Saturday, October 28

Apparently Fame was the song at No. 1 when I was born. It has been noted by someone that if you read the lyrics in a certain light, they appear to bear some resemblance to who I am (or will be). I think it's all pretty funny.

7:35 PM | permalink | discuss

Sorry for the lack of updates recently, but I've been spending a bit of time overhauling and adding content to the new, spiffy-looking Generation Mars website (large parts of which now unfortunately look better than this weblog). I have an ambitious secondary goal for Generation Mars (apart from the obvious educational/publicity side) - to create a vibrant, self-sustaining Mars and space-advocacy community that actually does something.

The thing with the Mars Society's major projects (i.e. the Arctic Research Station) is that they only involve a miniscule proportion of the near 4000 members we have now; probably at least 90% of the members don't actually do anything in between conventions. So what can they do?

The party line is that there are many things they can do; they can give talks, they can approach government representatives and so on. The thing is, is that this not only requires a surprisingly large investment of time (and courage), but it's just not really suitable for many people. I would think that most members wouldn't be comfortable in front of an audience of any size, talking about Mars. And if they were, as I've said, it is difficult to set these things up.

How does Generation Mars help? It puts things into context; it helps people latch on to a tangible project and work within it. It provides a framework. When the competition launches, people will be able to look at the posters and news articles and say - hey, I can actually help out with this. Instead of approaching a school out of the blue, asking to give a talk, they'll be able to say 'You know that Generation Mars competition that we sent a info pack to you about? How would you like an official representative to give a talk?'

I also have very high hopes for the messageboard that's being set up in the website (online next week); ever since the death of the Mars Society webboards, the community has never really felt the same.

But perhaps the most original thing about Generation Mars is that it will be open. If you've got a good idea and people support it, then it'll be implemented. If you make a valid criticism, then the person responsible will be held accountable. No good ideas will go to waste.

Yes, I have considered the fact that I am highly idealistic and have far too much faith in human nature, but you've got to give people a chance, at least.

Obligatory blogger community comment of the month: Unbelieveable though it may be, I will finally be showing my face at a UK blogger event this Friday - the elusive Adrian Hon himself. Although to be honest, the only reason I couldn't come to the other events is because they were either too far away, or I had lectures. I'm quite looking forward to meeting the faces behind the weblogs (and I do read them, it's just that I never mention them here).

7:23 PM | permalink | discuss

Thursday, October 26

Some snippets from today's Times newspaper:

Keep astronauts on the ISS happy: send up psychiatrists and surprise gifts.

An interesting take on the situation of dot-com companies in California. For example, Cisco Systems is a Bay Area firm with just 34,000 employees which supplies some of the networking equipment that shoots electronic signals around the Internet. Its stockmarket value is $400 billion, even after the recent declines in technology shares. This is more than the combined value of all the world’s car companies, steelmakers, aluminium companies and aircraft manufacturers.

I quite like The Times' new web design, in that it doesn't look competely hideous any more. Could do with being sped up a little, but can you really complain when they're putting an entire newspaper onto the Internet for free?

3:00 PM | permalink | discuss

Wednesday, October 25

There's something almost seductive about popcorn; despite, objectively, not tasting that amazing, it retains the addictiveness of take-away food laden with MSG. I seriously considered bringing my fairly large popcorn maker to Cambridge but then balefully decided that it would take up too much space in the car. Since then, I've been seen to prowl around the various stores in Cambridge looking for good popcorn machines. And here it is.

Coincidentally, the day on which I bought the popcorn machine was also a DVD night at a friend's house and so it received its inaugural corn-popping. It's all very simple, you just get your corn, toss a bit of it into the compartment in the middle and switch it on. We first put it in my friend's bedroom, thinking that such a small machine couldn't really do any harm, and placed a bowl underneath it to capture all the popcorn. After a minute or two, small bits of popped corn started sailing out of the machine to land neatly in the bowl, and we were extremely pleased. Within the space of ten seconds, the popcorn machine started firing popcorn at an ever-increasing velocity so that it'd bounce off the bowl and fly across the room. It was incredible, popcorn flying everywhere and both of us trying frantically to switch it off.

After it was switched off, we surveyed the damage. The room looked like some kind of war-zone, with random pieces of popcorn over the floor and floating forlornly in half-drunk cups of coffee several metres away (this gave us the idea of using the popcorn machine as some kind of weapon).

So the moral of the story is: If you buy a Prima Popcorn Maker, make sure that you take the appropriate precautions before turning it on, i.e. constructing a shield encircling the machine so that no high-velocity popcorn particles can escape.

And yes, the popcorn did indeed taste mighty good.

4:59 PM | permalink | discuss

I have to confess that I am absolutely amazed by the novels available at Bookface.com now. A couple of months ago there were only mostly second-rate books or short stories with the occasional gem scattered here and there. Now, for some bizarre reason, you can read the entirety of Moonbase and Moonwar by Ben Bova (very fun books to read) and Eon by Greg Bear. Clearly Bookface must be making money now. I believe that the Yanks can also read one of the latest SF short story anthology by Gardner Dozois as well as the Neutronium Alchemist by Peter F Hamilton (Brits can't read them due to publishing rights).

Not, of course, that I'd bother reading the books on computer anyway unless I was really bored or strapped for cash, since I'd rather read the physical book. But it's still a great idea and they have catapulted themselves into my list of favourite sites.

There are many unfortunate stories about kids drinking orange-coloured and appetizing-looking bottles of antifreeze and then consequently dying, most of which are true. This will form the basis of Today's Biology Factoid, and also ties in to the alcohol story I made a couple of days back.

Antifreeze contains substances such as methanol and ethylene glycol. The body treats the latter substance just like it treats ethanol, the primary substance in alcohol; it uses the enzyme acetaldehyde dehydrogenase to break it down. What are enzymes and how do they work? Enzymes are biological catalysts - they speed up reactions. They do this because they have a part of their structure called an active site that twists and bends bonds in the substrate molecule (the thing they're working on) until it breaks apart or joins together with something else. So in order to acetaldehyde dehydrogenase to break down something, it needs to latch onto it using its active site.

So if you consume ethylene glycol, then your acetaldehyde dehydrogenase enzyme will think - 'Huh, that looks a bit like ethanol, but not identical... ah, who cares, I'll just break it apart like normal.' And it does, but unfortunately one of the products of this breakdown is oxalic acid. Oxalic acid forms crystals in our cells, which is a Bad Thing because these crystals tend to break apart cell membranes and generally disrupt the whole of the cell's operations.

So, let's say that little Timmy has espied a bottle of antifreeze and guzzled down a pint. Right now, his acetaldehyde dehydrogenase enzymes are unknowingly breaking apart the ethylene glycol and producing poison. Thus, you see Timmy hanging around looking very unhappy and think - 'Shit, I never should leave interesting bottles of antifreeze lying around the place in the kitchen.' And since he's drunk your antifreeze, and it's the middle of winter and freezing cold, you can't get your car to work and an ambulance can't get to your house in time.

What do you do? Well, remember that the acetaldehyde dehydrogenase enzyme is primarily structured to work on ethanol. If you go and flood the body's liver cells with ethanol, then the enzymes will work on that and leave the nasty ethylene glycol alone. Why? Because if you have (say) ten times as many molecules of ethanol than ethylene glycol, obviously more ethanol will be broken down than ethylene glycol. Which is a Good Thing. Coupled together with the fact that the ethanol molecule 'fits' into the acetaldehyde dehydrogenase enzyme active site better means that ethanol can easily 'outcompete' ethylene glycol to be broken down.

So, exactly what do you do? If Timmy has drunk a pint of antifreeze, then roughly five shots of whisky should be enough to save him. Incredible, no? And thus Timmy emerges out of the entire situation relatively unscathed and only a mild addiction to strong spirits to show for it.

1:37 PM | permalink | discuss

Tuesday, October 24

Interesting scene today: There was a BBC camera crew skulking outside King's College on my way to 'Goddamn QB' (Quantitative Biology is always preceded by some sort of expletive by all of those who attend it), preying on innocent students with questions about what Parliament did concerning various things. Well, not really a camera crew, but one guy mooching around with a professional digital camera and another guy in a suit holding a boom mic.

In keeping with my new daily instalments of biology, here's a great piece about how you'd go about identifying proteins if you've only got very small samples (thanks Jo!):

In the distant future, Jo is a molecular biologist working in a lab for the space agency and some astronauts find cells on Europa which they bring back in a bucket.

Astronaut: "Hey you're gonna love this! We got alien cells!"

Jo: *quails* "What, *Alien* cells? Oh, right, I see. Why are they in a bucket?"

Astronaut: "Well, we didn't know what to do with them, or how to grow them, and we could only find some. Plus the flight commander ate some by accident 'cos they look like the mushy peas...anyway, here's what we got. In the bucket."

Jo (suspicious): "They look dead."

Astronaut: "Well they were fine sixth months ago when we left and nobody's touched them since so...."

Jo: *groan* "Let me analyse what's left a minute....." Does a quick bit of chromatography and stuff on the alien cells. "There's no nucleic acid left. All I've got is a soup of lousy proteins, and not much at that. You go all the way to Europa and you give me *this*?!"

Astronaut: "Well....er..you can do something right?"

Jo: "Yes, but I'd wish you'd got me some DNA. Okay, first of all, I'm going to take a small sample of this and run 2 dimensional gel electrophoresis. This is capable of separating over a 1000 different proteins on the same gel, and gives an indication of their relative abundance." Jo does this, and in a perfect world it actually works. It works firstly by separation in charge differences alone, and then by
separation in size after rotating the gel the other way round.

Astronaut: "Wow, you have 100s there!"

Jo: "I know". *sighs*

Astronaut: "Now what?"

Jo: "Well, let's take one protein here as an example. Let's take this one because it's a rare one and Rich [for the purposes of this story, Rich is the evil overlord of the space agency] wants to make my life difficult. I want to know it's sequence, so the first thing I do is use some proteolytic enzymes. These will break the protein down into peptide chains, giving convenient chunks to work with. I can separate these by chromatography to give me an idea of their size too."

[Editor's note: Proteins are made up of building blocks called amino acids. Sequences of amino acids longer than, say, 50, are called polypeptides. Shorter sequences are called peptides.]

Astronaut: "Then what?"

Jo: "Then I can sequence the amino acids that make up the peptide chain by using a clever sequence of reactions, that are now done in an automated amino sequencer machine. What this does is, a weak acid is used to bind to the first amino acid at one end of the chain, on the amino group that is exposed because it's not stuck to another amino acid at one end. The reaction can split the amino acid off the end of the peptide chain. Viola, I have one amino acid, which is then identified by chromatography. This reaction is re-iterated 1000s of times until I have all the amino acids.

And even though you gave me a shitty sample, it works with only a few micrograms of protein. I can repeat the whole thing by breaking the chain down using other proteolytic enzymes and then finding out the amino acids in the different-length peptide chains, which will enable me to piece out their order on their chain. Hey presto one ordered amino acid sequence for one protein. Alternatively, I could get home at a reasonable hour by cheating. Once I'd sequenced about 20 amino acids, I could just not bother with the rest, and instead make a DNA probe. I'd then probe a whole cell with this, see what bit it labelled (usually visualise with radioactivity bound to the probe) then simply clone and sequence that bit of DNA. Once I have the DNA sequence, it's easy-peasy for me to deduce the protein sequence. I can then do it all again for every other protein. Asshole."

Astronaut: "Wow. What if the coding sequence is different?"

Jo: "I go the long way by sequencing all the amino acids first. Alternatively, I give up the day job. Or, you get me a better sample."

Astronaut: "How do you find out what all the proteins do?"

Jo: "With extreme difficulty and proper samples which I can grow. And complex biochemistry, and genetic knockout mutants, and antibody-labelling and location studies and X-ray crystallography and stuff. Actually, I don't, because there's no way I can do all those things. I'll just give a few genes silly names."

Astronaut: "Could you explain how all those different techniques actually work?"

Jo: "No! Not right now anyway, I have to rescue my restriction enzyme digest and then it's my tea break! Do you want your cells back?"

Astronaut: "Er, no thanks, you can keep them."

Jo: "I do hope you observed all quarantine levels for a foreign organism..."

Astronaut: "Er, I'll be going now then". [turns and falls down dead].

Jo is actually a third-year biologist in Cambridge - I am only a lowly first-year biologist but one day I will know the vast sums of knowledge that she does and be able to write stuff like this.

Why telling your kids 'That's great' is a bad idea. To be honest, even if someone does deserve a compliment, 'That's great' is disappointingly unimaginative. Which is why you'd do well by buying this book on the history of flattery.

6:06 PM | permalink | discuss

Monday, October 23

It's incredible what you learn here. Using the multifarous (not a word) disciplines of biology that I have learned thus far, I can answer the following question:

Why do I go red in the face after one drink (of alcohol)?

There are in fact three answers, all of which are correct.

Proximate Answer (aka causal, mechanistic, 'how?')

When you drink alcohol, there is a two-step process in which it is broken down. The active component in alcohol, ethanol, is broken down by an enzyme (a biological catalyst) into acetaldehyde. Acetaldehyde still needs to be broken down into sugars and whatnot by the enzyme acetaldehyde dehydrogenase.

Now, the interesting thing is that there are two types acetaldehyde dehydrogenase enzymes present in the human liver (which is where all of this is taking place). One of them is present in the cytoplasm (the 'goo') of the liver cells, and one is present within the mitochondria (the 'power plants'). There is a difference between the two types. The enzyme in the mitochondria has a low Km value whereas the enzyme in the cytoplasm has a high Km value.

What is Km? Well, now we have to go into enzyme kinetics. Enzymes essentially work on 'stuff' (the substrate) by binding to it and doing other 'stuff' (breaking bonds, making bonds, etc.) to the aforementioned 'stuff'. If there is a lot of substrate present but a low number of enzymes, then all the enzymes will be working flat out because they need a certain amount of time to catalyse each reaction. So, with more substrate present, the enzymes will be working faster (they will have a higher velocity) than if there was less substrate - simply because if there's more, then it will take the enzyme a shorter amount of time to bump into a new bit of substrate to work on. But obviously when you have loads of substrate - an infinite amount - then the enzyme will be working at its maximum velocity and it won't be able to go any faster.

The Km value of an enzyme is the amount (concentration, really) of substrate that is required for the enzyme to be working at half its maximum velocity. So if an enzyme has a high Km value, then it needs a lot of substrate to get working fast. If it has a low Km value, it needs less substrate.

Therefore, the enzyme in the mitochodria, with a low Km needs less acetaldehyde, and thus less ethanol, to get working fast and breaking it apart. The enzyme in the cytoplasm has a high Km, so it needs more acetaldehyde to get working fast.

In other words, people with the type of acetaldehyde dehydrogenase enzyme in the mitochondria can break down alcohol than people with the enzyme in the cytoplasm. And you guessed it, asians have the enzyme in the cytoplasm whereas caucasians have the enzyme in the mitochondria. It makes perfect sense...

Ultimate Answer (aka functional, adaptive value, 'why?')

But exactly why do I (and other asians) have the cytoplasmic enzyme instead of the mitochondrial enzyme? Well, I don't know for sure, but there is a nice evolutionary story behind this which is probably not true. In Asia, people boiled water before drinking it so that it'd be clean. In Europe, people didn't bother doing this and drank beer instead, so essentially Europeans drank more alcohol than Asians. Presumably this exerted a selective pressure on the humans in Europe so that people with the fast, mitochondrial enzyme tended to live longer and have more children than people with the slower cytoplasmic enzyme. Or something like that. Anyway, it's a bit of a dumb story but you see what I mean.

Common Answer (aka dumb answer put forward by so-called friends of Adrian)

Apparently I have a 'low alcohol tolerance' and must build this up by drinking more alcohol. I doubt this has any biological basis (although I'm not sure - perhaps having more ethanol would make the body produce more acetaldehyde dehydrogenase enzymes, I don't know).

I hope you enjoyed all of that because I'm probably going to write more posts like that. Hey - tell your friends - 'visit Vavatch and learn all the biological secrets of the world!'

Anyway. I learned a lot of this at a lecture this morning, after which I went to a Evolution and Behaviour preparation practical. I was feeling rather pleased with my new-found knowledge, which was about the point when I realised that I was wearing my sweater inside-out. Alas, I hadn't noticed before because I had my coat on and there wasn't anything I could do about it at the time since I didn't have a T-shirt on underneath.

12:36 PM | permalink | discuss

Sunday, October 22

I had the opportunity to watch some of my newly bought DVDs last night, and during a viewing of The Rock, an interesting discussion about the film took place [minor spoiler ahead, but it's not as if they give much away].

Early on in the film, we find out that there are 81 hostages held on an island along with a large quantity of nasty biological missiles. Said hostage-takers are demanding a Large Sum of Money for their release. I sincerely believe that the different solutions people find for this problem reflect very well on their personality and mental state. Which doesn't say much for ours, because the conversation went something like this:

"I still think that a tactical nuke is the best way to go."

"Yeah, a backpack nuke would be brilliant. You'd have to get it there, though. How about some Tomahawk cruise missiles?"

"Nah, far too slow, they'd detect them on radar and launch the missiles."

"Well, obviously the only other option is to nuke -"

"- them from orbit? Exactly."


"Now, supposing that the loss of 81 hostages is not a factor in the decision-making process, I would agree that a nuke would be good."

"Yeah. I forgot about them."

"Stupid hostages."

David Brin is always full of interesting ideas about how to change the world. Evidently not satisfied with his excellent book on the virtues of transparency, his newest mission is the Eon Project. The Eon Project would create a 100-page catalogue of projects for philanthropists between $100 million to $50 billion that would endow varying amounts of 'immortality' for their name thereafter. For example, a Mars mission would cost $25 billion, have a 60% chance of success, have little chance of making any money but a 95% chance of bestowing immortality to the benefactor.

Conversely, developing Wind Tunnel and Water Tower technology for desert nations would be much cheaper and have far higher likelihoods of making money and being successful. It would also of course reduce the 'immortality-ness' of the benefactor - chances are that people will remember a Mars mission more than they would a few water towers.

I think the Eon Project is a wonderful idea, but I don't believe that there will be many takers. It's easy enough for Mr. Gates to have a look at the catalogue decide to get his credit card out and pay for a Mars mission, but far more difficult to work out the details.

There used to be a lot of talk in the Mars Society about some heaven (or Mars) sent benefactor with a bulging wallet and a starry-eyed visage to donate a few billion towards the cause. While we have had a few million thrown our way, we haven't had much more than that. And I personally don't believe that a Mars mission could be funded by a benefactor (or group of benefactors) alone. Who would do the mission? NASA? I don't think so. They're not a company, they're a government institution and they have other (so-called) work to do. Besides, do you really think that the US government would appreciate some yahoo beating them to the punch?

Having said that, there are always Ways and Means of doing things, and a few billion would be bound to have a positive effect. And of course, if there are any billionaire philanthropists reading this page, you know your money would be greatly appreciated...

8:36 PM | permalink | discuss