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A Brief (and probably wrong) intro into the influenza virus

Ok so this deserves some quick context. Basically I was reading through The Verge and I made the mistake of clicking on a medicine related article. I say mistakenly because all things medical science related has been my life these past few years and most things published is more often than not misinterpreted and makes me a little angry at the journalists involved. This time, however, I didn't get angry at the journalist but actually someone in the comments complaining about what a waste of money it is to invest in research of the influenza virus when there's more important viruses out there like HIV and the common cold.

So yea, this made me angry and so I channelled that anger into the following explanation that I doubt anyone will ever read:

I’m not really understanding where you’re coming from. The common flu is caused by the viruses from what is essentially the ‘influenza’ family and hence any research on the strains mentioned above could potentially hold benefits for this ‘common flu’. In fact all antiviral research is beneficial in terms of treating disease.

The hard thing about influenza (and by extension Acquired ImmunoDeficiency Syndrome, ie AIDScaused by you guessed it another virus called aptly the Human immunodeficiency virus) is that they’re RNA viruses.

I’m going to give anyone who wants to read a little intro into virology here and I’ll try and simplify it as much as I can to make it easier on y’all.

This means that the virus attaches to a host (or animal) and injects its own RNA into a host (or animal) cell. Normally in our bodies DNA is converted (without loss of the original DNA and hence we call this step transcription) to RNA and RNA is then translated into chains of amino acids which then to put it simply combine into proteins. Notice here that there are two steps where the same information is essentially being copied. That is the information from DNA is being ‘copied’ toRNA and again RNA is being ‘copied’ into proteins. The things doing the DNA>RNA conversion are what we call transcription enzymes and the RNA>Protein conversion is done mostly by ribosomes and I’ll refer to them and those that do similar duties as being ‘converter’ proteins to try and limit confusion.

We’re now going to side step a bit into genetics and mutations and cancers!

These ‘converter’ proteins then spend their days doing thousands if not millions of these conversions in our cells continuously and so naturally there will be mistakes made. These mistakes are what is colloquially referred to as mutations and viable mutations, that is mutations from which the cell can still survive, cause benign cancers. And if this mutation is replicated as that cell divides and then again as that cell divides and again and again etc. then we get problems. We start to develop lumps or spots and then we see it visibly and go to the doctors. The worry at this point is then of the cancer spreading to more important bits of the body (if it isn’t already at an important bit…) and they spread by what’s called metastasising, or breaking through into the host blood circulation and consequently resulting in cancers every which place.

I’ve digressed a bit but the point I wanted to make is simply that mutation is natural but our body has some safeguards in place. Our ‘workers’ (these are the conversion proteins in case you forgot) have some ‘proofreading’ in build in them and can tell if they’ve made a problem a lot of the time. Things which inhibit this function of theirs or can somehow circumvent it by say inducing mutations via chemical reactions (like UV light which can change the shape of DNA to put it simply) are what we call carcinogens.

Back to these RNA viruses. After they have injected their RNA into the host cells the RNAmust first be converted to DNA for the host cell to ‘force’ the host cell into using it. Now as I’ve kinda explained beforehand RNA is meant to go towards proteins and it doesn’t normally go back to DNA and so the virus brings with it a special protein that does this job. The important thing to notice with this protein is that there is no proofreading ability and if it makes a mistake it just keeps on chugging along and no one will know any better. Now to put this fact into perspective, if you were ‘knockout’ the proofreading ability in your ‘converter’ proteins, then you would rapidly develop cancers and to put it bluntly die. Very early in life. But there’s only one of you. There’s hundreds and thousands, millions even, of virus cells that could have infected you. So what if one of them dies, another will survive. Natural selection then on a massive scale will occur in your body where the fittest virus cells will survive and spread.

With influenza the main mode of spread is through aerosol particles as the infected person sneezes or coughs and the infectious dose (smallest number of virus/bacteria etc. needed to infect a person) could be quite low and even be single digits. For the sake of story and a nice logical progression I’m going to make a stupid statement (which is a little true but definately not the whole story) and say that the lower the infectious dose then means that the virus would probably be good at sticking to the host cells.

This is where things get more complicated. The proteins that the influenza virus uses to ‘stick’ to host cells and insert it’s RNA are different from what HIV uses. Influenza uses the haemagglutinin and neuraminidase (H and N respectively of the H1N1,H5N1 etc. nomeclature where the numbers represent different strains of H and N). HIV’s a different beast altogether and I’ll stop speaking about that… Anyway these H’s and N’s are the important bits as they can determine how well the virus will transmit and infect people. H1N1 or swine flu was all the rage because it could transmit and infect people really well! It was, however, a bit sensationalised as it had a low virility and hence didn’t really do much damage.

The virility or simply ‘killing ability’ of the influenza virus depends on the animal it’s in. The swine flue for instance is found in pigs and pigs can display no symptoms at all, you wouldn’t even know it’s infected. The swine flu in humans though results in the usual runny nose, sneezing, coughing and general bad feeling. How did the swine flu jump from pigs to humans?! Well to put it simply it mutated. A pig could have had the usual H1N1 virus that naturally likes to inhabit them (a ‘natural reservoir’ if you will), but then it could also have in it a H250N20 (picked random numbers out of a hat) which presents itself in pigs as a flu. Now if this H250N20 virus infects a cell that has already been infected by H1N1 then these two viruses could combine. When the RNA of the virus is converted into DNA in the host cell theDNA then combines into the host’s DNA. This is a pretty shitty process and doesn’t happen most of the time but all it needs to work is some similar bits of DNA in both the host and virus created DNA. If two strains of virus are in the one cell then you can see that it’s possible for thw two to combine in the host’s DNA.

Now let’s continue this made up scenario and say that there’s now a new virus called H250N1 now present in the pig due to this recombination event. But the thing about H250 is that it attaches really well to human cells! If the pig then got some snot on the vet that went to check it, and the vet then went on to sneeze on the hand he’ll use to give 2 dollars to the person at the cash register etc. You can see then how easily the virus will spread.

H5N1’s natural reservior is the bird (hence bird flu) and luckily we things that the virus likes attaching to in birds is not really found in us humans but after enough random mutations it can which is why you can see the sporadic cases popping up. The major problem comes when you get overlap in ‘likeable’ attachment areas between animals. For example the H5N1 virus might like things about bird cells which happen to be in pig cells, but then H1N1 naturally resides in pig cells AND also likes humans. Uh oh.

So to bring it all back, mutating H5N1 in the direction of being likeable in humans is definately a viable terrorist threat (but could never be used as a bioweapon by any particular country because it’s just uncontrollable and there woudl be no way to stop the damage from splashing back) but it is also something that will happen naturally and there it’s not a case of ‘if’ it will happen but ‘when’. So hope that we do it first in a controllable manner and find a vaccine.

PS The important thing about science is to never accept anything for fact unless it’s been backed up by some evidence. Notice how I haven’t included any sources? I could have just made up all of this and taken you for a ride! I’d encourage you to read a bit about it yourself, and in this age of information, you pretty much have no excuse not to :P


Rage and I simply do not mix....

So I just bought myself an S27A950 monitor and I have to say it looks pretty amazing.

Unfortunately I'd just uninstalled all graphics intensive games so I couldn't really see all it had to offer aside from Uncharted 2 and watching Dark Knight on bluray (if you haven't seen the IMAX shots on an awesome screen the you are missing out on something huge!). I cleared up some space on my PC in time for Rage. This is pretty much where shit hits the fan for me. I install Rage, read around to see what drivers I should try with my AMD5770, install those (11.10 preview 2) and then boot up Rage. Lo and behold what greets me is pretty much the worst fuck up a game has ever done on me. First it started off as being the barest of textures, think Deus Ex but full bodied and well rounded instead of the sharp polygon edges. I try and run around but but as soon as I get out of the first room/spaceship or whatever shit just turns grey and things are barely distinguishable. I get the hell out of the game pretty quickly after that and spend the next few hours trying to get the game to run. Eventually I try using some older drivers, thinking hey it worked for some people it might work for me. I was wrong. So I give up and head to bed.

The next day after I get back from uni I jump on again and try to fix it. I used driversweeper to get rid of all my graphics card drivers, unfortunately this seriously messed with my computer so I had to system restore that.... I try reinstalling the 11.10 preview drivers tweak the Catalyst Control Centre a bit and see how that goes. It progressed! But ultimately failed. Instead of plain boring textures appearing before my eyes I see a twisted Picasso collage of shit. Once again I hastily leave the world of Rage, on the computer at least.

I delve a bit deeper in to the forums and try out using the console as some people have suggested to load their custom made configuration files. I tried this a bunch of times with next to no progress. Sometimes I'd see the plain textures and sometimes I'd see the collage. At this point I'd almost given up but I thought that I may as well give it one more try. I clean my computer of anything AMD related, although this time not so swiftly and haphazard as with driversweeper. I then reinstall the preview drivers for Rage, turn everything to their lowest setting and BAM. It works.

I run a few more tweaks using what people suggested in the Steam forums. But frankly the game ran with about the same elegance as the old guy at the end of A Space Odyssey. That is not only was it tripping out and slow but I had no fucking idea why. I'd used all the launch options people told me to use. The game was on the lowest settings possible. It looked like shit with textures constantly popping in. The framerate would drop consistently whenever more that two people decided that I needed to die.

I think at this point I should say my computer is not shit. It's probably mid-end right now and consists of an i5-750, 4gb ram and the aforementioned 5770 running on 32bit Win7. It's more than enough to run any recent game....and yet that list doesn't include Rage.

At this point having spent around 10 hours trying to make the game work all I've managed to really do is develop an overwhelming hate for everyone at iD. Reading recent interviews and things I can't help but feel extremely frustrated over the fact that the game they made just did not want to run on my computer. Is it something they have against me as a person? If so why? You're hurting me far more than From Software ever has. At least they have a sick sense of humour when they send me off to die. I'm no developer, nor do I have any idea what goes on when developing games, but it's hard and I mean really hard to see how they managed to overlook such a flaw in their game. You can't just blame it on drivers being optimised for Battlefield because then the game should really have worked using drivers from months ago... I still don't understand how so many people could be bitching about the Battlefield 3 beta being so much like a beta, and yet there's a few articles here and there about this flaw that is so far inherent in Rage...

So yea, if you're still thinking about Rage and you have an AMD card, then I hope you have the luck you will most certainly need.

For me that's about as far as my Rage adventure will get and to put it bluntly, fuck it I'm gonna play Dark Souls.