A Teleological Hypothesis about a
Machine
How is it that we can use a teleological
perspective to guide research in the laboratory? Consider the basics of the
scientific method: you make observations; the observations, in the context of
background belief, lead to a tentative explanation called the hypothesis; the
hypothesis is often then formed with the help of "if,then" logic that allows for testing; the
results of the testing then can be viewed as supporting the hypothesis
(positive evidence) or weakening (even refuting) the hypothesis (contrary
evidence). In this case, I would argue that the initial observations used to
infer the hypothesis do count as evidence. That is, hypotheses themselves are
formed from evidence. The experimentation is simply an attempt to confirm the
hypothesis with additional evidence (it also helps to ensure we are not arguing
in a circle). Once enough evidence has been accumulated, the hypothesis becomes
established and can then be used as part of a larger theory.
I have consistently stated that I view ID as
a hypothesis. Thus, it builds on observations that function as evidence. For
example, that life itself is built upon encoded information is an observation.
That intelligent causation is closely matched to the origin of codes and
information is also an observation. Thus, since life possesses an attribute
closely correlated with intelligent design, a reasonable hypothesis is that
life owes its origin to intelligent design.
At this point, one can begin to phrase the ID
hypothesis in testable "if,-then" terms. Put simply, if life owes its
origin to intelligent design, then high resolution studies will uncover further
phenomena that echo origins through biomolecular
engineering at the hands of rational agents.
One way to help us detect such bioengineering
is through the use of Michael Behe's concept of
Irreducible Complexity (IC). Since all machines demonstrate IC at some level,
detecting IC is an important first step in detecting machinery. And as an added
bonus, IC can help us gage the likelihood that non-teleological forces were
behind the origin of such a machine (1,2)
The Degradosome
A recent article from Trends in Genetics
(3) made the following observations:
The degradation of mRNA used to be viewed as an unsophisticated
process in which a hodgepodge of ribonucleases
attacked any accessible RNA. In contrast to mRNA, transfer and ribosomal RNAs were believed to be protected by their rapid folding
into compact structures. This simplistic view has been made obsolete by the
discovery of multiprotein machines with the capacity
to unwind and degrade structured RNA.
One such multiprotein
machine is the degradosome from E. coli. It
can be viewed as a modular system composed of four parts: an exoribonuclease (PNPase), an endoribonuclease, an RNA helicase,
and enolase. The apparent function of the degradosome is to serve as a universal RNA degradation
machine (capable of digesting any RNA in the cell). There already seems to be
suggestive evidence of its IC state (4).
First, three of the four components have
interacting activities - endonuclease, exonuclease, helicase. These
three functions may act in concert to degrade any RNA and are probably required
to give the machine its universal functional role.
Secondly, biochemical tests support the
importance of individual components:
Thus, it seems clear we have an IC complex
here that depends on at least three protein components. However, the IC to ID
inference is shaky here. This is because each of these three components could
conceivably function independently or as part of another IC complex.
Thus, at this point, I would say this
particular IC system does not clearly indicate ID. However, it does fit nicely
into a view of front-loaded evolution. That is, if the degradosome
represents an original state, things have been set up so that it would be
easier to incorporate the three activities of the degradosome
in different contexts. In other words, instead of viewing the origin of the degradosome as three separate activities that converged
during history, it could be viewed as three coupled activities could split
apart in history. One way to test for this is to determine how ancient this
complex really is. Thus far, it has been identified and studied in E. coli.
What about gram positives, for example?
But now we turn to the really fun part. What
about enolase? No one knows what it is doing with the
degradosome. No one expected to be associated with
the degradosome, as it doesn't bind RNA. On the
contrary, it's an enzyme that is part of glycolysis
(a core metabolic pathway that breaks down glucose). But what is really
interesting is that it catalyzes its glycolytic
reaction just as well as its cytoplasmic
counterparts. So let me be the first to propose a
hypothesis for the function of enolase as part of
this degradosome complex by using ID logic.
ID Sheds Light on Enolase
ID entails that these cellular processes are
quite sophisticated. Consistent with this prediction is a quasi-solid state
cell, where order is paramount and random processes are minimized. Science, on
the other hand, is defined by its attempt to understand all biotic reality in
purely non-teleological terms. Thus, it perceives the OOL as a series of very
simple events building on each other to eventually create the complexity we
call life. The result? It envision
the first cells as rudimentary and sloppy entities. In contrast, I envision the
OOL of life on this planet as a consequence of biomolecular
engineering at the hands of some form of advanced intelligence. I envision the
first cells as complex and sophisticated entities. And while the introduction
of such cells were probably followed by a long history of evolution, I expect
to find traces of such initial states because, as I have explained elsewhere,
such a state is front-loaded and would be continually exploited by evolution.
So I will make a prediction about enolase function from this perspective.
First, IC critics might cite enolase as an example of an alternative function. Because
of my interest in identifying and defining IC systems, as a function of my
interest in ID, I took notice of this system and looked around. Without an
interest in ID, degradosomal enolase
would have been just one of those weird things in
biology. As I began to think about enolase, in light
of its lack of a role in RNA processing, I began to ask if this type of
arrangement might reflect the sophisticated, machine-like context of the cell.
So let's add a few observations.
1. The helicase in
the degradosome is ATP dependent.
2. Enolase, along
with PNPase and the helicase,
form a multimeric complex docked on the C-terminus of
RnaseE (the endonuclease).
3. Experiments in other cells show that enolase can form high-affinity complexes with pyruvate kinase and phosphoglycerate mutase, the two
enzymes that flank enolase on each side in the glycolytic pathway.
4. Pyruvate kinase carries out a reaction that forms ATP.
These observations, seen in the light of my
ID perspective, lead to an obvious prediction about the function of enolase in the degradosome:
Enolase functions in the degradosome
as a prong that plugs the degradosome into the glycolytic pathway so that ATP generated by pyruvate kinase is then quickly
channeled to the helicase to fuel its unwinding
activity.
That is, the degradosome
is a dynamic modular machine that literally is plugged in to turn it on. But it
can also easily be unplugged to turn it off, which is why scientists don't pull
out other glycolytic enzymes attached to enolase. The reversible nature of degradosome
function makes it possible to regulate its activity. The nice thing about this
hypothesis is that it explains why enolase is still
functioning as a glycolytic enzyme. But it also means
enolase is not an example of an alternative
function.
In fact, I recently came across an article
which supports my prediction/model (6):
The Escherichia coli degradosome is a multienzyme complex with four major protein components: the
endoribonuclease RNase E,
the exoribonuclease PNPase,
the RNA helicase RhlB and enolase. The first three of these proteins are known to
have important functions in mRNA processing and degradation. In this work, we
identify an additional component of the degradosome,
polyphosphate kinase (PPK), which catalyses the
reversible polymerization of the gamma-phosphate of ATP into polyphosphate (poly(P)). An E. coli strain deleted for the ppk gene showed increased stability of the ompA mRNA. Purified His-tagged PPK was shown to bind RNA,
and RNA binding was prevented by hydrolysable ATP. Chemical modification of RNA
by PPK, for example the addition or removal of 3' or 5' terminal phosphates,
could not be detected. However, polyphosphate was found to inhibit RNA
degradation by the degradosome in vitro. This
inhibition was overcome by the addition of ADP, required for the degradation of
polyphosphate and for the regeneration of ATP by PPK in the degradosome.
Thus, PPK in the degradosome appears to maintain
an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP.
This paper provided evidence that the degradosome is functioning in a specialized
environment that is coupled to regulating ATP flux.
So there you have it. A
specific prediction about the world of the cell from a teleological
perspective. You heard it first and only here - on some obscure ID web
page. So let's watch the literature for the developing story.
Recap
ID allows me to take a view of the cell more
as a sophisticated, machine-like entity rather than a jury-rigged hodgepodge
cobbled together by the Blind Watchmaker. This is because biomolecular
engineering at the hands of an advanced intelligence is likely to express its intervention
such that the products of design reflect a state that is elegantly coherent.
The expectation of a jury-rigged hodgepodge makes more sense in light of
non-teleological views, which begin with the random mess of the prebiotic soup and not the watch-type reality Paley once invoked.
So I begin to think that the degradosome could indeed reflect an originally designed
state given its basic house-keeping role. If so, what is enolase
doing there? A non-teleological view gives me no reason to expect a logical
reason for it being there, as evolution doesn't have to be logical,
in fact, it often simply jury-rigs hodgepodge things together. But if enolase was originally part of the degradosome,
which in turn was originally designed, I expect a logical reason for it
being there.
I then took notice of one glaring fact from
the Nature paper cited below (4) - while enolase
doesn't bind or alter RNA itself, it does still
function as a glycolytic enzyme. As I began to think
of a sophisticated, machine/factory-like state in the cytoplasm, it occurred to
me that the helicase was ATP-dependent and enolase normally interacted with another enzyme that
generates ATP. Now I typically envision ATP floating about and randomly
becoming available to ATPases. But ID allowed me to
lay this aside and consider that at least in this case, ATP could be funneled
almost directly to the helicase as a consequence of
its binding to enolase. This then led me to think of
the degradosome as a regulated module which could
literally be plugged in to an energy source (where the analogy to man-made
machines was not missed by me). This then added to the logic of the
system.
The Bottom Line
My prediction about degradosomal
enolase function could turn out to be false. Or even
if true, one might easily fit such a finding in a non-teleological view. But
what matters is this example demonstrates a teleological approach CAN be used
to guide lab research and, along the way, generate insight into the living
world. Of course, I have previously demonstrated this with another topic(6),
but with two concrete examples in hand, there is no reason to think ID can not
be used to generate 3, 4, 5, etc. concrete examples. Thus, I would even go as
far as to maintain the notion that ID is a "science stopper" or
nothing more than a "god-of-the gaps" approach has been effectively
refuted.
Citations
1. IC Debunked?
3. Carpousis AJ,
4. Py
B, Higgins CF, Krisch HM, Carpousis
AJ. A DEAD-box RNA helicase in the
Escherichia coli RNA degradosome. Nature
1996 May 9;381(6578):169-172.
5. Blum E, Py B, Carpousis AJ, Higgins CF. Polyphosphate kinase
is a component of the Escherichia coli RNA degradosome.
Mol Microbiol 1997 Oct;26(2):387-398.
6. Using ID to Infer Molecular
Events
[edited