Re: [asa] Amazing Proteins

Hi, Mike,

I am still confused as to the direction you are trying to take this.
All that you write about the amazing nature of proteins is very
interesting in itself, but where is it taking us, bearing in mind that
this group is for discussion of where Faith and Science intersect, or
at any rate, interface.

If you are saying, for instance, that it is just too amazing that
proteins could exist, and that this speaks of the intervention of a
designer, for example, then I could see where you are coming from,
though I might not agree. But you do not make such a point - but is
this the point we are to infer from your essay?

I agree that there is an unsolved chicken-and-egg type riddle in that
the situation we have now is that proteins are necessary for DNA
replication and DNA is necessary to encode for the proteins. (Well,
I'm sure that's an oversimplification, as I'm no biologist, but I hope
it illustrates the point). I guess what I'd like to see you address
is what does this imply, if anything, in a Faith/Science context?

You also didn't attempt to answer my points about the alphabet, and
musical scales. If you say the Blind Watchmaker would be nowhere
without proteins, could you not also say that Shakespeare would be
nowhere without the alphabet, or Mozart would be unheard of without
musical scales? Everything has to build on something else in music,
for example.

A good example of the "evolution" of music is the famous "Tristan
Chord"; the notes F-B-Dsharp-Gsharp form an intriguing and ambiguous
chord that had a profound effect on the development of 20th Century
classical music. The reason is that the chord doesn't appear to
belong to any key, and could "resolve" in a number of different ways (
Wagner introduces it in the first few bars of the opera Tristan und
Isolde and never shows us the final resolution till four hours later).
 That particular chord became famous, and paved the way towards
"atonal" composers of the 20th Century, such as Schoenberg, Berg and
Webern, who abandoned the notion of keys altogether. It can truly be
seen as a "mutation" that gave rise to entirely new species of music
emerging. But to pursue your analogy of the Blind Watchmaker being
impotent without proteins, one might also say that the Tristan chord
was meaningless unless viewed in the context of the traditional major
and minor scales. So does Wagner deserve the credit for it (or the
blame if you don't happen to like atonal music)? Are we to say,
instead, that the major and minor musical scales are so amazing (yes
they are amazing), that what the composer does is of lesser
importance?

Iain

On Sun, May 4, 2008 at 6:22 PM, Nucacids <nucacids@wowway.com> wrote:
> Hi Iain,
>
>
>
>
> "But when you make the statement "how much credit does the blind
> watchmaker really deserve?", it has set me thinking."
>
>
>
> Now *that* is the main point of my questions. The vast, vast majority of
> our empirical evidence of the blind watchmaker comes from studying and
> analyzing a protein-dependent reality. As such, it is easily to lose sight
> of them in the background. Maybe we should not treat that as brute givens
> when thinking about evolution.
>
>
>
>
> "Surely the reason for the amazing variety of proteins is due to the fact
> that
> they are long chains of around 20 different building blocks (I see
> this as a kind of molecular alphabet), so the possibilities for
> variety are astronomically large. One might say that only a tiny
> fraction of such sequences are going to be useful, and fold over in
> the right way, but this still leaves an immense number of
> possibilities for evolution to discover."
>
>
>
> I would agree that this is part of the story, as proteins connect function
> to sequence (which itself is an amazing thing). But is that surely the only
> reason? If having 20 different building blocks is all we need, it would
> seem the RNA would more likely to have expanded its alphabet than learn a
> new language. Carbohydrates too are made up of subunits, but have limited
> utlity. Or we could replace the 10 hydrophilic amino acids with 10 new
> hydrophobic amino acids and we'd lose a ton of functions. If it is simply a
> question of having 20 subunits, then you'd have to make the case that any
> polymer could replace proteins.
>
>
>
> The vast and immense Tree of Life is a protein-dependent output. Point to
> some evidence of evolution and I'll point to the proteins that underlie it.
> Without proteins, would there be a Tree of Life 3.5 billion years after the
> RNA world took root? How do we know? If we believe so, would the Tree be
> as immense and vast as it is today? A life form composed of nucleic acids,
> carbohydrates, and lipids would suffice for the purposes of the blind
> watchmaker. But could the blind watchmaker turn this material into
> something that is analogous to an Ash tree filled with squirrels, beetles,
> and birds?
>
>
>
> Look at it this way. What do we need for the blind watchmaker to exist? A
> finite, changing world, something that replicates, and imperfect
> replication. The first and the third are givens due to the nature of
> creation. The second is more iffy. In living cells, proteins play the key
> role in replicating things (they replicate the DNA, they divide the cell,
> and coordinate both). But if we entertain the notion of an RNA world, the
> proteins are not needed for replication (then again, proteins are not needed
> for chemical reactions to take place). But what the proteins do is amplify
> and enhance this replication property, and thus enhance the blind
> watchmakers' abilities. What's more, the same molecule that enhances
> replication also opens up a whole vast world of phenotypes not available to
> the blind watchmaker earlier. You can almost think of proteins are a form
> of tech material designed to exploit and prop up the blind watchmaker. And
> maybe even give the blind watchmaker a little guidance. ;)
>
>
>
> -Mike
>
>
>
> ----- Original Message ----- From: "Iain Strachan" <igd.strachan@gmail.com>
>
> To: "Nucacids" <nucacids@wowway.com>
> Cc: <asa@calvin.edu>
> Sent: Sunday, May 04, 2008 6:34 AM
>
> Subject: Re: [asa] Amazing Proteins
>
>
>
> >
> >
> >
> > Hi, Mike,
> >
> > Reading through this conversation, I'm trying to get to the bottom of
> > what you are saying. I guess the following paragraph gets to the
> > heart of it; you write
> >
> >
> > > For example, without proteins, and their manufacturing process, what
> > > becomes of the blind watchmaker? Without proteins, and the latent
> functions
> > > contained within, might not the blind watchmaker exist as the impotent,
> > > crippled, blind watchmaker with no one to notice its existence? If so,
> how
> > > much credit does the blind watchmaker really deserve?
> > >
> > >
> > >
> >
> > In other words the watchmaker wouldn't have the basic materials to
> > make the watch, and by implication your amazement that such materials
> > exist? One might infer that there is a "fine-tuning" argument to be
> > made here - how amazing that the laws of the universe allow such
> > things as possibilities. However, you don't appear to make that
> > point.
> >
> > But when you make the statement "how much credit does the blind
> > watchmaker really deserve?", it has set me thinking. Surely the
> > reason for the amazing variety of proteins is due to the fact that
> > they are long chains of around 20 different building blocks (I see
> > this as a kind of molecular alphabet), so the possibilities for
> > variety are astronomically large. One might say that only a tiny
> > fraction of such sequences are going to be useful, and fold over in
> > the right way, but this still leaves an immense number of
> > possibilities for evolution to discover.
> >
> > I wonder if a similar analogy can be made by considering the 26
> > letters in the English alphabet. A random arbitrary sequence of the
> > symbols is likely to be meaningless, but consider the immense variety
> > of different forms of textual communication; the Shakespeare sonnet,
> > the bawdy limerick, the lyrics of a pop song, the news items you read
> > in the newspaper, the endearments lovers whisper to each other, and
> > the staccato utterances of text messages (sorry txt msgs).
> >
> > Now, when you say "how much credit does the blind watchmaker really
> > deserve", is this not equivalent to saying "how much credit does
> > Shakespeare deserve for 'shall I compare thee to a Summer's day"
> > because if you take away the letters of the alphabet, he would be a
> > nobody without the means to create his literature". Similarly perhaps
> > Mozart doesn't deserve credit for the complexities of the last
> > movement of the Jupiter Symphony, because if the notes of the musical
> > scale (and all the latent functions and harmonies within them) didn't
> > exist he wouldn't have the means to compose melody.
> >
> > In summary, if even intelligent designers, such as Shakespeare and
> > Mozart are utterly dependent on a small finite set of elemental
> > building blocks that they can string together, then shouldn't one also
> > give the Blind Watchmaker some credit for being able to construct
> > living organisms from a similar set of molecules?
> >
> > What I am wondering is how my two examples differ from yours?
> >
> > Regards,
> > Iain
> >
> >
> >
> >
> > --
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> 11:22 AM
> >
> >
> >
>
>
>
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