Sunday, November 14, 2010

A potentially amazing idea.

I have been reading the book "Microcosm: E. coli and the New Science of Life" by Carl Zimmer. Already it has been an amazing read, I recommend it to anyone who wishes to garner a greater understanding of microbiology, micro-ecology, and molecular evolution. In one of the sections, Carl Zimmer explains the cycle of evolution that E. coli go through in certain situations. This is displayed rather dramatically when different strains of E. coli compete amongst one another for survival.

Each strain will often grow together as such communal behavior allows for greater survival of a strain. When a bacteria begins to act as a group instead of free roving individuals, they form what is known as a biofilm. Within this biofilm different individuals of the same strain might take over different roles. This is all done by chance, the random turning on and off of genes that occur naturally throughout a microbes life cycle. When a biofilm is threatened by a competing strain of E. coli, there is a chance for certain individuals in the group to sacrifice themselves for the greater good of the colony. They do this by producing a protein known as colicins. Colicins destroy bacteria in many ways. Some doe so by essentially destabilizing the cellular membrane so that all that is contained within can seep out, effectively shutting down the microbe. Others block protein formation while still others target the victims DNA While there are multiple forms of colicin, there is only one way to deliver the them in large numbers. Colicins are rather large by protein standards, as such when an individual E. coli begins to fill up with them, there is no easy way for them to escape. Normally they are produced in small numbers and are pushed out of the cell through certain channel proteins. But with such a large number of colicins, the bacterium gets far too full and lyses (explodes). The act of lyseing is not done by the pressure of the internal environment but by a specific suicide function of the bacterium.

Now you may be asking yourself, why don't the colicins released by the lysing E. coli also effect the neighboring members of the same strain and biofilm? The reason for this is that colicins are naturaly produced in small quantities by all E. coli in biofilms to begin with. To counteract this, they also produce an antitoxin that destroys the colicins before they do any damage. It also has to do with the fact that due to slight genetic differences within strains, the colicin proteins will be shaped slightly different. Each strain produces an antitoxin that is most effective against its own strain's colicins. But other strain's antitoxins won't be as efficient at disabling a sudden burst of foreign colicins and some will slip through the defenses to destroy the competitors.

Now when a certain biofilm is faced with such an attack, random mutations will cause a select few to produce more effective antitoxins. These random survivors will then propagate and begin to out compete the attacking colony. As evolution causes yet another shift of power and the attacking colony begins to shrink due to limited resources, there will often be a chance for a mutation for a yet more potent colicin.

This cycle would seem to be endless, but evolution favors the bold. At some point a random mutation may arise that causes a certain strain to only produce the currently strongest antitoxin, but none of the colicin. While this would, at first seem like an absurd tactic, it is one that works quite well over the long duration. The reason for this goes back to the size of colicins. Remember that colicins are naturlly large proteins to begin with. Any stronger variants of the colicin will be even larger still. It takes a lot of energy and resources to produce all that colicin as well as the antitoxin to protect against it. I'm sure you can now see why the seemingly useless mutation would actually be successful in such an environment. While its competitors are busy wasting all their energy on expensive colicins and antitoxins, this new strain can focus only on producing the strongest antitoxin and reproducing. Over time, it begins to out compete the strong colicin producers entirely.

But it doesn't end here, now that all the colicin producers have been killed off, the area is left clean for the original strain of E. coli to move in. The original strain isn't going about wasting any energy on excess colicins or antitoxins and it can quickly out compete the previous victors of the arms race. This leaves us back where we started. This cycle takes place consistently all the time. What started out as an arms race became a game of rock, paper scissors. Eventually, the cycle will continue on through another rotation.

Now that I have put forth all the background information, I would like to share an insight I had while reading this book. The idea of an evolutionary rock, paper, scissors game led me to a thought that left me rather excited. What if we apply this very same rule of evolution to our current problem of antibiotic resistant bacteria?

Antibiotics and antibiotic resistance work in quite the same way as the colicin antitoxin cycle work. Bacteria produce specific proteins that destroy or deactivate the antibiotics (which are often proteins in their own right). The only thing differentiating a resistant strain from a non-resistant strain is that the resistant strain is constantly pumping out these defensive proteins.

They evolved in much the same way as the antitoxin producing E. coli I mentioned earlier. They began as a normal strain that happened to have a random mutation that allowed for the production of the defensive protein. Over time, these resistant strains came up against more and more types of antibiotics. Each time, the arms race I mentioned earlier takes another step forward.

My idea is this, instead of fighting an arms race with these antibiotic resistant strains, why don't we simply use their own strategies against them? Just as the super antitoxin producers from earlier could out compete the strong colicin and antitoxin producers, so would a common strain out compete an antibacterial resistant strain. But we can do one better then blind evolution. If we were to introduce a strain that was not producing the antibiotic defense proteins but instead devoted all of its energy to reproduction, it would quickly out compete the resistant strain.

All one would have to do in the case of infection of an antibiotic resistant strain is to introduce a group of quickly dividing non-resistant bacterians to the site of the infection and soon the new strain will begin eating up all the resources that the slower resistant bacterians were using until there is nothing left but the non-resistant strain and possibly some mutations within the resistant strain which will have given up some of its defense protein production in favor of faster reproduction. Either way, within a few days you are left with an individual who is not a whole lot more ill then they began but now they are ill with bacterians that would respond to antibiotic treatments.

This kind of treatment would of course be a last resort, but it could very well be the answer to one of the most serious medical problems of our day. This concept would need thorough testing before it could ever be tried in a human patient, but with all that we are uncovering, I would not be surprised if this is the answer that so many have sought for.

Now because this solution is so elegantly simple, it is quite possible that I am not the first to stumble upon it, in fact I would be quite surprised if I was. If anyone has heard of such research, I would love to hear about it in the comments.

--------------------------------

References:

Carl Zimmer. (2008) Microcosm: E. coli and the New Science of Life. New York, United States: Pantheon Books.
Facebook Digg Stumble Delicious Twitter Reddit Technorati

Sunday, September 19, 2010

The failing of a legacy and a bit of neuroscience

One of my sources of income involves me working as the projectionist for the local Air Force base theatre. Before the start of many films geared towards younger audiences there often tend to be various shorts. The film company Pixar has become quite notable for the creativity they put into these shorts. However the short I saw just the other day was not done by them and did not have anything remotely similar to creativity. In fact I would go so far as to say it was the very opposite of creative and nothing more then a cookie-cutter style cartoon.

Now generally I would not have much to say about such a forgettable animation. But this was different, as when it started I was actually a bit excited to watch what I was sure to be an enjoyable cartoon. Why was I so sure of this at the start and thus, left with such a feeling of emptiness upon its conclusion? I was so sure because it was a Wile E. Coyote and Roadrunner cartoon.

I remember especially loving these cartoons when I was younger. I knew they were absurd and filled with gratuitous violence. And I also knew what to expect when I watched each one. But this is not why I have always loved them. What drew me to them was the fact that they were the perfect juxtaposition of Goldbergian and Murphian philosophies. It was the fusion of the ideas of "anything worth doing is worth over doing" and "anything that can go wrong, will go wrong". The two concepts play off one another so perfectly that each episode of the original cartoon offered a new example of engineering absurdity failing in the most spectacular fashion possible.

But the cartoon that I watched was nothing more then repetitive slapstick. There was no variation, no build up as we watched a ludicrous series of contraptions failing or working too well, just the Coyote jumping off a bridge with a bungee cord to grab the roadrunner who was feasting on a strategically placed pile of bird seed. The series of events were nothing more then just a play of the same theme over and over, Coyote jumps off the bridge, when he reaches his nadir he is struck by an on coming truck and flung away. In successive attempts, he is volleyed between trucks or is stretched and then released. There are no other apparatuses or contrived schemes. Just the same concept done over in differing ways. It lacked the finesse of the original cartoons and left me with a feeling of hollowness.

Must all cartoons be dumbed down to the lowest common denominator like this? What happened to playing to the intellectual audience while still giving the child the laughs they sought? Do the producers think so little of the current generation or have they lost that spark of creativity and now only create to make a pay check? Is comedy that requires a bit of thought to appreciate really too much to ask of an audience?

Now some have criticized these cartoons as being overly violent and conditioning children to laugh at the pain of others. While I will agree that one does get a hearty serving of Schadenfreude with every episode, I would not say this is inherently a bad thing. We as humans are naturally conditioned to laugh at the pain of others. This is not because we enjoy inflicting harm upon others. But because we are an empathic species.

Our brains are loaded with mirror neurons, a genius innovation by evolution that fires whenever we see someone doing something or experiencing something. These mirror neurons and mirror neural pathways allow us to learn by proxy. This is why we can see something done and put ourselves in the place of the person doing the action. It is also why our hands flinch when we see another persons hand injured or wince when someone else is harmed. They are both a wonderful learning tool as well as an invaluable capability for empathic bonding and interpersonal understanding. In fact, the evolutionary trait of having such unprecedented levels of mirror neurons is what contributed to the development of our social system and intrinsic moral compass.

As a side effect of having all these mirror neuron complexes is the problem of dealing with the emotional strain of feeling the pain of others so often. If we did not have an outlet for this, the emotional turmoil we would suffer from seeing others injured would tear us apart. So an outlet did form, our natural reaction to laugh when we know there is nothing that can be done to help the person and that the injury is not life threatening. When such injuries occur we often cannot help ourselves but laugh, this is because when the mirror neuron systems fire and our brain recognizes the situation as one that is not life or limb threatening and one we cannot do anything to assuage the pain of the other, our limbic system kicks in and releases endorphins and various parts of the brain that involve emotional and pain responce such as the amygdala, hippocampus, periaquductal gray and hypocampus all start firing sending us into Gelotoleptic fits, otherwise known as laughter. This whole series of events is an emotional survival mechanism, one that if we lacked, we would soon all become so emotionally frail that seeing the slightest injury inflicted upon another would send us into extreme duress.
Facebook Digg Stumble Delicious Twitter Reddit Technorati

Tuesday, September 14, 2010

Fox news, ever the source of honest journalism...

For those of you who did not notice, the title is dripping with sarcasm. I'm sure most of my readers picked up on that, but I also know the intellectual aptitude of humanity at large; so I wanted to clarify. The title is in reference to this recent article put up on the Fox News website. I'll give you a chance to read through that great example of journalistic integrity.

I have the misfortune of currently living in the state where this event is unfolding. What you might immediately notice is Fox News' attempt to link the atheists who funded this billboard and satanists. Yes, the journalist who wrote this article is doing his best to make his audience of gullible readers think that atheists are in league with satanists. Now I personally know that satanism is not actually about worshiping the devil figure from Christian mythology but more about poking fun at the system and irritating the status quo. But your average Christian reader does not have the slightest inclination towards this fact. Most honestly believe that there are people out there who truly see Lucifer as their ruler and perform various horrible acts to gain favor with this imaginary character. I also know that Fox news is well aware of this fact as well and they are using it to stir up commotion and public outrage in the hopes of increasing their ratings and site hit counter.

So is there an actual connection between the Oklahoma Atheists and the satanist group? Kind of. The only link they have is that the satanist group rented part of the same building the atheist group will be using. Yes, that is the one and only link. So other then trying to get more of a reaction, there is absolutely no reason to even mention the satanist group who did not offer any funding for the billboard or are associated with the atheist group in any way.

In a strange twist, near the end of the article, there are a couple quotes from a local minister, Robin Meyers, who says "It's not the people who don't believe in God that worry me, it's some of the people who do" and "Fundamentalism is the enemy worldwide, no matter what the strain." I believe that Mr. Meyers and myself would have quite a few things that we would agree on. This heartens me quite a bit, to hear about religious moderates who are standing up against the more fundamental groups.

So in the end, we have another case of Fox news writing things in a way that will get them the most ratings; while laying their intellectual integrity down as a sacrifice to the ignorant hordes. If only such half-truths and bending of facts were punished instead of being rewarded by the masses.
Facebook Digg Stumble Delicious Twitter Reddit Technorati

Wednesday, September 8, 2010

A random insult at humanity.

The people who wear fanny packs are those who are so mediocre in absolutely every way that their existence has become an unending cycle of monotony and their only comfort in life rests in the knowledge that by wearing such an aesthetic monstrosity they might pull down those around them into the gaping maw of banality that they have no hope of ever escaping.
Facebook Digg Stumble Delicious Twitter Reddit Technorati

Sunday, August 22, 2010

Now that is just sad.

Iran. If you believed the former Bush administration, then Iran is the next greatest threat to American Freedom (C). Now what exactly would Iran use to threaten our freedom? Well...not very much. They tried, they really did. In fact I can almost see where the Iranian President painted a smiley face on the corner of their 'weapons' for such good effort!

Take for instance their 'brand new' and 'advanced' fighter jet, the Shafagh.



According to the commander of the Iranian Air Army, General Attollah Salehi, the new fighter is "similar to the F-18 fighter jet, but it is more capable and has been manufactured domestically… designed, remodeled, optimized and made more capable by our engineers… no country has aided us in its production." So apparently it not only is similar to a F/A-18, but superior, well we better be sure to keep our fighter pilots on high alert. And it gets even better. Yes, those amazing Iranian engineers and scientists have made it a stealth air craft! But not the stealth like we are used to. No, instead of absorbing or dispersing radar waves, you know, the way us silly Westerners go about doing it, the Shafagh is "more difficult to pick up on the radar systems compared with the normal version due to its higher maneuverability". Yes, the Shafagh is so advanced it out maneuvers those pesky radar waves.

What I find a bit sad though is that it isn't a newly developed airframe at all. It you take a close look, it is just a modified F-5E Tiger II, take a look:



In fact the US sold a few F-5's to Iran and many other countries. They were outdated versions of the T-38 trainer and giving such technology to independent nations would make them feel good about themselves (they have big boy toys now!). Other then turning the single tail into a twin and some possible avionics upgrades, there really isn't much distinguishing it from the old 'Tigersharks' that we sold to them. Which were outdated back in the 1970's.

So we know that Iran has 'Advanced Stealth Fighters' but they recently showed their newest piece of doomsday warfare, the unmanned bomber named the Karrar (the Farsi word for Striker). This terror of the skies is..well...I'll just let you see for yourself:



Wow...I wonder if it was one of those snap together models or one of the super hard ones that require glue and stuff. But it gets worse. Yes, it can get worse. Not worse as in terrifying (as, honestly, I would be more worried that it would lose control and end up crashing on me then able to actually hit it's target) but worse in how the Iranian's describe their new 'toy'. President Mahmoud Ahmadinejad said that "The jet, as well as being an ambassador of death for the enemies of humanity, has a main message of peace and friendship,". Wait...what? So this is the happy drone of sharing and friendship? What about that whole 'ambassador of death', was that just a joke? I really don't know how else to say how sad this is. There just are not proper words for this level of fail.

So those are the latest threats coming out of Iran. This is the best Iran has to offer. In all honesty, if I was an American fighter pilot or controlled a UCAV (Unmanned Combat Aerial Vehicle), I would almost feel bad if I ever had to go toe to toe with these feats of Iranian ingenuity. I would imagine it would have the same feeling as pushing over the little kid who just really wants to play with the big kids. You could do it quite easily but you would feel horrible afterward.
Facebook Digg Stumble Delicious Twitter Reddit Technorati

Friday, August 13, 2010

Conservapeida.

Conservapedia: where rational thought, skeptical inquiry and general sentience goes to die. The land of tinfoil hats, martyrdom envy, and where batshit insanity is the preferred standard.

Come and prostrate yourself on one of our many crosses for your amusement, now in children's sizes! Do you find thinking for yourself or forming rational coherent sentences far too difficult for your underdeveloped and religion addled brain? Then stop by one of our many retailers for pre-packaged life choices and modes of thinking, one size fits all!

Afraid of life's many mysteries and complex questions? With our new and improved 'godidit' super-deluxe package, all your fears and concerns can be assuaged in single motion. Never have to think or say anything again!

Now open: Kids Corner! Where you can drop off your annoying children with their ever present questions so that you may continue your mindless and loveless existence free of the possibility of taking responsibility for anything! Here your precious spawn will have every last bit of curiosity and creativity wiped and replaced with mindless genuflections, pre-programmed responses, and a deep seated terror of everything good in the world, just like you! Act now and get a free 'if it feels good, you will burn in hell forever' kids coloring and activity book!

So next time you have one of those horrible things known as independent thought creep up in your mind, stop by and have people tell you exactly what you want to hear so that you can, once again, go back to your mindless existence as God's good little sheep. Remember only God loves you...unless you screw up then you will burn forever! Have a pleasant day.
Facebook Digg Stumble Delicious Twitter Reddit Technorati

Wednesday, August 4, 2010

Sanity starts to return to California

That little bit of idiocy known as 'Proposition 8' in California has been over turned. Sorry Mormons, looks like you went and spent all those millions to sway voters to enact Prop. 8 for nothing. Just like with that whole racist thing you went through quite a few years back, it looks like, once again, the courts have moved in and stomped on all your discriminatory fun.

But the religious 'right' did their best to try and fight this...wait...no they didn't. They were so sure that they were going to win they only had two witnesses. You know, for once, I'm actually glad that fundy conservatives are idiots, it made granting basic freedoms that much easier.

Now, unfortunantly, this isn't a dead win. Those with small minds and large mouths are already appealing the decision. So the judge has held off on enacting equal marriage in the state until the hearings are over. While I would like for things to start as soon as possible, I can see the logic in this. By doing this, he shows that he isn't an 'activist' judge (whatever the hell they are anyway) as well as preventing and dashed hopes in case things go badly during the appeal process. Though, at this point, I think there is very little reason to suspect that this will occur.

The way that this discriminatory law was overturned was simply brilliant. Instead of trying to argue that same-sex marriage should be allowed, they put forth that by denying same-sex couples the ability to marry, the state effectively was upholding negative stereotypes and discrimination for which there is no evidence to support. And this is exactly what such laws do. They make it ok to make a certain group of people second class citizens. Something that flies right in the face of the 14th Amendment to the Constitution (The 14th Amendment, infuriating bigots since 1868).

One can only hope that this will be the turning point leading to equal marriage laws being passed in other states that used similar arguments. This sets precedent and that was one of the biggest things holding back such laws. Part of me actually hopes the angry peons defending the 'sanctity' of marriage push this to the supreme court only to have the ruling upheld and turning a state concept into a national one. Now wouldn't that be a bit of wonderful irony?
Facebook Digg Stumble Delicious Twitter Reddit Technorati