Re: [asa] Amazing Proteins

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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>

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Received on Sun May 4 13:25:06 2008