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.

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.

Spearfishing in Borneo.

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?

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.