The blogosphere has been reporting a story via the Associated Press about an experiment performed on a recent space shuttle flight involving Salmonella bacteria. It turns out that during the 12 day flight the bacteria grown in the shuttle mutated to become significantly more virulent than the same strain grown under controlled conditions on earth.

Salmonella grown on board the space shuttle was many times deadlier than its terrestrial counterparts.
Researchers led by Cheryl Nickerson, associate professor at the Arizona State University Biodesign Institute, found that Salmonella grown during space-shuttle mission STS-115 in 2006 underwent major changes in the expression of 167 genes. When administered to mice back on Earth, the bacteria proved many times more deadly than an equivalent strain grown on the ground.
Technology Review

Here’s what happened. The bacteria spent 12 days in space during which time they replicated in an environment radically different[1] to that on earth. An associated effect of the lack of gravity is a reduction in pressure of the fluid passing over the bacteria cells. It is believed that this changed the gene expression[2] of 167 genes(73 proteins) producing a more virulent strain of the bacteria.

yellow and red

The response from the internext has been predictably ludicrous with titles like Spaceflight makes germs deadlier, stronger and Germs In Spaaace! Bugs Deadlier In Study. While they might report the facts correctly I’m ticked off that they misrepresent the implication of this experiment.

Some of the blame for this has to go to the lead researcher, Dr. Cheryl Nickerson[3] quoted as saying ‘These bugs can sense where they are by changes in their environment. The minute they sense a different environment, they change their genetic machinery so they can survive’. Bullshit.
It’s very likely that Dr. Nickerson was simply speaking colloquially, but this statement is totally incorrect. ‘These bugs’ don’t sense shit about changes in their environment and the sure as fuck don’t ‘change their genetic machinery’. What happened here is that the change in the environment meant that, as the bacteria replicated(had kids) and, in the process mutated, child cells that responded well to the low gravity environment were naturally selected as more successful. This was a simple, ordinary example of the process of natural selection causing the phenomenon of evolution. To say that the bacteria looked around and used their temporary environment to make themselves more poisonous is naivefuct.

What is amazing is that the mutation occurred so rapidly. From what I could find it seems that the generation time[4] of salmonella seems to be about 40 minutes under normal conditions. This means that 36 generations were produced per day, 432 generations in total. That’s very few generations in which to produce such a radical change. As always the secret to the speed at which the mutation spread is due to the large number of individuals per generation. Let’s assume the experiment started out with 105 cells[5]. I’m not going to risk the calculation of how many cells they would have ended up with by the end of the 12 days[6] but we’re talking here about a gabazillion cells per generation. And with the radical change in environment it means that those cells with a beneficial mutation(improving their survival rate) would’ve kicked ass and dominated their colonies, thereby setting their offspring up to be even more likely to succeed.
Each new report like this illustrates the incredible rate at which natural selection – the simplest of processes – can produce a solution to an environmental challenge that is wonderfully elegant. No cosmic watchmaker could do this in 12 days[7].

The second thing that the internext is completely misrepresenting about this story is the effect of space on bacteria. Sending bacteria into space does not ‘make it more dangerous’, as if zero gravity equips the little cells with sharper teeth the better to bite us with. The fact that in this particular case the bacteria mutated into a more virulent form says nothing at all about the effect of space on poisonous organisms. All that it says is that in this particular case, in this colony the offspring became progressively more virulent. Of course there is a good likelihood that if they were to send up another batch they would become more virulent again, simply because the environment is so radically different that it would likely favour the same type of mutation.
But this does not mean that all bacteria become more dangerous in space. There is an equally good likelihood that the bacteria would have become less virulent or even completely harmless. Somehow I don’t think that if this were the case it would have made much news. I can see the headlines now ‘Bacteria in space stay exactly the same!’.

Natural selection is a fantastic, elegant and powerful process. It’s effects continually astound us, its solutions to environmental problems are consistently ingenious. There is no need to jazz up its entirely purposeless workings by imagining some form of intent or will to change on the part of its subjects.

[1] near-zero gravity
[2] the process by which inheritable genetic information is turned into a physical product such as a protein.
[3] who appears to have first published research on microgravity’s effect on bacteria way back in November 2002
[4] The time required for a bacterial cell to divide
[5] From what I’ve found this seems to be the ballpark number of cells per mm2 in your average, healthy salmonella colony.
[6] Given the attrition rate, space constraints etc.
[7] And let’s not talk about what’s possible in 6 days of intelligent design.

While I put the finishing touches on my Facebook rant I thought that some good news might be fun.
I’m always surprised when people comment on how elegant the idea of natural selection is when applied to man-made items (such as in this story) but that they remain uncomfortable with the idea that the same process created the massive complexity that we see around us, including them. Here is a very worthwhile article on natural selection as applied to computer hardware[1].

Dr. Thompson dabbled with computer circuits in order to determine whether survival-of-the-fittest principles might provide hints for improved microchip designs.[...]
[When he] peered inside his perfect offspring to gain insight into its methods, what he found was baffling. The plucky chip was utilizing only thirty-seven of its one hundred logic gates, and most of them were arranged in a curious collection of feedback loops.[...]
Five individual logic cells were functionally disconnected from the rest– with no pathways that would allow them to influence the output– yet when the researcher disabled any one of them the chip lost its ability to [function as required].

The fact that the naturally selected winner used a design which was not only completely foreign to what a human would have created, but also simply could not work on paper shows one of the most elegant aspects of natural selection. Its utter simplicity(the best ones are replicated) produces solutions beyond our wildest dreams.

The more time I spend writing software[2] the more convinced I am that natural selection provides an answer to every evolutionary question and requirement.

Hooray for simplicity. God may not do so, but natural selection certainly does shoot craps.

Wanna dice?

[1] ignore the crappy images – the text makes up for it
[2] which basically involves glueing small blocks into bigger blocks into bigger blocks into bigger blocks

Prozac celebrated(!) its 20th birthday recently. The world’s first[1] superstar drug arrived on the golden shores of our minds in 1987 – the year Bon Jovi made it big with Livin’ on Prayer. I can’t think of a better companion piece[2].

P-zac

In 2001 Prozac alone brought in $2.7 billion for Eli Lily & Co. The mega success of this drug and successor blockbusters allowed big pharma to go from geek-street types who marketed to doctors with paperweights and golf umbrellas to hight street lifestyle vendors who market to consumers directly on prime time television. And the transition has been telling. Eli Lily no longer bother developing drugs that they do not believe will realise at least $500 million in annual sales.
The following is from BusinessWeek in 2001 (which also contains the above figures)

Says Mara Goldstein, an analyst with CIBC World Markets: “Sometimes products look good on paper, but they don’t turn out that way in reality.” In 1998, for instance, the company launched Evista–which can prevent and reverse osteoporosis in older women–in the hopes that it would become an overnight success. But first-year sales came to a less-than-spectacular $144 million. Why? Taurel says it was harder than expected to convince women to buy the drug before they have symptoms of the degenerative bone disease. But after Lilly tweaked its marketing effort, the drug took off, with sales expected to top $700 million this year. It is a blockbuster after all.

Prozac changed the game on better living through chemistry. Medication has become a personal choice and we are embracing its promise to bathe our neurons and genitals in a soft golden light.
I myself have a chronic prescription for a mood stabilizer – Lamictogrine, marketed as Lamictin in South Africa. The dose that I’ve been prescribed (50mg) is apparently just about the threshold dose(placebo?) – but my life is better through chemistry. In my case I don’t feel dependant on it for my ability to function – but I am concerned that I’m becoming fearful of not having it. What if something happens? In some small way I’ve become afraid of being scared of my brain without its medication.
But that’s a topic for a different post. This is about the evolution of big pharmaceutical companies into lifestyle giants and their bitches, pharma-ho’ doctors.

classic Adbusters

The Guardian has a look at 20 years of happiness in Eternal Sunshine. From this article there is one paragraph in particular that blew my mind

Enter liquid Prozac in peppermint flavour. In the US, a survey of drug companies found that between 1995 and 1999, use of Prozac-like drugs for children aged seven to 12 increased by 151 per cent, and in those aged under six by 580 per cent. In 2004, children aged five and under were America’s fastest-growing segment of the non-adult population using antidepressants. ‘Selective mutism’ (fear of speaking in social situations) is one affliction common in preschoolers and has been treated with Prozac.

Peppermint Prozac – could it be any simpler[3]?

But of course I shouldn’t be surprised in the least at Peppermint Prozac. Jonathan Franzen sees the truth in The Corrections

Golden sunlight fell across the blankets in her windowless room.

[1] That other pharma-juggernaut, Viagra, only became available in 1998.
[2] Except, of course, for Van Halen’s Jump! But that was 1984.
[3] It’s also available in chewable tablet form for that on-the-go bliss.

Time flies when you’re having fun.
Or just when the world is swallowing you whole.

I’m fascinated by the brain[1]; its origin, its work and its deterioration.
More than anything I’m fascinated by its ability[2] to observe itself.
Right now I’m observing a phenomenon related to the plasticity of time in the brain; I’m madly accelerating towards each year’s end.
It’s almost May, soon it will be July and then it will be October – each year accelerates.

July will be October -

It turns out that this sense of acceleration that overwhelms me is very real.

The brain has two distinct time keeping modes: a Circadian rhythm (aka the body clock) and a momentary perception of time passing.
From what I’ve read, these are intertwined and are both controlled by the Suprachiasmatic nucleus. However, they function separately.
The body’s circadian rhythm is relatively fixed[3], but it seems that our perception of time and the real time in which our senses operate is changeable.
The Suprachiasmatic nucleus controls these independently, separating our body’s concept of time, from that of our conscious mind.

Research is showing that a variety of factors influence the functioning of this tiny instrument to the extent where time really, physically, perceptually speeds up.The most common such influence is age[4].
My grandparents have many times mentioned that the days pass really quickly, even though they are retired and spend all of them sitting in different chairs humming to themselves.
Remember how long a school term was in primary school? A week took fucking forever to pass, never mind an entire term!
Your Suprachiasmatic nucleus is accelerating. The world really is moving faster.

Acceleration -

Here’s a fascinating experiment that shows the real plasticity of not only our perception of time, but of the rate of our brains’ internal clocks.

Psychologist Dr David Eagleman, [...] asked volunteer Jesse Kallus to perform a terrifying backwards free-fall of 33 metres.
If the [theory was] correct, Jesse’s perception of time would be slowed by the terrifying experience.[...]
Dr Eagleman came up with a cunning device: the “perceptual chronometer”, a wristwatch-like device which flicked blindingly fast between two LED screens.
Normally the flicker would be so fast Jesse could only see a blur. But if time slowed down for him, he might be able to discern the two different screens and read a random number on one of them.
All Jesse had to do was jump, and read. As he ascended the 33ft metal cage no-one seemed to believe this curious experiment might work.
When Jesse landed, he noted he had seen “98″. [...] In fact the number was 96. Not quite spot-on, but the two numbers look very similar on a digital screen.
Further jumps got similar results – all suggesting that time did seem to slow down for Jesse during the jump.

Whether or not the science of this experiment is sound, we cannot deny the evolutionary imperitive for this in the brain.
When we are not under threat and simply need to operate efficiently under rote conditions (performing a repetitive piece of work, walking far etc.) the brain can safely speed up time, thereby reducing the energy that it consumes in processing events in real time.
But when reaction time is crucial (e.g. in dangerous situations) the brain’s clock speeds up, processing more information, consuming more energy, slowing down time.

Of course, none of this helps me to catch a hold of the days that zoom past the foot of our bed.

[1] Not just the human brain. Sure, it is the most complex we know of, but even the common house fly’s brain is radical. The house fly’s optimised neural wiring gives it a reaction time of one 50th of a second, twelve times faster than a human’s.
[2] At least in humans
[3] Michel Siffre spent 2 months in a cave in 1962 foregoing any means of telling time – his circadian rhythm remained relatively in tact, but his ability to measure the passing of time (guessing what time it was) was totally lost.
[4] There are numerous scholarly articles on this topic – but they don’t make for good reading so I won’t cite any.

Over the last month or so I’ve been building up to the most important races of the running season[1].
Part of this is this weekend’s Kloofnek Classic 21Km which has one of the toughest routes in Cape Town.

I’ve for some time now been using a small selection of mineral supplements aimed at sports-type use. Some of them have worked, others not so much.
But I’ve recently come to terms with the fact that I need to look into Creatine.
I don’t like Creatine, or rather, I don’t like the whole culture that comes with Creatine. Crew-cut sales assistents that pound the Dis-Chem pharmacy ailes in crazy-tight shirts that say ‘Get Hard… or go home!‘.
I particularly dislike the USN brand with its mega-tubs of power whey whatever and multi-coloured ultra-max phedra-cut tablets[2].
However, Creatine is a naturally produced by the body and is a legitimate(crucial) part of the standard muscular metabolic cycle.
So despite not really being into the whole Better Living Through Chemistry thing[3] I decided to brave the muscle-bound commission earners and get me some of the good stuff.

Here is some of what USN tried to sell me.

• Phedra-Cut XT
• Protein Plex
• Cytopower SF
• Mega Anabolic Stack
• Dynamic EnerG

Damn! Just looking through the tubs of stuff featuring bronzed muscle temple and foil-embossed labels made me feel all mega-powerful and ripped! Whoo-whee! That’s damn hot!

USN Product Bonanza!

In the end, after comparing a bunch of basic Creatine Monohydrate products with various compound formulations, I settled on a USN product – CreatineX4. Yeah!
It is an Ethyl Ester form of the acid, which makes it fat soluble, and features DRT (Dynamic Release Technology supplied by the mega-folks from Calpharm) which is, I guess, what gives it the vaunted X4-ness.
It’s somewhat more expensive than the monohydrate products (around R180 per month), but not nearly in the league of the specialised badass motherfucker Creatine supplements that can clock in at around R600 per month. You should see the rad packaging on those things – the bottle all but has airbrushed flames and 3-D holograms.

USN CreatineX4

The bottle all but promises that if I drop 4 of these a day I will be endowed with ‘lightningquick muscle recovery during workouts’.
So let’s have a look what’s in this bad boy.

Phew! That’s some nasty shit right there!
Well, not quite.
Creatine is creatine and is natural. Glycine is a simple amino acid which is present in most sports supplements. Taurine is like Glycine but with a bit more bite. Beta Alanine is another amino acid, but with less bite. Let’s not even mention Magnesium Chelate which is basically standard Magnesium in an easily absorbable form.
CalPharm Tech Dynamic Release Formula? Hmmm… now we might be on to something.

Joking aside I’ve come to realise(through personal experience) that the efficacy of supplements often has less to do with how many crazy things are crammed in there and more to do with in what form the compounds are and how they relate to one another.
Comparitive to other sports supplements that I’ve used this one’s list is relatively standard, though the milligram contents of each is significantly higher.

I’ve been using it for about a week and a half – and qualitatively I can say that so far I’ve really felt a marked improvement in muscle endurance.
I was expecting a significant amount of the benefit to be deferred to the day after a training session (i.e. muscle recovery) but it’s been my experience that the real benefit has been to my actual training sessions.
I’m actually quite impressed[4] by it.
Now I just need one of those ‘Get hard!’ t-shirts.

MegaRunner EC (Extra Cool)

[1] The Peninsula Half Marathon on 18 February and the big day at the Two Oceans Half Marathon on 7 April.
[2] Not to mention the fact that moronic Mark Pilgrim is their spokesdude.
[3] I lean more towards Having More Fun Through Chemistry
[4] Just as impressed as I was by the much less high-end glamarous Fast Fuel Lactic Buffer – a simple sodium phosphate supplement.