streamspace

There seems to be some confusion as to what these concepts mean and how they differ. I'll make an attempt at clarification and explain what these three terms - Synthetic biology, DIYbio, Biohacking - mean to me. Synthetic biology (synbio) : This is an academic field of study that moves the focus from biology as an activity of observation to one of manipulation. One motivation here is that of understanding by synthesis, much like a beginning electronics enthusiast would build a circuit from scratch to understand how the different components interact, what happens when you leave out one component, how the behaviour of the circuit changes when you use a different resistor etc. Apart from this, one important idea in the synbio community seems to be that biotechnology should become a true engineering discipline, which requires standardization, abstraction, modularization, and componentization. This is the spirit behind BioBricks and the Registry of Standard Biological Parts . DI...

When researching material for a term paper on biocomputing, I came across a fascinating group of critters called ciliates. Ciliates are unicellular organisms that process their genomic information in a peculiar and unique way, one that was fascinating to study for the computer scientist side of me. In ciliates, we find a very illustrative example of how biological systems use structure as information. Plus they use pointers and linked lists.   There they are. Some ciliates. [Image from http://www.liacs.nl/~rbrijder/views_gene_assembly/ ] Ciliates, unlike other eukaryotes, have two different kinds of nuclei: macronuclei and micronuclei. A macronucleus is used in the everyday operation of the organism, for synthesizing the proteins it needs to survive. A micronucleus only comes into play during sexual reproduction (I'm stressing this because ciliates can also reproduce asexually). During sexual reproduction, two ciliates recombine their genetic material. The result is somewhat un...

In a previous post , I wrote about the controversy around a toxicity study of Monsanto crops. This post got a very valid comment, which I'd like to respond to here. Paul wrote: "de Vendomois' statistics are poor and not applicable to the Monsanto research data they used. The funding for their research was also funded in its entirity by Greenpeace. You have to ask yourself why Greenpeace/de Vendemois used the statistical approach they did knowing its flaws (as pointed out to them by the European Food Safety Authority in 2007). A cynic would suggest they conspired to use whatever method appeared to shed a negative light on GM crops. Would this collaboration have published truly independant research that showed no difference in toxicity between GM and Non-GM plants? I'm no fan of multinational corporations profiting from our basic food needs, but the dodgy, deceitful and blindly prejudiced approaches used by NGOs such as Greenpeace as part of their scaremongering campa...

It's a public secret: The world of social networks is about constructing identity. Let's be honest: Every one of us has probably tweeted about the cool club we've been to, or what airport we're currently stuck at, or that we're reading poems in some cool foreign language, to make our lives appear intriguing and cosmopolitan. Social networks are as much about constructing identities as anything else. They have enabled a construcivist approach to that elusive beast, identity, and Google Xistence is merely taking this a step further. Inside rumours that shed a bit more light on how Google Xistence works have reported that there will be a host of preset identities to mix and match - start with a "Renaissance Man" baseline, then throw in some "World Citizen" and "Political Activist", and Xistence will generate status updates, photos, locations and more that fit this synthetic persona. But who wants to be stuck with a static identity? Th...

A recently circulated paper by Vendomois et al takes an independent look at data from food trials of genetically modified (GM) corn on rats. The data was originally obtained in studies conducted by Monsanto as part of the application for market approval of these GMOs. I'd like to highlight a few points here. But first, some introduction. The original data stems from a trial where a population of rats was fed different kinds of GM corn over a period of 90 days. The GM crops in question were Monsanto's NK 603, MON 810 and MON 863. NK 603 is one of the Roundup Ready crops. Roundup Ready crops are genetically engineered to withstand large doses of Monsanto's herbicide Roundup. The idea is that fields can be sprayed with Roundup, the genetically engineered Roundup Ready crops survive, and all the weeds around it die. Let it be mentioned here that this approach has drawbacks all its own, as weeds have started to develop a resistance to Roundup over the years, which led to e...

Reading Stubben et al: " Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens" BMC Genomics, Volume 10, Issue 501, 2009 http://www.ncbi.nlm.nih.gov/pubmed/19874620 I found this paper interesting for several reasons: first, it follows a metagenomics approach, second it involves data mining work, and third, it's a step towards making an abstraction from individual pathogenics organisms to a more general understanding of virulence at a biomolecular level. In the abstract, the authors summarize the objective of their work: "New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can identify potential generic (i.e., conserved across multiple pathogen spec...

A few words on the posts labeled with "paper-a-day": Every day, I'll try to write about one paper I read that day. I mainly do this because writing about a paper helps me understand and remember its contents better. And maybe someone out on the interwebs gets something out of these summaries, too. P.S.: I renamed the category to "paper-a-week", for obvious reasons.