User:Jszab:m13-2

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1) The band lies 10mm above 5kb, 16 mm above 3kb marker, 22mm above 2kb marker. This gives about 9.5kb if read from logarythmic plot. It is not what was expected, although my measuring procedure was not perfect. In the case of big bands, the distribution of sizes is usually less well resolved. In order to get better results, I would run less dense gel for a longer time. 2)0.01*10^12*10^-8 = 10 plaque forming units. Zero for DH5 strain.
3) http://tools.neb.com/NEBcutter2/index.php

4) Synthetic biology is about engineering while genetic engineering is about biology.

Oxford dictionary states that genetic engineering is: "the deliberate modification of an organism by manipulating its genetic material." It does not say what are the details of these modifications. The brief introduction in class taught us that synthetic biology is also done by intended changes to genetic material - for example refactoring of a phage genome. However those fields of science differs, as can be expected, in details.

Genetic engineering has emerged as a discipline of biology more than 30 years ago thanks to design of major extraordinary DNA technology methods: PCR amplification, DNA sequencing, Southern blotting and hybridization, and clearly restriction nucleases and molecular cloning.

However, the technology of manipulating nucleic acids and their introduction to nucleus was not enough to modify phenotypes of organisms. It appeared that more knowledge is necessary in order to understand interactions within living systems. Since then large databases containing sequences of DNA and proteins or signal transduction pathways were created. Another approaches to understand living organisms were set - including establishing the field of systems biology. Even though we got to know about myriad of mechanisms which could be potentially useful, and there is more data then we can analysz, it still does not allow us to change organisms freely.

What opposes genetic engineering enterprise is complexity and integrity of biological systems. Living cells over the last hundreds of millions of years were subjected to evolutionary pressure. The basic mathematical idea that what can divide faster will become eventually more prevalent is, as for me, the axiom of life. But unlike other axioms it does not mean that it makes the life simpler. It does not make it simpler, and it does not make it tougher. This statement is simply irrelvant for evolution. Simplicity is does not necessarily make the spreading of organisms faster, nor does complexity. If we are lucky - the simplicity goes along with functionality and evolutionary fitness. It allowed us to achieve some minor goals - lack of strong evolutionary pressure on the size of bacterial genome allowed us to find genes separated from each other by small pieces of DNA. Each of the genes also had its own promoter and terminator. Moreover, nature allowed us to introduce additional DNA to bacteria on easy-to-use plasmids. The situation was not that easy in the case of sequencing of human genome - we got unlucky in this case. Long tandem repeats made it so hard to assemble contigs from early sequencing reactions that it took us over 10 years to complete the human genome sequencing project, in spite of a grand share of resources used.

What is necessary to understand is that an organism evolves as a whole system. A single change in a gene is likely to affect another one. We, as engineers, work by making single changes to achieve a specific goal. However, in the case when a single change creates plethora of random and undesired changes - we are not always able to perform our task. In cases where we want to take advantage of useful genes in an organism,we have to first understand the whole system, and then slowly start decoupling the biological mechanism of interest.

Evolutionary fitness does not apply to Synthetic biology. Instead scientists developing it use simplicity and verstaility as the main values. This approach assumes collection of all simple "parts" of biological systems, and creation of new ones which will work independent of all conditions that we may want to change in our design. It also is meant to create a finite set of applicable mechanisms which work in a strictly predictable way. These conditions allow to go from design to a working prototype without doing research on the way. Contrary to genetic engineering in which the design has to include some uncertainty - which has to be explained by research.

From my personal experience in research I can tell that the principle of synthetic biology are already being applied. There is a pressure exerted by researchers to make their life easier and more goal-oriented. Genetic engineering is a non-standardized synthetic biology. A genetic engineer, like any other engineer, is supposed to build a working prototype. We could use the analogy with an mechanical engineering and building a vehicle. A genetic vehicle engineer needs to build themselves every small part - no matter whether it is a 'screw', 'engine' or a 'windshield' analogue in biology. All of those pieces must be specific to the project: they have to fit into an obsolete, old-fashioned vehicle created. Moreover it was made by extraordinarily smart designer which is rather sloppy and hard to understand. Therefore there is no simple pattern which would allow to automatize the process of producing any of those parts. The complexity of constructions forces engineer to do the construction most of the time - instead of design. In this case the construction is laboratory research and the sloppy designer - an evolution. In the case of synthetic biology vehicle, an engineer would be provided with standard screws, engines or windshields so he could let robots perform the construction. However, in order do follow this simple protocol, we need to dispose old vehicles, even though they still contain some value. But this is a part of another chapter.