Synthetic Bio Midterm

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Synthetic Biology

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The intentional design of artificial biological systems.

Synthetic biology is a maturing scientific discipline that combines science and engineering in order to design and build novel biological functions and systems. This includes the design and construction of new biological parts, devices, and systems (e.g., tumor-seeking microbes for cancer treatment), as well as the re-design of existing, natural biological systems for useful purposes (e.g., photosynthetic systems to produce energy). As envisioned by SynBERC, synthetic biology is perhaps best defined by some of its hallmark characteristics:

* predictable, off-the-shelf parts and devices with standard connections
* robust biological chassis (such as yeast and E. coli) that readily accept those parts and devices
* standards for assembling components into increasingly sophisticated and functional systems
* open-source availability and development of parts, devices, and chassis.

Synthetic biology will help develop the foundational understanding and technologies to build biological components and assemble them into integrated systems to accomplish particular tasks. Synthetic biology will improve researchers' understanding of the natural world and holds great promise in producing socially valuable advances in information processing, energy production and environmental applications, chemical and materials manufacture, and human health.

Synthetic Biology is
A) the design and construction of new biological parts, devices, and systems, and
B) the re-design of existing, natural biological systems for useful purposes.

Goals: predictability, reliability, standards

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Parts

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Leader: Wendell Lim

SynBERC will computationally design and construct cellular “parts” that can be assembled into “devices” (Thrust 2). We define “parts” to be any genetically encoded, basic biological function (e.g., a ribosome binding site, transcription termin-ator, or phosphorylation motif). A key component in the “parts thrust” is developing a framework for parts design that takes into account part function, and part-part interactions.

UC Berkeley, UCSF (Lim)

Layers 1-3 occur within a single cell. We call everything that occurs here a biological part.: Layer 3 Protein dimerization interface
Layer 2 RNA PoPS
Layer 1 DNA BioBricks assembly

Promoters
Ribosome Binding Sites
Open Reading Frames
Terminators: a section of genetic sequence that marks the end of gene or operon on genomic DNA for transcription.

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Thrusts

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SynBERC has identified four research thrust areas: parts, devices, chassis, and human practices.

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Devices

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We will assemble cellular “parts” into “de­vices” that can be reused in a combination of “systems.” Here, “devices” are defined to be collections of parts that perform one or more human-specified functions under defined con­ditions (

Relates to Pops through a pattern

We see that in the definition of the device given here, almost anything can be considered a device as long as it is characterized according to a standard with well-defined inputs and outputs. The same component, uncharacterized, is not a device, as it is does not provide a useful device abstraction layer.

Output: The quantity that is delivered by an instrument or a component of an instrument

Input: Information sent

Thus, if you have an increase in Pops then more RNA is formed (input) which in return makes more protein (output)...right? So, the device is the whole system including the electrical current that controls the Pops...right?

GFP Producing Device: Green Fluorescent Protein

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Chart of Thrusts

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4 Population cell-cell signaling Design interactions between different cells
3 System Signaling molecules, fluorescence Design system to process external inputs into detectable outputs
2 Device PoPS, RiPS Use parts to design device with particular transfer curve
1 Part BioBricks assembly Plan and assemble
0 Materials nucleotides/amino acids Choose the materials

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Chassis

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Backbone on which a car is based.

Leader: George Church

Our overall goals require that we build parts, devices, and systems that work inside living cells. In an engineering sense, our cells must act as “power supplies” and “chassis,” providing materials, energy, and other basic resources that are needed for proper system function. Here, we will develop and characterize a small number of “naïve” cellular power supplies and chassis that can be used to sustain the proper operation of any synthetic biological system over a range of defined operation conditions. As a result, systems engineers will be able to focus on system design, and cell engineers will be able to focus on the design of cells as power supplies and chassis.

Harvard

Well-described: E coli, yeast

want the smallest operational unit that is still a living being

by reducing interactions, increase capacity to handle a load.

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Bacteria, like E Coli

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Bacteria are microscopic (very tiny) organisms that are unicellular (made up of a single cell). Bacterium is the term for a single bacteria.

Evolution of Bacteria: These primitive organisms were among the first to appear on Earth; bacteria evolved roughly 3.5 billion years ago. The oldest-known fossils are those of bacteria-like organisms.

Discovery of Bacteria: Bacteria were unknown to people until the 1600s, when Antony van Leeuwenhoek first observed them in his newly-made microscope.

Cells of Bacteria: The cells of bacteria are different from those of plants and animals in many ways, the most obvious of which is that bacteria lack a nucleus and other membrane-bound organelles (except ribosomes). Unlike animals and plants, bacteria have pili, flagella, and most have a cell capsule.

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Human Pratices

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In addition to numerous bioscientific challenges, the vast potential of synthetic biology to play a formative role in contemporary human life raises new questions for bioethics, biosecurity, biosafety, health, energy and intellectual property. To date considerable focus has been given to the so-called dual-use challenge. For example, while the study of synthetic biology can lead to more efficient ways to produce cures (e.g. against malaria), it may also lead to synthesis or redesign of harmful pathogens (e.g., smallpox). In addition, scientists, funders, policymakers, ethicists and others have recognized challenges presented by a post 9/11 political milieu. A new range of potentially malicious actors and actions (i.e., terrorists/terrorism) must now be taken into account by those seeking to govern scientific domains; and the internet and other new media provide global access to technological know-how and scientific knowledge. Such global access cannot be addressed using existing models of nation-specific regulation. (New Scientist, November 12, 2005). Some detailed suggestions for licensing and monitoring the various phases of gene and genome synthesis are beginning to appear. There is also an ongoing, comprehensive, and open discussion of so-called “societal issues” online at OpenWetWare.

Recently, efforts have been made to think beyond the “societal issues” model of ethics, politics, and science in relation to synthetic biology. This effort refuses the established convention of imagining society outside of and downstream of scientific practices, such that bioethics is assigned the task of limiting the negative impact of science on society. By contrast recent approaches focus on the integral and mutually formative relations among scientific and other human practices. These human practices approaches attempt to invent ongoing and regular forms of collaboration among synthetic biologists, ethicists, political analysts, funders, human scientists and civil society activists. To date collaborative work on “governance” or “society” or “ethics” in relation to synthetic biology has largely consisted either of intensive, short term meetings, aimed at producing guidelines or regulations, or standing committees whose purpose is limited to protocol review or rule enforcement. Such work has proven valuable in identifying the ways in which synthetic biology intensifies already-known challenges in rDNA technologies. However, these forms are not suited to identifying new challenges as they emerge. An example of efforts to develop ongoing collaboration is the Human Practices component of the Synthetic Biology Engineering Research Center (SynBERC), an NSF funded collaboration among a number of leading research universities. In Europe, the multi-partner project SYNBIOSAFE is investigating the biosafety, biosecurity and ethical aspects of synthetic biology.

Co-Leaders: Paul Rabinow and Ken Oye

The defining goal of SynBERC is to make biology into an engineering discipline. To this end, Thrusts 1 through 3 link evolved systems and designed systems, with emphasis on organizing and refining elements of biology through design rules that enable the engineering of complex integrated biological systems. Thrust 4 examines synthetic biology within a frame of human practices, with reciprocal emphasis on ways that economic, political, and cultural forces may condition the development of synthetic biology and on ways that synthetic biology may significantly inform human security, health, and welfare through the new objects that it brings into the world. It includes both applied research modules under the leadership of Kenneth Oye of MIT and fundamental research modules under the leadership of Paul Rabinow of the University of California at Berkeley.

Module 1: Applied Research on Intellectual Property and the Commons
Analysis of approaches to sharing and/or guarding the parts, devices, chassis, systems, protocols, standards and design rules that constitute synthetic biology; focus on effects of property rights and sharing regimes on incentives for investment, advancement of knowledge and diffusion of benefits of innovation; potential practicums in Registry of Biological Parts; Office of Biological Disenchantment; copyright and public licensing of protocols and standards.

Module 2: Applied Research on Security, Health and Environmental Effects
Analysis of benefits and risks associated with the development of synthetic biology in security, health and environmental affairs; assessment of methods of engaging with uncertainty over effects; analysis of methods of enhancing benefits and containing risks; potential practicums working with governmental and nongovernmental organizations in risk assessments; developing educational materials on synthetic biology for the policy community; and working with synthetic biologists on ways to limit risks through self governance.

Module 3: Fundamental Research on Ethics
Rethink the relationship of ethics and science in view of the highly innovative assemblage of objectives and practices in synthetic biology; analysis of the limitations and advantages of recent bio-ethics projects, including Belmont, Asilomar, ELSI, and Presidential Commissions; empirical research on evolving ethical practices in synthetic biology (including IP and security), monitoring differences in context and practical experience; design and develop collaborative ethical practices that reconfigure science and ethics for synthetic biology; eventual standardization of these practices.

Module 4: Fundamental Research on Ontology / Emergent Objects
Reflect on the form and essence of the parts, devices, chassis, and systems being created by synthetic biology; analyze the differences between the objects created in older recombinant technologies and those projected in synthetic biology; empirical research tracking how these parts, devices, chassis, systems, and test beds are designed and the ways that evolution and contemporary synthetic approaches differ from and enforce each other; observe and design new institutional arrangements and interventions appropriate to the new objects being brought into the world; eventual standardization of this new mode of productively assembling scientific, technological, economic, cultural, ethical, and security components.

The two applied modules will serve (in part) as test beds for foundational modules on ethics and ontology, in much the same way that SynBERC test beds on tumor seeking microbes and microbial drug factories motivate work on the foundational infrastructure on the design and construction of engineered biological systems. The pragmatic tasks of evaluating conventions for intellectual property, appraising risks, and benefits associated with synthetic biology, and developing educational materials on synthetic biology for the scientific and policy communities rest on implicit ethical and ontological assumptions.

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Parts, simple definition

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Genetic material encoding biological function. ie a piece of DNA that works with a matching binding protein to regulate gene activity.

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Devices, simple definition

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Combinations of parts that perform discrete tasks.

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Systems

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Combination of biological devices that perform functions encoded by humans.

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Genetic Pathway

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Collection of genes

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Gene

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The basic unit of inheritance. A gene is a segment of DNA that specifies the structure of a protein or an RNA molecule.

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Parts Biobricks

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Every BioBrick coding region consists of the following structure:

* It begins with a standard start codon: "ATG"
* It ends with two "stop" codons: "TAA","TAA", i.e., "TAATAA".

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Rational Design

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The first of these two terms sounds remarkably like “Intelligent Design,” which evolutionists reject. However, rational design is clearly Intelligent Design undertaken by human beings. The two scientists wrote: “Rational design, also known as computer modeling, attempts to modify or create [protein] molecules for specific applications by predicting which amino acid sequence will produce a protein with the desired properties” (Ibid.).

Example from Keasling Lab: With the maturation of systems biology it is now possible to study the physiological response of an engineered bacterium to synthetic pathway expression at all levels of the biochemical hierarchy: mRNA, enzyme and small chemical. Previously, E. coli was engineered to produce large quantities of amorphadiene, a precursor to the anti-malarial drug artemisinin, by creating a mevalonate-based isopentenyl pyrophosphate biosynthetic pathway (Martin et al. 2003. Nat. Biotech. 21:796). The engineered E. coli produced high levels of this isoprenoid, but optimization for higher titers elucidated several constraints imposed by interactions between the host organism’s metabolism and the exogenous synthetic pathway. Using a combination of DNA microarray, proteomic, and metabolomic approaches we have studied how E. coli responds to the synthetic metabolic pathway in an effort to further our rational design of this isoprenoid–producing bacterium.

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DNA Synthesis

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DNA synthesis takes place during S phase of the cell cycle; the two strands of a DNA double helix separate and each serves as a template for synthesis of complementary daughter strand.

1. DNA is unzipped by an enzyme called helicase. (mention that all enzymes end in -ase and that the enzyme responsible for unzipping the DNA is called "helic"ase because it acts on the helical strucute of DNA)

2. The enzyme DNA polymerase moves in and fills in the complimentary sequence of nucleotides on each of the parent strands. (In diagram have students fill in the complimentary nucleotide sequence).

(mention about enzymes)

3. The two developing DNA strands separate into two new DNA strands.

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Metabolic Pathway

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In biochemistry, a metabolic pathway is a series of chemical reactions occurring within a cell.In each pathway a principal chemical is modified by chemical reactions. These reactions are accelerated, more accurately catalyzed, by enzymes. Dietary minerals, vitamins and other cofactors are often needed by the enzyme to perform its task. Many pathways are elaborate. Various metabolic pathways within each cell form that cell's metabolic network. Pathways are needed by an organism to keep its homeostasis.

By adding new genes and engineering a new metabolic pathway in Escherichia coli bacteria, the researchers can quickly and cheaply synthesize a precursor to the chemical compound artemisinin. This next-generation antimalarial drug has proven to be effective against strains of the malaria parasite that are resistant to current front-line drugs, but it is far too expensive right now for the countries in Africa and South America where it is needed most.

"By inserting genes from three separate organisms into the E. coli, we're creating a bacterial strain that can produce the artemisinin precursor, amorphadiene," says chemical engineering professor Jay Keasling, who is leading the research. "We are now attempting to clone the remaining genes needed for the E. coli to produce artemisinin."

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PoPs, Polymerase

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Polymerase per Second

We can solve this problem by reorganizing the parts that make up our inverter [Figure 2, right]. Now, the input signal to the inverter is carried by polymerase per second, or PoPS. PoPS is the flow of RNA polymerase molecules along DNA (i.e., 'current' for gene expression). The PoPS level is set by the amount of RNA polymerase molecules that trundle past a specific position on DNA each second. Importantly, the output signal from the inverter is also carried by PoPS. The inversion function of the device is still executed by a repressor protein acting on its cognate site at the operator DNA, but all details specific to this interaction are internal to the device. As a result, an inverter only involves one protein and a complete set requires only one inverter per protein.

Polymerase chain reaction (PCR): A method for amplifying a DNA base sequence using a heatstable polymerase and two 20-base primers, one complementary to the (+) strand at one end of the sequence to be amplified and the other complementary to the (-) strand at the other end. Because the newly synthesized DNA strands can subsequently serve as additional templates for the same primer sequences, successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample.

Polymerase, DNA or RNA: Enzymes that catalyze the synthesis of nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides.

an enzyme that catalyzes the formation of new DNA and RNA from an existing strand of DNA or RNA

DNA polymerase adds nucleotides to match to the nucleotide present on the template strand. A is paired with T and G with C. Because each molecule of DNA contains one strand from the original strand, the replication process is semiconservative replication.

The nucleotides used for synthesis are ATP, GTP, CTP and TTP. Each of these DNA nucleotides has three phosphate groups. Two of the phosphates will be removed when the nucleotide is attached to the growing chain of new DNA.

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Enzyme

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Protein made by the body that brings about a chemical reaction, for example, the enzymes produced by the gut to aid digestion.

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Protein

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A molecule composed of a long chain of amino acids. Proteins are the principal constituents of cellular material and serve as enzymes, hormones ...

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Amino Acids

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Amino acids are the building blocks of proteins. There are 20 natural amino acids.

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Codon, Amino Acids, Nucleotides

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The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon.

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Biobricks assembly

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Physical parts in the DNA Repository have been designed to be assembled into systems using normal cloning techniques based on restriction enzymes, purification, ligation, and transformation - with a twist: BioBrick parts are composable. The result of assembling two parts is a new part that may be used in future assemblies. Certain RBS-CDS issues must also be considered.
Standard Assembly

Bricks.png


BioBrick parts can be assembled to form useful devices, through a process often referred to as 'Standard Assembly'. This uses normal cloning techniques based on restriction enzymes, purification, ligation, and transformation. Find out more about Standard Assembly.

Standardization

BioBrick parts can be assembled to form useful devices, through a process often refeed to as 'Standard Assembly' This uses normal cloning techniques based on restriction enzymes, purification, ligation, and transformation. BioBrick parts are composable; allowing endless numbers of biobricks to be pieced together to form higher systems.

The assembly to the left shows 3 BioBricks assembled to create a simple device.

Devices

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Parts Registery

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BioBricks is a standard for interchangable parts, developed with a view to building biological systems in living cells.

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Parts Registery Part 2

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In specifying your parts you must clearly understand the relationship between parts and plasmids. You must be explicitly aware that a part does NOT include the flanking restriction enzyme sites (called BioBrick prefix and suffix if you are using the BioBrick™ standard for which the restriction enzymes are: EcoRI, XbaI, SpeI, PstI). These sites must instead be specified in the plasmid that your part is in. Your part, then, begins with the first letter (A, C, T, G) following the prefix cloning site of the plasmid and ends with the last letter preceding the suffix cloning site of the plasmid.

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Beruf (Vocation)

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Beruf- Calling Pursuit of knowledge as a calling

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PoPs, continued

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PoPs is the flow of RNA polymerase molecules along DNA

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Wissenschaft (Science)

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The creation of knowledge

relates also to science as any prusuit of knowledge (ie anthropology)

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Demagification

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"One need no longer have recourse to magical means in order to master or implore the spirits, as did the savage, for whom such mysterious powers existed. Technical means and calculations perform the service. This above all is what intellectualization means.

"Progress:" Do they have any meanings that go beyond the purely practical and technical?"

"For civilized man death has no meaning"


Because death is meaningless, civilized life as such is meaningless

Has progress a recognizable meaning that goes beyond the technical... It is no longer the question of man's calling for science, hence, the problem of what science as a vocation means to its devoted disciples...to ask for the vocation of science withtin the total life of humanity. What is the value of science?


Science is meaningless because it gives no answer to our question, the only question important for us: What shall we do and how shall we live?

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Key points on Weber

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External Conditions: American versus German

American- football coach is most respected figure

Institutions and labor conditions are a part of the form of labor


Internal: Personality versus Character

Personality is shallow, 300-400 people courses,

Character: deep, vocational commitment to subject matter, ethically in pursuit, requries a great deal of work on self (modes of subjectification of Foucault)

Based on external conditions of the academy, the best people dont get the best jobs.

Can you stand to watch those inferior to you succeed?

Nature of institution where committees make decisions

Protestant view: no deep meaning to work, one has to work for the sake of working

One must work hard: Enthuasiasm is a dangerous sign that you are being lead astray.

The more science advances the less hte public knows about the external conditions

We are blindfolded from our own human condition.

Knowledge and Discipline without magic is a source of great power.

Science will not answer your question about whether or not what you are providing is meaningful, but self-clarification can later tell you that.

science presents itself as being self-evident and not needing to justify itself and has this concept of progress. it does not matter that there is not a meaning that science is working with. it is with the understanding that what you study will be outdated quickly.

Science as technical mastery is the ultimate truth about that which it is the truth about, thus it is a mistake to conclude: 1)there are not other forms of knowledge that could take up questions of worth or meaning and 2)we need to denounce science for having a limited function

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Wissenschaft

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Systematic pursuit of knowledge

Science is not to be concerned with immediate pleasures

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Demagified Universe

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Everything is ultimately calculable, but not on the intention of human actions. Meaning becomes the question that is put on the table.

This is the price you pay to know the truth.

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Tumor Killing Bacteria and Christopher Anderson

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*Bacteria can sense their environment, distinguish between cell types, and
deliver proteins to eukaryotic cells. Thus, can be designed to produce therapeutic agents like probiotics or as targeted delivery systems.
*Anderson: 1) Utilizes ribosome binding sites (mRNA that is bound to the ribosome when initiating protein translation), sensors, outputs, and genetic selection. These together help to engineer bacteria to sense the environment of a tumor by finding the cancerous cells and releasing a “cytotoxic” agent.
*Cites “Hellinga” and “Arnold and Coworkers” people from Berkeley and UCSF
*Inv (protein) E Coli can invade a broad range of tumor cells and is amenable to positive selection.
*Ground-up Genetic or Cellular Engineering,
we add DNA sequences into well characterized
model organisms to understand
biological behavior or construct useful
organisms
*Makes relation to Lunar Rover
*CalTech uses viruses to modify bacteria chassis (has one MIT prof on team... Endy researches same bacteria of bacteriophage t7), Princeton utilizes plasmids, Anderson uses other bacteria.
*Oragenics wants to use live bacteria for dentistry and probiotics for IBS.
* As it grows in tumors the engineered Salmonella Typhimurium expresses an E. Coli enzyme.
*1) Engineered bacteria are injected into the bloodstream; polysaccharide molecules on their surfaces allow them to evade the immune system
2) When they detect the low-oxygen environment of a tumor, the bacteria produce invasin, a protein that allows them to infiltrate the cancer cells
3) The invasin binds to the cancer cells, prompting the cells to engulf the bacteria
4) The cancer cell bursts the bacterium, releasing a toxic enzyme that kills the cell.

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Metabolic Pathway

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A series of chemical reactions catalyzed by enzymes in a living system. The products of the pathways have vital functions. For example, the Kennedy metabolic pathways found in plants are involved in producing various types of seed oil.

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Amyris

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Amyris Biotechnologies is dedicated to improving the world by leveraging breakthroughs in synthetic biology. Amyris' technology is able to provide a consistent, cost-effective supply of biofuels and other high-value natural compounds, including pharmaceuticals, fine chemicals, and nutraceuticals.

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Abstraction

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Abstraction Hierarchy allows one to make from scratch a system for human life saving bacteria as opposed to bioengineering

Abstraction: BioFab, Endy, Abstraction Hierarchy method
-John Goller: black boxing

Inverter: Computer Aided Design or BioJade (illustrates what abstraction comes out to); whatever comes out is opposite of what is inputted.

Abstraction is the process of describing some system in a way that highlights relevant properties and suppresses irrelevant details.

Abstraction hierarchies are a human invention designed to assist people in engineering very complex systems by ignoring unnecessary details. If the process to design a biological system was to write down the string of nucleotides, it would immediately become untenable even for experts to design anything but very simple systems. Most people just aren't capable of processing that kind of detail all at once. If instead, an abstraction hierarchy is specified, it allows the designer of a biological system to ignore some of the implementation details and focus only on the high-level design issues.

Engineers in all disciplines take advantage of abstraction hierarchies to design and build complicated systems. For instance, software engineers write in high level programming languages like C++ or Java which are designed to be easy for humans to read and write. These programs are then translated into lower level sets of instructions that are more easily translatable to bit strings that are machine interpretable and implementable. Thus, the people who write C++ programs do not need to know how to translate their programs to machine code and the people who work on instruction sets do not need to envision all possible programs that the software engineer might write.

Endy/Anderson model:

Layer name Definition Example
1)DNA:sequence of nucleotides ATGGATCATGATG:
2)Part: a finite sequence of nucleotides with a specific function; RBS, CDS, promoter, terminator
3)Device: multiple parts with a higher level function inverter
4)System: multiple devices hooked together; ring oscillator

An abstraction hierarchy can be used with other technologies (e.g., ‘standard part families’) to quickly design and specify the DNA sequence encoding many integrated genetic systems. For example, a ring oscillator system can be built from three inverter devices. Each inverter device can in turn be built from four parts, and each part can be encoded by a pre-specified sequence of DNA. Other systems can be quickly specified as different combinations of devices, and so on.

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Modularization

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: a part in the registry can be reintroduced into any system that works with the same standards. Any part can be attached to the other. The division of material into parts that can be reassembled.

The process by which courses are divided into separate elements - modules - which are self contained.

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BioFabs

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essentially talking about factories with technicians, workers, and parts

A Fab means flexible, reliable standardized methods and design libraries that enable complex applications.

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Standardization

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he process of establishing standards that are documented agreements containing technical specifications or other precise criteria to be used consistently as rules, guidelines, or definitions of characteristics. This ensures that materials, products, processes and services are fit for their purpose.

Began in 57 in silicon valley with planar technology and the use of photomasks for the production of standardized simple circuits instead of building circuit by circuit.

Without standardization, every DNA assembly is an experiment in and of itself.

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Collaboration

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Recognition of shared problems, stakes, challenges, and evolving norms

SynBerc is an organization that seeks to define this emerging field with the distinction being that they use collaboration.

Interdependent division of labor on shared problems. Thus, as MIT makes toys and we makes artemesinin, not collaborating. Is biobricks a shared problem? Different approaches prevent collaboration 100 percent. Does occur with some research.

Mutual work on commonly defined problems.

Usage of human practice thrust. Thus, demands new practices, new equipment, etc. to solve problems

Equipment here means a set of truth claims, affects, and ethical orientations all put together into practices that can be utilized for specific problems.

Call to Collaboration: Recognition of shared problems, stakes, challenges, and evolving norms

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Approaches MIT versus Cal

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1)MIT: John Goller: electrical engineering, if you can make all possible parts in the world, then ideas will come from that
2)Berkeley: Chris Anderson uses mechanical engineering, but actually uses all thrusts (thus has a stronger, more round understanding); We are more interested in the bigger application (don’t tell me how to understand it). We want to make systems and if this is a way to do that…great. But we won’t just make parts for sake of making parts. Keasling: MIT is big on producing toys and we are trying to make something.

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Cooperation

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Demarcated (separated, boundaried) work with regular EXCHANGE. It does not include common definition of problems or shared techniques of remediation.


Relates to CP Snow and two cultures. Can two cultures (say bio and human ethics) do more than cooperate when language is not shared?

ELSI model

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ELSI

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ELSI stands for Ethical, Legal and Social Issues. It's a term associated with the Human genome project. This project didn't only have the goal to identify all the approximately 24.000 genes in the human DNA, but also to address the ELSI that might arise from the project.

5% of the US annual Human genome project (HGP) funds is allocated to address associated ELSI of the work.

ELSI Research Goals

* Examine issues surrounding the completion of the human DNA sequence and the study of human genetic variation.
* Examine issues raised by the integration of genetic technologies and information into health care and public health activities.
* Examine issues raised by the integration of knowledge about genomics and gene-environment interactions in non-clinical settings.
* Explore how new genetic knowledge may interact with a variety of philosophical, theological, and ethical perspectives.
* Explore how racial, ethnic, and socioeconomic factors affect the use, understanding, and interpretation of genetic information; the use of genetic services; and the development of policy.

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more on berk v mit

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MIT wants to make synthetic bio. and engineering discipline whereas Berkeley wants to use engineering principles with immediately appliable function

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Mode One

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*Inventorying, cooperating, and consulting with experts
*The CORE assumption being that the expertise of existing specialists in one domain is adequate without major adjustment to emerging problems.
*Expert knowledge functions as means-end maximization
*It is only functional when that which counts as a problem is given in advance, stabilized, and not subject to further questioning
*In an emergent situation like synthetic biology, neither problems nor goals are settled, and so technical expertise cannot be effectively marshalled.
Two types of Mode one Social science practicioners 9 that represent existing expertise):
This first order observer takes the world as it comes to them. The second order observer observes actors acting. However, always a first order observer in as much as they must look through they must pick out another observer as their object to see through them.

Problems: 1)In emergent problems, experts do not necessarily exist; 2)When experts do exist, their very usefulness involves the bracketing of goals- in emergent situations, even the bracketing must be subject to scrutiny; 3)When hiring new experts to prepare for impact, 1 and 2 still apply; 4)Based on idea that there is a society with a government through which issues can be debated- however, world is now globalized... Is there even society?

Mode one operates within a realm of certainty. Thus, when taking up uncertainty, mode on looks to precedence from past successes in similar circumstances and uncertainty is a boundary condition (--on the horizon--).

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Mode Two

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"Science and Society"


*MTwoP are facilitators who bring heterogenous actors (scientists, tech experts, civil society actors, political activists, gov, industry, funders, etc)together into a common venue. This venue is often created by a particular crisis or event but then is often standardized as a place for representation and expression.
*Takes "social values" as norms for discriminating which activities are appropriate and then elaborates values as basis for organized activities.
*Center for Nanotech and Society at ASU is finding new ways to organize research through reflexiveness and social learning that will signal emerging problems, enable anticipatory governance, and guide trajectories away from undesirable ones. Utilize real time technology assessment (RTTA) that engages researchers with the public and monitors changing values. This places researcher as servant to the public. Wish to understand beforehand the strength and weaknesses of tools.

Problems: 1) Although trying to move away from experts, must use experts for polling, etc. Thus in moving beyond demand new experts 2)assumes that ethical science is science that benefits society; 3)Has no technique for producing society's representatives. 4)Who is society/the public? 5)Can never answer the question of whether something is good or bad, right or wrong.

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Mode Three

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Inquiry + Equipment

Goal to bring biosciences and human sciences into a mutually collaborative and enriching relationship. In order to do so, one must invent, design, and practice new equipment (truth claims, affects, and ethical orientations designed and combined into practices useful for work on specified problems and objects).
*improved pedagogy, vigilant assessment of events, and focused work on shared problem-space. Pedagogy meaning how one's practices form or deform one's existence and how science enriches or impoverishes those dispositions. Events cause specific changes in objects, relations, purposes, and modes of eval/interaction (Thus, while in mode one events occur and are later analyzed for their effect and in mode two the analysis of events is on wht it does for other people and its effects before it happens, in mode3 some events do occur but are examined for not only their emerging affect on society, but also on the scientists concurrently with their research and goals. reminds me of how anderson changed definition (equipment) of part 8 months ago and it is constantly changing...This has broader affects and changes goals and orientations).

Emergence is in when multiple elements combine to produce an assemblage.
*Can be used to spot dubious orienations
*Live action field work: Rabinow and Iceland Genome Project. How would someone know that science is being done differently in different areas? Must be done in real time and on ground.

Constant interchangeability between case materials, fieldwork in biotech, and concept work

Constantly poses and reposes the question of what does it mean to have a flourishing existence and the place of science in this form of life. How does science contribute or disrupt this? Must be posed and re-posed.

Although asked to call in experts, etc. mode three cannot but it is working with an emergent problem-space. Fluidity versus static knowledge.


From theory to inquiry

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Test-bed

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A test bed is a concrete research project designed to function as a proof-of-concept for work in the three thrusts. The three test beds right now are bacterial foundries, tumor-seeking bacteria, and biofuels. The MIT group would function as a testbed for for Berkeley's experiments. This is collaborative, but working with mode one to be able to produce such things as workshops, conferences, and so on.

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Scenario thinking

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Mode Two and SynBerc and Human Practices

Scenario thinking identifies a range of logically distinct futures and helps to tease out and pull apart assumptions. Helps identify the critical contingencies about the future that may play a formative role in the shaping of synthetic biology.

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Mode Three and Human Practice

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Biosecurity: Recombinations/Configurations of existing expertise is required if a biodefense system is to be constructed that is adequate for emerging problems. Human practices can take up problems in a way that experts at a distance cannot. Not concerned with IP and applications, but what kind of objectives exist and are really at stake in specific projects.

Three primary challenges:

1)To accept is positionality as adjacent and second-order, as opposed to one and two being first order. Thus, must have a tool kit of responses and practices that temper and reformulate to different demands.
2) Collaboration: Precise form cannot be settled in advance. Ongoing reconstruction.
3) Reconstruction: Directed inquiry that is progressive to the moral facts of an emerging situation, while creating equipment that facilitates forms of work and life.

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Equipment

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Truth claims, affects (A disposition, feeling, or tendency), ethical orientations

It is a word, a concept, and a referent/

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Notes on Patzek lecture and Writings

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1. As I show here, significantly more efficient individual transportation systems are possible
and ought to be implemented. Wherever sensible, individual transportation should be
replaced with public transportation systems.
2. The average rate of decline of conventional petroleum production in the world will gradually
increase to about 6% per year, and only some of this production will be temporarily
replaced by unconventional petroleum sources (tar sands, ultra-heavy oil, oil shale, etc.).
6. Because of the planetary physics of the Earth, agrofuels produced each year will always
be inadequate to make up for the decline of liquid transportation fuels from petroleum
accumulated over 460 million years or more.
9. Photovoltaic cell (PV) and battery R&D and implementation of already existing technologies
would have a much greater impact both near- and long-term than agrofuels, and
are presently underfunded by two orders of magnitude compared with agrofuels.
11. The EU ought not subsidize commercial energy sources. Research funding is constructive;
subsidizing commercial-scale processes is not. If corn ethanol, cellulosic ethanol, hydrogen
buses and other pseudo-green solutions had to be financed by investors instead of
taxpayers, they would die a natural death and we could concentrate on approaches like
PV (photovoltaic cell/battery) that might work.
1) With business as usual there is no long-term solution to the problem of liquid transportation
fuel supply for the US alone, much less for the entire world. For this very reason, the US
and the rest of the world soon will be on a head-on collision course.
2) Business as usual will lead to a complete and practically immediate crash of the technically
advanced societies and, perhaps, all humanity.
5) If all mass must stay on the Earth, all her households must recycle everything;
6) !!!!!!!!!!!!!!!! Unlike agrofuels, the solar cells will not take away food and environment from the largest
part of the human population in the tropics, and they will not contribute to untold corruption,
human misery, squalor, and slave labor. P 39
*We burn for transportation 34 times more energy than we need to live.

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Biofuels

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Fuels made from cellulosic biomass resources. Biofuels include ethanol, biodiesel, and methanol.

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CP Snow "The Two Cultures: A Second Look"

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Sputnik: West is now not the only superior group

American Medical Association and Sputnik: Too much time is spent reading boos and learning languages- great change in core curriculum and rise of suburbs

National Defense and Rise of National Science Foundation; Nixon and National Institute of Health

Watson and Crick, 1962, place of science had turned from physics to MCB

Americanization of Science: Science is now based on achievement and merit; Science is about technical mastery and specialization; It was always assumed that access to truth had a tie to moral training (Harvard demanded Christian training) Religion (is Bush and other presidents) is a precondition to leaderhsip

Division of value spheres: They do not fit together

Freud: humans seem to need meaning

If an idea spreads quickly with quick response, then it is unlikely that it is original. They were in the air, only needing the form of words. Secondly, with such a response, the ideas must be ideas of some substance.

Basic statement of lecture: In our society, we have lost even the pretense of a common culture. Persons most educated in their fields are unable to cross-communicate. The effects of this are wrongful interpretations of the past, the present, and to deny many hopes of the future.

'The Two Cultures'
1)The Scientists:
2)The Literary Intellectuals: These represent, vocalize, and shape/predict the mood of non-scientific culture. They do not make decisions, but their words affect those that do.

There is near hostility between these two groups.

Def of culture 2 (1=to be cultured): A group of persons withshared habits, assumptions, and ways of living.

Scientific culture would feel certain that research is the primary function of the University (Keasling EBI)

Literary culture hates censorship.

The more that technology goes to work, the harder of a line it is to make between science and technology.

The scientific process has two motives: to understand the natural world and to control it. These are interchangeable.

Science is driven by war.

Third culture is coming that will soften some of the difficulties in communication between cultures one and two. Some social historians have crossed both cultures in their examining of such things as organic community and scientific revolution.

For non-scientists to understand a discussion on thermodynamics, they cannot just read the encyclopedia. To speak with scientists, they need a legitimate understanding. Snow believes buildling this understanding should be a part of the building of 20th century culture.

MCB is more likely to affect the way that men seee themselves than any other discovery in science since Darwin.

Applied science has made it possible to remove unnecessary suffering.

It is inhumane to deny one's elemental needs when they are provided for you.

Most people are rushing into a scientific revolution, not aware of the massive changes. Ie Thoughts on the Industrial Revolution demand questions on what life was like in the pre-industrial era as compared to industrial society.

Solution: education in primary and secondary school.


From physical ailment example, Snow believes we share a common humanity (85) Therefore, social condition is with us and we are a part that cannot deny it.

Like Dostoevsky and his old man diary of anti-semetic rantings, your actions have an effect on society.

Modernist movement is defined by Western literature.

Major theme: It is dangerous to have two cultures that can't or don't communicate, especially in a world where science is determining much of our destiny and scientists can give bad advice. They provide knowledge on potentialities which is theirs alone. We (non-scientists) are trying to hear messages on our future in a foreign language we hardly understand. Sometimes the logic of applied science thus defines the political process itself. OBomb.

Changes in eduation will not solve all problems, but are a start. We can no longer have the Pascalian Renaissance man, but we can educate people toward imagination and of responsibility to prevent suffering.

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Wendell Lim Test-beds

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* Signal transduction
* Protein-protein recognition
* Protein switches and networks
* Signaling protein and network evolution
* Systems biology
* Biological computation
* Synthetic biology

To achieve these goals we take a highly interdisciplinary approach that incorporates diverse techniques including:

* Mechanistic biochemistry
* Biophysical methods
* X-ray crystallography, NMR
* Molecular biology
* Cell biology
* Yeast genetics
* Protein, pathway engineering

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Laurie Garrett on Malaria/HIVAIDS

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I found it very “enlightening” for understanding the medical world to have this article and the Keasling article lumped into one week. While I read this article first and felt the shock of all that needs to be done to fix our world and, more poignantly, at the situation with malaria in Africa, while reading the Keasling article’s I felt entirely removed from it all. It was as if being placed in an entirely separate world and I can see how easy it must be for 1) scientists to lose sight of the actual goal by losing themselves in the micro and 2) to not be concerned so much with anthropology and ethics. The science of metabolic engineering really does seem so logical and systematic that it feels almost as if the ethics should be built into the cells.
Moving to the actual content, what I found to be one of the greater points of the article was the emphasis on the effects, advantageous and detrimental, of NGO’s on developing nations. While companies such as Merck, Bristol-Meyer, and the Gates Foundation have helped to greatly lower the amount of deaths annually due to the AIDS virus in such countries as Botswana (also a special case based upon its higher employment rates and wealth from the diamond trade), they have done so at the expense of many other health care initiatives, not helping to raise the life expectancy of a citizen of Botswana to over 34 years of age.
As Garrett describes, the massive amounts of funding being poured into these nations is possibly yielding a dependency on foreign funding, to the effect that some of the smartest businessmen of Mozambigue and Uganda have well-established careers in the profitable “AIDS Industry.” Secondly, because HIV/AIDS spending is “sexy” to the donors of today, many other diseases and infrastructural problems are being ignored, such as a lack of doctors and nurses (many of which these same donating NGOs are sending to the US to practice for a better paycheck); care for mothers before, during, and after childbirth; and jobs for their husbands.
However, quite refreshingly, Garrett does offer a solution, as difficult of one as it may be. She states the following: “…The world health community should focus on achieving two basic goals: increased maternal survival and increased overall life expectancy” (9). Granted, if everyone that needed them was given ARVs as is the goal of many NGOs, life expectancy would increase drastically. However, ARVs are not the only thing needed to prevent people from dying of AIDS. First, HIV has to stop spreading, be it through handing out condoms at every church door. Secondly, there needs to be enough doctors and nurses to educate and administer ARVs. Lastly, people need to have their health cared for in other ways (fight against malnutrition, malaria, etc.), so as to not die of another disease while their immune systems are down. Secondly, by taking care of her first goal of care for mothers and babies, simple mathematics would take care of the second one. Hundreds of zeros when calculating average ages of death will bring a number down drastically.

Key points:
1)NGOs having detrimental affects- lowering AIDs in Botswana, but causing dependency on money, brightest minds going into non-profit "business"
2)Not buildling infrastructure in other areas like jobs for husbands, helping mothers have safe births, malnutrition
3)Doctors and nurses being recruited for our nations
4)too much bureaucracy involved in solving problems... Does aid even get to the right people?
5)66 percent of global funding goes to fighting TB and malaria
6)Clinton: First use HIV to build infrastructure, then malaria, tb, infant death will follow suit.
7)As in Haiti, even as money has poured into Ghana for HIV/AIDS and malaria programs, the country has moved backward on other health markers. Prenatal care, maternal health programs, the treatment of guinea worm, measles vaccination efforts -- all have declined as the country has shifted its health-care workers to the better-funded projects and lost physicians to jobs in the wealthy world.
8)There is also an intimate relationship between HIV and malaria, particularly for pregnant women: being infected with one exacerbates cases of the other.
9)Doc in a box

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Keasling and Engineering of Artemisinin

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Engineering synthetic metabolic pathways in microbes for the production of pharmaceuticals and complex chemicals is an attractive alternative to traditional chemical synthesis. Yet, the incorporation of an exogenous biosynthetic pathway into a host organism often abolishes the original, native regulation of carbon flux through the pathway causing the accumulation of toxic intermediates or altered levels of key endogenous metabolites. With the maturation of systems biology it is now possible to study the physiological response of an engineered bacterium to synthetic pathway expression at all levels of the biochemical hierarchy: mRNA, enzyme and small chemical. Previously, E. coli was engineered to produce large quantities of amorphadiene, a precursor to the anti-malarial drug artemisinin, by creating a mevalonate-based isopentenyl pyrophosphate biosynthetic pathway (Martin et al. 2003. Nat. Biotech. 21:796). The engineered E. coli produced high levels of this isoprenoid, but optimization for higher titers elucidated several constraints imposed by interactions between the host organism’s metabolism and the exogenous synthetic pathway. Using a combination of DNA microarray, proteomic, and metabolomic approaches we have studied how E. coli responds to the synthetic metabolic pathway in an effort to further our rational design of this isoprenoid–producing bacterium.

Artemisinin, according to Keasling, is extracted from Artemesia Annua L, or, more colloquially, sweet wormwood. This plant, while able to be found all over the world, grows wildly in Central China and is now being concurrently farmed there for the production of this compound. However, because of the rarity of this plant (yielding a cost that has quadrupled since artemisinin was discovered) and its low yield of artemisinic acid that can be actually used for the production of this anti-malarial drug, the drugs being produced today are too expensive to be utilized in poorer regions, namely in Africa, where they is needed most. Thus, through the concepts of metabolic engineering, Keasling and others succeeded at producing a yeast that is capable of producing higher levels of artemisinic acid, the precursor to artemisinin, at a cheaper cost and more efficiency than farming wormwood.
The process of producing this acid is threefold. First, a change was made to the FPP biosynthetic pathway. This change involved upregulating one gene that increased FPP synthesis and downregulating another gene that converted the FPP to sterols. By reducing the production of sterols, more of the FPP producer was left to produce amorphadiene. The production of amorphadiene was done by introducing the amorphadiene synthase gene from A Annua (sweet wormwood). Amorphadiene synthase, what is produced in step two, in an enzyme that, when oxidized, catalyzes a synthesis reaction. This oxidization is threefold and defines step three. For step three, a novel cytochrome (a hemoprotein found in plants and bacteria) P450 was produced in which certain genes were selected for (I believe through the use of splicing E Coli for gene selection, but I am not quite sure) that would enable an efficient and quick three-step oxidization process that turns amorphadiene into artemisinic acid as found in A Annua. It is then expressed in an amorphadiene producer.

Uses sacch which is a yeast instead of a bacteria for production of acid, I believe. A Yeast is also unicellular and self-replicating, but is a byproduct of a eukaryotic cell, not like a bacteria. Thus, they have a nucleus.

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Keasling on Biofuels (Note: mentioning of needing to find BIOLOGICAL ANSWERS for cellulose)

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●Sunlight produces energy which produces biomass (plants, etc.). We would like to take this biomass (much of which is polymers), break down into smallest denominator (monomer) to produce/synthesize fuels.
●Microbe is a small organism. Perhaps can use microbe to turn sunlight DIRECTLY into energy.
●Ethanol: Sun breaks down plants into starch using enzymes to make sure which is eaten by microbes that produce ethanol
●Corn based ethanol- water and fertilizer needed
●Ethanol cannot be piped from production plant to distributors bc it gathers water and must be redistilled
●Ethanol is not as good of a gas
●Biofuels from biomass: using cellulose instead of starch (corn)
●biomass is an excellent starting material for biofuels- switchgrass, like a weed
●Maybe even use our trash
●Photosynthesis has low efficiency
●If we can understand how cell walls are made naturally, maybe we can figure out how to break them down better
●Need cellulose from walls, but hemicellulose/lignin are too “sturdy.”
●Cellulase is a set of proteins that can break down cellulose
●After producing glucose from cellulose, need to find a pathway that gets one from having glucose to a biofuel. Synthetic Bio. Can builds pathways from scratch
aaaaaaaaKeasling said work at the lab will focus on breaking down plant cellulose, drawing on research on microbes found in the gut of the common termite, where they break down wood into digestible sugars that fuel the termite’s ravenous rampages.

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Endy "Refactoring Bacteriophage t7"

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Turns the genome of a natural biological system to a more structured design. They used a practice of refactoring, a process that is typically used to improve the design of legacy computer software. Saw that in restructuring that T7 had other elements, but then realized that they did not all matter (black boxing). ie ignore protein coding domains and other promoters

shows trying to make biology linear "Element overlap also prohibits element manipulation"

Produced a t7.1 genome that was easier to model and study and was linear. (all overlapping functions are nonessential)

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Interesting note on Keasling

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in 2003 was using ecoli as chassis and discovered it didnt not work and is now using the sacch yeast?

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Promoter (Endy)

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A contiguous stretch of DNA that interacts with an RNA polymerase molecule and allows for the intitiation of mRNA synthesis.

The design of the t7.1 genome allows for the simple deletion of parts.

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Rabinow and Caduff

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MCB uses terms like code, information, instruction, etc. that mimic lingiustical code. Thus, life is now framed in terms of organization through information.

Thus, analyzing Weber, the very core of life has information that needs to be learned.

This has been somewhat left, but now biologists turn genomic information into biological knowledge.

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Class notes, Patzek v Keasling

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The question is not technologies or not, but which technologies and how, etc.

One may say that both Patzek and Keasling are both mode one guys, kind of the same. Neither really address how science goes within society… Patzek wants a technical solution- everyone should consume less. What do you do in Mississippi in hot summer with mosquitoes?

Answers: Trains, Protestant ethic of frugality, bikes (SOCIAL Technologies= means/ends relations…ie how to get people from their home to their work place… involves people, construction, zoning, etc.) Mode Two and One.. Issues of social justice are involved…How?

People consuming less is simply a technology solution because it simply means just using less technology. It brings no social change.

Health care for Toyota workers- Japan has a health care system- cars cheaper- social technology

When its all or nothing….Polemic and not going anywhere….Keasling and Patzek

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Wendell Lim's Test beds address most specifically:

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TKB and Biofuels

Is this collaboration btwn Cal and UCSF?

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Biofuels also

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EMPHASIZES
three important societal concerns that are addressed by a conversion to bioenergy: security of
supply, lower greenhouse gas emissions, and support for agriculture.
We believe that bio-energy production and policies need to be based on.

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Project Group Malaria

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S.Africa,

1) Artemisinin might also provide a solution for breast cancer and leukemia. If a biosynthetic version were to be produced and modified, this could yield to whoever has rights wishing to develop drug further to solve these more “modern” world, money-making problems. This would prevent the allocation, at least with some level of swiftness, to third world countries

Artemisinin ProjecT: i. “Each partner is committed to keeping the cost of the drug as low as possible by foregoing profits and royalties on sales of the drug to the poorest people in the world, mainly in Sub-Saharan Africa.”


ii. One World Health: Non-profit pharmaceuticals in conjunction with profit-based companies possible solution

South Africa has a well-established private voluntary health insurance sector. At present, only 16% of the South African population are members of these medical schemes. The rest of the population depends on public sector health care. Yet more than 60% of resources are located in the private sector

Amyris is mking drug independently, but is this a model that others can follow in regard to one world health. If they had used the “parts” of other groups, would this cheap redistribution be so simple?

What about competition?

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Biosafety

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Maurer

Acutal potential of an organism to cause biological harm

Workers at Asilomar

Biosafety would be related to the potential breakout without intentionality of the plague.

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President Bush and BioShield

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I ask you tonight to add to our future security with a major research and production effort to guard our people against bioterrorism, called Project Bioshield. The budget I send you will propose almost $6 billion to quickly make available effective vaccines and treatments against agents like anthrax, botulinum toxin, Ebola, and plague.

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Biosecurity

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Intentionality

Endy on DNA Synthesis: biosecurity can be seen as the protection against the potential use of biological organisms as a form of weaponry, closely linked to terrorism

“…synthesis might provide an effective alternative route to those who would seek to obtain specific pathogens for the purpose of causing harm”

Biocitizenry

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Preparedness

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stockpile effective vaccines just in case of an attack being a perfect example of this term. As described by Caduff in his article “The Futures of Risk: Insurance, Precaution, Preparedness,” we are now moving into an age where risks are too great to be calculated and prepared for by traditional systems of insurance."

In other words, if someone was to scale an all-out biological attack on San Francisco, insurance companies would go broke in the damage control. Thus, a new field of risk management is forming called “preparedness.” Just as with Project BioShield, preparedness involves preparing ahead of time vaccinations and other solutions to potential biological hazards (intentional and non-intentional) in order to quarantine and cure the infected with the most sufficiency possible.

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synberc definition of preparedness

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also refers to situations that cannot be predicted and havgin a toolkit of appropriate reactions... not necessarily national preparedness.

solutions: collaboration, remediation of problems into a form that has multiple solutions, and pedagogy (reflective thinking)

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Maurer versus Endy approaches to security

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Maurer: screening, watchlists, hotlines, affirmation of ethical obligation, community-wide clearinghouse for tracking, endorse R and D in field of saf/sec, puts humans to cost-benefit analysis, no placing orders with companies that do not comply to standards, make advice free to members and non-members, code of ethics,

Endy: focus on DNA synthesis, less trusting, wants to work with law enforcement and FBI, international solutions, does not want to limit access, thus wants development of good computer programs

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Notes on Asilomar

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brought together scientists to discuss recombinant DNA. Paul Berg selected people for Asilomar


Feb 75, would plasmid-infected e coli go loose and hurt people? moratorium on research.

to make rules that prevent government and police interference in science.

also issues with studying a monkey virus

labeling of level of risk

Results:

The first principle for dealing with potential risks was that containment should be made an essential consideration in the experimental design. A second principle was that the effectiveness of the containment should match the estimated risk as closely as possible.[10]

The conference also suggested the use of biological barriers to limit the spread of recombinant DNA.

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Areas of human practices

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1) problematization:taking on assertions
2)raising questions: what is the good life?
3)calls for collaboration

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Restriction Enzymes

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Proteins that can chop DNA to protest from viruses

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Levels of standardization

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1) Compositional: parts are predictable
2)Physical Construction: biobricks
3)Functional composition: input/output

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Bayh-Dole

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All publicly financed research must seek commercial applications

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part

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object that has a defined function and can be put with another part

sensors

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ELSI

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mode two, science would happen and people downstream would study

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synberc has five sections that all get seeded through with HP

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parts, devices, chassis, hp, test beds

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Keasling JBI

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