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:

Linker histone proteins (also known as H1) play an important role in packaging the large chromosomes of plants and animals. Although they are present in all eukaryotes, they are not essential for survival and reproduction in filamentous fungi, such as Ascolobus and Aspergillus. If H1 function is eliminated in these fungi, the cells are perfectly viable with no deleterious consequence on the sexual reproduction cycle. The same results were previously seen in the protozoan Tetrahymena. However, in the fungi mentioned, elimination of H1 does result in the cessation of growth within a week or two. So H1 does not affect viability or reproduction, but only the life-span of the individual organism (however, with Aspergillus, elimination of H1 does not even effect the life span of the organism and has no apparent effect). This all means that the linker histones may not be crucial for single-celled existence. Juan Ausio, from the Department of Biochemistry and Microbiology at University of Victoria, notes, “while linker histones may be dispensable for the relatively short life span of an individual cell, they are most likely indispensable for survival of higher eukaryote organisms.”16 Ausio argues that H1 may be essential for multicellular organisms because compaction of the genome is an important ingredient in the regulatory schemes used in generating and maintaining a multicellular body plan. If H1 was indeed designed, given its minimal role in protozoa, it might constitute a very good example of front-loading evolution such that the initial eukaryotic state was prepared to evolve a multicellular state. In other words, the existence of H1 in protozoa may best be explained by the existence of H1 in metazoans. That is one hypothesis that simply cannot be entertained, for the briefest of all moments, from a non-teleological perspective.

The PREPA pattern thus emerges as some biological feature that is strange and non-essential in its ancient state, yet makes sense and is essential in its modern state.  We can objectively determine if a feature is essential through genetic and phylogenetic analysis, as a non-essential element can be removed through experimental or natural mutation without causing lethality.  Keep in mind that non-essential is not the same as useless.

However, whether or not a feature is “strange” or “makes sense” depends on our mind’s eye and how we perceive things in their larger context.   Thus, there is a distinct subjective element to PREPA.  Nevertheless, what’s important is that PREPA can serve as a springboard to make testable hypotheses that help us to better understand our biotic reality.

So let’s now return to the archaeal RNAP.

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9 responses to “PREPA

  1. Whoa! You made clear what “strange” objectively means: “non-essential”.

    You made clear what “makes sense” obectively means: “essential”.

    Where’s the subjectivity?

  2. Hi Bilbo,

    I’m thinking of strange and non-essential, not strange and non-essential. You are stripping out the strange/makes sense aspect of the perception.

  3. Could you give me an example of an ancient biotic feature that is non-essential but not strange, and which is presently essential, but does not make sense?

    And if such a feature exists, are you saying that it would not qualify as a candidate of foresight?

  4. Or perhaps what you mean by strange is that the archaeal RNAP has so many more components than the bacterial RNAP, and in fact almost has as many as eukaryotic RNAP.

    In that case, “strange” seems to be a function of improbability. The more components the stranger it seems.

    And perhaps you’re tying “make sense” in with optimality. Not only is the component essential, it is optimal. But I think we can come up with an objective criterion for optimal, as well.

  5. The irony is that the one ID guy who is doing the best science, refuses to call it science, and doesn’t really like the term ID, either.

    Now that is strange. And it probably makes sense in some Kafkaesque world.

  6. Speaking of optimality, interesting article about the optimality of the genetic code:
    Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement.
    Link: http://pre.aps.org/abstract/PRE/v79/i6/e060901

    Abstract:
    A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.

    Conclusion:
    In conclusion, earlier estimates of code optimality were understated by a statistically significant amount. The extent of optimality and its dependence on metric revealed here further support the notion that the genetic code must have evolved during an early communal state of life

  7. Hi Techne,

    Were you able to read the paper?

  8. Hi Bilbo,

    Yes, it is one of the perks of being a student :p.

  9. So how optimal is the code? And what other evidence do they offer that it evolved?

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