Monthly Archives: April 2010

RNAPs and Another Front-loading Prediction

As you now know, the bacterial and archaeal RNA polyermase (RNAP) differ in complexity.  Despite the fact that the cell plan of both life forms is small, relatively simple, and streamlined, the RNAPs differ remarkably in terms of complexity, where the bacterial version is built from four parts, while the archaeal version is built from 11 parts.

The non-teleological perspective would “explain” this disparity by simply informing us that there are many ways to transcribe DNA into RNA and these two RNAPs would merely reflect the many roads to Rome.  At that point, we might remind people that this non-teleological perspective led biologists astray, as it prevented them from anticipating the widespread phenomena of deep homology.  But worse than that, this explanation doesn’t work with these cellular RNAPs.

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PREPA

In The Design Matrix, I explore the four criteria used to assess any putative design inference in an open-ended manner.  One such criterion is Foresight.  Let me share a couple of excerpts from the book that outline one way to recognize foresight has been in play:

The second phenomenon that speaks to foresight involves a shift in the way we look at history. Normally, to understand the present, we explore what happened in the past, trying to uncover all the relevant past events that led to the present state. Th is is the standard historical approach. For example, if a historian wants to understand how America became involved in World War II, he will explore the history prior to America’s entry into war and consider all the relevant events associated with America’s relationships with Asia and Europe. But if we are, in fact, dealing with foresight in action, we can reverse this approach and attempt to use the present to understand the past. I will call this new perspective PREPA (the present explains the past). How does PREPA work? Consider a mundane example. Your friend becomes concerned because his wife has been acting strangely lately. On Monday, she stayed away from home for an uncharacteristically long time. “She said she was shopping, but she rarely shops on Monday,” he explains. On Tuesday, he says he entered the bedroom and she quickly hung up the phone. He asked her who she was talking to, and she fumbled about with words and eventually said it was one of her friends. On Wednesday, she gave the house a good cleaning, “Which is odd,” he says, “because she normally does that on Saturday.” On Thursday evening, she tells him that he should go bowling with his friends Friday evening. “Now, she normally complains when I go bowling,” he explains. So you take your friend bowling. After one game, you take him home early to check on his wife. He enters the door and it is dark. He then flips on the light and people everywhere jump out and shout, “Surprise!” At that moment on Friday evening, suddenly the present explains the past (his wife’s behavior Monday through Thursday). She was acting according to foresight, as she planned for the surprise party. What did not make sense in the past now all comes together.

I then offer a biological candidate for PREPA:

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Shallow Water

Jerry Coyne just reviewed the books of Richard Dawkins and Jerry Fodor and Massimo Piattelli-Palmarini.  I can’t comment on the books themselves, as I have not read either one.  However, shocking as it may be – are you sitting for this? – Coyne lavishes great praise on Dawkins’ book and sneers at Fodor and Piattelli-Palmarini’s book.  Never saw that one coming, did ya?

In one part, Coyne gushes as follows:

Dawkins describes selection as an “improbability pump,” for over time the competition among genes can yield amazingly complex and extraordinary species. Here’s how he describes the evolution of tigers:

“A tiger’s DNA is also a “duplicate me” program, but it contains an almost fantastically large digression as an essential part of the efficient execution of its fundamental message. That digression is a tiger, complete with fangs, claws, running muscles, stalking and pouncing instincts. The tiger’s DNA says, “Duplicate me by the round-about route of building a tiger first.””

Only Dawkins could describe a tiger as just one way DNA has devised to make more of itself. And that is why he is famous: absolute scientific accuracy expressed with the wonder of a child–a very smart child.

So Dakwins writes yet another book about Darwinian evolution that recycles his signature argument from 35 years ago and Coyne squeals like a young school girl.

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The Archaeal RNA polymerase

Given that the archaeal RNA polymerase is needlessly complex when compared with the eubacterial RNA polymerase, let’s take a closer look.

The bacterial RNAP contains four subunits, the yeast RNAP contains 12 subunits, and the archaeal RNAP contains 11 subunits.  So when it comes to complexity (the number of parts), we would group the archaeal and eukaryotic versions together.

Yet when it comes to size (HT to Guts), the archaeal and bacterial version group together, both being around 400 kD.  In contrast, the yeast RNAP is around 600 kD.  So we do see evidence of streamlining in archaea – it’s simply in the size and not the complexity of the RNAP.  And this makes the needless complexity of the archaeal RNAP even more perplexing.

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Deep Needless Complexity

In the previous entry, I showed you how the eukaryotic cell plan is far more complex than the bacterial cell plan on multiple levels.  We might add the existence of introns in protein-coding genes, and thus the need for a spliceosome, to the picture.  And we’ll  add more in the future.  But for now, we have enough to acknowledge the existence of a mystery.  Since bacteria teach us that life is possible without all this complexity, we can explore questions that remains in the collective blind spot of the non-teleologists – Why is the cell plan of the eukaryotic cell so needlessly complex?

We could try to explain this by invoking the large population sizes of bacteria and hypothesize that this difference is the consequence of purifying selection.  After all, it is well known that natural selection streamlines bacteria for efficient replication.  Yet while this may be part of the explanation, it leaves too many stones unturned. For example, does this mean that life originated from complex, rather than simple, beginnings, and natural selection has pruned away much of this ancient complexity?  And how did the eukaryotic cell plan emerge in such a way as to escape the pruning shears of purifying selection?  And why hasn’t purifying selection streamlined the machinery inside the yeast cell, an organism which exists as large populations?

To show you how deep this mystery goes, let’s focus on one example of needless complexity – the RNA polymerase.

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Eukaryotes: Needlessly Complex

It is well known that eukaryotic cells are more complex than prokaryotic cells. For example, while the typical eukaryotic cell is 10-100 micrometers in diameter, contains numerous membranous organelles, has an elaborate cytoskeleton, and reproduces through mitosis, the typical bacterial cell is only 0.2-2.0 micrometers in diameter, lacks organelles, and reproduces through binary fission. Clearly, the cytological complexity of the eukaryotic cell is not needed in order to be alive.

Yet the theme of needless complexity repeats itself at increasingly smaller scales like a fractal image.

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Deja Vu

Here’s a nice example to show how our culture is so deeply influenced by scientism:

Such scenes are speculative, but Hawking uses them to lead on to a serious point: that a few life forms could be intelligent and pose a threat. Hawking believes that contact with such a species could be devastating for humanity.

He suggests that aliens might simply raid Earth for its resources and then move on: “We only have to look at ourselves to see how intelligent life might develop into something we wouldn’t want to meet. I imagine they might exist in massive ships, having used up all the resources from their home planet. Such advanced aliens would perhaps become nomads, looking to conquer and colonise whatever planets they can reach.”

Hold on. Why does this sound so familiar?

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