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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Why it's so easy

Posted on June 25, 2009 by Michael

The more and more I think about it, the more and more I recognize just how easy it is to understand evolution.

Evolution is the change within populations over time. This change is continuous. Take birds, for instance. They are descended from dinosaurs. Depending on who you ask, you might even hear them referred to as dinosaurs. However, for the sake of argument, let’s draw a line in the sand. Let’s say birds are birds and dinosaurs are dinosaurs. There is no single point to which we can point that says “Ah-ha! This is the generation in which birds originated!” Evolution doesn’t work that way.

Life is gradual in the big picture. The lines are blurry as to where one species begins and where another ends. It is simply a matter of convenience that we are able to make the distinctions we make. Ancient birds weren’t great at flying. Less ancient birds were better. Even less ancient birds were even better. And then, sometimes, extant birds are back to being terrible at flying. It just so happens that we’ll never know what every year of every species was like. If we ever do, we won’t be able to say “Such-and-such is Species X and this other example is Species Y”. We’ll be looking at Species X.1, X.11, X.111, X.112, etc.

To be this all another way, mother birds (or bats or monkeys or humans or bears or prarie dogs) only give birth to daughter birds (or bats or monkeys or…etc). But over time, small changes accumulate. Think of how much you probably resemble your father in some way. Now think of how much you resemble your grandfather. Odds are, you resemble him less than you resemble your father. Go back further and you’ll see more changes. And that’s just on a phenotypic (for purposes here, “physical”) level. Go to a genotypic (genetic) level and there’s no questioning the facts. You are more similar to your close relatives than to your distant ones.

Now we have to extend this concept over time. We have plenty of it. Evolution has been playing out for nearly 4 billion years. Think about that for a moment. You’ll live around 80 years. If you’re lucky, you might hit 100. A tremendously long human lifespan would be another 20 years on top of that. It’s all a blip on the timescale of Life on Earth.

So here’s what you should be thinking. Every generation is similar to the previous generation. It doesn’t matter what species we want to specify. It’s always true. But the further back we go, the fewer similarities we see. But importantly, we still see similarities.

Take the bones in the wing of a bat. They are easily matched with the bones in the hand of a human or the paw of a cat. They are the same bones but shaped vastly differently. It isn’t simply a huge (convenient) coincidence that this is so. Bats share a common ancestor with other mammals. This common ancestor, being that it is found deeply in time, would hold notable similarities with all extant mammals, but it obviously wouldn’t visually match with every single organism (or even a majority).

But the visual match isn’t all with which we need to concern ourselves. That common ancestor wouldn’t be able to breed with anything alive today. The changes have been far, far too considerable since its time.

I’m breaking stride for a moment because I want to note something. The changes which occur over time in a species are what cause it to be considered a new species. In other words, when two populations cease to be able to breed and produce fertile offspring, we have a two separate species (which one we want to call the “new” one is somewhat subjective, but usually it’s the one least resembling the common ancestor). As I said, there is no single point where speciation happens, but imagine for a moment approximately the time where two populations cease to be able to breed. It won’t be one defined generation where it occurs, but there will be some generation somewhere where some members of a population cannot successfully produce fertile offspring with members of another population.

On the face of it, this sounds like I’m contradicting what I’ve been saying all along about not being able to pinpoint one generation. I’m not.

Remember I talked about the lines being blurry. While some members of one population probably won’t be able to breed with some members of another population, that won’t be true for all members of both groups. Much breeding will still be possible. With time, those possibilities dwindle. Eventually, the line begins to come into focus. That is how evolution works: It’s gradual.

So again, the more and more I contemplate evolution, the more and more it makes so much sense. Of course, the evidence is crystal clear and I don’t need this contemplation to confirm the theory. However, it is through this focus that I’m forced to wonder why we had to wait until Charles Darwin and Alfred Wallace to really recognize how new species come into existence. The truth is that changes occur in populations over vast expanses of time. Then most of the world’s populations either continue to evolve or, more likely, go extinct. In hindsight, we observe definitive periods of stasis, almost leading one to believe in static, unchanging species. Almost.

Forelimb morphology

Filed under: Evolution | Tagged: , , , , , , | 19 Comments »

Why it’s so easy

Posted on June 25, 2009 by Michael

The more and more I think about it, the more and more I recognize just how easy it is to understand evolution.

Evolution is the change within populations over time. This change is continuous. Take birds, for instance. They are descended from dinosaurs. Depending on who you ask, you might even hear them referred to as dinosaurs. However, for the sake of argument, let’s draw a line in the sand. Let’s say birds are birds and dinosaurs are dinosaurs. There is no single point to which we can point that says “Ah-ha! This is the generation in which birds originated!” Evolution doesn’t work that way.

Life is gradual in the big picture. The lines are blurry as to where one species begins and where another ends. It is simply a matter of convenience that we are able to make the distinctions we make. Ancient birds weren’t great at flying. Less ancient birds were better. Even less ancient birds were even better. And then, sometimes, extant birds are back to being terrible at flying. It just so happens that we’ll never know what every year of every species was like. If we ever do, we won’t be able to say “Such-and-such is Species X and this other example is Species Y”. We’ll be looking at Species X.1, X.11, X.111, X.112, etc.

To be this all another way, mother birds (or bats or monkeys or humans or bears or prarie dogs) only give birth to daughter birds (or bats or monkeys or…etc). But over time, small changes accumulate. Think of how much you probably resemble your father in some way. Now think of how much you resemble your grandfather. Odds are, you resemble him less than you resemble your father. Go back further and you’ll see more changes. And that’s just on a phenotypic (for purposes here, “physical”) level. Go to a genotypic (genetic) level and there’s no questioning the facts. You are more similar to your close relatives than to your distant ones.

Now we have to extend this concept over time. We have plenty of it. Evolution has been playing out for nearly 4 billion years. Think about that for a moment. You’ll live around 80 years. If you’re lucky, you might hit 100. A tremendously long human lifespan would be another 20 years on top of that. It’s all a blip on the timescale of Life on Earth.

So here’s what you should be thinking. Every generation is similar to the previous generation. It doesn’t matter what species we want to specify. It’s always true. But the further back we go, the fewer similarities we see. But importantly, we still see similarities.

Take the bones in the wing of a bat. They are easily matched with the bones in the hand of a human or the paw of a cat. They are the same bones but shaped vastly differently. It isn’t simply a huge (convenient) coincidence that this is so. Bats share a common ancestor with other mammals. This common ancestor, being that it is found deeply in time, would hold notable similarities with all extant mammals, but it obviously wouldn’t visually match with every single organism (or even a majority).

But the visual match isn’t all with which we need to concern ourselves. That common ancestor wouldn’t be able to breed with anything alive today. The changes have been far, far too considerable since its time.

I’m breaking stride for a moment because I want to note something. The changes which occur over time in a species are what cause it to be considered a new species. In other words, when two populations cease to be able to breed and produce fertile offspring, we have a two separate species (which one we want to call the “new” one is somewhat subjective, but usually it’s the one least resembling the common ancestor). As I said, there is no single point where speciation happens, but imagine for a moment approximately the time where two populations cease to be able to breed. It won’t be one defined generation where it occurs, but there will be some generation somewhere where some members of a population cannot successfully produce fertile offspring with members of another population.

On the face of it, this sounds like I’m contradicting what I’ve been saying all along about not being able to pinpoint one generation. I’m not.

Remember I talked about the lines being blurry. While some members of one population probably won’t be able to breed with some members of another population, that won’t be true for all members of both groups. Much breeding will still be possible. With time, those possibilities dwindle. Eventually, the line begins to come into focus. That is how evolution works: It’s gradual.

So again, the more and more I contemplate evolution, the more and more it makes so much sense. Of course, the evidence is crystal clear and I don’t need this contemplation to confirm the theory. However, it is through this focus that I’m forced to wonder why we had to wait until Charles Darwin and Alfred Wallace to really recognize how new species come into existence. The truth is that changes occur in populations over vast expanses of time. Then most of the world’s populations either continue to evolve or, more likely, go extinct. In hindsight, we observe definitive periods of stasis, almost leading one to believe in static, unchanging species. Almost.

Forelimb morphology

Filed under: Evolution | Tagged: , , , , , , | 19 Comments »

Obese sex is unnatural

Posted on June 24, 2009 by Michael

Sex with obese individuals is unnatural, not intended by God, and thus wrong and immoral.

People are naturally attracted to healthy individuals. The obese are definitively not healthy. It follows, plainly and clearly, that any attraction to these people is a sexual perversion. Furthermore, those who are obese are gluttonous and thus sinners.

As a result of these facts, I propose a ban on all marriage to the obese. They harm society through their added burden to the healthcare system. They encourage children to think that obesity is acceptable, even though the Bible clearly bans it. Obesity is a scourge on the world which must be destroyed.

Only things deemed ‘natural’ and ‘intended by God’ can be considered normal, good, even moral. All else must go. It makes me go “Yuck!”

Filed under: Politics and Social | Tagged: , , , , , , , | 54 Comments »

Charles Darwin and the Tree of Life

Posted on June 23, 2009 by Michael

I recently watched a BBC America special by David Attenborough titled Charles Darwin and the Tree of Life. It was excellent. I’m familiar with Attenborough. Any fan of science probably is. However, I’ve had limited exposure to the man. He isn’t as popular in America as he is across the Pond as far as I can tell. At the very least, he isn’t promoted much on most of the science shows and networks I watch. I’ve been missing out. He has a passion about him that is as strong as the passion that was within Carl Sagan. I was especially struck by an absolutely beautiful segment in the show which broadly walked through the history of life. The video description says it will make one feel insignificant. It should. At the same time, though, it shows a grandness in Life, and that’s something of which we are all apart.

Filed under: Evolution | Tagged: , , , | 1 Comment »

Cowardice and lies

Posted on June 19, 2009 by Michael

I recently wrote a letter to the editor of my local newspaper, the Kennebec Journal. Here it is.

My very first job was at Hannaford on Willow Street. Starting pay for a high school student was relatively good, key word “relatively”. My friends made minimum wage whereas Hannaford started me a quarter above. That’s not fantastic, but again, I had good pay relative to my peers.

It has recently come to my attention through acquaintances working at that dingy, grimy, ugly little place more commonly known as Ghettoford, that they have a coworker – an employee of 12 years – who has just reached the $9 mark. Nine. Really? I mean, REALLY?

I quit that job for the very fact that said employee was making under $8 in 2005. Inflation is apparently a concept foreign to Hannaford.

The manager at the time, John Gibson – now demoted to assistant manager for Skowhegan – touted the company line and refused to admit that less than $8 was a livable wage for an adult.

When pressed to actually be human, he reverted to the company line that Hannaford pays ‘well’ relative to other human-hating stores. The man had no good answer. Bad wages are bad wages, even if the next guy is worse.

Gibson knew $8 was an insult then, and I’m sure he knows $9 is an insult now. Worst yet, he is representative of the culture that Hannaford promotes. The people in charge of forcing poverty upon the employees at this wretched business are filthy trash who don’t give a damn about anything but their vacuous bottom line.

I have no link to offer because, well, it never got published. I received an email from Opinions Page Editor Naomi Schalit. Here it is.

Dear Michael,

Thank you for your recent letter to the editor. Your letter contains some
allegations which we are unable to verify. We will not be able to publish
your letter as it would be unfair to print just one side of the issue.

Please feel free to write us on other topics.

I am honestly torn. I’m sitting here wondering if I should begin my response on FTSOS “HAHAHAHAHA” or with simple dismay.

This response is an act of cowardice. Furthermore, it is a lie. I’ve been losing confidence in this paper for quite some time now. This only solidifies my dismissal of the majority of this publication as worthwhile.

Letters to the Editor are not held to nearly the same standard as the journalists who fill all the other pages. It is not unfair to offer one side of an issue. Come on. That’s the whole point of an editorial page! What’s the alternative? Should individuals only submit their opinions if they are also submitting the opinions of others? Perhaps the Kennebec Journal would like readers to collaborate and only submit joint letters.

This woman is outright lying to me, though. She isn’t refusing to publish my letter because she couldn’t verify my ‘one-sided point of view’. She publishes thousands of unverified claims every year. The issue here is that I gave a specific name – John Gibson. He was a shitty manager. He’s probably a shitty assistant manager now. The fact that I’m willing to say this is what’s causing the ruckus. It’s a lie to tell me that she can’t verify claims.

Furthermore, it’s an act of cowardice for the KJ to not publish this letter. It is my thought that they believe they may be liable for my words. I doubt that’s true, but if it is, what could possibly happen? John Gibson is a complete corporate hack. He isn’t going to agree with me that low wages are deplorable. That’d jeopardize his career. His only route would be to admit that he believes low wages are fair at Hannaford. That’d ruin his whole libel case since it’s precisely what I’m saying. And even if all that falls through, it’s just a case of he-said, he-said. Libel is very hard to prove. It can’t be done in this situation.

The Kennebec Journal needs to be taken to task. This blog post will reach a few, but not enough. I am going to launch a monthly publication in my local area late summer/early fall. Costs will be relatively low and there are good businesses for liberal advertising around here. At the very least I expect to get my voice out there (along with some like-minded friends). The subject matter will be much like FTSOS, so this isn’t simply a response to this denial to publish my letter. However, the KJ may very well start making the news rather than just reporting it.

Filed under: News, Politics and Social | Tagged: , , , , | 1 Comment »

The purpose of purpose

Posted on June 19, 2009 by Michael

Filed under: Atheism/Humanism, Evolution | Tagged: , | Leave a comment »

The stupidity, it doesn't stop

Posted on June 17, 2009 by Michael

This is currently on Conservapedia’s front page:

The killer at the U.S. Holocaust Memorial Museum, James von Brunn, was a white supremacist and also an evolutionary racist. James von Brunn wrote that “Only the strong survive. Cross breeding whites with species on the evolutionary scale diminishes the white gene-pool while increasing the number of physiologically, psychologically, and behaviorally deprived mongrels.” The evolutionist Charles Darwin was also an evolutionary racist. The shooter, James von Brunn, also appears to have had close ties to neo-Nazis and his ex-wife said his anti-semitism and racist hate “ate him alive like a cancer”. Adolf Hitler was also a rabid evolutionary racist.

Aside from reading like a child wrote it, this is just the same old creationist appeal to emotion. These people have no evidence to back up their horribly stupid views, so they resort to dumb things like this; evolution means racism!!! It’s therefore wrong!!1!!

But here’s the kicker. Even if one were to ignore the glaring logical fallacy in the wee little minds of Conservapedians, the argument still fails. Being wrong is also a major no-no when making any argument.

James von Brunn’s beliefs are not based upon any real understanding of evolution or genetics. If they were, then he’d know that two white people can be more genetically diverse between each other than a white person and a black person. In other words, race doesn’t have any biological grounding. So if Conservapedians actually think it is a valid tactic to judge the merits of scientific evidence based upon inconveniences that it may give, then the real argument here is that evolution informs us that racism has no good basis and is therefore stupid.

von Brunn’s idea of evolution is very close to the creationist idea of the theory. Neither one is anywhere near correct. They both use their particular versions of this revolutionary concept to suit themselves. von Brunn thought there was a significant genetic basis for races. Creationists think evolution actually says that. The only difference between these abuses is scale. von Brunn is one guy with wrong ideas and the crazy to back them up. Creationists are a huge group of poorly educated, unfortunately ignorant individuals* who harm the progress of science by rejecting the most fundamental concept to an entire field.

The Conservapedia piece mentions that Charles Darwin was an “evolutionary racist”. This is more conservative screaming and kicking. Reasonable people keep pointing out just why they are wrong, but the conservatives just switch to more convinced language. That’ll do it.

Darwin held many of the racist beliefs of his day, but he didn’t need evolution to get him there. His science stands firm, regardless of what he may have believed. But for what it’s worth, he was ahead of his time with his race views. He also was a big abolitionist.

As for Hitler, he suffered from the issues as von Brunn. In addition, however, the man may have just been abusing any old idea for his purposes. He invoked all sorts of beliefs, including the words of Jesus, to rally support for his plans, actions, and goals. This says nothing of whether or not he was right.

*Ignorance is no crime. We’re all guilty of it. Fortunately, there are remedies.

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