technology to the Rescue: Determining Genetic Ancestry.

Humans look off the earth to determine Extra-Terrestrial Life. Or try to figure out Alternative Life paths. Or determine if the Composition of Comets could have contributed.

For years, evolutionists have left this topic largely alone. The point of creation was something so unknown and so speculative that there was little of note to report. Now, however, we understand a little more. It's time for speculation once again.

Links of Interest
Faux Consumer Watchdogs in Canada
Biggest Drawing in the World
Drivers, +, Hedgehogs, -
Europe's Manned Space Craft
Pterosaur paleobiology. And here. Wikipedia.
TSA vs. Art

Tuesday, May 20, 2008

Gay Marriage

Well, it's just before another presidential election and another state supreme court has weighed in on gay marriage. I don't know why they choose this particular point in the election cycle to bring this up but there it is.

And along for the ride comes the usual collection of foolishness. Sorry. Usually, I'm not so judgmental (right, says my wife) but these guys are idiots.

Let me say right up front: I'm a happily married heterosexual guy. I have a son. And I am absolutely in agreement with the Supreme Court of the State of California. Gays should have the same right to marriage as anybody else. The text of the actual decision is here.

There are a lot of reasons to be in favor of the decision, most of them in the decision itself and I won't elaborate them here. But there is one that is not so addressed. That is the compelling need of the state.

It is in the best interests of the state to bring marginalized populations, be they marginalized by race, orientation or religion, into the mainstream. The state-- by which I mean ourselves-- benefits. Tensions within society are reduced. Polarizing influences are ameliorated. We all benefited when African Americans started being brought in. We benefitted by different points of view, increased awareness of the breadth and depth of our country and, most of all, from the society not being so damned white all the time. Gets pretty boring around the suburbs when that sea of white faces drive by in their SUVs. Looks a whole lot friendlier when there's a little color leavening the view. Not to mention that making people's acts clandestine is the quickest way to make them criminal. Things that are criminal acts should be criminalized. But by taking something that is already happening and making it clandestine you make it open to manipulation by the unscrupulous and insure that participants will not have legal recourse.

The opposition to this have a standard litany of issues: sanctity of marriage, slippery slope, child rearing and dissolution of society. That's pretty much the gist of their problems. Let's take them one at a time.

Sanctity of Marriage:Look at that statement. Sanctity? Since when has the state been in the business of bestowing sanctity on any religious institution. Personally, I don't think the state should be in the business of marriage at all. The state is a secular institution. Marriage is a religious institution. The best the state can do is bestow recognition of a contractual state-- a civil union to coin a term. All state licenses can only truly be is a recognition of a contractual relationship that has for reasons that escape me termed marriage, thoroughly confusing the issue since it uses the same religious term. So: it's not the state's business to keep up your religion so get over it. I like the idea of the "enduring union" proposed in the decision to replace the word "marriage". Go for it.

Slippery slope: This means that once we recognize gay marriage, we'll be forced to recognize marriage of three people, five, hundreds, dogs marrying cats, humans marrying horses, George Bush marrying Ken Rove.

First, I'm much more concerned about a country that let's sixteen year olds get married. That's a much bigger assault on the concept of marriage than a couple of lesbians in Lawrence getting hitched. Second, I think the institution is obviously limited to human adults for a couple of reasons. One, few other species would have us without coercion and second, until the day that dogs talk, we'll never be able to determine consent.

As far as the idea of multiple marriages, so what? I question the sanity and self-esteem of an adult woman who would want to share a man with someone else. Although, I could possibly see the idea that two women sharing a man might also be sharing a burden. Regardless, I don't care. It doesn't change my marriage, or that of anybody else's, one whit.

In fact the slippery slope argument is one of the arguments for gay marriage. Mainly in how we handle polygamy. From the recent FLDS cases in Texas, we've already heard that polygamy is generally not prosecuted unless some other criminality is involved such as child abuse, etc. This has two very interesting effects. First, it's made polygamy acceptable in those regions where it is practiced. And, in those same regions, it's under the control of some fairly nasty people. Since it is illegal and since the participants (the women) have only the legal recourse of reporting their participation in something illegal, the participants have entered into a place where they have no rights. They have no right of divorce. They have no right to marriage property. They have no right to debate custody. They have only the blunt instrument of bringing charges of a crime in which they have participated. If polygamy were legal, these people would have right of divorce, right to determine custody, standing in a court of law, etc. At least all of those arranged marriages by Reverend Moon were binding contracts and could be negotiated under the law.

Of course, multipolar marriages and divorces are going to be a lot more complex than bipolar marriages. I wouldn't want to be in one but there you have it.

Child rearing: They trot this one out all the time. Last time I looked there was no vast gang of gays searching parking lots for stray children. Gay men have to adopt. While I don't have any particular faith that DSS or China can pick a good adoptive family, they're certainly not going to do any worse with gays than they already have with heterosexuals. I think we can safely say that most gay men who married would likely be childless not because they didn't want children but because the hurdles and hideous expense of adoption would be just as tough on them as any other couple. As long as adoption is this hard and this competitive, couples who can't or won't have children of their own have a better than even chance of being childless regardless of their gender makeup. Although, in this area it's possible that gay men might be more receptive to adopting older children and not be so infant obsessive as heterosexual couples. Gee: a loving gay adoptive pair of parents or an endless series of foster homes. Which do you think the average DSS six year old would choose?

I think this one is a low blow aimed at lesbians. After all, any lesbian couple with a turkey baster and a sperm donor has a good chance of starting a family. God forbid they might actually be legitimate.

If the opposition really wants to help kids, get single mothers who are already at the brink health care. Get the single mothers education and child care. Going after gay marriage and leaving single mothers to rot is the rankest sort of hypocrisy.

Social dissolution: You have to work a little bit about this one. In a culture where marriages have as good a chance of failing as lasting, where a significant number of homes have only one parent, where people are having to choose between food, health insurance and rent, where nearly half of the men of one particular ethnic group is in jail and their families torn apart. Somehow the idea of a same sex marriage will bring the whole society to its needs. Yeah. Right. That's enough about that.

I do think marriage and families are under attack. It's being trivialized by those who marry frivolously. By bridal magazines who try to milk as much money as they can from it and are right there to milk gays the same way they go after high school girls. By having state laws allowing kids to marry before they can drink-- in some places before they can get a driver's license. By extremely successful celebrities making sex tapes of thirteen year olds. By television shows that can't seem to show a marriage that lasts more than a season without affair or death. By television shows that glorify the nastiest and most self-destructive relationships so that we can all participate. By stagnating wages so that both parents and sometimes a parent have to work just so the family survives. By ignoring economic changes that either destroy families outright or make it nearly impossible to stay together. By building schools that are monuments of architecture but not allocating enough money to pay the teachers. By ignoring substance and embracing illusion as fact.

By going after silly issues like gay marriage.

Links of Interest
NOTE: This week the ISS will be very visible: Check it out here.
Sex Science
Left Brain/Right Brain localization of emotion.
Shermer's A New Phrenology?
Rolling Europa
The Utility of Physics
Redesign of the One Laptop Per Child
Fear of a White Planet

TED Talks
Our Cellphones, Our Selves
Robert Ballard on the Sea

Nature's Idea of Free Will

Here's an article in Nature Neuroscience regarding ongoing research with decision making. The experimentation has been around for some time now. It goes like this: put the subject in an MRI and observe the neural activity in the brain. Present them with a task involving a decision on what button to push. The subjects have some methodology that signifies when the decision is actually made. Observation of neural activity shows a pattern that highly predicts when the decision will be made that occurs significantly prior to when the subject says he's made the decision. Conclusion, decision is made prior to when the subject is aware of it.

Or is it?

Let's take this apart for a moment. We have a subject indicating a previous event as indicative of when the decision is made. Where does "awareness" come into it?

I recently went to buy a car to replace my lamented Geo. I bounced around several possibilities and settled on a 2004 Ford Focus. We go down to see the car. We like it and put money down on it based on some things that had to be done to it. We go back down a week later when the done things have purported to be actually done. By and large they have (though with buying a car the dealer never quite gets it exactly the way they say it will be) we give them the rest of the money and take home the car.

When was the actual decision to buy the car? When we went down? When we put a deposit down? When we checked what the dealer had done? When we gave them the money?

I submit to you that the actual decision to buy the car was represented by the act of putting the remainder of the money in the dealer's hot little hands. Up to that point are a set of increasing biases towards that decision, all of which indicate an increasing probability of the final decision being the same as the predicted decision. Was I aware of this increasing bias? Absolutely. Would it have been hard to walk away close to the decision? Absolutely. Could I have done it? Again, absolutely. If the dealer had done something to sour the deal, I would have walked away and left the deposit instead of the final payment. Certainly the probability was low. But it was still there.

Back to the Nature article. The conflating of bias and awareness is just plain silly and not supported by the article. The statement that people might "not become aware of their decisions until after they are made" is not a conclusion based on the experiments. Do subjects have subconscious biases? Sure. That's why they're called subconscious biases. Are decisions subconscious? Maybe. I doubt it. But it's not proven by this research.

Links of Interest
Interesting analysis of the gender gap in science and engineering
Syntho virus for delivering good things to the cell
In Myspace no one knows you're a dog until prosecuted
First Frogs. Now Birds.
Iceland hunts whales.
The Tasmanian Tiger Returns. Sort of. And here.
Odd Animals: The Glyptodont.
Let the computer drive your car.
Ultra-portable, low cost PC Comparison
Phoenix's mission.
White House causes EPA reversal. Surprise!

Friday, May 2, 2008

Niche Religion

The concept of "niche" came out of ecology a number of years ago. A niche is a place in the ecological system a species can exploit. It can be a predator who preys on a specific prey or a herbivore that eats a particular plant.

I think of niches from the viewpoint of thermodynamics. All biological systems operate by taking energy of a higher level, absorbing a bit, and emitting a little less energy. Plants take a photon, use a bit of energy to take CO2 and water to make sugar, releasing some energy (heat) in the process. The Krebs Cycle, that venerable biochemical system that derives energy from the burning of sugar, does the same, chewing up two carbons at a time, dumping CO2 and water and a little heat and getting energy in return. The three laws of thermodynamics says you can't win, you can't break even and you can't get out of the game. But that doesn't say you can't make a profit on the trip downhill. Think of the ecology living on the back of an elephant or in the human gut.

It shouldn't be surprising that humans do the same thing economically. Small businesses get their start finding a service or product that is unexploited. Commerce makes money on the transfer of energy whether the energy is represented by product, service or money itself.

I was out in Missouri a couple of weeks ago to the funeral of my brother-in-law. Not being a believer of any kind, it's odd for me to go to funerals. I've been to a lot of funerals in the last two decades: frinds, uncles, aunts, cousins, parents, in-laws of the same sort of relations and, now, brother-in-law. Most of these funerals had a minister of some sort.

On such occaisions, the service and sermon follow a set pattern. Step 1: Comfort the bereaved. This is where heaven comes in. Step 2: Exalt the departed. This can be considered part of step 1 but it is usually separated out. Step 3: Place the event in religious context. These steps can happen in any order. Some steps are infacted at the cost of other steps.

Step 3, which I also call putting grief in harness to a greater good, is the part that pays the salary of the minister. This is the part of the service that shows the necessity of God, the religion, and, by extension, the minister. It's niche exploitation, pure and simple. Grief is the consequence of a thinking monkey observing the death of a loved one. It's as inevitable as a predator/prey relationship. Religion injects itself into the heart of this transaction, serving up comfort and context and taking advantage of the emotions as they transiton from bereavement to acceptance. No differet from a tiger or a tape worm.

When my father died this Baptist minister showed up at the funeral. I didn't invite him. My Mother didn't invite him. My sister didn't invite him. There's some evidence he was brought by my aunt but there's no confirmation.

He comes in, talks a little about my Dad in a way guaranteed to show he had never met him. My Dad had left Baptists far, far behind. He'd become an athiest in the latter days of his life and it made him happier in many ways. He said he felt free.

It was clear the minister had either not been informed of this fact or conveniently chose to ignore it. Since we were not paying him we were not his constituency. I was pretty angry at him at the time but I'm not now. Religion is the parasitic load of culture. We might not like it but it seems that we're stuck with it the same way we're stuck with E. coli STDs.

But thinking of religion in this way has given me a bit of freedom, too. After all, if religion is inevitable, there's nothing to be done about it. Besides, if religions are biologically part of us like an appendix or a tonsil, it means that none of them have any better claim to truth than any other. It's like head lice in schools. It happens.

And if all religions are more or less equal, we shouldn't be so upset with upstarts. After all, a couple of hundred years ago the Mormons were just some personality cult in New England. Now they're a world religion with their own parasitic load on society. So don't think of David Koresh and the FLDS as cults.

Think of them as start ups.
Links of Interest
Decreased oxygenation of the ocean
Send your name to the moon
Fertile women have sexy voices. Really. I'm not making this up.
O disquiet death
Human and Neanderthal skull differences due to random chance and here
Cultural Evolution vs Biological Evolution
Genetic mechanism for the difference in evolution between men and women
Stalin's ape hybrids
Satellite pictures of the Burma cyclone floods
Volcanic eruption in Chile
Truly Strange Films: Microbia
Regulating Evolution
Learning is Bad. Dumb is Good.
Mathematical Art