Materials science and transgenic animals

Oil spill analysis equipment

One of the most interesting ongoing developments in materials science involves the borrowing of biologically originated materials and processes. The development is old news for people who follow science news, but seems worth mentioning to others.

In the first instance, there is the copying of chemical tricks that exist in nature. People have speculated about copying the wall sticking abilities of gecko feet, for instance. By artificial producing structures similar to those on the feet, excellent non-chemical adhesives could be made. Gecko feet are sufficiently adhesive to hold several hundred times the weight of the animal. Furthermore, they can be attached and detached at will by altering the geometry of the setae that produce the adhesion using Van der Waals force.

In the second instance, people have been exploiting biological processes to produce existing things in more effective ways. A favourite way to do this is through pharming: where new genes are introduced into species in order to turn them into pharmaceutical factories. For instance, goats have been genetically engineered to produce an anti-clotting drug in their milk, which can then be extracted, purified, and used by humans. The drug, called ATryn, treats hereditary antithrombin deficiency: a condition that makes people especially vulnerable to deep-vein thrombosis. The principle benefits of using goats are financial, as described in The Economist:

Female goats are ideal transgenic “biofactories”, GTC claims, because they are cheap, easy to look after and can produce as much as a kilogram of human protein per year. All told, Dr Cox reckons the barn, feed, milking station and other investments required to make proteins using transgenic goats cost less than $10m—around 5% of the cost of a conventional protein-making facility. GTC estimates that it may be able to produce drugs for as little as $1-2 per gram, compared with around $150 using conventional methods.

Transgenic goats are also being used to produce spider silk on an industrial scale. That super-strong material could be used in everything from aircraft to bullet-proof vests. Different varieties of spider silk could be used to produce materials with varying strengths and elasticities.

While the former behaviour seems fairly unproblematic (we have been coping from nature for eons), the latter does raise some ethical issues. Certainly, it involves treating animals as a means to greater ends – though that is also an ancient activity. People have generally been more concerned about the dangers to people and the natural world from such techniques: will the drugs or materials produced be safe? Will the transgenic animals escape and breed with wild populations? These are reasonable concerns that extend well beyond the genetic or materials expertise possessed by the scientists in question.

The potential of such techniques is undeniably considerable. One can simply hope that a combination of regulation and good judgment will avoid nightmare situations of the kind described in Oryx and Crake. So far, our genetically modified creatures tend to be inferior to their natural competitors. According to Alan Weisman, virtually all of our crops and livestock would be eliminated by predation and competition in a few years, in the absence of human care and protection. It remains to be seen whether the same will be true of plants and animals that currently exist only in the imaginations of geneticists.

On technology and vulnerability

The first episode of James Burke’s Connections is very thought provoking. It demonstrates the inescapable downside of Adam Smith‘s pin factory: while an assembly line can produce far more pins than individual artisans, each of the assembly line workers becomes unable to produce anything without the industrial network that supports their work.

See this prior entry on Burke’s series

Protecting sources and methods

Rusty metal wall

By now, most people will have read about the Canadian pedophile from Maple Ridge who is being sought in Thailand. The story is a shocking and lamentable one, but I want to concentrate here on the technical aspect. INTERPOL released images of the man, claiming they had undone the Photoshop ‘twirl’ effect that had been used to disguise him initially in compromising photos. While this claim has been widely reported in the media, there is at least some reason to question it. It is also possible that INTERPOL is concealing the fact that it received unaltered photos from another source, which could have been anything from intercepted emails to files recovered from an improperly erased camera memory card. It could even have been recovered from the EXIF metadata thumbnails many cameras produce. It is also possible this particular effect is so easy to reverse (and that the technique is so widely known to exist) that INTERPOL saw no value in keeping their methods secret. A quick Google search suggests that the ‘twist’ effect is a plausible candidate for easy reversal.

Providing an alternative story to explain the source of information is an ancient intelligence tactic. For instance, during the Second World War an imaginary spy ring was created by the British and used to justify how they had some of the information that had actually been obtained through cracked ENIGMA transmissions at Bletchley Park. Some have argued that the Coventry Bombing was known about in advance by British intelligence due to deciphered messages, but they decided not to evacuate the city because they did not want to reveal to the enemy that their ciphers had been compromised. While this particular example may or may not be historically accurate, it illustrates the dilemma of somebody in possession of important intelligence acquired in a sensitive manner.

Cover stories can conceal sources and methods in other ways. A few years ago, it was claimed that Pervez Musharraf had escaped having his motorcade bombed, due to a radio jammer. While that is certainly possible, it seems unlikely that his guards would have reported the existence of the system if it had played such a crucial role. More likely, they got tipped off from an informant in the group responsible, an agent they had implanted in it, or some sort of communication intercept. Given how it is now widely known that email messages and phone calls worldwide are regularly intercepted by governments, I imagine a lot of spies and informants are being protected by false stories about communication intercepts.

In short, it is fair to say that any organization concerned with intelligence gathering will work diligently to protect their sources and methods. After all, these are what ensure their future access to privileged information in the future. While there is a slim chance INTERPOL intentionally revealed their ability to unscramble photographs as some sort of deterrent, it seems unlikely. This situation will simply encourage people to use more aggressive techniques to conceal their faces in the future. It is also possible that, in this case, they felt that getting the man’s image out was more important than protecting their methods. In my opinion, it seems most likely that ‘twist’ really is easy to unscramble and that they saw little value in not publicizing this fact. That said, it remains possible that a more complex collection of tactics and calculations has been applied.

…in order categorical

All of the entries on this site have been sorted into one or more categories. Just for the sake of experimentation, I will use the next 21 daily posts (the ones with photos are generally the ‘official’ daily posts) to go through my whole list of categories one by one. This will occur in no particular order. Some posts are likely to fall into multiple categories, but they will only count as the most relevant one for the purposes of the tally:

The numbers beside each category indicate the number of posts so far.

Best Ottawa bike shop

Milan Ilnyckyj on a bike

When I moved to Ottawa, I didn’t know where to go to buy a bike. With the benefit of experience, I can tell other newcomers that their best bet is to go to G.M. Bertrand Cycles in Gatineau. They are at 167 Wellington Street. I recommend them because they have the most knowledgeable and helpful staff of any of the ten places or so I visited. Many of their staff members are bilingual and the rest have been happy to put up with my broken French. They have good products at reasonable prices and they stand behind them. When the front light they sold me failed after three weeks, they replaced it with a better one with no questions asked.

The Bike Dump seems to be the Ottawa bike shop that gets the best press. While I may not have had a representative experience, I saw no reason for which that praise is justified. Their bikes were overpriced and not in terribly good condition. They have bad hours, only accept cash, and have an indifferent staff. G.M. Bertrand is a much better choice.

Cleaner coal

Coal is a witches’ brew of chemicals including hydrocarbons, sulphur, and other elements and molecules. Burning it is a dirty business, producing toxic and carcinogenic emissions including arsenic, selenium, cyanide, nitrous oxides, particulate matter, and volatile organic compounds. Coal plants also produce large amounts of carbon dioxide, thus contributing to climate change. That said, some coal plant designs can reduce both toxic and climatically relevant emissions to a considerable extent. Given concerns about energy security – coupled with the vast coal reserves in the United States, United Kingdom, China, and elsewhere – giving some serious thought to cleaner coal technology is sensible.

Integrated Gasification Combined Cycle (IGCC) plants are the best existing option for a number of reasons. Rather than burning coal directly, they use heat to convert it into syngas, which is then burned. Such plants can also produce syngas from heavy petroleum residues (think of the oil sands) or biomass. One advantage of this approach is that it simplifies the use of carbon capture and storage (CCS) technologies, which seek to bury carbon emissions in stable geological formations. This is because the carbon can be removed from the syngas prior to combustion, rather than having to be separated from hot flue gases before they go out the smokestack.

The problems with IGCC include a higher cost (perhaps $3,593 per kilowatt, compared with less than $1,290 for conventional coal) and lower reliability than simpler designs (this diagram reveals the complexity of IGCC systems). In the absence of effective carbon sequestration, such plants will also continue to emit very high levels of greenhouse gasses. If carbon pricing policies emerge in states that make extensive use of coal for energy, both of these problems may be reduced to some extent. In the first place, having to pay for carbon emissions would reduce the relative cost of lower-emissions technologies. In the second place, such pricing would induce the development and deployment of CCS.

One way or another, it will eventually be necessary to leave virtually all of the carbon that is currently trapped in coal in the ground, rather than letting it accumulate in the atmosphere. Whether that is done by leaving the coal itself underground or simply returning the carbon once the energy has been extracted is not necessarily a matter of huge environmental importance (though coal mining is a hazardous business that produces lots of contamination). That said, CCS remains a somewhat speculative and unproven technology. ‘Clean coal’ advocates will be on much stronger ground if a single electricity generating, economically viable, carbon sequestering power plant can be constructed.

Mac security tips

Gatineau Park, Quebec

During the past twelve months, 23.47% of visits to this blog have been from Mac users. Since there are so many of them out there, I though I would share a few tips on Mac security. Out of the box, OS X does beat Windows XP on security – partly for design reasons and partly because it isn’t as worthwhile to come up with malware that attacks an operating system with a minority of users. Even so, taking some basic precautions is worthwhile. The number one tip is behavioural, rather than technical. Be cautious in the websites and emails you view, the files you download, and the software you install.

Here are more detailed guides from a company called Corsair (which I know nothing about) and from the American National Security Agency (who knew they used Macs?). The first link is specific to Tiger (10.4), while the latter is about the older Panther (10.3). I expect they will both remain largely valid for the upcoming Leopard (10.5).

Some more general advice I wrote earlier: Protecting your computer.

PS. I am curious about the one person in the last orbit who accessed this site using OS/2 Warp, back on February 17th. I hope it was one of the nuns from the ads.

Poison-absorbing plants

A recent article in Scientific American describes the use of transgenic plants to remove toxins from contaminated sites. The plants have genes for toxin and carcinogen metabolisis (for instance, using the enzyme cytochrome P450-3A) inserted into their DNA. The technique has been tested with plants intended to address trichloroethylene, chloroform, carbon tetrachloride, vinyl chloride, and benzene contamination. Such plants have also shown promise in removing remaining concentrations of the explosive RDX from soil in test ranges. At present, there is sometimes no choice but to scoop up huge amounts of contaminated soil and put it into landfills; plants that are able to seperate the toxins from the soil could promise to facilitate the process, as well as reduce costs.

The article is not entirely clear on whether the plants simply absorb the chemicals, becoming contaminated by them in turn, or whether they actually break them down. In the former case, they might be useful for concentrating air, water, and soil contaminants into plant matter than can then be disposed of as hazardous waste. In the latter case, they could perform remediation without the need for such careful treatment of their remains. Another question is how the plants would deal with combinations of chemicals, such as might be found in actual contaminated sites.

All told, it seems a promising potential use for biotechnology. The world is certainly well saturated with contaminated sites and having more cost effective means of reclaiming them could be a boon to both nature and human health. It remains to be seen whether these limited trials can be scaled up and made cost-effective for commercial or governmental use.

Unlettered society

National Archives of Canada

My ongoing fruitless search for lined correspondence paper has hammered home the degree to which letters have faded from our society. Not even specialized paper stores have ordinary letter paper for sale, it seems. This is no surprise, really, given how much more immediate and immersive other forms of communication are. The societal forces at work lead me to wonder whether we are even capable of writing letters anymore.

There was a long span of time during which letters were the only low-cost means of maintaining personal relationships at a distance. This began in the ancient world (though only because popular with the rise of mass literacy) and persisted until the rise of affordable long-distance telephone calls and the internet. Now, there are a myriad of more rapid and personal ways through which to exchange all manner of personal thoughts and information. Email was the dirt on top of the well-nailed coffin: allowing people the permanence and clarity of written language in a much quicker and more versatile way. Now, every office tower is stuffed with BlackBerried workers.

Yet the letter persists as an aesthetic ideal. People value them because of the time they take to construct and their enduring quality. I still have letters that Kate wrote me a decade ago. Still, I wonder whether people who are utterly acquainted with rapid communication are generally capable of writing things in a style suited to this slow and permanent route. Our communication styles have simply become too dynamic – we expect things to change quickly and for responses to be fluid. At the same time, all but a tiny minority of people have become utterly unpracticed in letter writing. Just as poetry and public speaking are no longer taught as a skill in schools, so too has letter writing been marginalized due to a lack of need and a lack of practice.

Overall, I cannot help but think this is a change for the better. People can remain in contact more vividly and extensively, despite how they tend to have groups of friends who are ever more spread out. Letter writing is destined to become an occasional curiosity – like the ‘paper making’ workshops that sometimes happen in elementary schools or craft stores (usually just re-assembling cut up bits of previously made paper). Hopefully, people who are engaging in the kind of correspondence that will eventually be published in books (if those do not vanish as well) have been keeping accessible and reliable paper copies. Digital media are fickle, and it would be rather tragic to lose such a historical record to failed hard drive bearings and changed file formats.

Fixed-wing / helicopter hybrids

A good number of readers probably know something about the V-22 Osprey tilt-rotor aircraft. They may recall the ad that Bell Helicopter Textron ran in The National Journal which explained that the aircraft “descends from the heavens” but “unleashes hell.” This would probably have attracted less controversy if it hadn’t shown American troops rappelling onto the roof of a mosque.

Many people argue that the V-22 is unsafe. Fewer people realize that it was a second attempt at this sort of vehicle. A predecessor called the DP-2 was even less successful.

What is it that makes Vertical Take-Off and Landing so difficult?