Re: Is evolution really the central theory for all of biology?

From: Pim van Meurs <pimvanmeurs@yahoo.com>
Date: Fri Sep 23 2005 - 11:17:28 EDT

Cornelius Hunter wrote:

> Jim:
> This is a knowledge-based approach that does not require evolution,
> per se. We call it an evolutionary approach in normal science because
> evolution is the paradigm, not because evolution is required, per se.
> This is an excellent example of what Phil is talking about. You can,
> for example, replace "evolutionary" with "design" and have the same paper.
> --Cornelius

With the understanding that evolution presents the best theory about the
'designer', your comment may hold some relevance. But in general the
term design, is much vaguer than the more specific term 'evolution'.
For instance look at ID which tries to explain the 'design' in nature by
appealing to something supernatural. While surely such an 'explanation'
is possible, it lacks much of the scientific aspects required of a
plausible explanation. Calling something design leaves out any detail as
to means, opportunity, motives and so on. Evolutionary theory provides
pathways, plausible and observed mechanisms.
Check out the latest issue of Nature to see some great examples of
science progressing our knowledge. Imagine that just a decade or less
ago, some ID proponents argued against the evolutionary probabilities of
the immune system.. Or against the evolvability of proteins....

    Immunity with complements

------------------------------------------------------------------------

The complement system is a key component of innate immunity that kills
microorganisms directly. It is evolutionarily ancient, predating the
immunoglobulins. The crystal structure of the human complement component
C3 has now been determined. As well as revealing some of the mechanisms
involved in its immune function, the structure has evolutionary
implications for mammalian large multi-domain proteins in general and
it may be the largest protein structure (the longest chain and the most
domains) so far determined.

        Structural biology: Origins of chemical biodefence p484

The idea that complex biological systems can evolve through a series of
simple, random events is not universally accepted. The structure of a
vital immune protein shows how such evolution can occur at a molecular
level.

Robert Liddington and Laurie Bankston

        Structures of complement component C3 provide insights into the
        function and evolution of immunity p505

Bert J. C. Janssen, Eric G. Huizinga, Hans C. A. Raaijmakers, Anja Roos,
Mohamed R. Daha, Kristina Nilsson-Ekdahl, Bo Nilsson and Piet Gros

doi: 10.1038/nature04005

Abstract: The mammalian complement system is a phylogenetically ancient
cascade system that has a major role in innate and adaptive immunity.
Activation of component C3 (1,641 residues) is central to the three
complement pathways and results in inflammation and elimination of self
and non-self targets. Here we present crystal structures of native C3
and its final major proteolytic fragment C3c. The structures reveal
thirteen domains, nine of which were unpredicted, and suggest that the
proteins of the alpha2-macroglobulin family evolved from a core of eight
homologous domains. A double mechanism prevents hydrolysis of the
thioester group, essential for covalent attachment of activated C3 to
target surfaces. Marked conformational changes in the alpha-chain,
including movement of a critical interaction site through a ring formed
by the domains of the beta-chain, indicate an unprecedented,
conformation-dependent mechanism of activation, regulation and
biological function of C3.

    Follow the sequence

------------------------------------------------------------------------

It is widely believed that a protein's amino acid sequence contains all
the information needed to dictate its structure, but exactly what
information is both necessary and sufficient for generating a folded,
functional protein is not clear. Two papers by Rama Ranganathan and
co-workers tackle this question using computational protein design to
construct artificial WW domains, small proteins of approximately 40
amino acid residues that bind to proline-rich sequences. The synthetic
proteins adopt the characteristic WW structure and recognize typical WW
target sequences. Since the information used in designing these proteins
was obtained from multiple sequence alignments only, with no prior
knowledge of three-dimensional structure, it is clear that for some
proteins, a relatively small quantity of sequence information is
sufficient to specify the complex amino acid interactions that make up a
functional protein.

        Structural biology: Form and function instructions p486

How much and what kind of information is required to fold a chain of
amino acids into a functioning protein? It seems the problem may not be
as daunting as once thought the solution is in the coevolution data.

        Evolutionary information for specifying a protein fold p512

Michael Socolich, Steve W. Lockless, William P. Russ, Heather Lee, Kevin
H. Gardner and Rama Ranganathan

doi: 10.1038/nature03991

Abstract: Classical studies show that for many proteins, the information
required for specifying the tertiary structure is contained in the amino
acid sequence. Here, we attempt to define the sequence rules for
specifying a protein fold by computationally creating artificial protein
sequences using only statistical information encoded in a multiple
sequence alignment and no tertiary structure information. Experimental
testing of libraries of artificial WW domain sequences shows that a
simple statistical energy function capturing coevolution between amino
acid residues is necessary and sufficient to specify sequences that fold
into native structures. The artificial proteins show thermodynamic
stabilities similar to natural WW domains, and structure determination
of one artificial protein shows excellent agreement with the WW fold at
atomic resolution. The relative simplicity of the information used for
creating sequences suggests a marked reductio
Received on Fri Sep 23 11:18:00 2005

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