July 23, 2010

The Obesity Epidemic

A recent study has shown that the skinniest state in the U.S. is fatter than the fattest state only 20 years ago. The thinnest state currently in the union is Colorado with 55% of the population overweight and 18% obese... So 1 in 5 people in the thinnest state is considered a health risk. Only a few decades ago this wasn't the case, there was obesity to be sure, but it was more a sign of prosperity or the like, rather than regarded as the illness it has been called today. The main difference in our interpretation of the condition appears to be its prevalence..

So what happened?

As with most problems, there is never a single cause to it, but rather the culmination of many factors coming together.

Firstly, since the industrial revolution the amount of physical jobs has decreased sharply, in favor of using machines and automated systems, with the workforce shifting towards more sedentary jobs, like the one I possess. Going along with this many works of media (television, video games, computers, etc) all consist of sitting down and little movement.

This is not to say I'm an advocate for being a Luddite, this is progress encourages a more cerebral society that values knowledge over brute force...hopefully. Exercise is not our cultures definition of a good time, we get home and we want to relax, in general. Sociology isn't my specialty... Anyhow, moving on...

Genetics are also at play here. A study conducted by Tulane's Department of Epidemiology has shown that there are heritable phenotypes for obesity that range from as low as 6% of a group to as high as 85%. There are a number of conditions as well with obesity as a symptom. These of course tend to be very rare conditions, but none the less inflate the numbers of the whole. Far less rare conditions however, include diabetes and depression, two conditions that are extremely pervasive in the US, both of which have been linked to obesity (and both links are shown to be causative).

The next issue comes to a very simple cause. Our food and drink. Let us first be honest about something, it is not cheap to be healthy in the U.S. Not only that, it's time consuming to eat healthy in the U.S. Making a home cooked meal, in general, is almost always healthier for you than going out to eat, not only are you doing the work (and burning off calories) but you can control precisely what it is the meal. The reason that most restaurants taste so good is because they tend to slather their product in fat and salt. And going out to a 'healthy' restaurant is more expensive, being a specialty shop they raise their prices to match with a limited clientele.

Now to address the elephant in the room....

High fructose corn syrup.
High fructose corn syrup, as the name implies is made from corn. It is originally a syrup of glucose (the natural sugar in sweet corn) and is enzymatically converted into fructose (which is in fruit). In theory it is 50% glucose 50% fructose, but it can contain up to 80% fructose and 20% glucose. It is frequently used as a sugar substitute

I've seen some ads recently advocating the stuff saying that 'it has the same effects as sugar'. This is, in part, true. High fructose corn syrup in terms of caloric intake is no worse than regular sugar, honey, and other sweeteners... There are other issues with it however. For one thing a study has shown that it contributes more towards obesity than other sugars, due to it's ability to repress the chemicals behind your appetite, making the consumer unaware of when they are in fact 'full'. Another is that apparently there is mercury found in about half of all HFCS tested, mercury contaminated caustic soda has been used to produce HFCS in some companies...

Ignoring the possibilities of neurotoxins and enzymatic inhibitors there is an even larger problem with the stuff.

It's everywhere.

A cursory look over my pantry revealed it was in yogurt, industrial bread, cookies, salad dressing, tomato soup and ketchup. The issue is that this ingredient, and the calories it packs, is virtually in every processed food out there.

This brings back another question... Why use it?

The simple answer? It's cheap. Without delving into politics, the U.S. government subsidizes corn production, making the product dirt cheap. While this does allow for many people to be fed that wouldn't it causes the opposite problem of people becoming too fat (corn was cheap before however, the government simply made it cheaper).

So what comes from this long rant? Obesity is caused from a variety of sources and preventing it would be a herculean task. Or the fact that diabetes, closely related to obesity, has risen sharply in the past few decades limiting the lives of many. Or perhaps simply that high fructose corn syrup has many chemical properties that have enzymatic and neurochemical ramifications?

I think it means I'm going to stick with my caffeine addiction...
Thanks for reading


July 21, 2010

Synthetic Biology, Bioethics and Unicorns, oh my!

Our current vision of reality is slowly but surely being taken over by the world of science fiction.
And I heartily approve.
There have been many recent advances in the fields of bioengineering. There are obviously the pest and disease resistant crops that most of us now eat (a matter of transplanting genes mostly) as well as various thoughts on RNA and DNA therapy for people with genetic conditions. In addition, for a fee, we can map our genome and determine what of the myriad of diseases we may be affected with in the future, as well as discovering our maternal line, people we never knew we were related to. On the whole, we've made massive movements towards sci-fi use of biochemistry.

But most amazingly. We've managed to edit the genetic code, and are able to make biological proteins not seen before. Recently scientists in Cambridge, specifically a one Jason Chin has managed to creature a codon that can code using four nucleotide bases.

To explain, a three base codon it part of DNA and RNA that encodes for all proteins, enzymes and biological materials that are made in the body. A codon is, simply, the blueprints for designing every part of a living thing, humans, plants, animals, everything. To change the number of nucleotide bases that are read by the codon changes how business is done, it's like switching from our Phoenician alphabet with 26 characters to an Asian character system with hundreds. To do this they had to make new ribosomes which they selectively inserted into strains of E.Coli.
What this means is that it opens up a whole new area in terms of amino acids, proteins and enzymes, which in turn opens up a whole new field entirely. That of synthetic biology.

Speaking of which...

Across the pond that very instance has taken place. By engineering a strain of DNA they were able to insert it into a bacterium, which then proceeded to replicate, forming an entirely new strain of bacteria, which successfully went through cell replication. Forming the first entirely engineered form of life that has never been seen on this planet before.

The consequences of this find are astronomical. Instead of genetically modifying a creature, we are able to fully create a life form from the ground up (albeit inefficient and not particularly cheap...nor particularly viable on large scales). Like the previous discovery this opens up the doors for new sorts of medicine and biotechnology (and possibly food)

But as with all discoveries, it also opens up the door for ethical and moral quandaries. And I'm pleased to say that the U.S. court's at least are taking this seriously. There was an idea that specific genes created by companies could be patented, but the issue becomes what happens when someone possesses the gene? Who's property is it? Worse yet, if a single company owns the patent on a cancer gene, that bottle necks the companies able to study and cure said cancer... Luckily such a ruling is meeting legal action

In addition to this there is the fear that a synthetic organism, if released into the wild would then run amok with the native ecosystem. Being that it a completely nonnative being it is possible that the immune systems of living creatures would not be able to handle it, causing an epidemic almost overnight. Then of course there's the fear that someone would do this on purpose as an act of biological terrorism. AS before, there are growing watchdog agencies who are beginning to try and monitor just that sort of thing.

So as we see, biology is making great stride and becoming a greater behemoth in how it will affect our daily lives, not that it wasn't already. I'm personally excited about the possibilities, and the thought that science fiction is quickly becoming science fact

I didn't forget unicorns.... As it turns out in Italy there was found a single horned deer, which a lot of people seem to believe may have been the beginning of the original unicorn myth.

Personally I want to genetically engineer a unicorn... but, you know, gotta wait for progress and all that

Thanks for reading,


July 20, 2010

Swine flu will come around for another try

A few weeks ago 40 million vaccinations against Swine flu expired, and by the year's end 70 million will have expired, around 40% of the total reserved for public use and about a half billion gone to atrophy.... I remember about a year ago when all of the panic began surrounding the swine flu, it's funny looking back given how few people even remember that time. It largely was a mass panic attack on the part of the American public... which seems to be our natural state.

I'll admit it, I caved into the pressure and got the vaccine at the urging of loved ones. I never considered the swine flu to be a very big issue however. Some can chalk it up to me being a college kid and thinking myself invincible, but really I based it off the fact that it typically only killed people with compromised immune systems and otherwise was the plain old flu (which, for the record, kills about 500,000 thousand people a year, about 40,000 of which are in the US. as opposed to swine flu where 17,700 deaths)

I was never terribly worried and, not to pat myself on the back, but it appears that my feelings were justified given a Spanish Flu study. For those who don't know, the Spanish flu of 1918 infected 40 million people and had a 50% mortality rate, killing 20 million, making it one of the worst epidemics in history far outweighing the death toll of WWI and WWII combined. The Spanish flu was in fact a version of the H1N1 avian flu (which is communicable to both pigs and humans). So why then did the current strain not do what our paranoid fears promise? Two reasons, a massive amount of vaccine was made and given out, more than was needed in fact. The other reason is by virtue of being a virus, the flu's genetic code (And it's deadliness to humans) is in a constant state of flux, and is different from one generation to the next. Viruses can absorb new DNA and become a different strain very easily, which is why the normal flu even today is a potentially deadly circumstance, it is the same reason why someone can get the flu multiple times.
However, specific genes can give a person a hint as to how severe a virus can be. Sequencing the virus' RNA, it was found what gene's it held in common with other comparable flu's. Two genes specifically show this, H1 gene(the virus is technically known as A(H1N1)resembles the H1 gene of strains that reach their victims’ upper respiratory tracts, but not their lungs. When flu enters the lungs, chemical fallout from a body’s immune response can cause severe damage. H1 gene — the virus is technically known as A(H1N1) — resembles the H1 gene of strains that reach their victims’ upper respiratory tracts, but not their lungs. When flu enters the lungs, chemical fallout from a body’s immune response can cause severe damage. Another gene, NS1, belongs to a family of genes that seem to modulate immune response. The swine flu version resembles other NS1 variants that trigger a mild reaction. These two genes had they shared more in common with more virulent counterparts would have made the swine flu a potential epidemic maker...luckily for all of us this was not the case
Now the question. Where did the swine flu go? Surely we destroyed it? Wrong. The swine flu, following it's erstwhile name, has returned to it's native land of pork, where it can combine with other flu strains substantially more deadly, such as the normal human flu and the avian H5N1 flu.

Swine flu has actually been a part of the American experience, with breakouts occurring in 1918, 1976, 1988, 1998, 2007 in the Philippines and of course 2009. Ultimately, viruses such as swine flu will become more and more common as the world's population explodes, offering fertile grounds for these sorts of disease. With such high concentrations of people, we sit on a time bomb waiting to go off.

I still love pork though

Thanks for reading,


July 17, 2010

Oil cleanup options

So BP finally capped the oil spill.... Without getting into the long blame game who who caused it and their punishment, I've decided to go a slightly more... optimistic approach? Perhaps not the best phrase, perhaps more 'pragmatic'

I view oil spills a bit like I view innocents being convicted in the justice system. In spite of all our hopes, and whatever faith we may have in the system, at some point it will fail, if just by random chance alone, it's hard to deal with so many variables. I'm not going to say for a second that we should just go 'cold turkey' off of oil, that is at best a very poorly thought out bit of propaganda. Oil, whether we like it or not is an intricate part of our economy and how we build things. To go 'cold turkey' would lose many people their jobs and let's be honest, none of the current 'clean' methods of powering the country are currently at a level where it would support our needs. The only methods that would are nuclear, natural gas and coal(all of which have their own problems)...and even then we would still use oil as a way of making plastics, as well as other petroleum based products. This isn't to say I think we shouldn't research alternative fuels, far from it. the hippy in me would love to have the whole 'love mother earth' sort of movement go forward... I just don't believe for a second that it will magically change overnight.

Disregarding oil's problems ecological, technological and economical this leaves the issue of how to clean up oil when it does spill(and as resources become lower and we dig for it more zealously it most certainly will) how do we fix it? As shown with the gulf coast oil not only affects the local ecology, but the local economy adversely. So how does one clean up oil spills effectively, keeping in mind both the economic and ecological ramifications? How can I do this while making it both informative and not completely depressing?

The answer is simple. I will rate the current ideas in order of what I view as effective and just plain cool

Burning off the Oil

The current modus operandi of most clean up efforts, namely simply burning the oil off. It is by far the cheapest way of doing it and it does indeed get rid of the oil, plus it has the added benefit of setting water on fire, which I'm always for, being that I have a strong connection to Cleveland Ohio and all.

Unfortunately, burning the water surprisingly isn't the best option. First of all it dumps a ton of pollutants into the air which not only affects the atmosphere but otherwise is harmful to plants, animals and people, lung cancer and all that. In addition, the fact that the water itself is actually ON FIRE doesn't particularly bode well for the creatures that dwell underneath, and by extension harms the fishing and tourist industries. And to top all of this off, the oil itself is burned off so there is no return on the investment, just pure destruction

Overall grade: F
This isn't the way you want to clean oil, it causes more problems than it solves, you exchange one ecologic disaster for another one. I'll grant you it is cheap, efficient and does technically get rid of the 'oil', but the side effects aren't worth it

Coolness factor: C
Fire.... on water! Need I say more?

Bacterial Clean up

Being a biochem major this one has a special place in my heart. There are already microbes that eat methane, so why not make some that eat oil? Well we're in luck, such creatures exist already...though they are not adapted to the environment and thus would die quickly. Given that this is a bacteria however and have such quick breeding cycles, selective evolution (usually known as breeding) would be a potentially viable solution.

The issues that arise however are twofold. Firstly it takes time to engineer creatures like this for a specific purpose, so even if it were developed it wouldn't be useful for some time. Luckily (or rather unluckily) oil spills take a long time to clean up, and that time could be used to tailor the organism to the specific environment.

The other issue to this though, is the simple fact that in ecology, once you start a system, it is very hard to stop it. The oil spill will kill off most of the native fish anyhow, especially given how slowly it would take to clean this up, and the dead fish would then sink to the bottom of the ocean, decaying and releasing more methane, which in turn, would kill more fish and give these bacteria more food in addition to the oil. When the bacteria die, they sink to the bottom, release methane, and supply the next generation. On the bright side it's a sustainable ecologic cycle... just not the one we want.

In related news, apparently you can buy them too!

Grade: C+,

Less overall impact but would change ecosystem for sustainable future. Still lose the oil. On the bright side, we would ensure more oil in the next few thousand years for our descendants.

Coolness: C+ .... I'm a bio nerd....Don't look at me like that

Nanomachine 'Grey Goo Scenario'

This one is for all of the engineers, and really only deserves a mention because it's a staple of sci-fi destruction of humanity fiction. The basic idea is that you create self replicating nanomachines to clean up the oil for us. This solution is a lot like the bacteria solution, except without the sustainable ecosystem, get rid of the oil, clean up, shut down robots, problem solved.

In theory anyway.

The first clear issue would be the sci-fi worry of these things taking over the world and consuming all organic life. Realistically, we need to have a much higher level of tech for this to be a worry, but it should still be a concern (why else have sci fi). Self replicating machines have yet to be found outside of science fiction and we are still quite a distance away from developing such things. Leaving aside that, the far bigger issue is the time frame it would take to design and make the machines, let alone the cost/reward of it. Things that are very small are notoriously hard to build and expensive by design, and it is not even the current thought in how to clean up the oil. It's not the most practical method of cleaning oil, unfortunately I feel this is the sort of thing that will remain in the realm of science fiction for some time

Grade: D+

Theoretically sound, but still far off and impractical in the face of cheaper and more effective options

Coolness: A

Anything that could possibly kill all life gets an automatic A in my book. Bonus points for being a man-made disaster, the most common in sci fi.

Skimming the Oil. AKA Kevin Costner is...Right?

Perhaps the least exciting, but the most likely to succeed, the idea of skimming the oil off of the surface of the water. Oil and water, as the saying goes, doesn't mix and it's still true. Literally picking up the oil does effectively clean up the pollutant (using water permeable nets no less), and not only that, but it actually reclaims the oil, which can then be sold and recoup whatever loses may be incurred. Simple enough right? It's not terribly efficient however...

Enter Kevin Costner, who just so happens to have this kind of technology, which he bought the patent for back in the 80's around the time of the Exxon Valdez oil spill (which by the way, we're STILL cleaning up). The basic idea comes from centrifuges, oil and water have different densities and by spinning them the two will separate from each other easily. Not only that, but the oil is usable again. This is actually one of the things BP has done recently, buying several ships from Costner. BP has bought 32 of the machines, which in theory could clean 6 million gallons of water a day. The one minor hiccup to this whole thing is the disperants that were placed in the oil, which has caused the oil to be under the water and not necessarily seen by the naked eye, making clean up more difficult. However this is easily fixed with the use of sonar and a hose to reach it. Over all I am actually very hopeful for this sort of clean up...

Grade: A
Clean, simple, effective and we get the oil back. What prevents it from being an A+ is the cost, but should these machines become more common, that should go down.

Coolness: D-

Do we really want to live in a world where Kevin Costner's vision of the future is correct?

July 16, 2010

Immortality has been achieved!... In Jellyfish

So occassionally things will just catch my attention.... Immortal hydrozoa happens to be one of those things.

Turritopsis nutricula, now otherwise known as IMMORTAL jellyfish has a similar life cycle to other jellyfish, egg, larva, polyp (Which are alot like coral...in fact coral and jellyfish are related) and then finally the medusae stage (the actual jellyfish we're used to thinking of). This in itself isn't particularly astounding, most jellyfish do this the same way, with more or less steps depending on the species. The medusae stage typically has a fixed lifetime that can range from a few hours to a few months.
What makes this one special is the fact that they can revert back to a previous life stage, reverting from it's adult stage back into the polyp stage, effectively staving off death and resting, preparing to breed again. This process is accomplished by a process called transdifferentiation which alters the differentiated state of the cell and transforms it into a new cell. In this process the medusae of the immortal jellyfish is transformed into the polyps of a new polyp colony. The jellyfish reabsorbs its tentacles and umbrella in this process, repurposing the cells to form the polyp colony. This process, in theory can go on indefinitely...making it effectively immortal, avoiding the pre-determined death of the medusae stage.

There are alot of ramifications of this discovery... and how it affects us as humans. It has been thought for a long time that telomeres (the repeating sequences of DNA at the end of chromosomes) are directly linked to aging (they do shorten as we age). However in the case of the jellyfish, there appears to be no link to telomere length and the lifestage of the jellyfish... While we are significantly different animals, DNA tends to operate similarly in most eukaryotes and casts doubt on previous hypothesises on the link between telomere's and age.

A more pragmatic, and disturbing, ramification is that without proper predation, these creatures can very easily take over the oceans...and that seems to be what they are doing. The immortal jellyfish can now be found across the world in virtually every ocean. Given that overfishing has made several fish likely to go extinct within my lifetime... with their natural predators gone the immortal jellyfish could take over entirely

I personally would like to welcome our future immortal overlords with open arms...tentacles... Or something like that

Thanks for reading,


Graphene, not the stuff in your pencils

Graphene is potentially the new material of the future.

There I said it. I try to avoid that sort of over the top inflation but in this case I feel it may actually be true. I've always had a fascination with carbon based materials and their formation (carbon nanotubes, buckyballs, even lonsdaleite and diamond). I mean carbon is one of the most abundant elements in the universe after Hydrogen, Helium and Oxygen, why not exploit it?

Now why is Graphene important? It's because of Graphene's shape and electrical conductivity has many potential uses, specifically in the field of electrical engineering. Among the potential uses for graphene: single molecule gas detection, electrical conductors and transistors, electrodes, capacitors and biodevices for use in diagnosis and microbial detection. On top of this graphene has been shown to be at least 200 times stronger than steel so may be used as potential building materials as technology advances

Graphene on the molecular level looks like a series of sp2 bonded carbon molecules strung together in a honeycomb shaped crystal lattice...looking a bit like molecular chicken wire. Graphene is really the originator of several materials anyhow, the most notable of course is graphite (used for, among other things, as lubrication and in pencil lead) carbon nanotubes and fullerenes.

The fact that graphene has been used to so many applications now anyhow is impressive given that the substance was only capable of being isolated in 2004. Graphene is found in small amounts in ordinary graphite, though it is incredibly difficult to retrieve given our current level of technology. At the current state, as with most next gen materials, it is not cost efficient at all until newer technologies are developed.

I have to say I am excited by the potential prospects and applications of this new substance. I'm not much for the business side of things, but if i were (and had the money) I'd be investing in company's producing graphene. Given that currently a square centimeter of the stuff costs around 100 million dollars(as of april 2008), one can already tell just how this substance has grown in importance already

That being said, given how the business world works, I wouldn't expect any of this for public use for several years now, I expect industrial usage, particularly to produce and maintain energy to go up significantly in the next decade or so, with personal useage following in the 20-30 years

Thanks for reading


Let's start on a light note

Avatar the Last Airbender

Let me start by saying I’m a big fan of the series, it surprised me in many ways (namely the fact that it was made in America among others...there are still people who refuse to believe that). The series was complex, with fantastic visual elements, complex characters, interesting plots and much more to the point....it was fun. I was eager to watch new episodes, and I genuinely cared about the characters all of them

This unfortunately is not the case for the movie. I didn’t care about the controversial casting decisions and hell I was willing to give M. Night another chance. I even tried to shed my fanboy preconceptions and try to enjoy it for what it was, a movie.
From that aspect it was....alright. The visual effects were impressive and I’ve always had a soft spot for filmed martial arts. Even the story, while different from the source canon was alright, it was a new take on the classic. Now for the but.... The acting was blocky and wooden, it felt like the actors didn’t particularly care about the movie and they were simply going from scene to scene doing their lines. The mark of a great movie to me is when you forget the actors are in fact, actors...this is not such a movie. Now even that I could chalk up to several young actors who haven’t quite gotten their acting chops yet (though the Harry Potter series should show that shouldn’t be an issue). But the worst part of it...it didn’t have the same amount of fun. The same charm and humor that was found in the original.
Putting my fanboy cap back on I must ask, did you watch the show? Oh, and a final thing. It’s Aang (A-ng) Sokka (Sock-a) and Iroh (I-roh). NOT Ung Soe-ka and Uroh.... The mispronouncing of the names killed it for me more than anything



Despicable Me

Perhaps the reason why I judged the previous film so harshly was because I saw it during the same weekend as this movie. Despicable Me fills out my primary criteria for a movie... It’s fun. It’s full of charm, wit and action, and does have a lot of heart (for those who care about that). The film features Steve Carrell as Gru, the incompetent villain, three orphan girls, a shrink ray and a hoard of asexual minions, and a general good time.

Despicable Me fulfills the wonderful role that all kids movies should, being written on two levels. This movie can be enjoyed by little kids and adult (and those who are somewhere inbetween like me)There's a ton of physical humor, as well as some subtle bits that go over the heads of little kids (The Bank of EVIL is formerly named Lehman Brother's for instance)
I honestly have nothing bad to say about this movie, the animation was different and stylistic but still good, the plot made sense, and the girlfriend and I enjoyed it the whole way through. What that I would say of this movie is that it should’ve gone further, more jokes, more physical humor, just...well more of everything. As said however, I enjoyed it overall, I definitely recommend for people to see it and deepen Mr. Carrell’s pockets.

Grade: B +


The Sorcerer's Apprentice
I'm going to be honest with you, and it makes me feel dirty. I love Nicolas Cage. There, I said it. I'll take a shower to wipe away the shame later.
The fact that he's a giant nerd who's attracted to geeky movies does a great deal for me (the fact that Vin Diesel plays D&D may be the only reason I watch any of his movies). Getting rid of that though, this movie fulfills my primary requirements for a movie of this type to be passable.
It's fun.
The effects are wonderful, the scenery is fantastic and the plot does in fact make sense (albeit if you ignore all sorts of contradicting stories and mythology...but you have to for most disney movies).
Nick Cage I'm convinced always looks a little haggard...so makeup for him turning into Balthazar was likely easy. He was also playing the same person he plays in every disney movie, the quick thinking smart, dry, witty hero....with a touch of magic this time around. This isn't to say it's a bad thing however, as he plays the role well. Jay Baruchel as always plays the awkward teen who reminds me, frankly, a bit too much of my own high school years...but he invariably gets the girl. Baruchel's scene that's reminiscent of the Fantasia scene with the same name definitely steals the whole show. Alfred Molina as always plays a wonderful villain and may be the most interesting character in the whole movie. Teresa Palmer rounds out the cast as the obligatory love interest who actually DOES do something useful in the movie!!! Granted until that times she's at best eye candy, but still.
Don't get me wrong, there's plot holes a plenty, some deliciously awkward scenes and the villain does certainly hold the ball at certain points. And as with most Disney movies, they never really tries to push limits and of course all of the good guys are alive at the end...even when they make the quote 'ultimate sacrifice'. The movie ultimately sticks close to the time honored stereotypes, but does warp and play with them occassionally
Ultimately? The Sorcerer's Apprentice is a fun ride, it's just a ride we've been on before without any twists and turns to surprise you. I recommend seeing it, if not for full price then certainly at the dollar theatres, it's a fun two hours
Grade: B-
More science-y posts later