Friday, July 10, 2015

The New Paradigm: The Physical Universe Is Mostly Machine - 3

Putting a face on machine mutation
This series is about molecular machines (see the first post The New Paradigm: The Physical Universe Is Mostly Machine for a list of Dredd Blog posts about it going back to 2009).

With all the Dredd Blog posts about molecular machines over the years, I am pleased to see it now go mainstream.

The science that we are composed mostly of molecular machines such as RNA, ribosomes, and DNA, can't be held back any longer I suppose.

So, The New Your Review of Books indicates:
Today, driven by ongoing technological innovations, the exploration of the “nanoverse,” as the realm of the minuscule is often termed, continues to gather pace. One of the field’s greatest pioneers is Paul Falkowski, a biological oceanographer who has spent much of his scientific career working at the intersection of physics, chemistry, and biology. His book Life’s Engines: How Microbes Made Earth Habitable focuses on one of the most astonishing discoveries of the twentieth century—that our cells are comprised of a series of highly sophisticated “little engines” or nanomachines that carry out life’s vital functions. It is a work full of surprises, arguing for example that all of life’s most important innovations were in existence by around 3.5 billion years ago—less than a billion years after Earth formed, and a period at which our planet was largely hostile to living things. How such mind-bending complexity could have evolved at such an early stage, and in such a hostile environment, has forced a fundamental reconsideration of the origins of life itself.
[The ribosome] is an entity so tiny that even with an electron microscope, it is hard to see it. As many as 400 million ribosomes could fit in a single period at the end of a sentence printed in The New York Review. Only with the advent of synchrotrons—machines that accelerate the movements of particles, and can be used to create very powerful X-rays—have its workings been revealed. Ribosomes use the instructions embedded in our genetic code to make complex proteins such as those found in our muscles and other organs. The manufacture of these proteins is not a straightforward process. The ribosomes have no direct contact with our DNA, so must act by reading messenger RNA, molecules that convey genetic information from the DNA. Ribosomes consist of two major complexes that work like a pair of gears: they move over the RNA, and attach amino acids to the emerging protein.

All ribosomes—whether in the most humble bacteria or in human bodies—operate at the same rate, adding just ten to twenty amino acids per second to the growing protein string. And so are our bodies built up by tiny mechanistic operations, one protein at a time, until that stupendous entity we call a human being is complete. All living things possess ribosomes, so these complex micromachines must have existed in the common ancestor of all life. Perhaps their development marks the spark of life itself. But just when they first evolved, and how they came into being, remain two of the great mysteries of science.
(How You Consist of Trillions of Tiny Machines, emphasis added). Those "mysteries of science" are still "mysterious" because we can't yet grasp that the facts of abiology are not the facts of biology.

Abiology is the absence of biology, having evolved billions of years prior to biological life forms coming into existence (e.g. cosmology).

The trance some scientists harbor, or at least the group trance that some science writers are in, is illustrated by this sentence in the piece I just quoted from:
"One of the most ancient of ... biological machines is the ribosome..."
(ibid, emphasis added). No, Tim Flannery (author of the piece) there is no such thing as a "biological machine," so that verbiage is more bad nomenclature (Good Nomenclature: A Matter of Life and Death).

Machines are all abiotic, thus, molecular machines, being machines, are abiotic, not biotic.

There is no more reason to call a ribosome "biological" than there is to call your lawn mower "biological."

Both are used by biological entities, but that does not change their abiotic machine nature (a lawnmower does not become biological merely because it is used by a biological entity).

This same confusion about what is "bio" (life) and what is "abio" (non-life) has been perpetuated about viruses for a century:
For about 100 years, the scientific community has repeatedly changed its collective mind over what viruses are. First seen as poisons, then as life-forms, then biological chemicals, viruses today are thought of as being in a gray area between living and nonliving: they cannot replicate on their own but can do so in truly living cells and can also affect the behavior of their hosts profoundly. The categorization of viruses as nonliving during much of the modern era of biological science has had an unintended consequence: it has led most researchers to ignore viruses in the study of evolution. Finally, however, scientists are beginning to appreciate viruses as fundamental players in the history of life.
(On The Origin of the Genes of Viruses). I also hypothesized that viruses are candidates for being the first abiotic molecular machine entities to morph or evolve into cyborgs, i.e., the first to become composed of both abiotic and biotic components (compare The Uncertain Gene - 9 with On the Origin of the Genes of Viruses - 2).

Thus, I have also advocated for a discipline called "Abiology 101," so that the confusion and cacophony about these two opposite realms can begin to go away:
The subtitle of today's post could be "The Abiology Rebellion."

That is because, in today's post, I am going to talk about Abiology, a subject that is not yet in some of our parent's dictionaries.

Abiology is an area of science that is like Rodney "I don't get no respect" Dangerfield when it comes to the entirety of evolution.

Regular readers know that in various and sundry posts on the Dredd Blog System we have bemoaned the dearth of research within evolutionary circles concerning the subject of abiotic evolution or Abiology.

I have even done so to the point that I now encourage more scientific textbooks with the title "Abiology 101" in addition to and in contrast with "Biology 101" (see e.g. Did Abiotic Intelligence Precede Biotic Intelligence?, Putting A Face On Machine Mutation - 3).

A fair definition of Biology is:
... the science of life or living matter in all its forms and phenomena, especially with reference to origin, growth, reproduction, structure, and behavior.
(Dictionary, emphasis added). A fair definition of Abiology, then, ought to be:
... the science of non-life or non-living matter in all its forms and phenomena, especially with reference to origin, growth, reproduction, structure, and behavior.
(see e.g. abiological).
(Weekend Rebel Science Excursion - 27). I have also done two series which look closely at the evolutionary "abio" events that took place billions of years prior to the advent of carbon based "bio" (life).

Those two series are: On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11.

The first proto-ribosomes (which I call robosomes in On the Origin of the Genes of Viruses - 6) were abiotic molecular replication machines prior to the existence of biological life.

My guess is that one of the next areas of discovery to make it to Mainstreamville will be to realize that wireless communication is done by molecular machines, and also by biological entities using those molecular machines.

Whether done by exclusively abiotic dynamics or by cyborgs (symbiotic combos of both abiotic and biotic entities), it is a reality:
It is well accepted that all objects, whether living or nonliving, are continuously generating electromagnetic fields (EMFs) due to the thermal agitation of their particles that possess charges. Interest in EMFs as alternative forms of cell-to-cell communication can be traced back to at least the second decade of the 20th century. Interactions between EMFs and biosystems have been intensively studied for over a century and a quantitative understanding of many interaction mechanisms exists, There is much evidence that biological processes can be induced or modulated by induction of light of characteristic frequencies.

Recently, distant interactions between mammalian cells through EMF coupling have been shown. Distant (non-chemical) interaction in biosystems is not limited to interactions at the cellular level. Biosystem interaction has been reported at the level of plants, insects and other biosystems.

In 1997 Cosic proposed that there is a resonant interaction between macromolecules that plays an essential role in their bioactivity. The key point of Cosic's finding is the assignment of specific spectral electromagnetic (EM) characteristics of proteins to their specific biological function. Proteins with common biological functionality are known to share one significant peak, called the Consensus Frequency, which is acknowledged to represent the region responsible for the biological functionality. Bio-molecules with the same biological characteristics recognize and bio-attach to themselves when their valence electrons oscillate and then reverberate in an electromagnetic field. Protein interactions can be considered as resonant energy transfer between the interacting molecules. In simple words each protein and biomolecule has its fingerprint electromagnetic characteristics that can be used for its identification. In living systems long-range electromagnetic fields exchange messages across a distance because of matching emissions and absorption spectra. Non-resonating, unwanted random signals are excluded simply because they do not resonate.
(On the Origin of the Genes of Viruses - 11). An interesting candidate for analysis was written about recently in National Geographic (With Sonar-Reflecting Leaves, Plant Lures Bats to Poo in it).

This post is getting a bit long, so I will get more into the world of molecular machines, which make up the foundation upon which biological life is based, in future posts of this series.

The previous post in this series is here.

Enjoy the paradigm shift Hue.

1 comment:

  1. Since there is no "Weekend Rebel Science Excursion" post this week, consider a post in that genre over at Toxins of Power Blog (Hypothesis: Toxins of Power Originate in Molecular Machines - 2 ).