Monday, February 17, 2014

The Uncertain Gene - 9

~14 bn. yrs. of evolution
The Oxford Dictionary tells us that "evolution" means "the gradual development of something, especially from a simple to a more complex form", and in terms of living things, evolution means "the process by which different kinds of living organisms are thought to have developed and diversified from earlier forms during the history of the earth" (Oxford).

The graphic to the left shows a 14 billion year time line of both types of theoretical evolution, i.e., gradual development of non-living things (abiotic evolution) and the evolutionary process involving living things (biotic evolution).

The two sections of the graphic are designed to fit the two definitions of evolution; the top section in red as abiotic, the bottom section in blue: biotic.

This is in accord with the dictionary which also tells us that "abiotic" means "physical rather than biological; not derived from living organisms, devoid of life; sterile" (Oxford), and that "biotic" means "of, relating to, or resulting from living things" (Oxford).

Thus, abiotic evolution is shown taking place from the Big Bang, circa 14 billion years ago, until circa 3.5 billion years ago when biotic evolution began on Earth.

The sequences of development in the abiotic time line portion are not in actual, detailed sequence (for that, see e.g. Graphical Timeline of the Big Bang), because that detailed precision is not required for the general ideas in today's post.

Notice that in the time line depiction RNA/DNA is shown as a late development in the abiotic time line, and that viruses cross over from abiotic into biotic.

More about that follows.

Note that RNA/DNA are abiotic molecules rather than being live biotic entities, as has been discussed earlier in this Dredd Blog series:
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 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.
(The Uncertain Gene - 8, see also this and this). Additionally, the viruses have given scientists classification problems at times:
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.
(Scientific American). More recent research indicates that those virus entities do fit on the border line between abiotic and biotic, or perhaps fit in both:
If viruses were already present in the biosphere when LUCA [the Last Universal Common Ancestor, or the Last Universal Cellular Ancestor] was living, one would expect to find some common features between viruses that now infect members of different domains. This is precisely the case.
The idea that viruses are very ancient and have co-evolved with the three cellular lineages from the time of LUCA and even before has recently led to several hypotheses posing that viruses have played a major role in several critical evolutionary transitions. For instance, it has been suggested that DNA and DNA replication machineries first originated in the viral world (Forterre 1999; Villarreal and DeFilippis 2000; Forterre 2002), that virus-induced transition of cells with RNA genomes into cells with DNA genomes triggered the emergence of the three cellular domains (Forterre 2006), that the nucleus of eukaryotic cells originated from a large DNA virus (Takemura 2001; Bell 2001), or even that the selection pressure to prevent the entry of virions promoted the evolution of cell walls (Jalasvuori and Bamford 2008). All these hypotheses are not easily testable, but recent findings make them reasonable.
(Defining Life: The Virus Viewpoint). What the new research is getting at is that the abiotic molecular machine realm existed prior to the biotic / biological realm, and in some sense the viral realm is seen as a fusion of, or cross-over, from one realm, abiotic, into the other realm, biotic:
The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes that went uninterrupted from the precellular stage of life's evolution to this day. This concept is tightly linked to two key conjectures on evolution of cells: existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes, and origin of the eukaryotic cell by archaeo-bacterial fusion. The virus world concept and these models of major transitions in the evolution of cells provide complementary pieces of an emerging coherent picture of life's history.
(Koonin 2005, emphasis added). So, consider molecular machines such as a primitive virus, that is, consider a collection of molecular machines of various sorts.

Consider further that molecular machines are not fanciful:
An industrial revolution on a minute scale is taking place in laboratories at The University of Manchester with the development of a highly complex machine that mimics how molecules are made in nature.

The artificial molecular machine developed by Professor David Leigh FRS and his team in the School of Chemistry is the most advanced molecular machine of its type in the world. Its development has been published in the journal Science.

Professor Leigh explains: "The development of this machine which uses molecules to make molecules in a synthetic process is similar to the robotic assembly line in car plants. Such machines could ultimately lead to the process of making molecules becoming much more efficient and cost effective. This will benefit all sorts of manufacturing areas as many human made products begin at a molecular level. For example, we're currently modifying our machine to make drugs such as penicillin."

The machine is just a few nanometres long (a few millionths of a millimetre) and can only be seen using special instruments. Its creation was inspired by natural complex molecular factories where information from DNA is used to programme the linking of molecular building blocks in the correct order. The most extraordinary of these factories is the ribosome, a massive molecular machine found in all living cells.
(Science Daily, emphasis added). These ideas are part of a new paradigm shift in science:
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.
(Molecular Machines, A New Paradigm). 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.

Regular readers know that Dredd Blog has considered these issues for several years now (The New Paradigm: The Physical Universe Is Mostly Machine).

It is "The Abiology Rebellion" of "microabiology" (consider macroabiology too).

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

1 comment:

  1. Abiotic evolution in the form of asteroid impact dynamics is being considered as an important factor in early Earth and other planets' atmospheric dynamics: link