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Tuesday, December 13, 2011

Wondering About Ourselves: An Excerpt from WONDERING ABOUT

To our astonishment, our common sense view of things biological begins to disintegrate the moment we apply curiosity and imagination to it, to dissect it and look into it at the finest levels science allows us to probe.  In doing so, try as we might, we never encounter this special essence or quality which seems so obvious at first sight.  Instead, what we do find, when we break out our detectors and other scientific instruments, is that living things are composed of atoms and moledcules like everything else, albeit not in the same elemental proportions, yet acting according to the same laws of physics and chemistry as everything else.  The mechanical, Newtonian universe of objects and forces, modified by quantum effects on the smallest scales, appear all that is needed to explain why butterflies fly, or mate, or find food, or stare at us with the seeming same curiosity that we feel gazing upon it.  All our initial impressions, and all the stories that have been told and retold aside, there appears no miraculous special something that we can affix to or inject matter with to make it come alive; no energy fields, no forces, no protoplasm, no elixir of the living, nothing we can pump into Dr. Frankenstein’s reassembled parts of corpses which will make it groan and open its eyes and have thoughts and feelings and break its bonds to move in accordance with them.  There is nothing like that whatsoever.  No, whatever it is that characterizes life lies elsewhere.

But the impression of such a force is so strong, so deep, so instinctual that, try as we might, we cannot simply abandon it without at least wondering why it is there, where it comes from, and what it tells us.  Something is there, of that there can be no question.

Intentionality.  Complexity.  Design.  Try to put aside your ordinary impressions and perceptions of things, and seed your mind, germinate in your mind, take root and push out of the soil and put forth leaves and vines in your mind, the theme that to satisfy our curiosity we must look at the world from a different perspective, the one that imagination unlocks.  Very often, we find that when we look closely, what we thought we were seeing fades away, yet is replaced by something just as amazing – no, more so.

Let us start with the simplest of things that could be called living.  Consider the virus.  Here is something both considerably smaller and simpler than the smallest, simplest bacterium, all biologists would agree.  But on the most microscopic of scales, that of individual atoms and molecules, even the simplest virus turns out to be a machine of remarkable complexity.  At the very least it has to be able to recognize a host cell it can parasitize, whether it is a cell in your body or a bacterium (in which case it is called a bactaeriaphage), somehow figure out the molecular locks and other gizmos which cells use to protect themselves from invasion, penetrate the defenses, then usurp the molecular machinery the cell uses to replicate itself, perverting the cell into a factory for producing many more copies of the virus, copies which then have to figure out how to break out of the cell in order to repeat the cycle on other cells or bacteria, all the while avoiding or distracting the many other layers of defenses cells and bodies use to protect themselves from such invasions.

Biologists still debate whether viruses can be legitimately counted among the various kingdoms and domains of life, but there is no doubt that their hosts, whether bacteria or other single celled organisms or multicellular organisms, can be classified in the great Tree of Life, from which all other living things, be they plants, animals, fungi, or you, diverge from.  And what dominates this tree, right down to the most primitive beginnings we have yet been able to detect, is a level of complexity that we simply do not encounter among the great many more things than don’t belong on this tree, from rocks to stars to solar systems to galaxies.

So after all this, have we cornered our quarry?  We started with the at first sight idea that life possessed some special quality or substance or essence, then realized that we could not find that essence however hard we looked.  But what we did find was that living things, even the simplest of them, showed a level of complex organization well beyond the most complex of non-living things.

Life is special.  I don’t want to lose sight of that.  We are fully justified in our grand division of matter into the non-living – things we explain only by the laws of physics and chemistry at a simple level – and the living, all the things we must also apply whatever biology has to teach us.  What I have been trying to show is that, whatever that specialness is, it isn’t as obvious as it appears upon first sight.  It is more subtle, involving a number of characters and qualities, one of which is complexity and another the appearance of design or purpose.

*          *          *

Again, I say that life truly is special.  It is early May, and I have just come home from a walk through Pennypack Park, one of the many lovely natural places which skirt the city where I live, Philadelphia, one of several cities along the  eastern edge of North America.  I would love one day to walk on the moon or on the red soil of the planet Mars, but what I have just experienced would be utterly lacking in those dead, albeit fascinating places.  In the spring in this part of the world, as in many other parts of our planet, every sense is roused to life by the call of the wild.  Not only are you surrounded by the verdant green of new buds and flowers and grasses, but also by a cacophony of whistles, chirps, tweets, and other rhythmic sounds which reminds you that you that new life is all about, some of it still rustling itself to full wakefulness after winter but much of it already in the air and alit on the many twigs and branches.  And even without vision and sound, you can still smell the musty beginnings of stirrings things, the scents of enticing blossoms and irritating pollens, and you can still feel the grass between your toes and the softness of young leaves on your skin as you brush by the undergrowth.

Here I have spoken of complexity and the appearance of purpose and meaning, and perhaps that is exactly what our scientific mission into the heart and soul of biology requires, but this is one place where, I have to submit, we will never really capture the essence of what we are studying.  Life is something that has to be experienced, and only living things themselves have the capacity, as far as we know, to experience anything.  So, in a sense, our quest to satisfy our curiosity begins with the admission that, at least for the world of the living, we never can completely satisfy it.
Am I going to give up, then?  No, because, as I have maintained up to this point, curiosity combined with imagination and the scientific method can undo any knot, unlock any riddle, however baffling and impervious it may seem.  I have even suggested a starting place even, this idea of complexity combined with apparent purposefulness, an idea I hope to build upon and demonstrate just how powerful it is.  I think we can agree that it is a good starting place.  Biological things, even the simplest of them, are highly complex, we now see, and there does seem to be something to this notion of being imbued with purpose, however that comes about.  If we can make some progress on this front, then perhaps in the end we will satisfy our intellects after all, as impossible as that seems looking at things from their beginnings.

Quadratic Fitting of Data

I recently had to tear my hair out finding an algorithm for the coefficients of a second order fit for a set of data points ( first order fits are easy).  I found this below, in FORTRAN, and translated it into VB:

  Sub QuadFit(N As Double, P As Double, i As Integer, X() As Double, _
              Y() As Double, Q As Double, N As Double, R As Double, _
              S As Double, T as Double, U As Double, V As Double, _
              W as Double, as As Double, b As Double, c As Double)
  
    P = 0


    For i = 1 To N
      P = P + X(i)
    Next i


    Q = 0

    For i = 1 To N
      Q = Q + X(i) ^ 2
    Next i


    R = 0

    For i = 1 To N
      R = R + X(i) ^ 3
    Next i


    S = 0

    For i = 1 To N
      S = S + X(i) ^ 4
    Next i


    T = 0

    For i = 1 To N
      T = T + Y(i)
    Next i


    U = 0

    For i = 1 To N
      U = U + X(i) * Y(i)
    Next i


    V = 0

    For i = 1 To N
      V = V + X(i) ^ 2 * Y(i)
    Next i


    W = N * Q * S + 2 * P * Q * R - Q ^ 3 - P ^ 2 * S - N * R ^ 2
    a = (N * Q * V + P * R * T + P * Q * U - Q ^ 2 * T - P ^ 2 * V - N * R * U) / W
    b = (N * S * U + P * Q * V + Q * R * T - Q ^ 2 * U - P * S * T - N * R * V) / W
    c = (Q * S * T + Q * R * U + P * R * V - Q ^ 2 * V - P * S * U - R ^ 2 * T) / W


  End Sub

I hope you can use it.

Black Sea deluge hypothesis

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