Oh, Jesus

Posted on July 9, 2009 by Michael

There’s a story floating around the interwebbings that says “Study shows evolution guided by ‘invisible hand'” or some variation of that. Most of the actual articles take this idea too far.

A study in the University’s School of Psychology sought to explain how turn-taking has evolved across a range of species. The conclusion is that there is an “invisible hand” that guides our actions in this respect.

That isn’t really the conclusion. The researchers did use the phrase “invisible hand”, but they didn’t come to a scientific understanding that, “OO! Magic!” is what’s going on here. Here’s some actual meat.

The researchers state: “Turn-taking is initiated only after a species has evolved at least two genetically different types that behave differently in initial, uncoordinated interactions with others. Then as soon as a pair coordinates by chance, they instinctively begin to play ‘tit for tat’. This locks them into mutually beneficial coordinated turn-taking indefinitely. Without genetic diversity, turn-taking cannot evolve in this simple way.”

Tit-for-tat is a model of behavior that results in a form of altruism. It’s pretty much what it sounds like: you scratch my back, I’ll scratch yours. A lot of organisms have it, and it’s especially strong among kin or even likely kin. The basis is that closely related organisms tend to have highly similar genes. While helping out (in one form or another) one’s brother may seem detrimental, it actually isn’t. That brother has 50% of the genes, on average, that the helper has. He’s really helping a lot of his own genes. On top of that, the brother is likely to help back at some point in the future (afterall, genes for altruism, if in one brother, are likely to be in the other brother).

What happened in the aforementioned study is that tit-for-tat is already assumed in the model. That is, it has already evolved within groups. What needs to be explained is specific turn-taking. And that’s exactly what the researchers did. They showed that it takes a random throw of the dice to find the right gene combination, so to speak. Once that point is reached, the non-randomness of natural selection can subject those genes to adaptations.

Professor Colman added: “In our simulations, the individuals were computer programs that were not only dumb and robotic but also purely selfish. Nevertheless, they ended up taking turns in perfect coordination. We published indirect evidence for this in 2004; we have now shown it directly and found a simple explanation for it. Our findings confirm that cooperation does not always require benevolence or deliberate planning. This form of cooperation, at least, is guided by an ‘invisible hand’, as happens so often in Darwin’s theory of natural selection.”

Let’s be fair to Professor Colman. There’s no way of telling from this if he too is trying to sneak a vague concept of a god into all this. I doubt he is. Unfortunately, it doesn’t matter because he’s a scientist and his languages suggests religious connotations. That is why the media especially latched onto this story. It isn’t like turn-taking grabs the attention of the average layman.

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Dawkins

Posted on July 9, 2009 by Michael

What has theology ever said that is of the smallest use to anybody? When has theology ever said anything that is demonstrably true and is not obvious? I have listened to theologians, read them, debated against them. I have never heard any of them ever say anything of the smallest use, anything that was not either platitudinously obvious or downright false. If all the achievements of scientists were wiped out tomorrow, there would be no doctors but witch doctors, no transport faster than horses, no computers, no printed books, no agriculture beyond subsistence peasant farming. If all the achievements of theologians were wiped out tomorrow, would anyone notice the smallest difference? Even the bad achievements of scientists, the bombs, and sonar-guided whaling vessels work! The achievements of theologians don’t do anything, don’t affect anything, don’t mean anything. What makes anyone think that “theology” is a subject at all?

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Bats

Posted on July 8, 2009 by Michael

We’ve had an abundance of rain in the past month in my area. As such, we have a lot of standing water. To make matters worse, I live near a lake, which often means there’s standing water nearby anyway (and that’s definitely the case here). This all adds up to mean a deluge of mosquitoes. Fortunately, there are also a lot of bats around here. But it isn’t all gum drops and soda. Sometimes having a lot of something means things will start showing up where you don’t want them to show up.

In the past two days, I’ve encountered three bats in my apartment. The first was dead. I’m not sure if a cat killed it or if it died naturally or if it was white nose syndrome (though there was no visible fungus). The second was among a series of shirts I have layed over a large change bottle. I got that guy downstairs before he decided to take a quick aerial tour of the area. I eventually got him out the door. The third one, which showed up tonight, almost victimized by the hungry mouths of several cats, decided to go for the extended stay with optional aerial tour of the living room. It was fascinating watching it flying back and forth and back and forth and back and forth. After waking some sleeping roommates, we got it sequestered in the sun room/porch. Unfortunately, there’s no light in that small room, so there was a lot of fast ducking and thrown blankets in response to the constant dives and erratic motions of the bat. With time and a little help from an empty Yahtzee box, we got it out one of the windows.

So, in honor of this story (which I don’t think is over – we have little idea of where these things are originating), I am reposting some bits from a Carl Zimmer piece on bats. Be sure to click “Bat in wind tunnel” and “Vampires running!” to watch the videos. For whatever reason, I cannot embed any better than that.

Bats evolved about 50 million years ago from squirrel-like ancestors. They probably made their first forays into the air as gliders. Like living gliders, they used flaps of skin to increase their surface area, letting them glide further. Their hands evolved long spindly fingers that were joined by membranes. Some early bat fossils suggest that they may have shifted from gliding to alternating between gliding and bursts of fluttering. Eventually bats evolved sustained powered flight.

Bats evolved a way to take advantage of the same laws of physics birds use to fly. And many scientists who have studied bat flight in the past have basically treated bats like leathery birds. Yet there’s no reason to assume that this should be so. After all, it would not be surprising to find that the way the feathers on a bird’s wing react to air pushing against them are different from the way the stretchy membranes on a bat react. Birds don’t have wing surfaces connecting their front and back legs, like bats do. And while birds only have a couple joints in their wing skeleton, such as at the elbow and wrists, bats have lots of knuckles they could, in theory, bend selectively to alter their wing surface. Bats also have lots of sensitive hair cells on their wings that appear to track the speed and direction of the air flow, and the information they get from the hairs may help them make fine adjustments to their wings many times a second.

Bat in wind tunnel from Carl Zimmer on Vimeo.

I think the creepiest thing about this whole event, other than the possible rabies, was the way I watched the third bat walk. It landed on the floor a couple times and crawled around a bit. I wish I could have had more light to really observe it.

Vampire running! from Carl Zimmer on Vimeo.

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Obama continues to fix the errors of Bush

Posted on July 6, 2009 by Michael

Scientists will be allowed to make the guidelines surrounding use of embryonic stem cells.

The government issued final rules Monday expanding taxpayer-funded research using embryonic stem cells, easing scientists’ fears that some of the oldest batches might not qualify and promising a master list of all that do.

President Barack Obama lifted previous restrictions on the field in March, but left it to the National Institutes of Health to decide just what stem cell research was ethically appropriate: Only science that uses cells culled from leftover fertility clinic embryos — ones that otherwise would be thrown away — the agency made clear in draft guidelines.

This is precisely how it should be. It is those well versed in science who should be making the relevant decisions within science. Politicians rarely ever know much of anything about how science needs to work. This is doubly true for Republicans. So it comes as no surprise that it has taken the election of Democrats to at least get a few things right.

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DNA Portrait

Posted on July 6, 2009 by Michael

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Hawking

Posted on July 4, 2009 by Michael

The intelligent beings in these regions should therefore not be surprised if they observe that their locality in the universe satisfies the conditions that are necessary for their existence. It is a bit like a rich person living in a wealthy neighborhood not seeing any poverty.

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It seemed so innocent

Posted on July 3, 2009 by Michael

I wrote this for the purpose of a Facebook note, but I would love to make it more public. So, here ya go.

~~~

As I returned to town with girlfriend in company, I had a sudden idea. I had recently purchased a new driver from Play It Again Sports on Bangor Street. Good investment from a good business. The employee there – almost certainly still in high school – went so far as to virtually insist on carrying out my other, bulkier purchases for me. If not a good business sense, then he at least at a solid grasp on common decency. So in my desire to complete the satisfaction around my recent acquisition, I decided to stop by T’s Golf in Manchester to hit a couple balls.

It wasn’t far from closing time and I didn’t want to make anyone wait around for me to hit a full bucket. Besides that, I had a lovely lady to entertain. As such, I only wanted to hit 3 or 4 balls. Purchasing a full bucket wasn’t in my plans.

Upon arriving at the range, I noticed the empty lot. I always wondered why I rarely saw many vehicles at this business. This night I chalked it up to the late time and gloomy weather.

I grabbed my clubs, a few balls and set up at one of the deserted tees. It didn’t take long for Rawn “Misspelled-Name-And-All” Torrington to come out with his wife Judy. When he asked “Are you hitting your own golf balls?”, I naturally assumed the best in him, thinking he was making some friendly chit-chat. Just imagine it. The local proprietor seeking quality relations with his customers. It happens all the time, every day. As much as I’ll rag on Hannaford or McDonald’s or any other lowing-paying retail location, they usually higher good people who usually treat customers with kindness; if not always great service, then at least kindness. But we all know what happens when one assumes. It makes an “ass” out of “u” and “me”.

Rather than being the savvy owner I expected, Torrington instead showed a complete disregard for good business sense, not to mention common decency. He opened by chiding me for daring to use his facilities for free. “I have $200,000 invested in this operation!” he wailed. Okay. Let’s hang on a second.

It’s fair enough that he wouldn’t offer his services for free. It doesn’t seem unreasonable to let a person take a whack or two on range where a roaming tumble-weed may be expected, especially if said person is using his own equipment. There’s no gain or loss, regardless of the operation being worth $2, $200,000, or $2,000,000. But again, it’s fair enough. It’s his business and he isn’t supplying anyone with a free playground.

That isn’t the problem.

The problem is that Torrington’s blood was virtually boiling. He had no justification for his reaction. He was perhaps only rivaled by Mrs. Torrington’s immaturity.

I say without embellishment or revision, our reaction was nothing if not mild. I briefly explained that I just wanted to hit a ball or two to try out a new club. Judy Torrington tore into us, foam not far behind her lips.

“You should know better!”, she screeched.

Know better than what, Torringtons? Than to innocently hit a few balls into a field? I’ll concede that asking would have been prudent. But whether or not I should have known better or done differently is far from the point. The point is that bad behavior is rarely justified. This falls under no exception of which I can imagine, if there even are any.

In the interest of full disclosure, I let fly some colorful language. I regret ceding the high-ground, though not the sentiment behind the words.

We packed up our gear, constantly reminding these two horrible business owners that we weren’t maliciously attacking their livelihood. They seemed convince that any action which does not result in profit for them must also be a personal slight.

And here’s the kicker. Had either of these individuals simply explained, with calm and composure, that they didn’t allow people to hit their own golf balls, I would have asked how much a small bucket cost. I assumed at least $5, not to mention the time it’d take for me to hit them when I arrived. As it turns out, according to their website, I could have gotten 10 balls for a buck fifty. I have no doubt that I would have made the investment.

As a result of the – to be frank – dumb business practices of T’s Golf in Manchester, they have forever lost my business. In reality, I didn’t contribute an arm and a leg in the first place. Independent of all this, I’ve always thought their mini golf was one of the worst I’ve ever played; it has no pop, no pizzazz. What’s more, they don’t provide the clubs for their driving range. T’s Golf, regardless of the poorly customer-versed owners, is not a good facility from the get-go. This recent debacle only ensures that even less of my money – precisely zero dollars – ever gets spent there.

But the story doesn’t end here. And I’m not alone.

Immediately following this incident, I headed over to All Steak Hamburger on Hospital Street. It was there that I spoke with the owner (whose name I missed).

Because he has a driving range (as well as a restaurant and batting cages) I asked him what he would do if someone wanted to hit a couple of their own golf balls from his tees. He said it didn’t matter to him. Anyone who does it will obviously lose anything they hit, but people can bring entire bags of golf balls for all he cares (and they have). That’s good business sense.

After he explained his casual position to my scenario, I told him that I had just come from T’s and…his laughter quickly cut me off.

“Well, there’s your problem.”

As an anecdote, he told me that he gets about 1 customer per week as a result of Rawn and Judy Torrington and their bad business sense. I believe it. In speaking with further friends and family, that anecdote seems to be slowly morphing into a pattern.

So let’s break down what happened. I went to hit a few balls into a field. Rawn and Judy Torrington not only said no, but they practically cried it. It would be fine for them to kindly object to what I was doing. My actions were reasonable, but quality justifications can certainly be made against them. But, again, that isn’t the point. It’s the reaction to my actions which deserve the attention here. The bad moral and bad business decisions of the Torrington’s forever cost them my dollars. It wouldn’t be a stretch to say it has cost them the dollars of anyone reading this. Furthermore, it damages their reputation. Granted, the anecdotes appear to indicate that they already have awful reputations, but this certainly doesn’t help.

I guess I can’t just blame the rain for their empty parking lot. After all, All Steak Hamburger had both of their parking areas filled. Funny that.

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New information

Posted on June 30, 2009 by Michael

I’ve posted about “new information” in the past, but I recently wrote this for some friends and figured it may as well go up here, too.

~~~~~
This is from a YouTube video by some dishonest creationists who poorly edited a video to make it look like Richard Dawkins couldn’t answer a question. It doesn’t deserve to be linked.

“[Is there] an example of a genetic mutation or an evolutionary process which can be seen to increase the information in the genome?”

The answer is yes. But I won’t get to the heart of the question right away. It needs explaining.

A definition of “information” is drastically needed here. It’s a term that doesn’t really mean anything in the given context. However, we can ascribe it some definition which is useful. My best proposition is that it can mean DNA itself (nucleic acids), amino acids, or genes. I’ll tackle DNA first.

Our genetic code consists of four ‘letters’, A, C, T, and G (or adenine, cytosine, thymine, and guanine). These four letters are mixed in a huge number of ways in order to form amino acids. It is amino acids which compose our genes. But let’s slow down.

An amino acid is composed of 3 letters. Let’s say we have CGU. That makes arginine. If we replace that final letter with, say, another “C”, we have CGC. As it happens, that still gives us arginine. Different letter combinations can make the same amino acid. When a mutation occurs which does this, it’s called a silent mutation. It’s neutral and natural selection is blind to it.

Now let’s say we change that middle “G” to an “A”.That gives us CAC, or histidine. This is a completely different amino acid. It’s presence in a given gene in place of arginine can have potentially huge consequences. This single letter substitution is called a missense mutation. (It is also called a point mutation because just one letter was changed; the same applies to the arginine example.)

So as should be clear, single letters of DNA can be considered information because they can have profound effects on genes, which in turn affect how proteins are made. However, we have another avenue.

An amino acid can be considered information because it is more directly responsible for the changes to how a protein operates than a simple letter. Personally, I prefer this option the least, but I digress.

Genes are composed of chains of amino acids. Some can be quite short while others range into the hundreds, even thousands. Recall how an amino acid is composed of a series of 3 letters of DNA. That means those letters go back to back to back to back to etc…, each set of 3 making an amino acid. After one triplet, there’s another. And another. Each “another” is an amino acid. (Eventually, a gene can be defined, at least one way, by identifying where the stop codons are – triplets which tell the gene that it is at its end, thus releasing the amino acid chain.)

But if we’re going to call amino acids information, we may as well go a step further and just say genes. And this gets more to the heart of the question. Genes essentially determine what protein will be made (epigenetic or environmental factors are important, but there’s no need for those here). A mutated gene is mutated information, at least in a sense. So how can an evolutionary process be seen to increase the information in a given genome?

It’s actually pretty simple. DNA is far from perfect. It has incredibly high fidelity, meaning it makes few copying errors, but it isn’t perfect. That’s one way we get mutations. Another thing we can get is extra copies of genes. There are a myriad of ways this can occur which I will not discuss here. But it does occur all the time. In one recent text, I read of 12 copies of a gene for seeing green in relation to eyesight.

So what does it mean to have too many copies of a gene? Sometimes it can mean a lot. A lot of the time, though, it doesn’t have to mean too much, such as with the aforementioned case. But what happens to all those extra copies in the next generation, especially if they have no real world (phenotypic) results? They are not subject to the pressures of natural selection. They are free to mutate in whatever way they ‘please’. This gives these genes a huge range to become useful in other ways. In this case, they may affect vision acuity or color sharpness and that may be an advantage.

This is, for all intents and purposes, new information.

A gene gets duplicated. It mutates. It becomes useful, by chance, in some other way. It is subject to the pressures of natural selection. For that reason, it is maintained in the gene pool. Those with this gene have increased the size of the ‘information’ in their genomes.

Filed under: Evolution | Tagged: , , , , , | 3 Comments »

How apt

Posted on June 28, 2009 by Michael

From Conservapedia:

Attention Canadian evolutionists! Conservapedia now nearly ranks in the Google top 10 for the very popular search “evolution” at Google Canada! The Conservapedia evolution article ranks #12 at Google Canada for the search evolution![8] The article appears to be rapidly gaining prominence on the Canadian internet. Will this creation science wildfire spread to the USA, UK, and beyond? Please stay tuned for further developments!

They got their analogy right. Well, partially. Creationism is very much like a wildfire, though it isn’t anywhere near science. It’s a destructive force for not only science, but good in the world.

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Michael Jackson

Posted on June 26, 2009 by Michael

I don’t care that Michael Jackson is dead. I just know this will add to my blog stats. All aboard the exploitation train, right?

That is all.

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