The Emergence of an Engineered Enzyme

Ask a chemist or any scientist in general what would be one of the top currently-nascent technologies they would want to mature quicker, and they would surely name protein engineering as one of them. A recent paper in Science brings us closer to this reality.

Just quickly, for the non-scientists: proteins are little molecules in your body that catalyze many reactions (called enzymes) that help you digest food, get energy, and just LIVE in generally, they also make up a lot of the building blocks for various parts of your body.

To be able to create proteins with various non-natural functions, as well as create enzymes with better activity, it is sometime necessary to predict the conformations that these synthetic proteins will take. The interactions of the amino acids (protein building blocks) on various parts of the proteins can be mindbogglingly varied depending on the length of the protein and environment. Computer programs are often used to predict the lowest-energy configurations and the final products. Not only do you need powerful computers to run the simulations, but you need efficient and realistic simulator programs, of which there is a whole slew out there (with no clear winners).

The quest towards engineering any protein on demand is one that is slowly but surely being achieved with the help of better predictive computational algorithms. Here's part of the abstract of the paper:

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity.

This reaction is widely used in synthetic chemistry, so this means that much time and money could potentially be saved by using an engineered enzyme such as this.The team chose to build an enzyme using a design method called Rosetta. I don't pretend to know anything about it, but in the case that someone is interested, I just put that up here. The researchers then prepared an in silico model of the shape that they'd need to accommodate the transition state for this reaction (high energy intermediate - remember chemistry class?). They then added amino acids to their protein that would hold the reactants in place.

Their first calculation showed that 10¹⁹ theoretical active sites matched several parameters they specified for the two molecules they wanted to join. They then used the RosettaMatch program to screen all these possibilities against already-known protein scaffolds and narrow down to 10⁶ possibilities that were stable.

This was further modeled and the number of enzymes was filtered down to 84, all of which the researchers expressed and purified. Of those, 50 turned out to be soluble and two had Diels-Alderase activity. The enzymes were also tuned to increase their activity.

That's the gist behind the rational design approach for protein engineering. This is of course very laborious, but is state of the art at the moment. There are certainly other approaches, such as protein evolution using single amino acid mutations, but these have their own problems and an in-depth look is beyond the scope of this post (though of course not the blog as a whole).

Protein engineering has a myriad of uses besides making enzymes for chemical synthesis. Imagine piecing together parts of different proteins to make them work quicker, attach more strongly to certain surfaces, play novel roles in signalling, etc. I personally cannot wait until this field matures and we can realize all it's possibilities.

To Grow or Not To Grow, That is the Question

In biology class we all learned that "winning the game of life" means that you leave more hardy offspring than your competitor. That is the goal of all life - to propagate and expand; to leave tons of children running all over the world.

Humans, more than any other species, strive for growth and expansion. We've all seen the human population growth curve, with it's exponential line of doom pointing towards the heavens.

By and large, most of our technology and culture aims at growth - prolonging and preserving human life, expanding human knowledge, creating music, art, and literature, spreading a country's influence and boosting it's economy, inventing robots that will allow us to produce more Hershey's Kisses than we can eat. Such growth, though, sadly, is not without consequence. This main consequence being that we do not live in a world of infinite resources, and that our production and growth rate (read: overpopulation and overconsumption) is certainly out-pacing our ability to gather enough resources (any RTS player knows that this usually leads to an early loss). Anyway, not that any of you didn't know this already or that there aren't a billion articles written about this...

What brought this topic to my attention was this editorial in Chemical & Engineering News, titled "Addicted to Growth", that puts forth that the human addiction to growth stems from our greediness. In our greed we have destroyed our planet, and instead of pushing forth to overcome our problems with technology and more growth "we should be able to create social structures and an economic system that do not depend on growth." The author reviews positively a book with the opinion that "Growth is a religion...that flies in the face of physical reality, and as such, cannot be maintained". Really?

First of all, the assumption that growth is bad and is a consequence of some inherent human greediness is inaccurate, to say the least. When you look on a smaller scale, maybe your neighbor buying five flat-screen TV's and driving that Hummer and not giving a crap about the "problems of tomorrow" is greedy. I'm not saying that greed doesn't exist in the world. But isn't the growth and expansion of human civilization a result of something else other than greed? Isn't it, like I mentioned earlier, simply the driving force of life? Can any of you envision a society that you'd want to live in that did not want to grow and expand in the many domains of life? It would be a boring and stagnant society, a society without a greater purpose - one that I certainly wouldn't want to live in.

I think the problem that the author has with all this growth and expansion is the fact that it is often unchecked and it's consequences are not realized until it is too late. On the grand scale, humanity wants to advance itself and expand wherever possible, but on an individual scale, people can be greedy, ignorant, and plain stupid. It's often a much easier life to live where you only care about your own good today (and in the near future) and not think whether your actions will have a negative impact on others in the future. Indeed, it is our nearsightedness that often blinds us to the problems that could be avoided if only we took the time to think things through, play some possible outcome scenarios, and just plain keep technological, economic, and population growth in check.

As a scientist, I may find all those "ethics committees" frustrating, as they will be the ones evaluating whether my cyborgs could take over humanity or not, but ideally they would be making the best decision for the long term. This job, of course, currently rests with all of humanity as well to a much larger degree.

What the author lauds is the idea that we should "focus not on growth but on maintenance". Now, I didn't read the book that he reviews/cites this from, so I can't say what these suggestions really are, but if they indeed forgo any growth, then I certainly disagree with them.

The whole "green movement" is not something that I disagree with, however, as I do think that overconsumption and wastefulness is a problem and should be kept in check by individuals as well as groups. But that is not the answer to our dwindling resources. The answer lies in finding new resources and in finding ways to expand the use of resources we already possess. Scaling everything down and settling back into some sort of "maintenance" mode is going to lead to decline (back to horse and buggy, I guess). We need to strategically scale down on use and pump money into energy research as well as travel to nearby planets for resources. It's pretty much inevitable.

I don't think humans will ever stop growing and expanding, and suggesting that these are the result of greed is like smacking all the progress in science, the arts, economics, (and pretty much every other domain) very hard in the face. The long term solution (once we get over this fossil fuel and sorta-overpopulation hump) is to try to have more stringent control on consumption and production (of everything from energy, to information, to babies [production of babies, not consumption]). Will this work? Does this sound too much like all those dystopian sci-fi movies and novels? Who knows... We will certainly need to be more considerate, but never stop cultural, technological, and physical growth and expansion, as that is what makes us human.

Roller Coasters!

I'm a huge roller coaster fan, and recently a good friend and I ventured over to Six Flags Great Adventure in Jackson, NJ to ride as many of them as we could. It was a semi hot-and-humid Monday and there weren't many people there. Weekday theme park visits are always better than weekend visits. Anyway, without further ado, here are my official reviews of the roller coasters we went on:

• Kingda Ka: This is a VERY tall coaster, and very fast. So fast in fact, that it's over before you know it. Now this is definitely a ride to go on at least once, but honestly if the wait is over 30-45 minutes, your time is better spent in other lines. Thankfully our wait was within this time limit. I waited for three hours once for this one, only to watch the ride be closed due to thunder storms when I was 5 minutes away from getting on it. The coaster shoots you up very fast and pauses for a tiny bit at the top, from where you can see miles around you. The ride down isn't as scary as you'd think because the tracks are sort of twisted, and you don't see as much. You also don't get a weightless feeling when going down. All in all, going up is better than coming down on this one.

• El Toro: This is one crazy wooden coaster. I'm not a fan of Rolling Thunder, another wooden coaster in the park, because it just shakes the whole time and I get thrown around way too much (bruises anyone?). This coaster surprised me with its awesomeness. It's a relatively long ride, and there are some very high points. There are a lot of parts when you're going under wooden beams at a high speed and just feel like you have to duck! Very much a scary ride the whole way. This one was my favorite that day, and was worth the 30 or so minute wait.

• Bizarro: This ride replaced Medusa, which was a fun short/medium length ride. It's pretty much the same. There is some fire spewing on the sides and some mist and scary spikes.

• The Dark Knight: This one's an indoor coaster, like the Skull Mountain (which is really no fun). It has a better "intro" while you wait in line - going along with the whole Joker taking over town theme from the movie. The ride itself is only okay though. Such are the afflictions of many indoor roller coasters. There were barely any other cool themed things inside the ride (unlike rides like Spiderman in Universal, which ROCKS). Also way too many sharp turns (I got thrown around a lot in this one!). If the wait's long, it's not worth it.

• Batman: This ride is another mediocre ride, in my opinion, but I still always go on it. It's fun, like Bizarro, but there's really nothing special about it.

• Nitro: This ride has to have the best first drop of any roller coaster that I can remember (and there are plenty that I don't). After a very slow ascent, you plummet down at incredible speed, feeling weightless as your insides get squeezed into places where they shouldn't be. Thankfully this lasts JUST the right amount of time without overwhelming you. From there it's a nice long ride, with all the usual thrills. There are some "rolling hills" around the end which are very fun, as you can throw your hands up in the air as you get thrown up out of your seat a bit. Overall, this is my favorite roller coaster at Six Flags, and is very beautiful in the dark.

• Runaway Mine Train: Meh.. just another short and not very eventful ride. The wait was about 2 minutes though (I wonder why), so we just went on it.

Rides that we didn't go on that day were Superman, Great American Scream Machine, and Rolling Thunder (out of the main roller coasters). I've been on all those before, and they're fine, but there just wasn't enough time for everything. Also, riding lots of thrill rides one after the other takes a lot out of you (that and the heat and standing/walking a lot). I'm not a roller coaster snob, but I do judge them, and I hope this little review helps anyone deciding on which ones to go on while in Great Adventure.

Technology's effect on boredom and creativity

Here's something to think about: This article at The Atlantic is very short, and has two premises:

1) With all the technology and instant access to entertainment and information anywhere, there is no way anyone can be bored.

2) Because we no longer have these "bored" moments where we can let our thoughts roam and daydream to entertain ourselves, we may be losing all-important "creativity/deep thinking time".

The article is titled "Boredom is Extinct", and in relation to the first premise, I think it sounds true at first glance, but not upon further analysis. (I will try not to make it one of those "oh what is happening to the world because of all this technology" posts).

Lets say you have and internet-access phone/ipod/ebook reader that you can take along anywhere. As long as it's in your possession, you technically have access to limitless information, or at least enough entertainment that you "shouldn't" be bored. While walking to class or doing any routine stuff you can be listening to music or podcasts, while waiting in line somewhere you can be reading my awesome blog, playing chess on the bus, or texting your ex while on a boring date.

I have to point out, as most of you would agree, that it's still possible to be bored while having an access to limitless information and entertainment. One can be "bored" with absorbing information, when the brain is just saturated and needs a break. At this point you need to go for a run (or a walk, or for some tea).

How much of the world has this limitless access? I don't have exact numbers, but I'd wager it's a small percentage. Only about 27% have internet access, so the number would be lower than that. Plenty of people can still be "bored" and daydream to solve this dilemma.

Lets look at the second premise, which makes even less sense. We are not losing our creativity because of this information accessibility, though we may have to make a conscious effort to sometimes "get away". I think the people who are more creative by nature or whose work needs them to be creative and spend considerable time brainstorming do so anyways. My labmates and I have plenty of idea-generating talks, lots of people go on walks for a change of setting and inspiration, video game development and movie teams have brainstorming sessions, etc.

So overall, just because people can have instant access and distraction, doesn't mean it always has to interfere with their creativity or work. Same goes with daydreaming. That's assuming that "daydreaming time" correlates with "creative time", which is certainly not the case. Some very creative ideas come out when interacting with other people or reading articles online. One may say that having an all-access pass is a boon for creativity.

I do think that for kids who are raised in this environment, life will certainly be different, as they are brought up with constant access. I won't go into this right now, but I do believe that there will still be plenty of people who can be creative and introspective in such a world. Who knows, in a few years, if we have an implantable all access "phone" (a la last Futurama episode), then maybe it truly will be impossible to "get away", and creative/introspective time will be harder to come upon.

I think maybe what the author of the article should say is that the constant access is making it harder for people to find quiet moments of solace with no distractions. (There are many articles out there exploring all the "horrible" consequences of this). Whether this correlates with daydreaming about nothing in particular, with introspection in general, or with creative activity depends on the individual.

Human behavior and thinking patterns are marvelously adaptable, and I don't think our creativity will be stifled by being able to google anything at any time and by receiving texts from our mom.

On a final note, I'm reading an interesting book on creativity, so I'll surely post some more about this topic.

Caffeine and sports performance: should it be banned?

Being a coffee drinker, I always look out for articles that shed my habit in a favorable light. Studies generally show that drinking less than 6 cups of coffee a day can have favorable health benefits. Anything more than that is usually a bad deal. Moderation is key.

I won't go into details about the health effects of coffee intake (perhaps later). What I want to explore here is rather the benefits of caffeine and coffee for sports performance, training, and exercise in general. Since I train quite a lot (and some of you surely do too), I think this is something interesting to know about, and coffee can be another tool to add to one's arsenal.

The effects of caffeine and coffee on sports performance in general are favorable, with a few more murky results. First lets see what science has to say about what caffeine may be enhancing, exactly.

For starters, caffeine has been shown to increase the pain and perceived effort thresholds during exercise, and very interestingly, in both habitual and non-habitual drinkers. Post-exercise pain can also be decreased with some java, by a hefty percentage too.

The effects on endurance performance are pretty well documented. Time to exhaustion as well as time-trial performance are usually enhanced (though sometimes with a lot of variability), especially during sleep deprivation.

For anaerobic exercises where the onset of exhaustion is within a short period of time, such as sprints, there is also evidence for caffeine's action as an ergogenic. Few studies exist for strength training, and usually the results are more "equivocal". Some studies show that in well-trained subjects there is an increase in maximal force generation, muscular endurance, and "vigilance", while others state that there is no significant strength increase for one-rep max lifts. There is certainly a consensus, however, that further study is necessary.

Then of course come the studies that are sport-specific, for sports such as soccer and rugby, which are classified as high-intensity intermittent exercises. As these involve endurance, strength, and anaerobic performance, one can see how caffeine would be considered an ergogenic in these cases.

The specific mechanism of caffeine's action is still questionable (that, and I will spare you all several paragraphs of physiology).

It's important to note to take everything with a grain of salt, especially since there are so many factors that influence the design of a human study.

Also, caffeine is not necessarily the same as coffee. Coffee has a whole slew of other ingredients besides caffeine, and it's effects are a little harder to study.

So if caffeine is such a performance enhancer, why isn't it banned from professional competition? Well, it actually WAS banned until 2004. Apparently it was just too hard to regulate.

The World Anti Doping Agengy, which "fight[s] against doping in sports" has a list of substances that are prohibited in sports.

Interestingly "gene doping" is on the prohibited list, or any pharmacological substance which may "alter gene expression". Also, alcohol is prohibited in competition for some sports where operation of machinery or a complex tool such as a bow is required. One can see why.

Stimulants, of which caffeine is one, are also well-represented on the list.

How does WADA decide what gets put on the list?

A substance shall be considered for inclusion on the Prohibited List if the substance is a masking agent or meets two of the following three criteria:

(1) it has the potential to enhance or enhances sport performance;

(2) it represents a potential or actual health risk;

or (3)it is contrary to the spirit of sport.

None of the three criteria alone is a sufficient basis for adding a substance to the Prohibited List. Using the potential to enhance performance as the sole criterion

would include, for example, physical and mental training, red meat, carbohydrate loading and training at altitude. Risk of harm would include smoking.

Requiring all three criteria would also be unsatisfactory. For example, the Use of genetic transfer technology to dramatically enhance sport performance should be prohibited as contrary to the spirit of sport even if it is not harmful. Similarly, the potentially unhealthy abuse of certain substances without therapeutic justification based on the mistaken belief they enhance performance is certainly contrary to the spirit of sport regardless of whether the expectation of performance enhancement is realistic.

Some think that as more and more evidence arises for caffeine's sports-enhancement benefits, it should go back on the list. (Though one would have to be a very serious coffee drinker to gather some of caffeine's benefits).

It's very hard to say whether it will ever go back on, since studies show that low to moderate consumption can have a performance boosting effect and coffee is such a prevalent part of society. I do think ideally, if the evidence keeps growing for its effects, then at least competitors at the highest levels (Olympics, Super Bowl, and other national or world championships) should be tested. Though perhaps a substance should be a "controlled" one to be on the list. Otherwise take specially formulated electrolytes - there are certainly benefits to be reaped from these during competition, and surely overdoing these would have deleterious effects on the athletes, but these are not going to be banned any time soon.

We have to realize though that there are many factors that are taken into consideration when such lists are formulated and when athletes are tested, and what ideally should be done is usually far from what is actually done. We all want to think that at the highest level of competition the field is as level in terms of doping and other unfair advantages as it can be. However, there are many other factors that account for performance, and they're all part of what's called TRAINING. Of course not everyone has the same access to coaches, equipment, nutrition, masseuses, or genetic benefits. Prohibiting a number of performance enhancing substances is the best that we can do.

Personally, I will keep drinking my coffee for its social reasons (coffee hour!), delicious taste, and the apparently significant kick it can give my training even if it doesn't always make me feel buzzed. No caffeine pills for me though. As for anyone else reading this who trains and is NOT a coffee drinker - just know that you may be missing out on some nice boosts without many deleterious effects.