Recombination hotspots

Ran across an interesting article here. Key quote:

The researchers also identified particular patterns in the DNA that play a role in hotspot activity. ‘That is very exciting because it takes us closer to understanding how recombination is controlled,’ explained Dr Gil McVean, the other senior author. ‘It looks as though there are patterns in DNA which effectively say “recombine here”. Finding out more about that is a step along the road to understanding one of the major mechanisms shaping genetic variation and its consequences.’

The idea that our genome "knows" where and how to recombine is fascinating. It leaves us with two questions: "How does it work?" and "How did it happen?" The first question is purely scientific -- it will doubtless be fascinating, but is unlikely to be particularly controversial. The second question introduces a lot of speculation and philosophy, and is likely to raise a lot of fists on all sides.

From an evolutionary perspective, the answer to the second question is, "More really lucky mutations we can't comprehensively name or describe, but can infer, based on the paradigm of common descent via mutation. Species which randomly developed the capacity to vary in areas of the genome where variation is useful (and not varying in the areas where it is not) had a competitive advantage, and spread."

From a creationary perspective, the answer is, "Maybe the Creator intended to build in the capacity for rapid variation to allow species to adapt quickly to changes in environment, and to continue replenishing diversity."

Neither of those interpretations is particularly falsifiable. Neither of these interpretations will interfere with the ability of scientists to empirically study the mechanisms of the targetted variation.

Nevertheless, both sides will no doubt use the fact of targetted variation to support their own paradigm, and attempt to "debunk" the alternative.

Science and Magic

Evolution and Intelligent Design are typically characterized as "Science" and "Magic," respectively.

But it occurred to me the other day: intelligent design of life is being performed every day, by scientists. They are genetically engineering and modifying life; they are even working diligently on creating it from scratch (and have succeeded, it seems, in creating a virus, although people debate whether viruses are actually life or not). At the very least, self-replicating RNA has been assembled from scratch by humans.

So intelligent design and modification of life is clearly science. If it isn't, then why is it being performed by scientists all over the world, every single day?

On the other hand, you have the two dominant "unintelligent origin of life" theories -- RNA world and metabolism world. But nobody's demonstrated how they work. RNA world says "Some RNA came together by sheer luck, and that RNA happened to have the capacity to reproduce." Metabolism world says "A primitive metabolism showed up first, and self-replicating RNA came later." Both are, of course, undemonstrated.

So given the choice between the observed, replicated, coherent explanation of a scientist or scientists intelligently designing life as is seen on a daily basis, and the unsupported, explained, "magical" explanations about how life came together by sheer luck ... which one is "science" again?

The only reason "ID" is considered magic is because of a particularly narrow and rigid theology: the idea that "God" (the creator) works only through 'magic,' not 'natural' means. Get rid of that assumption, and ID becomes significantly more "scientific" than any of the alternatives.

Which brings us to a second important point: what are we to do with this theology of "magic?" What is this "supernatural" of which we speak with reference to the Creator?

I don't think the word "Supernatural" means anything. If you define nature as "everything that is," (a reasonable definition, I think), then there cannot be anything "beyond nature," by definition. God may be somewhere well out of our experience -- he may not be visible from our point of view -- he may not be a part of His "Creation." But if He exists, he must be within the scope of "all that is," and must, therefore, be either part of nature of the substance of nature itself.

So if this God (or gods) created us, he must have done it by "natural" means. No other understanding of creation holds any real meaning.

How? No clue. As Arthur C. Clarke said, "Any sufficiently advanced technology is indistinguishable from magic."

I brought this up in a discussion the other day, and the gentleman objected, saying that he would define "supernatural" as things that cannot be observed and studied, and "natural" as things that can be.

I responded that this definition leads to a whole host of problems.

According to his definition, quarks were "supernatural" until we were able to observe and study them; at which time they become natural.

According to his definition, the boats used during the Trojan war were "natural" at the time they were used, but subsequently became supernatural when they were destroyed and were thus no longer available for observation or study.

Clearly, there are only two categories of things: things that exist/occur, and things that do not exist/occur. If something does not exist/occur, it is not supernatural -- it is fictional. And if something occurs, but we cannot observe it, it is not supernatural, but rather, not yet observed

All this comes down to bad epistemology -- a sin of which both evolutionists and creationists are often guilty.

Adnan Oktar

A well-known Islamic and Turkish creationist named Adnan Oktar was recently convicted and sentenced to three years prison. For what, we're not quite sure.

DISCLAIMER: I'm not arguing about whether he's innocent or guilty -- I don't know anything but what I'm reading on the web. But this case smells really bad.


Here's the Reuters account .

According to the story, he was accused and convicted of "using threats for personal benefit and creating an organization with the intent to commit a crime."

There are two causes for suspicion here:

1) "In that court case, Oktar had been charged with using threats for personal benefit and creating an organization with the intent to commit a crime. The charges were dropped but another court picked them up resulting in the latest case." In other words, Double Jeopardy.

2) "No further details were immediately available." In other words, we aren't given any of the facts underlying the allegations.

Procedural abuses by the authorities and vague claims always raise my hackles -- in my work, these have proven to be a common theme for trumped up charges.

Here is a video of a portion of a long press conference he gave a while back, to the European media. The rest of the press conference is on youtube, and is absolutely fascinating. What I found most interesting was the unsubstantiated allegations made by the reporter -- about his "suing scientists who talk about evolution." Oktar called the reporter's bluff, and the reporter had nothing to say.

That started to smell even more like trumped up charges.

And then you find blogs titled "Whoisharunyahya" that make all only generalized allegations, without any substantiating facts. I'm hurting here. Need more data.

I have a potential lead on what may have happened here. I didn't realize exactly how nuanced, subtle, and balanced his views were. He calls for tolerance of Jews and Christians here. He says that the Jews have a right to the land of Israel here.

Those two views are enough to make him a lot of enemies in the Muslim world. His opposition to Darwinism is enough to earn him no friends among the secularists.

This brings new light to the statement of a spokesman that "the judge was influenced by political and religious pressure groups." Maybe.

I'm open to the possibility that he's guilty. But I haven't seen any coherent allegations or facts to support them. Apparently he's also been accused of cocaine use, having orgies, molesting little girls ... and been acquitted each time. That makes these allegations stink even more.

Thank God for Due Process.

According to this blog, Harun Yahya got a ruling in Turkish courts blocking wordpress blogs in Turkey, for defamation and libel. I'm certainly no fan of censorship of any type, and I don't know much about Turkish defamation law. However, I do know that the few wordpress blogs I saw (like this one) about him were plainly defamatory and libelous. He was accused of just about everything under the sun, all without evidence.

Nested hierarchies

Also during the long discussion yesterday, the topic of nested hierarchies came up. This caused me to look harder into the topic, to try and understand it. I found something interesting.

First, the main point. Evolutionists use "nested hierarchies" as evidence of common descent -- that is, life can be categories along certain lines, and there are no characteristics that violate those hierarchal categorization. Therefore, those hierarchies constitute the "family tree" of life.

When I first heard the argument, I was struck by how "label over reality" it was. That is, we categorize life according to certain characteristics, and then treat the structure of those categories as being "real." When if we picked different characteristics, we'd certainly have different hierarchies.

In fact, it seemed, there are all sorts of traits that violate the "rule of nested hierarchies."

So with this in mind, I started reading about the marsupials and monotremes, because they seemed to be a great place to start in looking into these hierarchies.

And what did I find? I found placental and marsupial variants of a bunch of different animals. All of the photos on this page are of MARSUPIALS, either alive or extinct. Yet we know instinctively, from looking at them, that they are eerily reminiscent of placental counterparts.

For example, there is the placental wolf, and the "tasmanian wolf," which was hunted to extinction in the 30s. The two species share all the major "dog" characteristics, except radically different reproductive systems, and, apparently, minor differences in the palate bone. So I kept looking, and I found the "marsupial sabertooth tiger," the "marsupial lion," the "marsupial anteater," the "marsupial flying squirrel," the "marsupial mole" the "marsupial badger (or tasmanian devil), the "marsupial mouse" ... and it didn't appear to be ending anytime soon.

All the sources I found treat all these animals as "convergent evolution" -- that is, the "tasmanian wolf" is not a "wolf" -- it is a "marsupial that happened to evolve a lot of the same characteristics as wolves, because it filled the same niche." Maybe I could buy this once. But how many times? Dogs, lions, sabertooth tigers, anteaters, moles, flying squirrels?

How many times did this "convergent evolution" happen?

Or maybe these "nested hierarchies" aren't as involable as argued. Maybe these organisms originated fully formed, in two distinct variants. Or maybe they originated in a single, primal form with the capacity for both forms of reproduction in the gene pool, which "fixed" due to genetic drift over time?

Whatever explanation you choose, these "nested hierarchies" start to look pretty silly when you have such a long list of organisms that have such similar placental counterparts, with only one significant difference: the reproductive system.

(I got all the photos straight off Google Images, and claim Fair Use, as this is a not-for-profit, educational purpose that uses documents only in small part).

Recurrent laryngeal nerve

I got baited into another long, fruitless debate with some gentlemen, but in the process, I learned some cool stuff about biology.

The recurrent laryngeal nerve is a nerve that runs from our brain to our voicebox to provide motor function and sensation to the voicebox. Interestingly, though, instead of running a direct route from brain to larynx, it runs from the brain, all the way down the neck to the chest, and then back up the larynx. It doesn't take the straight path -- it loops. Hence, recurrent. This occurs in a whole bunch of animals, including the giraffe -- where "taking the long road" adds meters of nerve.

One gentleman in particular used this as evidence of common descent -- after all, why would the nerve take this inefficient path from the brain down to the chest and back up to the larynx in animals as diverse as men and giraffes, unless the two species were related? Having never heard of this before, and finding it interesting, I googled "laryngeal nerve," to learn what it was. On a whim, I then looked up "non-recurrent laryngeal nerve" and I found this abstract, among others, which indicated that non-recurrent laryngeal nerves occur about 1% of the time in humans.

I brought this to the attention of the gentleman, and pointed out that given the regular occurrence of non-recurrent laryngeal nerves, it would seen that if such a path were advantageous, it would have been selected by now. Thus, the fact that the other variant is set (or nearly set) in the population indicates that the recurrent version may well have some advantage. There was also another abstract which indicated that the non-recurrent variant was quite deletarious during surgery, as it increased the chance of injury. That at least provided a potential explanation.

He never responded. I wish he had. He obviously knew some stuff about biology. He obviously had a lot to teach me.

The eye

Another video reflecting profound ignorance:



Here are the errors:

1) Non-sequitor. Titling the video "creationism disproved?" As though the presentation of a hypothesis of the evolution of one organ, the eye, could disprove the idea that the organism itself was created. Silly, if course.

2) Oversimplification. The video starts out with "light sensitive cells," as though the development of such cells was "no big deal." But let's take a closer look at this. How much genetic information is required to transform a limited number of cells into light sensitive cells? First, the cell has to hyperpolarize in light. Then, it has to have the capacity to produce various neurotransmitters depending on its state of polarization, and transmit them. And it has to be connected via nervous tissue which can transfer that neurotransmitters. And it has to have some capacity to receive the neurotransmitters. And it has to have the capacity to use this information in a way that adds survival value. All this irreducibly complex functionality, glossed over in just the "first step." All the further steps similarly oversimplify the steps of development. Like all the genetic information required to construct the "rudimentary lens," including the differentiation of lens cells, and the mechanisms required to manipulate those cells in order to make the lens useful. She skipped those steps, too. Finally, by focusing only on mollusks, she doesn't even get to the real difficult stuff -- the development of the eye BALL, which moves freely inside an eye socket.

3) Hypothesis masqueraded as science. All they have presented is a hypothesis -- not a theory -- there is in fact no evidence to prove that these various forms of eyes actually, historically, evolved from one another. The evolution of the eye could have been radically different than the process presented here. Or there could have been no such evolution at all. There is no evidence to falsify either of these other possibilities, and therefore the "just-so" story presented is not science.

4) Non-sequitur. I think my favorite quote of hers is "If it can grow, it can evolve." How beautiful is that. Growth is the process by which an organism follows the instructions encoded as genetic information preprogrammed into the organism. Evolution is the process by which genetic information is modified through the generations. Radically different processes. But she argues that if an organism can follow its preprogrammed genetic instructions, then surely those genetic instructions could be programmed into the organism without any intelligent intervention. Nice:). Like if a computer can start up, following the instructions pre-ncoded in its hardware and software, then surely those instructions can develop through random variation and non-random selection.

Placental genes

Cutting through the obligatory evolutionary ranting here, I think it's some pretty cool stuff. Basically, during the first stage in placental development, we activate primarily genes shared by other species. But in the second portion, we activate species-specific genes.

How cool is that?

The evolutionary error, of course, is to conclude from these facts that all the species are related. No go. Just because the Model T and the Highlander Hybrid both have tires doesn't mean they're related. But it's still really cool. I'm interested in what gene (or other biological structure) controls the activation of the genes within the two stages. How does the embryo "know" when different genes need to be activated?

Dawkins. Yikes.

I can't believe what I'm hearing here. Richard Dawkins said that "In order to prove that a fossil was really 3000 years old, they would have to find igneous rocks which were found in proximity to the fossils, date these by radioactive dating, several different methods of radioactive dating, all of which give independent estimates of the date of the fossil."

That's simply not true.

When you date igneous rock by radioactive dating, you determine how long ago the igneous rock cooled from volcanic rock. You do NOT determine how long ago the sedimentary strata in which you find the rock were laid down. A rock may have emerged from a volcano 1M years ago, and been buried in sedimentary strata 10 years ago. Radiometric dating will still find the rock to be 1M years old.

But, of course, the date of a FOSSIL laid down in a sedimentary strata is not the date of the old rock that got buried there, but the new bones!

By Mr. Dawkins' reasoning, you could have an igneous rock that was 1M years old, bury it in the dirt next to my shoe, and then upon uncovering them both, conclude that my shoe was 1M years old.

But even further, radiometric dating of rocks assumes that the rock had a particular composition when it was initially formed. For instance, K-Ar dating assumes that the rock initially had no Argon. If there was in fact Argon in the rock initially, the rock itself will date millions of years older than it actually is.

And in fact, there are many examples of volcanic rocks being found with Argon in them.

It never ceases to amaze me how these "scientists" are either unwilling or unable to grapple with reality.

Hardware and software

I often hear people, the popular press, and even "scientists" say things like "DNA contains all the information necessary to create life." Seems to me pretty clear that the claim isn't true, for one simple reason: In order to function, DNA must be in a cell which already has all the structures in place to keep the cell alive, as well as to use the DNA to code proteins.

Seems analogous to a computer: DNA is comparable to the software, and the cell is comparable to the hardware. But in a computer, both the software AND the hardware contain information necessary to the function of the computer.

Same with a cell: DNA by itself doesn't contain all the information necessary for life. The rest of the cell probably contains just as much information (if not more) in the configuration and function of all its organelles.

How much of the total information necessary for life is in the DNA? And how did the rest of the information come to be encoded in the cell? Someday maybe we'll know.