Friday, March 28, 2014

The Uncertain Gene - 10

DNA: molecular machines
This is probably the final post in this series, a series about how abiotic evolution might take place, but it is not the end of this subject matter [there is a new post here].

Their will be additional new series on these type subjects as long as Dredd Blog is still a blog.

The list of posts in this series, and associated posts from other series, can be accessed from links on the Series Posts Tab, at "EVOLUTION (Abiotic Machine Epoch - the first ~10.21 billion years)" and "SCIENCE (of the rebellion - *subject" where the subject is listed as "Abiology" or "abiotic evolution."

To end or suspend this series on a good note, today I am focusing on a post from the Small Things Considered blog (STCB), which focuses on a particular molecular machine mentioned in the journal NATURE VOL. 386, page 299, "Letters To Nature" (March 1997), and in other places.

STCB and other blogs call the ancient dynamo, which existed billions of years before human evolution began, a "molecular dynamo."

They then go on to point out that we humans made our very first and much more primitive dynamo billions of years later:
The dynamo was invented in the early 19th century as a device to convert the mechanical movement of magnets—preferably by turning a crank—into electric current. Using the same machine some 25 years later people found that electric current can drive mechanical movement, and the electric motor was born.
(Small Things Considered - "The Dynamo at Work"). In "The Tiniest Scientists Are Very Old" it was noted that ancient microbes used quantum mechanical principles to do work with molecular machines.

What is interesting, comparing the way the rotor on the dynamo works, with proton tunneling (The Uncertain Gene), is that a less random and seemingly more stable technique of proton translocation is used in this molecular dynamo:
Rotation of the c ring is driven by the proton gradient across the membrane. The existence of such a gradient was first postulated as the 'chemiosmotic hypothesis' by Peter Mitchell in 1961 and was highly controversial at that time. Protons pass through a narrow canal formed by two neighboring c subunits and the α subunit of the Fo particle (see figure 3). This proton transport is known to involve the D61 residues of the juxtaposed c subunits and R210 of the α subunit (in E. coli). The 'handover' of a proton between two c subunits leads to small incremental movements of the c ring with respect to the a subunit, i.e. rotation of the c ring within the membrane, with the a subunit representing the stator. When during (aerobic) respiration the cytoplasm of the cell is depleted of protons, a proton gradient is established that allows protons to flow 'downhill' back into the cytoplasm through the Fo canal. This flow sets the c ring in motion, which in turn lets the F1 γ subunit rotate. The rotating F1 γ subunit then induces the conformational alterations in the β subunits of the α3β3, that are necessary to synthesize ATP from ADP and Pi. We can calculate that it takes—depending on the c subunit stoichiometry in the c ring—between 4 and 6 protons to synthesize 1 ATP.
(ibid, "The Dynamo at Work", emphasis added). This particular use of protons in this particular case of a molecular dynamo is "planned" or "controlled" rather than being the result of unplanned, uncontrolled, random action.

It is unlike the proton tunneling mentioned in the first post of this series (ibid, "The Uncertain Gene").

Both uses of protons also took place during ancient abiotic evolution, specifically during abiotic genetic evolution / mutation in the case of RNA / DNA replication (ibid, "The Uncertain Gene").

These examples of sophisticated proton-energy based molecular machinery add support to the notion that the viral realm is a viable place to look for the original transition from pre-carbon (abiotic) entities into carbon based (biotic) "life" forms:
The virus realm may be the bridge from the molecular machine realm into the biological realm, the bridge from the abiotic evolutionary realm into the biotic evolutionary realm.
(The Uncertain Gene - 9). In fact, the viral realm has been described as a realm of molecular machines:
One of the principal goals in biology is to be able to fully understand the mechanisms of an organism in atomic detail. Viruses offer the best opportunities to achieve this goal. Written by leaders in the respective fields, this book examines a variety of viral molecular machines, using the best examples from bacteriophages and animal viruses, many causing infectious diseases of public health importance. Beginning with the viral entry into a host cell, the book takes the reader through replication of the genome, assembly of structural components, genome packaging and maturation into an infectious virion. The book conveys the state of the art knowledge of the topic generated by combining X-ray crystallography, high resolution electron microscopy, molecular genetics, biochemistry, and single molecule biophysics. Viral Molecular Machines is not only a “must-have” book for virologists but it will also be broadly useful for molecular biologists in academia and industry as well as an educational tool for teaching graduate and upper level undergraduate students.
(Viral Molecular Machines, emphasis added). While I do not dispute or criticize that observation at the macro level, I do criticize the study of viruses and microbes when it is done as if they evolved in a vacuum devoid of any experience of catastrophe on this planet or in the Cosmos (e.g. The Evolution of Anthropogenic Extinction by Catastrophe, On The Origin of Catastrophe).

And, I do criticize the cop-out that utilizes "natural selection" devoid of the larger picture of abiotic evolution, which took place without any "natural selection."

That is because "natural selection" applies only to biotic evolution of carbon based life forms which showed up billions of years after "abiotic selection" was underway  (see e.g. On the Origin of the Genes of Viruses - 6, Did Abiotic Intelligence Precede Biotic Intelligence?).

We cannot remain in a Washington, DC type of bubble (Economists - Aliens From Cygnus?) while expecting to understand either the Earth or the Cosmos around us without understanding that the five mass-extinction events must have had an important impact on evolution (see e.g. Are Microbes The Origin of PTSD?, Weekend Rebel Science Excursion - 16, On The Origin of Propaganda - 2).

And we have to take a look at the larger map to get the larger picture (see e.g. On the Origin of the Genes of Viruses - 5Putting A Face On Machine Mutation - 4).

Have a wonderful weekend.

The next post in this series is here, the previous post in this series is here.

Wind of Change, by The Scorpions