Howdy t.o.-ers,

The ID debate over at the Chronicle of Higher Education website

(which published some articles on the ID movement in late December,
see:

http://chronicle.com/free/v48/i17/17a00801.htm
http://chronicle.com/colloquy/2001/design/design.htm
http://chronicle.com/colloquy/2001/design/re.htm )

has finally about wound down after 300+ posts, probably the most
active colloquy they've had (they have one every week, the other few
that I've checked get only a few posts).

Anyhow, I felt like someone had to add some biology back into the
discussion (which was getting very philosophical, not a bad thing but
not the whole story), so I wrote a number of posts:

http://chronicle.com/colloquy/2001/design/40.htm
http://chronicle.com/colloquy/2001/design/99.htm
http://chronicle.com/colloquy/2001/design/152.htm
http://chronicle.com/colloquy/2001/design/153.htm
http://chronicle.com/colloquy/2001/design/267.htm
http://chronicle.com/colloquy/2001/design/268.htm
http://chronicle.com/colloquy/2001/design/269.htm
http://chronicle.com/colloquy/2001/design/270.htm
http://chronicle.com/colloquy/2001/design/280.htm
http://chronicle.com/colloquy/2001/design/293.htm

...most of which is not particularly original and which most of you
will be familiar with, although they might serve as handy "pages o'
links".  I just wanted to point out one new tidbit I came across that
seems relevant to the evolution of one of Behe's systems (the
eukaryotic cilium) as well as being a particularly elegant case of
"How to evolve IC":

http://chronicle.com/colloquy/2001/design/269.htm

...which is about (the later bit of the post) about recent scientific
work on identifying simpler homologs to the dynein heavy chain (the
"motor" of dynein), one of the biggest proteins around.  I'll repost
the bit on dynein here, to see if there are comments (particularly
from someone who knows more about this example, I wouldn't be
surprised on t.o.), and perhaps for future reference as a particularly
good case of the evolution of "strict" IC (multiple parts required AND
interacting with each other AND well-matched AND machine-like --
dynein is described as the "Mack truck of the intracellular
interstate" [1] by one science writer).

The basic idea for the evolution of IC here is the specialization of
originally identical components (a simple prokaryotic homolog of
dynein is a hexamer, wherein six identical proteins from one gene form
a six-part ring) resulting in complexes with functions different than
the original.  This is something that is familiar in metazoan biology
(e.g. specialization of segments), but not really in biochemical
evolution (to my very limited knowledge; perhaps the "duplicate genes
to extend a metabolic pathway" idea is a version of this.  And
actually, now that I'm thinking about it, hemoglobin sort of is, also,
being made up of myoglobin-like subunits, although the specialization
is limited in this case, although on the other hand the cooperative
properties almost certainly are crucial to the "effective functioning"
of hemoglobin, so if Behe were consistent he would not exclude
hemoglobin from his IC classification -- but this is another debate).

I post the relevant bit here in case the CHE board gets deleted and to
see if people have comments/additional useful factoids/can find holes
in the argument:

[begin]
[T]he failure of IDists to address actual biology will not deter me
from posting more of it. While playing around on PubMed over the
break, I came across a fascinating article that shows yet another way
that IC, and even machine-like IC, can evolve.

Here is the article:

Mocz G, Gibbons IR. "Model for the motor component of dynein heavy
chain based on homology to the AAA family of oligomeric ATPases."
Structure (Camb) 2001 Feb 7;9(2):93-103

http://www.ncbi.nlm.nih.gov/entrez/query.fcgicmd=Retrieve&db=PubMed&l...
s=11250194&dopt=Abstract

I will attempt to give a summary of the conclusions for those readers
who may have missed biochemistry day in kindergarten ;-) , so that the
article excerpt that I quote will make some sense.

Those who have read Behe's book, Darwin's Black Box, may recall that
Behe's first example of an IC biochemical structure was the eukaryotic
cilium, discussed in his chapter "Row, row, row your boat." He
describes three main, key components of the cilium: tubulin (which
forms the microtubules of the axoneme, the 'rod' of the cilium),
dynein (which is the motor which moves the microtubules past each
other), and nexin (which keeps the microtubules from sliding apart,
which results in the bending motion of the cilium).

I posted some references on the origin of the cilium in post #153.
Some of those references discussed the relationship between the
simpler cytoplasmic dynein and the more complex cilial dynein. But
where did cytoplasmic dynein come from? The most common scientific
view of the relationship between eukaryotes (large cells with a
cytoskeleton and nucleus) and prokaryotes (smaller, simpler cells with
no nucleus and only recently discovered to have a simple cytoskeleton;
eubacterial and archaea are the two fundamental groups of prokaryotes)
appears to be (there is still much debate) that eukaryotes are derived
from prokaryotes. Specifically, the 'core' 'informational' genes of
eukaryotes are derived from a direct archaeal ancestor, and that many
of the current eukaryotic 'metabolic' genes are derived via lateral
transfer from eubacteria, something that has people like DI IDist
Jonathan Wells proclaiming the end of the 'Tree of Life' model, even
though it has been widely accepted since the early 1980's that the
mitochondria and chloroplasts of eukaryotes are in fact the
descendents of endosymbiotic eubacteria, and that many of the symbiont
genes have been transferred to the eukaryotic nucleus.

Anyhow, if eukaryotes did in fact evolve from prokaryotes (instead of
being specially created, as Todd Moody would apparently have it),
there ought to be evidence of this process in the form of prokaryotic
homologs to 'key' eukaryotic genes, for example the genes of the
eukaryotic cytoskeleton, one of the most distinct features of
eukaryotes. Such a homolog for tubulin was long suspected in the
prokaryotic cell-division protein FtsZ, a suspicion which was
dramatically confirmed by the independent solution of the structures
of FtsZ and tubulin. See these webpages:

On the evolution of tubulin:

http://www.cellbio.duke.edu/Faculty/~Erickson/FtsZ_tubulin_struct.html
http://octem.berkeley.edu/webpage/papers/nature/index.html

& this article:

Faguy, D. M. and Doolittle, W. F. (1998). "Cytoskeletal proteins: The
evolution of cell division." Current Biology, V8(N10): R338-R341.
Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=
PubMed&list_uids=9601632&dopt=Abstract

Dynein, however, is a tougher case. It is routinely referred to as a
'motor' protein, and in fact it is one of the biggest and most complex
proteins known. It powers the cilium, but other versions of the dynein
protein are used to push microtubules apart from each other during
mitosis (eukaryotic cell division), and to carry cargo along
microtubules.

The actual 'motor' of dynein is found in the 'dynein heavy chain'
(DHC). Various other dynein chains (referred to as light and
intermediate, depending on their size) perform regulatory roles (and
perhaps other functions; the newly-evolved Drosophila sperm dynein
intermediate chain gene, Sdic, has an unknown but evidently highly
selectable function; see refs in #153).

The problem was that, until recently, there was no likely prokaryotic
homolog to the dynein heavy chain. Indeed, what use would prokaryotes
have for dynein, having no cilia, mitosis, or long-distance transport
needs, or even any microtubules? It will not surprise biologists to
discover that the prokaryotic homolog has, in fact, an entirely
different function, and is structurally much simpler.

The Mocz and Gibbons (2001) paper identifies the homolog of dynein as
AAA ATPases (AAA stands for ATPases Associated with cellular
Activities; don't ask me why it's not AAWCA, I don't know). ATP is the
main energy molecule of the cell, and an ATPase is an enzyme that
breaks down ATP, releasing energy that can be used for work. Dynein
burns ATP to do its work also.

The various proteins in the AAA ATPase family have a number of
functions (click the 'related articles' button in the PubMed link,
above), but the interesting thing about them is their structure. The
simplest AAA ATPases actually have a symmetric ring shape, and are
actually made by a self-assembled hexamer of one protein -- that is,
one gene produces one protein, and six copies of this (wedge-shaped)
protein form a ring (hexa = six). Since all six 'parts' are in fact
identical, there is really no crucial 'part' -- remove one of the
subunits of the ring, and the same gene can produce an identical
replacement. One part only, so no IC here.

However, other AAA ATPases are more complex. Some AAA ATPases are
coded for by *six* genes, arrayed next to each other along the
chromosome. Six copies of the gene can occur very simply by gene
duplication; what is interesting about this situation is that the
duplication allows each copy to evolvely independently, and therefore
to specialize to perform nonuniform functions in the AAA ATPase ring.
Mocz and Gibbons (2001) note that in one AAA ATPase "this
differentiation of AAA modules has progressed to the point that the
deletion of the gene encoding any one of the six is lethal, indicating
that the individual subunits, although closely related in sequence,
are functionally noninterchangeable." If you blinked, you might have
missed it: we just moved from non-IC to IC using very simple, well
understood genetic processes -- and we're not even at dynein yet!

So where does dynein come it? Well, it turns out that the dynein heavy
chain, which is coded by a single large gene, ...

read more »

read more »

Here's the latest incarnation.  In the HTML version I steal some pics
from articles, but you'll have to use your imagination or look at the
articles via PubMed...

Begin paste
=======
The Evolution of the Dynein Heavy Chain and the AAA+ ATPase
Superfamily

by Nic Tamzek
Copyright © 2002

[posted [draft]: 1/2002]

Introduction
The Evolution of the Dynein Heavy Chain (DHC)
Summary
The Evolution of Cilial (axoneme) Dynein from Cytoplasmic Dynein
The Practical Results of Evolutionary Theory for Dynein Research
Endnotes
References

Introduction

I would like to point out one new tidbit of research that I've come
across that seems relevant to the evolution of one of Behe's systems
(the eukaryotic cilium) and is a particularly elegant case of "How to
evolve irreducible complexity (IC)" unto itself.  This material was
originally developed as a post for the Chronicle of Higher Education
(CHE) discussion on CHE's December 21, 2001 article on Intelligent
Design entitled "Darwinism Under Attack."

I would like to briefly review recent scientific work on identifying
simpler homologs to the dynein heavy chain (the "motor" of dynein),
literally one of the largest, most complex, and most important
proteins known.  I see it as a particularly good case of the evolution
of "strict IC" ("strict IC" having not only "multiple parts required
for function," but having a system with multiple parts required AND
interacting with each other AND well-matched AND machine-like; this is
important as IDists, Behe included, are inconsistent on whether
qualifiers beyond "multiple parts required" are really part of the
definition of irreducible complexity).

Dynein (Gibbons and Rowe 1965) is described as the "Mack truck of the
intracellular interstate" by one science writer [1].  Various versions
of dynein have functions like moving the cilium, carrying cargo down
microtubules, and pushing microtubules (and therefore chromosomes)
apart during eukaryotic mitosis (cell division).  The Dynein Heavy
Chain (DHC) is universally referred to as the "motor" domain of dynein
[2], and its size and complexity are commented on in the introduction
of every scientific article on the topic.  For example, Asai and
Koonce (2001) write,

        The dynein heavy chain is enormous, being approximately 4600
amino acid residues in length, more than twice the size of myosin II
and more than four times the mass of conventional kinesin. Unlike
myosin and kinesin, the predicted secondary structure of the dynein
sequence does not readily divide into a globular head and a tail
domain. However, genetic, molecular and structural analyses have
revealed several discrete functional domains, as summarized here (Fig.
1).

We will look at Figure 1 of Asai and Koonce presently.

The basic idea for the evolution of IC here is the specialization of
originally identical components (a simple prokaryotic homolog of
dynein is a hexamer,
wherein six identical proteins from one gene form a six-part ring)
resulting in complexes with functions different than the original.
This is something that is familiar in metazoan biology (e.g.
specialization of segments), but not really in biochemical evolution
(to my very limited knowledge; perhaps the "duplicate genes to extend
a metabolic pathway" idea is a version of this.  And actually, now
that I'm thinking about it, hemoglobin sort of is, also, being made up
of myoglobin-like subunits, although the specialization is limited in
this case, although on the other hand the cooperative properties
almost certainly are crucial to the "effective functioning" of
hemoglobin, so if Behe were consistent he would not exclude hemoglobin
from his IC classification -- but this is another debate).

Following is a more detailed review of Mocz and Gibbons (2001), who
provide a model for the origin and evolution of the dynein heavy
chain.  This is a
somewhat edited version of my CHE post.

  The Evolution of the Dynein Heavy Chain (DHC)

The failure of IDists to address actual biology will not deter me from
posting more of it. While playing around on PubMed over the break, I
came across a fascinating article that shows yet another way that IC,
and even machine-like IC, can evolve.

Here is the article:

Mocz G., Gibbons I.R. (2001) "Model for the motor component of dynein
heavy chain based on homology to the AAA family of oligomeric
ATPases." Structure (Camb).  9(2):93-103.

Here is the link to the PubMed reference, which links to the full-text
article if you have subscription access, for example if at a
university library.

I will attempt to give a summary of the conclusions for those readers
who may have missed biochemistry day in kindergarten ;-) , so that the
article excerpt
that I quote will make some sense.

Those who have read Behe's book, Darwin's Black Box, may recall that
Behe's first example of an IC biochemical structure was the eukaryotic
cilium,
discussed in his chapter "Row, row, row your boat." He describes three
main, key components of the cilium: tubulin (which forms the
microtubules of the
axoneme, the 'rod' of the cilium), dynein (which is the motor which
moves the microtubules past each other), and nexin (which keeps the
microtubules from
sliding apart, which results in the bending motion of the cilium).

I have cited some references on the origin of the cilium elsewhere.
Some of those references discussed the relationship between the
simpler cytoplasmic
dynein and the more complex cilial dynein. But where did cytoplasmic
dynein come from?  The most common scientific view of the relationship
between
eukaryotes (large cells with a cytoskeleton and nucleus) and
prokaryotes (smaller, simpler cells with no nucleus and only recently
discovered to have a
simple cytoskeleton; eubacterial and archaea are the two fundamental
groups of prokaryotes) appears to be (there is still much debate) that
eukaryotes are
derived from prokaryotes. Specifically, the 'core' 'informational'
genes of eukaryotes are derived from a direct archaeal ancestor, and
that many of the current eukaryotic 'metabolic' genes are derived via
lateral transfer from eubacteria, something that has people like
Discovery Institute IDist Jonathan Wells proclaiming the end of the
'Tree of Life' model, even though it has been widely accepted since
the early 1980's that the mitochondria and chloroplasts of eukaryotes
are in fact the descendents of endosymbiotic eubacteria, and that many
of the symbiont genes have been transferred to the eukaryotic nucleus.

Anyhow, if eukaryotes did in fact evolve from prokaryotes (instead of
being specially created, as Todd Moody would apparently have it),
there ought to be
evidence of this process in the form of prokaryotic homologs to 'key'
eukaryotic genes, for example the genes of the eukaryotic
cytoskeleton, one of the most distinct features of eukaryotes. Such a
homolog for tubulin was long suspected in the prokaryotic
cell-division protein FtsZ, a suspicion which was
dramatically confirmed by the independent solution of the structures
of FtsZ and tubulin. See these webpages:

On the evolution of tubulin:
http://www.cellbio.duke.edu/Faculty/~Erickson/FtsZ_tubulin_struct.html
http://octem.berkeley.edu/webpage/papers/nature/index.html

...and this article:
Faguy, D. M. and Doolittle, W. F. (1998). "Cytoskeletal proteins: The
evolution of cell division." Current Biology, V8(N10): R338-R341.
PubMed Link.

Dynein, however, is a tougher case. It is routinely referred to as a
'motor' protein, and in fact it is one of the biggest and most complex
proteins known. It powers the cilium, but other versions of the dynein
protein are used to push microtubules apart from each other during
mitosis (eukaryotic cell division), to carry cargo along microtubules,
and probably other functions (see e.g. Vorobjev et al., 2001).

The actual 'motor' of dynein is found in the 'dynein heavy chain'
(DHC). Various other dynein chains (referred to as light and
intermediate, depending on their size) perform positioning and
regulatory roles (and perhaps other functions; the newly-evolved
Drosophila sperm dynein intermediate chain gene, Sdic, has an unknown
but highly selectable function; see Nurminsky et al. 1998, 2001).

The problem was that, until recently, there was no likely prokaryotic
homolog to the dynein heavy chain. Indeed, what use would prokaryotes
have for
dynein, having no cilia, mitosis, or long-distance transport needs, or
even any microtubules?  It will not surprise biologists to discover
that the prokaryotic
homolog has, in fact, an entirely different function, and is
structurally much simpler.

The Mocz and Gibbons (2001) paper identifies the homolog of dynein as
AAA ATPases (AAA stands for ATPases Associated with cellular
Activities; don't
ask me why it's not AAWCA, I don't know). ATP is the main energy
molecule of the cell, and an ATPase is an enzyme that breaks down ATP,
releasing
energy that can be used for work. Dynein burns ATP to do its work
also.

The various proteins in the AAA ATPase family have a vast number of
highly divergent functions (see Neuwald et al. 1999, and Ogura and
Wilkinson 2001,
for reviews), but the interesting thing about them is their structure.
The simplest AAA ATPases actually have a symmetric ring shape, and are
actually made by a self-assembled hexamer of one protein -- that is,
one gene produces one protein, and six ...

read more »