Sunday, October 13, 2013

Putting A Face On Machine Mutation - 4

First Came the Machines
One statement gets our attention anytime we talk about machine mutation and/or machine evolution.

That statement is: DNA is not alive, is not life, it is a molecule, it is not living - it is a molecular machine.

Add to that peculiarity the narrative pointed out in this series, a narrative not always considered in discussions concerning evolution, which is that machine evolution has taken up the vast majority of evolutionary dynamics, especially in terms of the percentage of the span of the evolutionary timescale (Putting A Face On Machine Mutation - 3).

Thus, we come to the focus of today's post, which is the observation that one of the candidates for the apex of machine evolution, reached during the epoch of exclusive machine evolution (prior to biological evolution) is DNA.

Some students, when they begin to study college courses that focus on DNA, know that any DNA molecule is itself not alive:
... DNA is chemical compound ... DNA is non-living, because it is a molecule not an organism ... DNA is not living. It is a chemical - a large fragile molecule ... there is no debate in the biological community about this ...
(Is DNA living or non-living thing?, emphasis added). In other cases, however, students not only harbor the misconception that DNA is alive, they even have to be specially educated to "undo" that misconception:
We are involved in a project to incorporate innovative assessments within a reform-based large-lecture biochemistry course for nonmajors. We not only assessed misconceptions but purposefully
DNA molecule is not alive
changed instruction throughout the semester to confront student ideas. Our research questions targeted student conceptions of deoxyribonucleic acid (DNA) along with understanding in what ways classroom discussions/activities influence student conceptions. Data sources included pre-/post-assessments, semi-structured interviews, and student work on exams/assessments. We found that students held misconceptions about the chemical nature of DNA, with 63 % of students claiming that DNA is alive prior to instruction. The chemical nature of DNA is an important fundamental concept in science fields. We confronted this misconception throughout the semester collecting data from several instructional interventions. Case studies of individual students revealed how various instructional strategies/assessments allowed students to construct and demonstrate the scientifically accepted understanding of the chemical nature of DNA. However, the post-assessment exposed that 40 % of students still held misconceptions about DNA, indicating the persistent nature of this misconception. Implications for teaching and learning are discussed.
(Is DNA Alive?, Research in Science Education, Volume 43, Issue 4, Aug. 2013, pp.1361-1375, emphasis added). As that abstract points out, some students have a difficult time with the concept that a DNA molecule is composed of an arrangement of atoms which are not alive.

That difficulty continues into the concept of molecular machines, that is, it is difficult for us to conceive that atoms and molecules can be configured in such a way that they are actually machines:
The ribosome ... is a large and complex molecular machine, found within all living cells, that serves as the primary site of biological protein synthesis (translation)....
(The Uncertain Gene - 4). That "large and complex molecular machine" is only one among many thousands in cells:
"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.
(The Uncertain Gene - 3). That the complex machinations of DNA and RNA are considered to be of the realm of machines is not new nomenclature.

For example, "machine" or "molecular machine" has been the nomenclature used to describe other non-living entities within cells:
Dr Clarke said: “There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become livingeverything up to that point is chemistry.”
“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said.
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
The most complex molecular machines are found within cells.
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped."
(Do Molecular Machines Deliver Toxins of Power?, emphasis in original). Since RNA and DNA are required for carbon based life forms to exist and to continue to exist, we can argue that DNA is possibly the most evolved entity to have resulted during the epoch of machine evolution.

Before closing today's post, let's consider one of the causal factors leading to the inability of some students to fathom the concept of machine evolution:
Teleology in both science and religion appears in many forms, formats, and verbal expressions during many a dogmatic brainstorm.

Scientists complain that teleological  concepts exist at even the fundamental levels of our modern science (compare If Cosmology Is "Off," How Can Biology Be "On?" with The Uncertain Gene - 2).

In the series The Uncertain Gene, Dredd Blog posts attempt to discuss a pure, i.e. teleology free, account concerning issues about how abiotic machine-evolution intersects with biotic carbon-based-life-form evolution through the advent of the quantum tunneling dynamics of protons.

Specifically, I am referring to proton tunneling at the location of certain hydrogen bonds in gene related molecules (The Uncertain Gene).
(Weekend Rebel Science Excursion - 24). Teleological language is a problem because its users subconsciously or consciously use verbiage that connotes essences to machines or organisms which those machines or organisms do not have:
Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena ... except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes.
So, let's get back to the book (Quantum Aspects of Life) to further emphasize that physicists also can get loose with their discipline, i.e. can get off into the weeds of teleology, unless they are careful:
Expressed differently, how does a quantum superposition recognize that it has “discovered” life and initiate the said collapse? There seems to be an unavoidable teleological component involved: the system somehow “selects” life from the vastly greater number of states that are nonliving ... But this implies the environment somehow favours life—that life is “built into” nature in a preordained manner. So an element of teleology remains. (p. 11) ... an element of teleology is required; namely that the molecule must somehow know before hand what it is aiming for. (p. 42) There is no teleology needed here since we describe the measurement as a two-step process ... (p. 45) ... there’s the teleological point that, hey, we search for something ... (p. 357) ... As far as the teleological aspects are concerned (p. 360) ... Teleological aspects and the fast-track to life ... there is a teleological issue here ... (p. 392)
(ibid, Quantum Aspects of Life, emphasis added). The point being made is that "natural selection" discussions by either evolutionary biologists or physicists can become fundamentally teleological unless great care and focused technical language skills are employed ...
(The Uncertain Gene - 2). For those who want to go through that experiment, describe the machine epoch, beginning at the Big Bang then progressing through some ~10.21 billion years of machine evolution until finally molecules of DNA became part of the universe of machines, all of which transpired prior to the advent of any carbon based life forms.

Don't leave out some of E.O. Wilson's pleas for discourse and nomenclature on the evolution of morality, altruism, and ethics, especially as it has been considered on Ecocosmology Blog in the same vein that abiotic intelligence has been considered:
The stars like our Sun, at the center of all solar systems, will support life forms for an amount of time, but will then destroy life on the planets near them at an unknown time during each solar system's developmental life cycle.
This could be read to imply that abiotic evolution includes a process whereby undesirable carbon based biotic life forms that might later evolve will eventually be extinguished, will "automatically" become extinct, should they evolve/develop primarily "maladjusted behaviors."
It would seem to imply, then, the existence of some form of abiotic intelligence intent on preventing future undesirable biotic evolution from getting out of hand and populating the cosmos with undesirables
(Did Abiotic Intelligence Precede Biotic Intelligence?). How could any one describe "what is up with that", in terms of morality, ethics, and/or altruism, by using the nomenclature and theory of a "natural selection" apparatus which results in the mass murder extinction (Tenet One Basics) of innocent and/or helpless species?

Nevertheless, be sure to use the nomenclature of natural selection as your linguistic word source to describe machine evolution: beginning at energy evolving into subatomic particles like protons, then those subatomic particles evolving into atoms, the atoms into molecules, then molecules into compounds, then compounds into dust clouds which condense into planetoids, which eventually evolve into stars that create carbon within themselves, then release that carbon when those stars "go nova" or "go supernova."

You will find that you will encounter some teleological problems, just like the physicists in the book Quantum Aspects of Life who tried a similar teleological-language-free task (ibid).

For example consider the use of the word "behavior":

1. manner of behaving or acting.
2. Psychology, Animal Behavior.
a. observable activity in a human or animal.
b. the aggregate of responses to internal and external stimuli.
c. a stereotyped, species-specific activity, as a courtship dance or startle reflex.
3. Often, behaviors. a behavior pattern.
4. the action or reaction of any material under given circumstances: the behavior of tin under heat.
(Dictionary). The quanta (e.g. electrons, photons, protons, neutrons) will have "behavior" ... which carbon based life forms will also have ... so be careful that teleological language does not subvert your nomenclature:
On one planet — a most ordinary planet, orbiting a mediocre star, one speck on the spiral arm of a standard galaxy — surging continents and roiling oceans organized themselves, and out of the oceans an ooze of organic molecules reacted and built proteins, and life began.
(The God Particle, Lederman, p. 1, bold added). The assertions "organized themselves" and "reacted and built" are teleological slips (or are they inferences that abiotic intelligence existed?) that reflect a need for better nomenclature.

For another example, if you think "genes are selfish" you may tend to explain machine evolution in terms like "machines are selfish" (because genes are simply molecular machine entities which are not alive).

The language of that thought experiment could be extrapolated, if you are not careful, to a notion of "protons that became selfish" ... so those selfish genes protons gathered an electron to themselves to form a hydrogen atom.

Then later they became more selfish and therefore gathered a neutron to themselves too, so as to form other atoms.

Then atoms became selfish and gathered other atoms to themselves to form molecules, etc. etc.

With such contemplation you may expose more flaws in such teleological practices, which exposure may lead to some form of improvement over flawed historical teleological communications and misunderstandings (looking on the bright side that could lead to some remedy in the form of scientifically sound and improved nomenclature).

The previous post in this series is here.


Randy said...

Reminds me of "What Orwell Didn't Know" Link

Randy said...

New link to "What Orwell Didn't know"