SDSSB Comments 9 - Design and Aesthetics

“...art is about asking questions, questions that may not be answerable” (Maeda, 2012) Synthetic Biology has been able to bring different species together: artists, designers, scientists, and engineers. I think, an important discussion by Agapakis (2013) and Ginsberg (2014) is the differences in “design mindset” of these species in their respective fields....

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SDSSB Comments 8 - Past and Futures

Brown et al. (2006) gave us a good example of how scientific expectations, both hype and dissapointment, have shaped the history of scientific development in the case of Hematopoietic Stem Cell (HSC), which was stated as one of the most valuable stem cell in bioeconomy. I think, in 2006, Brown et al. addreses the change of interest from HSC towards human...

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SDSSB Comments 7 - Synthetic Biology and the Public Good

Calvert and Emma (2013) starts the discussion with an interesting argument: “science is part of society and society is part of science”. Even so, the paradigm lies to distinct between the scientist, engineers, and policy makers, with the public. Indeed, both scientist, engineers, policy makers, and industry regards “the public” as an important entity to...

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SDSSB Comments 6 - Governance and Regulation

The 1975 Asilomar conference was presented in the unique press narration, entertaining and satire, in the popular Rolling Stones magazine. The conference aims to come up with an agreed regulation on the new disruptive technology. The emerging recombinant DNA technology was predicted, and has been proofed, to have great impact on today’s biotechnology, with...

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SDSSB Comments 5 - Bioethics

Knowledge is value-neutral. The value depends on its user. Or is it? Douglas & Savulescu (2010) addresses three issues regarding concerns in Synthetic Biology: (1) it is playing god (?), (2) the distinction between living things and machines, and (3) knowledge misuse, which could leads to bioterrorism or warfare. On playing God, I think as long as it...

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SDSSB Comments 4 - Synthetic Biology as Open Science?

I envy Drew Endy’s vision on Synthetic Biology. I personally think that IGEM and the Biobricks Foundation starts because of Endy’s personal will to open biology and make it easier to engineer, because he himself was not a “life sciences-trained” academia. Nevertheless, in Endy’s plenary talk (2008), there are two solutions to make this dream happens: (1)...

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SDSSB Comments 3 - Ways of Owning

In the last decade, systems and synthetic biology has advanced biology with novel ideas and applications which interests the public, the enterprises, and the academia. As a “hot” topic, Nelson (2014) reported the current issues we have today, the two cultures which debates wether this domain should be “publicly owned” or “privately owned”. But, the question...

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SDSSB Comments 2 - Systems Biology and Science Policy

As science and technology deemed important in the progression of humanity, scientific findings moved from “individual artist” in their own laboratory into today’s global scientific society with its culture and policies. Science has come to be an important thing: it is a country’s asset, the driver of new business and industries, and a way to make a living...

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SDSSB Comments 1 - From Breeding Experiments to Synthetic Biology

Rather than just using philosophical context to define and “limit” a field, I find it more interesting to find what drives the scientific society to gave birth to a new field, both political and technological. It is why, to understand more about Systems and Synthetic Biology, we have to take a look back at the history of its root: Molecular Biology. The...

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FGT Part 9 - Genomic Profiling

Many diseases are associated with genomic changes in the genome. For example is cancer and genetic disorder. Changes in the genome can be in the form of gaining or loss of genetic material, or rearrangement of whole chromosomes or smaller section of the chromosome. But, difference in genomes between individual is also an important source of diversity. Therefore,...

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FGT Part 8 - Emerging Technologies

Technology is what drives Functional Genomics, it allows us to as new question int the genome level. It is possible because technology allows us to ask questions in parallel, through high throughput technology, giving more power to infer new insights. But, how do we evaluate the robustness of technology? Different risk and benefits conditions are...

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FGT Part 7 - RNA Sequencing

RNA sequencing is the alternative to microarray. RNA sequencing measures population of RNA by generating cDNA with adaptors. Why choose RNA seq over microarray? In functional genomics, we are not only interested to see differential expression of genes, but also to see combination of exons which give rise to RNA population. This is difficult because most...

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FGT Part 5 - Design of Microarray Experiments

Design consideration: -Identify the key aims constraining factors protocols for sample isolation and processing decide analysis decide validation aim to randomise nuisance factors 1. Replication averaging replicates will give better estimates of the mean. replicates allow statistical inferences to be made. Biological vs Technical Replication. Techincal...

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FGT Part 4 - Identifying Differentially Gene Expression in Microarray

Describe the strengths and weakness of filtering on fold change to identify differentially expressed genes from gene expression microarray data Fold Change Fold Filtering When analysing a microarray gene expression dataset it is important to assess the general quality of the data. Describe three methods by which data quality can be assessed. For each method indicate how low and high quality data...

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FGT Part 3 - Data Normalization for Microarray Data

Why is it important to normalize microarray gene expression data before carrying out data analysis? The goal of microarray experiment is to identify or compare gene expression pattern through the detection of the expressed mRNA levels between samples. Assuming that the measured intensities for each arrayed gene represent its relative expression level,...

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