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  • Jeffrey E. Barrick 23:23, 30 January 2013 (EST):It might be good to parse out the page into various headings so that it's easier to find the right thread.
  • Neil R Gottel 03:32, 28 January 2013 (EST): Technical question: how do I properly format quotes? I tried using formatting from wikipedia, but I couldn't get it to work properly, so I'm just using the blockquote command.
Evan Weaver 12:00, 28 January 2013 (EST): I was able to add quotes by adding " around the text. "Like this" Is this what you needed?
  • Neil R Gottel 15:14, 31 January 2013 (EST):Nah I was thinking something that would put the words into their own separate box. Jeff said that a lot of the more advanced wiki formatting isn't available on OWW.
  • Thomas Wall 21:32, 31 January 2013 (EST): I don't know if this is the appropriate place to throw out IGEM ideas that are chock-full of moral turpitude, but as one with the desire to be a bio-troll let me say my idea. We take bacterial photographs of religious figures and find some way for them to cry out a blood looking substance
    • Neil R Gottel 14:13, 4 February 2013 (EST):yeah we'll call that "plan B"


  • Max E. Rubinson 13:23, 28 January 2013 (EST): “Given the difficulties synthetic biologists have when trying to make genes from a different species function properly in another species, it seems unlikely that accidental transfers of genetic material could result in any significant biological hazards.” Comments like this seem rather arrogant. There will always be a potential for biological hazards that we may never fully understand or live long enough to realize. As Dr. Ian Malcolm aptly states in Jurassic Park, “…life, uh, finds a way.”
Andre C Maranhao 14:03, 28 January 2013 (EST): Maybe it is arrogant, but it's probably just an overreaction to all the sensationalism from anti-GMO groups and the bioethics community. Yes, there are hazards associated with any human activity and maybe to a greater degree the activities of synthetic biology. Still, take a look at hydrofracking. It utterly destroys the local water-table, which has serious, long-term consequences for the environment and biosphere. Yet, we as a country 'need' to tap that vast source of domestic energy. Now, the country is discussing how the technology will be used/implemented whilst minimizing the repercussion. The same thing is necessary for synthetic biology. So in the end, debate is good, but both side should avoid extremes of hand-waving disregard and doomsday fear-mongering.
  • Gabriel Wu 15:54, 28 January 2013 (EST): Minor point: It's good to keep the tone light, but captions for Cynthia--while funny, I admit--may be interpreted wrong by those who are looking for material to use against the synthetic biology committee.
    • Jeffrey E. Barrick 20:43, 30 January 2013 (EST):I added a "?" to the end of this caption, which might defuse it a little bit.
      • Neil R Gottel 15:21, 31 January 2013 (EST):Good point, I forgot that deadpan/sarcasm can be a dicey thing when communicating with text...
  • Gabriel Wu 16:22, 28 January 2013 (EST):Suggestion: Include discussion on flu debate?
    • Neil R Gottel 15:21, 31 January 2013 (EST):Good idea. I already have one of those controversial flu papers linked, but I'll put in a paragraph devoted to it, since that was a pretty big deal last year.
  • Kevin Baldridge 16:42, 28 January 2013 (EST):There was an interesting article on privacy with genomic information available in public databases in Nature doi:10.1038/493451a
  • Siddharth Das 17:31, 28 January 2013: Minor fix: Christina to Christian
  • Gabriel Wu 16:44, 30 January 2013 (EST): Very good (and recent) review on some of the considerations and current directions at addressing the risks involved in synthetic biology [1].
    • Jeffrey E. Barrick 23:23, 30 January 2013 (EST):This project mentioned in the article sponsored by the Woodrow Wilson International Center for Scholars has a LOT of information. Should be linked. If you click through, it seems like there is no audience for a lot of the stuff though. The "Ask a biosafety professional your question" seems to have only had one question, ever, in its history.
      • Neil R Gottel 15:43, 31 January 2013 (EST):Wow you weren't kidding, there's so much on here! I'll put it in. Also, I sent in a question for the biosafety professional about whether there are any plans for regulatory/certification of DIY Bio labs (either by the gov, or some a certification group like Underwriters Labs). That question page was only established on the 17th of Jan this year, so maybe they'll get more.
      • Gabriel Wu 17:15, 31 January 2013 (EST): This is a constant problem with this area. There are plenty of people who are willing to admit that it's important and we should talk about the ethics, but from a day to day standpoint and certainly from an academic standpoint, where's the incentive? For all the years I spent hanging out in the synthetic biology community, this was an issue. The scientists and the ethicists (which were anthropologists, political scientists, among other specialties) were fairly far apart in what they considered important. I think it goes back to what we've talked about earlier how characterizing parts would be so useful, if only someone else would do it and figure it out.

Black hat vs white hat hackers

Is it feasible to think that, just like today, "white hat hackers" for synthetic biology could create the "patches" or cures to counter the malicious work of black hat hackers, in a continually escalating yet mostly benign tit-for-tat? -*Dwight Tyler Fields 16:11, 28 January 2013 (EST):

    • Gabriel Wu 16:15, 28 January 2013 (EST): Problem is in software development it's easier to develop a patch then in biology. If we could "patch" human health the way we can computer hacks, we wouldn't be in such a panic about antibiotics and vaccines right now.
      • Catherine I. Mortensen 01:23, 30 January 2013 (EST)]]: Case in point, here's an interesting article about outbreaks of narcolepsy in Sweden thought to have been caused by the H1N1 vaccine. [[2]]
  • Kevin Baldridge 16:12, 28 January 2013 (EST):We talk about the doomsday scenario of "biohackers" ruining the environment to where you'd have to wear respirators etc. Is that a genuine concern as well, because we do have the hacker culture in the computer world, but it hasn't ruined our ability to use computers altogether. The regulatory/antivirus industries have stayed ahead as hackers develop their malware, would we see a similar development in the protective bodies against biohacker culture? Apologies if this repeats -- it seems that Dwight had the same idea during class.
    • Siddharth Das 17:30, 28 January 2013 (EST): Although the analogy may hold true in terms of understood constructs, for both electronic and biological, the emphasis of the possible dangers of synthetic organisms arise misunderstood regulatory metabolic pathways and moreover it evolution. For example, scientist can easily design organism with a "fail safe code" that terminates the organism before it grows beyond control. In the case of DIY biologists (a.k.a. biohackers), they can easily design an organism with an unrealized gene expression that harm an individual. Furthermore, unlike code, the genetic code in vivo can mutate dangerously and even out compete their wild-type counterparts. Thus, inexperienced biohackers can prove to be dangerous.
      • Jeffrey E. Barrick 20:15, 30 January 2013 (EST):There's a really good section in the paper Gabe cited above talking about strategies and problems with containment and another about detecting malicious sequences in oligo orders.
    • Catherine I. Mortensen 01:54, 30 January 2013 (EST): I guess it would depend on the viability of the harmful organism. If biohacking seriously became a problem, I'd expect the process of discovering and manufacturing a cure to be a much more timely process than that of creating antivirus computer programs. Complexity of the genome exceeds that of computer viruses and there would health risks involved with white hacking.
    • Benjamin Gilman 20:03, 30 January 2013 (EST): I think the argument that the government and private industry (i.e. antivirus software makers) have stayed ahead of malicious hackers is false, because they are always forced to react to unforeseen developments. Every time a novel computer virus is introduced, it takes time to come up with a defense against it. While those solutions often come in a matter of hours or days, they are the result of potentially thousands of programmers trying to correct a flaw that may have been successfully exploited by a lone hacker. This imbalance is even worse in the case of bioterrorism or state-produced biological weapons, because even with infinite resources it takes a significant amount of time to (hopefully) come up with a treatment or vaccine. Though we have some idea about what agents are likely to be weaponized, we've probably wasted billions of dollars researching diseases like tularemia when the next successful bioweapon will be based on an idea nobody else ever had.
        • Kevin Baldridge 18:33, 31 January 2013 (EST):You're not wrong that they haven't stayed ahead, but I guess the point I was making is the infrastructure and computer systems we use are still all just fine. I think the way the analogy translates into biology is worth discussing. In computers, malware finds a security flaw in a current program (which was written by someone else), something like a port that was left open or an ambiguous function call which allows the malware to enter. The antivirus side of things might notice this error in a program like Outlook after reports of security issues, and so Microsoft will come out with a patch which fixes that particular security risk. That's the reactionary, slow response that you are talking about, which would be analogous to someone developing a vaccine for the pathogen. But in an antivirus software, it's a more complex response, that involves a separate program (i.e. antivirus software) which kind of thinks for itself in how it scans your files. The antivirus software has heuristics that read the contents of a file and look for "risky" code that resembles known malware, in a very similar fashion to how our antibodies recognize peptide fragments which were associated with previous pathogens you encountered. So in a way, we have the "antivirus software" already installed, which puts the protection side ahead of the hacking side to begin.
    • Kevin Baldridge 18:33, 31 January 2013 (EST):In case you were drawing comfort from the success of computer antivirus protection, this should change your mind a little bit [| Red October]

Feasibility/probability of bioterrorism

  • Gabriel Wu 16:13, 28 January 2013 (EST): What are the major limitations to "successful" bioterrorism? We talk about accessibility to materials and equipment, but is that really the major barrier? The idea of chemical/biological warfare has been out there for a while. Heuristically, it feels like it's not been a easy as people fear. Is this true?
    • Benjamin Gilman 20:32, 30 January 2013 (EST): The idea of somebody engineering a weaponized virus in their garage is probably pretty ridiculous, but recreating a natural virus that you don't have access to isn't so far fetched. It wouldn't be fast, cheap, or easy, which is why we'd expect a well funded group or small nation to be the likely backers. Larger nations (US, Russia) have tons of effective biological weapons, we just know better than to use them.
    • Jeffrey E. Barrick 20:11, 30 January 2013 (EST):A lack of opportunities for testing? -- which slows down any development effort. You can test ballistic missles or nukes under realistic conditions and gather data about failures. Not so with a disease.
      • Benjamin Gilman 20:32, 30 January 2013 (EST): I'm not sure testing is really necessary in the case of bioterrorism because any attack doesn't actually have to be all that effective. If a few people die, it creates enough panic to achieve the goal, but if it doesn't work nobody notices and you can go back to the drawing board. There is also quite a bit of information out there from the instances where biological weapons have been tested on people (like the Japanese experiments in China during WWII) which might eliminate the need for testing of dispersal mechanisms.
        • Neil R Gottel 16:03, 31 January 2013 (EST):Your comment about attacks not having to be all that effective (i.e. body count) is a great point. The anthrax letters of 2001 killed 5 people, but it sparked off a huge investigation ("one of the largest and most complex in the history of law enforcement.") and decontamination of the various post offices and other buildings ended up costing over a billion dollars... and the delivery mechanism was probably one of the most inefficient ways to distribute a bioweapon! Same reasoning behind "dirty" (radioactive) bombs. The decon costs and panic caused would be crazy expensive.
        • Gabriel Wu 17:24, 31 January 2013 (EST): Interesting, I was thinking that inefficient dispersal mechanisms was a possible reason. Also, problems with stability of the biological material. In any case, I agree that currently people get very scared with just a minimal number of cases. I think that's because people fear the worse. But ultimately, that never really seems to be the case. Is there an inherent limitation here that prevents more widespread instances. For example, if you try to deploy using gas, how do you control for wind and prevent harming yourself. Yes, masks would work, but it'd be a little obvious who we should stop and arrest, no?
          • Neil R Gottel 14:26, 4 February 2013 (EST):Perhaps the difficulty in such an attack occuring is that you need all the pieces to come together. For example, I might know how to make a airborne version of avian flu (flu+ferrets+time=nastiness), but I would need engineers to create the dispersal device. Anything that requires technical know-how like that is going to increase the complexity of the project, and hopefully increaes the likelihood of the terrorists getting caught before they attack.
          • Aurko Dasgupta 20:59, 31 January 2013 (EST):Presumably, the terrorist won't be deploying the gas-dispersed agents in his own vicinity- maybe something like leaving a time-bomb that's set to disperse after the culprit is hours away? Not to mention suicidal attacks have proven somewhat popular in modern terrorism, so the footsoldiers of a terrorist organization may be regarded as expendable. Or just not instructed about the risks they face.

Biosafety and Safety Comments

  • --Alvaro E. Rodriguez M. 20:48, 3 February 2013 (EST)I consider the safety guidelines would be better as a subsection of Biosafety. Also this subject needs to be expanded somewhat, to include countries that signed each treaty and dates that they were signed.
    • Neil R Gottel 14:17, 4 February 2013 (EST):I didn't add this section, so I don't feel particularly attached to it. If we make a separate biosafety page, then it would certainly be better to move that section to the new page.

Bio Art

  • Jeffrey E. Barrick 12:02, 4 February 2013 (EST):There are some interesting ethical issues raised by the art exhibits of Oron Catts, esp. one involving tissue engineering where you can go to the museum and watch it grow. As an example, he grew "pig's wings". He directs this center called SymbioticA.