SPINNING
WHEELS
By
Mike Gene (
Biologist Robin Holliday published an interesting essay in the June 2003 issue of BioEssays [1]. In this essay, Holliday notes that the wheel has been one of the most important inventions (designs) of man, where even to this day, we store our high tech information on discs. Holliday then implicitly argues that if life was designed, we might expect to see such a useful device implemented in biology:
Since the
wheel has become so important for human motility and diverse other purposes,
one would think that it might also be used by animals in a variety of contexts.
Holliday that claims that no wheels are found in biology and asks:
So how do
the creationists explain why an all-powerful deity did not on any occasion design
an animal incorporating the enormously advantageous rotary motion of wheels? [2]
Holliday asserts that “creationists” have no answer for this
question and then explains how
The wheel is
a manufactured object that can only function when it is complete. One cannot
use a quarter or a half of the wheel; indeed they would be an impediment to any
animal. Therefore one cannot evolve a wheel in multiple stages, in the way that
one can evolve an eye, a brain or a limb.
So there can be no selection of advantageous mutations in the case of
the wheel, because they simply do not exist.
The problem with Holliday’s argument is that wheels do exist in biology – they exist at the nanotech level.
The classic example is the bacterial flagellum where the motor proteins form a ring that spins. For some reason, Holliday dismisses this example:
The
flagellae of motile bacteria that have a rotary propeller-like movement contain
a single structural protein called flagellin, but could scarcely be regarded as
wheel-like.
Yet as biologist Sutherland Maciver, from the
Bacteria
invented the wheel! The bacterial flagellum is a helical structure that drives
the cell through the media like a propeller. The structure is rigid and turned
by a rotatory motor at the base where it connects to the bacteria's body. The
rotary motor consist of several wheel-like discs one of which the M-ring
(and/or possibly the S-ring) interact with the C-ring and studs to rotate the
whole structure. The rotary motor is very like a stepping motor! [3]
In fact, even Richard Dawkins acknowledges the bacterial flagellum as a wheel. [4]
Yet the flagellum is not the only wheel inside the cell. Another classic example is the ATP Synthase, which is considered the smallest rotary engine in nature. One paper describes this complex as follows:
The rotor portion is proposed to consist of[b] a wheel[/b] of at least nine copies of subunits c, epsilon and a portion of gamma as a spoke, and another portion of gamma as a crankshaft. [5]
This motor has even inspired nanotechnologists. [6]
If we return to Holliday’s argument, in a sense, he is correct. If our inference to design stems, at least in part, from the analogies between life and technology, we should expect to see wheel-like structures incorporated among the machinery. Holliday notes, “Paley’s watch had cog wheels, but living organisms have no wheels…” Yet as I wrote a few years back, “In fact, I will now make a prediction: If the cell is designed, we will find that they look more and more like Paley's watch.” [7]
Yet I don’t think it’s simply a question of making superficial comparisons. In this case, I envision the cell as an artificial construct that entails coordinated movement. This vision is behind my prediction. If we consider the coordinated movement inside the cell, there is either linear movement or rotary movement. Concerning the latter, the wheel is a circular device that is well-suited to couple rotary motion to work. The advantage of a rotary motion device is that it can carry out such work indefinitely with minimal rearrangement of the surrounding structural architecture. Thus, from an design perspective, I would predict that the flagellum and ATP synthase represent only the tip of the iceberg.
To follow up this prediction, I poked around the literature and found another interesting example.
MCM (or mini-chromosome maintenance) protein complexes are essential the initiation of DNA replication in eukarya. They function as helicases that unwind the DNA. However, there are aspects of MCM function that are confusing in this role. For example, the MCMs are not located at the sites of DNA replication. Ronald Laskey and Mark Madine have proposed an intriguing hypothesis that resolves many of these odd features.[8] They propose the ‘rotary pumping model,’ where the MCMs act as rotating wheels that thread the DNA strands into the sites of replication:
We suggest
that the existing data are far more consistent with an alternative model,
namely that the MCM proteins are indeed rotary motors, but that they
translocate DNA along its axis by helical rotation, causing it to unwind at
distant, fixed replication forks (Fig. 2). This is analogous to a helical
threaded ‘bolt’ rotating through ‘nuts’ (see below), and there are several
precedents for such a rotational translocation of DNA. We envisage two steps,
both using the same postulated rotary function. First, MCM complexes would load
onto DNA at the origin of replication and move away from the origin by rotation
along the helical thread of the DNA. In this way, MCMs would disperse along the
unreplicated DNA….. Second, the dispersed MCMs would be anchored to an immobile
nuclear structure and the identical rotary action would be repeated. Now only
the DNA would be able to rotate, and this action would effectively pump DNA
back towards the origin of replication (Fig. 2). This would provide a simple
and efficient mechanism for spooling large quantities of DNA through ‘anchored’
sites of replication.
Given that there is growing evidence that DNA replication occurs in fixed protein factories, I expect this model to pan out. This would highlight just how artificial-like life is at its core. Here we’d have protein wheels being loaded on the DNA in their proper orientation and spinning down the DNA until they reached a proper location where they become anchored at fixed sites. Now, as they spin, the begin the thread the DNA back into replisome factories. And it’s also worth mentioning that the same MCMs also license the DNA for replication [9].
Let me suggest other candidate wheels. First, there is the rho transcription terminators used by eubacteria. These hexameric protein complexes help to extract the RNA transcription products. While no one has proposed rotary movement for the rho terminators, they are thought to be quite similar to the F1 component of the ATP synthases, where three of the six subunits hydrolyze ATP in a sequential fashion in a manner that tracks with rho’s movement across the RNA [10]. Also, it has been found that the RNA is threaded through the hole of the hexamer [11].
Secondly, there is the FliI component of the bacterial flagellum. It has been recently shown that FliI forms an ATP-dependent ring structure [12] and is thought to sit at the very base of the flagellum. FliI is also thought at act as the intermediary between the cytoplasm and the embedded protein secretion apparatus, recruiting flagellar proteins. Since many flagellar proteins are probably unfolded as they enter the secretion apparatus, one can envision FliI acting much like the MCMs, snagging and threading the amino acids chains into the apparatus as it spins.
What all these proposed wheels have in common is that they form ring structures and handle polymers in an ATP dependent fashion. I’ll label these machines as the molecular threaders. In a sense, cells do have “cog wheels,” only they are more sophisticated than Paley’s watch.
Above, I noted the advantage of a rotary motion device is that it can carry out such work indefinitely with minimal rearrangement of the surrounding structural architecture. Yet the cell is also very good at coordinating internal structural rearrangements, as its order is dynamic. Thus, the advantage of the wheel inside the cell may be minimal and restricted to certain functions. This is one reason why I propose the molecular threaders. The rapid threading of polymers is something a wheel could do very well.
Cites