Tuesday, January 14, 2014

The Uncertain Gene - 8

DNA is not alive or biotic
In this series we have been looking at surprising ways that genetic mutation takes place (The Uncertain Gene).

But before we move on into today's post, let's remember that reporting on scientific dynamics does not require that the reporter or blogger be a microbiologist, a genetic specialist, or a quantum physicist.

Citizen journalists who are bloggers have the same "freedom of the press" and "freedom of speech" that newspaper and other reporters have.

I mean that in the sense that we can report on various subjects without having a Phd. in that particular subject or field.

Just as main stream media reporters are allowed to report about nuclear power plants and other technical subjects, even though they are not nuclear or other types of physicists or scientists.

In that context, the exercise concerning what Dredd Blog reports is to make sure that the foundational materials come from competent sources that allow us to honestly and accurately communicate the dynamics that we are reporting on to other laypersons like ourselves.

This series, from the first post, has emphasized that we are talking about abiotic evolution and abiotic mutation, not biological evolution and biological mutation.

It is important to realize that scientists are calling aspects of this subject matter a new paradigm:
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
Ribosome: a molecular machine
unit acts as a molecular machine
... 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). That Dredd Blog post quotes from a U.S. Department of Energy entity, which is the Lawrence Berkley National Laboratory.

The first fundamental thing to understand about this current series is that what we are discussing is not commonly understood.

That is, it is not commonly known, even to university level students, that DNA & genes happen to be molecular machines, i.e. that they are abiotic entities in the sense that DNA is not alive, rather, it is an abiotic molecule:
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 changed instruction throughout the semester to confront student ideas. Our research questions targeted student conceptions of
Prokaryotic Translation
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.
(Putting A Face On Machine Mutation - 4). This new paradigm of scientists uses "molecular machine" nomenclature.

Perhaps, later on this ongoing discussion will also use the concept of molecular machine intelligence, a.k.a. artificial intelligence (Did Abiotic Intelligence Precede Biotic Intelligence?).

That has to be the case when considering the long, long past of machine evolution and mutation which took place prior to the existence of any carbon based organic life forms or any biological intelligence.

Anything else ignores the enormity of time before biological evolution "recently" emerged out of previous molecular machine evolution:
The Earth is said to have formed "around 4.54 billion ... years ago" (History of Earth).

Therefore The Big Bang happened about 9.21 billion years before the Earth formed (13.75 - 4.54 = 9.21).

Biological organisms formed on the Earth about a billion years later, which would be ~10.21 billion years after The Big Bang.

Humans, homo sapiens,  are said to have evolved about 200,000 years ago, which would be ~13.7498 billion years after The Big Bang (13.7498 + 00.0002 = 13.75 billion years). Homo sapien evolution is a very tiny 0.0002 billion years of the 13.75 billion year story.

The abiotic epoch which preceded the biotic epoch involved a vast amount of "time" as we know it ...
(Putting A Face On Machine Mutation - 3). By effectively ignoring the majors while hiding in the minors, we have let some of our science decay.

Take for example the need to adjust quantum mechanics and cosmology and then move them into the flow of time involved in molecular machine evolution and mutation:
Quantum mechanics is an incredible theory that explains all sorts of things that couldn’t be explained before, starting with the stability of atoms. But when you accept the weirdness of quantum mechanics [in the macro world], you have to give up the idea of space-time as we know it from Einstein. The greatest weirdness here is that it [quantum mechanics] doesn’t make sense. If you follow the rules, you come up with something that just isn’t right. [Penrose]
...
This is said to be the golden age of cosmology and it is from an observational point of view, but from a theoretical point of view it's almost a disaster. It's crazy the kind of ideas that we find ourselves thinking about.
...
And the metaphor here—which comes from atomism that comes from Democritus [c. 460 – c. 370 BC] and Lucretius [c.99—c.55 BC] —is that physics is nothing but atoms moving in a void and the atoms never change. The atoms have properties like mass and charge that never change in time. The void—which is
Eukaryotic Translation
space in the old days never changed in time
—was fixed and they moved according to laws ...

...
Why are we confident of that? We're confident of that because we have a kind of metaphysical belief that there are laws of nature that are outside time and those laws of nature are causing the outcome of the experiment to be what it is. And laws of nature don't change in time. They're outside of time. They act on the system now, they acted on the system in the same way in the past, they will act the same way in a year or a million or a billion years, and so they'll give the same outcome. So nature will repeat itself and experiments will be repeatable because there are timeless laws of nature.

But that's a really weird idea [for scientists] if you think about it because it involves the kind of mystical and metaphysical notion of something that is not physical, something that is not part of the state of the world, something that is not changeable, acting from outside the system to cause things to happen. And, when I think about it, that is kind of a remnant of religion. It is a remnant of the idea that God is outside the system acting on it.[Smolin]
(If Cosmology Is "Off," How Can Biology Be "On?"). These are great scientific problems that will therefore need great scientific solutions.

That is because of, among other things, the complexity of the molecular machines that make up everything genetic, such as the prokarotic translation which molecular machines perform within prokarotic cells (see graphic above).

Same with the eukarotic translation that molecular machines perform within eukarotic cells (see graphic above).

The work of molecular machines which fabricate genes, as well as fabricating other molecular machines, must have had an enormous part to play in billions of years of evolution leading up to genetic machines (The Tiniest Scientists Are Very Old).

Remember also that this vast amount of evolution and mutation had to have taken place billions of years prior to the advent of biological organisms, which only came on the scene relatively recently.

Failure to concentrate on that vast span of time of molecular machine evolution, which eventually relegated them to mysterious "junk DNA", when they are anything but junk, is junk science:
Here is what "junk DNA" or "dark matter" really is:
"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.
(Scientists Discover the Origins, emphasis added). One wonders why this was not contemplated prior to going off into junk science, especially since molecular machines are found elsewhere in cells.
(The Uncertain Gene - 3). A recent post on an excellent microbiology blog has indicated the degree of sophistication of some of these molecular machines (by calling one of them a "Molecular Turbine").

Anyway, in the next post we will take a look at how all of this impacts upon our understanding of the nature of viruses.

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

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