Friday, June 20, 2014

Autopoiesis: It's Not Just For Machines Anymore

SN-1987-A: Autopoiesis at work?
It is Friday, so let's do a weekend rebel science excursion just for the fun of it.

In today's post I want to once again bring up and then focus on aspects of denial which can be rife within the scientific development of the theory of evolution.

A denial that remains, and is perhaps even stronger in American science today than it has been at other times of great scientific discoveries in the past.

Like I have indicated in an earlier post, that would be the subject of the denial of the need for the discipline I call Abiology:
The subtitle of today's post could be "The Abiology Rebellion."
(Weekend Rebel Science Excursion - 27). But more than that, let's do so using the subject referred to in the title, the subject of autopoiesis.

Like "Abiology" the word "autopoiesis" is not in some dictionaries yet, but both words should be in all dictionaries:
"Autopoiesis" (from Greek αὐτo- (auto-), meaning "self", and ποίησις (poiesis), meaning "creation, production") refers to a system capable of reproducing and maintaining itself. The term was introduced in 1972 by Chilean biologists Humberto Maturana and Francisco Varela to define the self-maintaining chemistry of living cells.
(Wikipedia, links removed, emphasis added). Notice that biologists formed that word with the myopic application based only to their discipline ("chemistry of living cells").

I have criticized narrow, myopic types of nomenclature in some Dredd Blog series (e.g. The Uncertain Gene - 8, Putting A Face On Machine Mutation - 3) as well as some non-series posts (e.g. Did Abiotic Intelligence Precede Biotic Intelligence?).

The gist of this weekend rebellion is that evolutionists tend to apply nomenclature in such narrow ways that the nomenclature becomes incoherent to a broader interdisciplinary base:
The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century.
(On the Origin of the Genes of Viruses - 3, quoting Wikipedia: "Modern Evolutionary Synthesis", emphasis added). That type of myopic distortion has happened with the word "autopoiesis" too.

So, today we will apply it to the broad, long term time frame concept of abiotic evolution rather than pigeon holing it within the much shorter time frame of biotic evolution.

If you think about it, the Big Bang Theory is a description of spontaneous autopoiesis, because that cosmological, abiotic theory describes an abiotic, non-living, pre-carbon-based-life system-generating-event.

An event that is said to have resulted in a universe which has powers of replication (see e.g. the series On the Origin of the Genes of Viruses, especially On the Origin of the Genes of Viruses - 6).

Remember that a lot of current abiotic science was not known when Humberto Maturana and Francisco Varela coined the word "autopoiesis."

Furthermore, it was not known then that abiotic molecular machines generated many of the dynamics which they were observing.

They thought that the phenomena being observed were totally biotic or biological dynamics.

A new paradigm exists for understanding how cells function. Scientists are recognizing that the cell is a highly integrated biological factory with a modular architecture. Each modular unit acts as a molecular machine. These machines have highly specialized functions and are large assemblies of proteins and nucleic acids. They range in size from about 10 - 150 nanometers (10-9 m) and provide environments in which chemical species can interact in a highly specific fashion. Molecular machines also function as mechano-chemical energy transducers, converting chemical free energy into mechanical energy for cellular processes. They operate cyclically, and can reset themselves.

With the genetic information gained from the U.S. Human Genome Project and DOE's Microbial Genome Program, scientists now have the raw information with which to observe, manipulate, characterize and, ultimately, replicate these large protein assemblies. Using conventional and newly developed microscopy techniques, PBD researchers, through an initiative called Microscopies of Molecular Machines (M3), are creating a toolkit for probing the inner workings of these molecular machines.
(The New Paradigm: The Physical Universe Is Mostly Machine). Thus, much of what they saw as being purely biological functioning in cells was actually machine or abiotic autopoiesis, not biological or biotic autopoiesis.

This is also true for genetic dynamics (DNA is not alive, not biotic, it is abiotic) taking place within cells too:
"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant ["junk"] since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
(The Uncertain Gene - 8). When geneticists and microbiologists look inward they see evidence of autopoiesis in the micro-universe of microbes.

Likewise, V. G. Gurzadyan and Roger Penrose are advancing a kind of a never ending autopoiesis hypothesis called "conformal cyclic cosmology" (CCC) in the macro-universe of the cosmos:
According to conformal cyclic cosmology (CCC) ... what would normally be regarded as a probable entire history of our universe, starting with its Big Bang and ending with its accelerating de Sitter-like expansion (assuming a positive cosmological constant Λ ...), is taken to be but one aeon in a (perhaps unending) succession of such aeons, where the conformal 3-surface B representing the big bang of each aeon is regarded as the conformal continuation of the remote future (i.e. conformal infinity I ...) of the previous one. CCC takes there to be no inflationary phase in any aeon, the observational support that inflation enjoys being supposed to be equally supported by the existence of the final exponential expansion occurring in the previous aeon ...
(Concentric circles in WMAP data may provide evidence of violent pre-Big-Bang activity, cf. Phys Org). Their paper argues that the Big Bang is perhaps a regular intermittent event that takes place between aeons in a CCC.

A follow-up to their paper which address some criticism of their first paper: (On CCC-predicted concentric low-variance circles in the CMB sky).

Their hypothesis is somewhat akin to the old Oscillating Universe (the ultimate abiotic autopoiesis) hypothesis.

I now return you back to your regularly scheduled borgosphere programming.

Have a good weekend!

The Borgosphere ...


  1. History repeats itself, and that’s one of the things that’s wrong with history.” – Clarence Darrow

    Perhaps autopoiesis is a defect?

  2. "You're out of order, you're out of order, the whole trial is out of order!"

    Great post, Dredd. This is the kind of cutting edge thinking that shows how desperately slow and plodding our human knowledge is - taking millennia to come to this (which may have been even further refined if we had any time left). It seems like (the gaining of this knowledge via) our scientific inspection (which is part and parcel of industrial civilization) contains within itself the seed of our destruction (for doing so).

    It seems as if no matter what we would have done, we'd eventually come to the same end, like everything else in the universe. "Nothing lasts forever" may be true if we regard "nothing" as the (eventual) eternal state of being.


  3. also tangentially relevant:

    Meteorites hidden under Antarctic could hold clues to solar system’s origins