Archive for January, 2014

Doing what the internet does best

Posted in media, rant with tags , , , on 28/01/2014 by sangomasmith

Links and threats of violence, apparently.

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Inevitability Squared

Posted in Crop science, media, Science, screwed by the man with tags , , on 25/01/2014 by sangomasmith

So this puff piece came out in Wired, talking about Monsanto’s ‘new’ approach regarding plant breeding. It’s pretty weak suace: Marker Assisted Breeding is hardly new. Big M does, however, have a very strong pipeline approach which allows them to use these sorts of technology to the fullest. But enough about the details of what is actually happening.  Time to rant!


Reading the comments, I’m loving the outrage from people over teh ebil corporations now moving into breeding – as if that isn’t what they were doing all along (GM just puts a specific gene into an existing breed, folks). I’m sure that, somewhere in the bowels of Greenpeace HQ, they are already contemplating how to whip up luddite sentiment against MAB, or bioinformatics, or whatever it is that big Ag is going to use to do their thing once you’ve pushed through a ban on the other tools in the box. God knows the first thing they will do is paint the whole thing as a sign that they were right all along and GMOs are evil (look, they’re so bad that even Monsanto is going organic!).


This is inevitability squared. It was inevitable that once a bunch of environmental lobbying organisations made it really hard to use genetic engineering for political reasons (LOL @ 10 year field trials, compared to 0 years for ‘traditional’ crops) you would see large companies turn to other methods to generate a profit.

Just as it is inevitable that the same lobbying organisations will now find another thing to rail against once this happens. And, just as existing GMOs get grandfathered in before banning all future research on them (I’m looking at you, Hawaii), so too will the existing hybrids and MAB projects get quietly put into a safe category when we’re all taught to fear targeted mutants or something.

I can’t wait to see what the future brings…

A beer recipe: the Unqombothi-inspired ale

Posted in recipes with tags , , , on 17/01/2014 by sangomasmith

One of the weird advantages of living where I do is that when I wanted to be that guy (there’s always that guy) who brewed his own beer, I had access to the most important ingredients right from my local supermarket. This is because, in South Africa, we still have a strong tradition of home-brewed alcohol: ginger ale, pineapple beer and, most importantly, unqombothi (which is sort of an un-hopped ale).


Now, a lot of folks have hangups about the latter because a) it is a poor/rural person’s drink and b) it’s a bit of an acquired taste (cloudy, foamy, slightly sour and gritty). This isn’t helped by persistent rumours about the terrible things that supposedly go into the brew: shoes, old batteries and the like. Or the horror stories about methanol poisoning and cancer; which, like a lot of things, have grain of truth to them. Be careful when storing grain, kiddies. And never drink anything brewed on somebody’s roof.


What isn’t appreciated is that, for all intents and purposes, unqombothi is the ur-brew; the sort of grain-based thing we called ‘beer’ before the advent of hopping, lagering, clarifying and all the rest. And, as I’ve found out, it doesn’t take much to convert this venerable recipe into something that people who’ve grown up with lagers can appreciate. Even better, brewing this beer (your first, maybe) is a great way to get started in beer brewing in general.


So, without further yarbling, here is a full, explanatory recipe for the easiest (or at least cheapest) all grain beer you’ll ever brew.


The Unqombothi-inspired ale:


Ingredients (mandatory):

  • 1kg Sorghum malt

  • 500g maize grain: pap/maize rice/samp/grits etc.

  • 250g brown sugar/treacle sugar etc.

  • 5-20g hops (herbal hops if nothing else is available)

  • 5-20g Brewer’s yeast

  • Sugar for priming


Ingredients (optional and replacement):

  • Clear gelatine

  • 25g molasses

  • 5-20g extra hops for aroma

  • 1kg Other malts – barley, corn, etc. (replaces sorghum malt)

  • 500g Other grains – roasted barley, rice, etc (replaces maize)

  • 5-20g Baker’s yeast (replaces brewer’s yeast)

  • Suitable herbs (replaces hops)

  • Carbonation drops (replaces priming sugar)


Equipment (mandatory):

  • 5-10 litre brewing tub (a plastic or metal bucket of some sort, preferably with a lid)

  • Sieve or straining cloth

  • Large microwaveable dish or stove pot

  • Microwave or stove

  • Large spoon

  • Bottles


Equipment (optional):

  • Scale

  • Thermometer

  • Mashing tub

  • Oven

  • Fridge

  • Ice or freezer blocks

  • Hose

  • Bleach or other disinfectant

  • Lautering tub (replaces sieve)



  • Mashing

    • Take a suitable container (the lautering tub if you have it, your brewing tin or similar if not) and add in the sorghum malt and maize. Now fill it, as far as is practicable, with a 1:1 mixture of boiling and tap water (max volume of water = 5l)

    • Mix

    • Either cover with cloth or place in oven set at 50-65’C

    • Leave for 2-3 hours

    • Explanation: the mixture (called the mash) will use some of the enzymes in the malt to convert starches into sugars. This means that, as the mashing is going on, your malt and maize are slowly turning into food which yeast can use to make alcohol with. The ideal temperature (60-65’C) just happens to be what you get when you add 1:1 boiling and room-temperature water.


  • Lautering

    • After mashing, strain off the liquid by either squeezing it through the sieve/straining cloth or running it through the lautering tin. Reserve the liquid (now called the wort) in the microwaveable dish or stove pot.

    • Explanation: Lautering is just a synonym for filtering. If you’re wanting to use a lautering tin (which can be as simple as a tub with a small hole cut out of it at the bottom) then all you have to do is dump the mash into it, collect the resulting liquid and pass it a few times through until it’s more or less clear. An extra step is then usually added, where (after collecting the wort) you simply add some more 60-65’C water in to the tin to extract the last little bit of useable stuff from the grains. After this the grains are pretty much done – you can throw them away, boil them into porridge or give them to farm animals.


  • Boiling

    • Take the wort and either microwave on high or bring up to a boil on the stove. Once boiling, you then keep it there for an hour. Take care not to burn the wort.

    • Sometime during this process, add your hops to the boiling mixture. If you were only able to get herbal hops (which are usually a hallertau or similar), then this would be done at the beginning (60 min immersion). If you have access to something stronger (higher alpha acid content), then you can both use less and add it in later.

    • Explanation: The boiling step serves a bunch of useful purposes. Firstly, it sterilizes your wort so that other microorganisms aren’t messing your beer up from the start. Secondly, it drives off some of the more potent corn and chip flavours that tend to develop during the mashing step. It also serves to denature some of the proteins in the wort, allowing them to drop out of suspension once the whole thing cools down (which results in clearer beer). Finally, the heat of the boil is what converts the alpha acids in the hops into the bitter beer flavour that we all love so much. This is important in more ways than one, as this bitter stuff also makes the beer more resistant to outside contamination when the beer is brewing. You can (as has been mentioned) substitute certain herbs for your hops to get the same effect (albeit with different flavours), but this is not something that I have personally verified.


  • Brewing

    • Once your wort is boiled, transfer it to the brewing tin, add the brown sugar (and optional molasses) and measure the resulting volume. If it is less than 5l, then make up the shortfall with cold water.

    • Cool the wort as fast as possible. If you have no other options, simply stick the tub somewhere cold and dark (with a lid or cover on). If you have ice or freezer blocks, then make a container of ice-water and dunk the tub in that.

    • Once the wort is cooled down to room temperature you can add in the yeast and the optional aroma hops before sealing

    • lightly seal the tub (the lid or cover should not be airtight) and leave overnight to brew (in a cool, dark place 16-24’C).

    • The next day, use the large spoon (disinfected) to skim the crud off the top of the wort. Give the whole thing a stir to churn up the mixture before re-sealing.

    • Brew for 2-14 days in a cool, dark place (16-24’C)

    • Explanation: cooling the wort is important if you want clear beer, as it forces the denatured proteins out of solution. It also helps to keep some of the more pungent flavours (corn and chip smells, again) out of the brew. Brewing time both influences flavour and clarity of your beer. You can brew to completion within 3 days, but you’ll end up with the best product if you allow the process to carry on for longer. Of course, the longer your beer brews the more chance there is of something nasty getting into it and breeding. Which brings up the next point…


Very important: everything which touches the wort after it has boiled must be clean and disinfected (if at all possible). This includes the brewing tub itself, the spoon, the bottles you will be transferring the beer into, the siphon tube you may use to do it etc. The more obsessive you are about keeping things clean, the less likely it is that you’ll end up with an undrinkable beer that reeks of vomit.


  • Bottling and conditioning

    • Once your beer is ready, you should (if possible) lager it for a day or two before bottling. The easiest way to do this (if you don’t live somewhere reliably cold) is to just lump the entire tub into the fridge (4’C).

    • While you’re lagering, it’s also a good idea to add a flocculant to the beer to drag more stuff out of solution. A simple way of doing this is just to mix up a small batch of gelatine (one quarter of a cup of hot water plus a level teaspoon of gelatine) and add that in a day before you bottle.

    • Once you’re ready to bottle, make up a priming solution (30-40g of sugar dissolved in half a glass of boiling water) and add it carefully to your beer.

    • Allow things to settle, move the tub to where you want to pour or siphon, allow things to settle again.

    • Pour, ladle out or siphon your beer into clean bottles (siphoning works best, but can be a pain to do) and seal. Remember to leave a small air gap at the top of the bottle to provide something for the yeast to work with. You should count on getting around 4-4.5 litres out of the tub before the trub at the bottom begins to get into your bottles.

    • Check that bottles are airtight (invert and see if anything leaks) before storing in a cool, dark place (20-24’C). Allow the bottles to condition for 3-7 days before chilling.

    • Your beer is now ready.

    • Explanation: Lagering and flocculation seem to be the surest way to improve the clarity of your beer, if that’s what you’re interested in. The cold allows stuff to drop out of solution and form a thick, compact layer which you will then invariably stir up or suck up into one of your bottles. Keep this bottle for yourself, or make proper beer bread out of it. The priming bottle conditioning allows the residual yeast in your beer to make some carbon dioxide, which will then give your beer some fizz once opened. If you’re wanting to skip the priming step (which does, after all, tend to leave a residue on the bottom of your bottles) you should look for carbonation drops to add instead. I’d still allow the beer to condition, though, as it’s supposed to help with the flavour



  • ~4% abv (slightly under the lager range)

  • ~20 ibu (in the lager range)

  • ~8 srm (a tad darker than a standard lager)


Summing up:

As you can see, there is a lot of variation in this recipe. If you’re low on equipment, not that worried about clarity or just want something quick then you can skip the optional stuff and have something drinkable in a week. If, on the other hand, your process control is good you can have a very clear, well balanced brew in a month.

The amount of work required in each case is about the same – a few hours for the initial mashing, filtering and boiling, and a few minutes for the rest of the work. The cost is also low – R8/litre (not including price of containers) if you’re buying small batches of ingredients and getting shafted on the price of hops.

Miscellaneous notes:

  • Bleach is my go-to for getting things clean and disinfected. A capful per litre of water, with a minimum 15 minute soak, seems to work wonderfully. Just remember to rinse whatever it is you’ve cleaned before using it (especially the siphon tube if you’re using one) as bleach-flavoured beer is probably never going to be popular.

  • Counter-intuitively, you shouldn’t scour plastic surfaces when trying to get them clean. The problem is, apparently, that the scratches you make end up sheltering bacteria and fungi, which then go on to contaminate your beer.

  • Brew with your nose – you can usually smell if something has gone wrong before you bottle, which will allow you to skip the heartache of making all your friends and loved ones gag when they open a tainted brew. It also doesn’t hurt to reserve some liquid at some steps of the process (rousing the wort, bottling) to taste. Don’t be too worried if the taste is rough, though, as brewing and bottle conditioning tends to even out the flavours.

  • Iterate, iterate, iterate. You probably won’t get the first brew right, or the second. Just keep plugging away (hopefully learning as you do so) and it will all come right. And by the time it does so you will probably have a better idea of what you want in your beer. Feel free to add or subtract things to your taste.


Useful links:

  • A brewing calculator, which has become an indispensable tool for me when organising and testing recipes.

  • A wonderful paper on Sorghum malt properties, which includes a methods section that would allow you to make your own.

  • Some more articles on Unqombothi, all from the perspective of commercial brewers

  • An entire site dedicated to hop alternatives and traditional brewing

  • How to make your own malt (barley and corn). Fair warning – you will almost certainly have problems with bacterial contamination on your first few attempts.

Edge does a thing

Posted in Science with tags , , on 15/01/2014 by sangomasmith

A bunch of people weigh in on scientific ideas that should be retired.


Whenever these sorts of lists crop up, I tend to get that feeling people have when watching TV shows that feature subjects they know something about. There is this moment when you realise that the opinion being presented is shallow/glosses over important concepts/presents only one side of an ongoing debate/is just plain false. And so you begin to wonder: is the seemingly-plausible stuff you see being presented on a topic you don’t really understand just as bad?


Anyway, there is some interesting stuff in there at least. Have a read and make up your own mind.



The pitfalls of doing reactive science

Posted in Crop science, Science with tags , , , , , on 14/01/2014 by sangomasmith

Note:  A lot of the papers I’ve linked to are behind paywalls. Which is sad and sort of it’s own entire story. Nevertheless, you can read the abstracts and get an idea of what is going on.


One of the papers I’ve been wanting to talk about is this fellow from 2012. It’s a pretty boring, dry piece if you’re not intimately involved in the minutiae of crop research, detailing the results of a series of experiments (each the subject of it’s own paper) designed to see whether one particular form of BT-expressing corn (the MON 88017 line) is dangerous for non-target arthropods. This, it turns out, is done by feeding the stuff one way or another to an almost ludicrous number of creatures (caterpillars of various species, bugs, wasps, spiders, mites and on and on) and seeing if any of them suffer any sort of developmental damage or mortality. What the review found, in almost all cases, is that the risk to non-target organisms is minimal.

What this article represents – what makes it interesting beyond the dry recitation of tests and figures – is as a sort platonic ideal of the dangers of doing what I tend to think of as ‘reactive’ science (in that it’s a reaction to external events). This crop, which has been grown since 2005 (and had been in development and testing since something like 1995), has just been through 7 years of tests to determine if it has any effect on organisms which, from all that we know about the Cry toxin that Bt encodes, it should have no effect on. And the reason? This.


In may 1999, a paper was published in Nature which seemed to show that the larvae of monarch butterflies raised in an environment where they were exposed to the pollen from Bt-expressing maize plants were negatively affected by the experience (slower growing, less hungry and with higher mortality). Although issues were soon raised about the methods and applicability of the paper, it was seized upon by environmental groups as proof positive that Bt corn, and GMOs in general, were evil and dangerous. Following this, a flurry of papers were produced examining the the issue from every angle: how much Bt was in GM corn pollen, how likely it was to come into contact with the monarch larvae and how much would be needed to induce negative effects. A result of this can be seen in this 2001 review article on the whole affair.


And the result? Nothing. There isn’t much bt in the pollen, the amount of milkweed plants (which the monarch larvae feed on) hanging around close enough to get dusted is low, the amount of pollen that would actually land on one of these plants if it was in the right place is negligible and the timing of the pollination and the lifecycle of the butterfly is far enough off so that it would be very rare for this to happen anyway. Overall, the evidence overwhelmingly shows that bt pollen from GMO corn is not a threat to the monarch butterfly.

And yet, even today, you still have a good chance of this being brought up whenever GM crops are discussed in the public sphere.


This is the central problem of doing science when politics is involved – it takes exponentially more time to debunk something than it does to simply claim it. To rebuff a single, badly put-together study can take years of careful testing by scores of researchers and burn through massive amounts of money. And by the time you do so, public opinion has likely moved on. When doing science as a reaction to hysteria or panic, all you end up doing is wasting money and effort: the hysteria will have already solidified into common knowledge (which you then have to fight against) and the extra burden of research will have diverted effort away from more important things. Which is how you end up with dull, boring, meticulously-researched papers looking at the 1000-and-1 ways in which an existing product has no negative consequences.


This central asymmetry; between claiming a negative outcome and then proving the claim negative, is one of the central factors driving a lot of the stupid, anti-scientific debates that we as a society keep having. Scientists are prime targets for reactive science, we fall into this trap again and again. In the end, though, it isn’t scientists that pay the price (we still get to keep on doing our jobs, after all). It’s society at large, in the form of the lost opportunities that reactive science creates.

A more productive post

Posted in media, pedantry, rant, Science with tags , , , , on 12/01/2014 by sangomasmith

I recently went blog-diving and found this charming specimen who, between saying things that make sense, seems to be particularly vexed by feminists (and women in general, if his other mentions are anything to go by). Now, the combination of finding this particular rough diamond and hanging around here too much got me all het up to write a post blasting the smart misogynists for being the clueless dipshits that they are. Ultimately, however, I realised that (as Scalzi pointed out) you just cannot get concepts like ‘privilege‘ across to these bozos without whickering and whining. They are just too bitter, clueless and invested to hear. So instead I’m going to try for something a little more tangental: a brief explanation for why these guys may have a point about some of the people they find wretched or disgusting (thanks for that, Scott). And why it doesn’t much matter.


The problem is simple: it takes a certain amount of resources and connections to get the word out. This means that, barring miracles or outside intervention, a rich, upper-class person who works in the media is going to have an easier time reaching an audience than a poor person working as a janitor. Which means that, more often than not, the people writing about the poor and dispossessed are going to be neither. Which can be a problem if, for instance, you’re trying to dig down to the essence of what it means to be poor. It can also weaken your personal case for whatever it is you are arguing for – folks will inevitably leap onto the fact that your personal experiences are overblown or minor compared to the real suffering that you’re trying to connect to. And there is a core of truth to this – it really is hard for a white, cosseted, upper-class person to really get what it means to be down and out in a racist country. Or for a pampered, academic feminist to really get what it means to be a woman living in a world where your worth to society is measured principally by the number of male children you can raise to adulthood.


However, there is a known human faculty which is supposed to help alleviate this problem. We call it ’empathy’. It is, like all things human, not a perfect faculty – one’s personal experiences and biases will always creep in to colour things. But it is useful for that most human and humane of tasks: the long mile in someone else’s shoes. I should mention the word ‘useful’ again, because empathy is also about more than just getting the feels when you realise what someone else’s plight is. It is also a hard-edged tool: the culmination of our fine-grained, meta-cognitive, social senses. Which is why it tends to be the first thing that tends to go whenever a brain is damaged or malfunctioning.


Most feminists, whatever I may think of their individual lives or arguments, tend to at least display empathy. That the ones with the biggest platforms may also tend to be the ones who encounter the least actual sexism in their daily lives (you know, aside from the inevitable rape threats any time they say anything in the public sphere) does not mean that what they say has suddenly been rendered worthless. What unites my little collection of misogynist  internet assholes, on the other hand, is a stunning lack of empathy. This may not even be their fault – it is one of those biological failings of the male gender (along with stupid risk taking and much higher crime rates) that we tend to be more afflicted by neurological disorders.


So when they accuse those evil(or wretched, or disgusting) feminists of being self-serving, vain, deceitful, clueless, arrogant, out of touch, creepy, grasping, pathetic etc. perhaps they are just looking into the mirror and failing to see any reflection but their own?

Something about biotech for a change

Posted in Crop science, rant, Science with tags , , , on 07/01/2014 by sangomasmith

This is an interesting piece on the problems associated with trying to legislate GMOs – namely that being anti-GMO is turning into the climate change denialism of the left.  And to think I’d allowed a shred of optimism to colour my worldview on the subject.


Way back at the beginning of 2013 Mark Lynas, who played a pretty big part in getting the anti-GMO ball rolling in the first place, issued a public mea culpa for his past actions. This, along with some encouraging news about the use of GMOs to counter citrus greening, led me to briefly become optimistic that the worst of the stupidity was over.


It was not to last

Mark Lynas’ speech led to a backlash from his previously loyal supporters rather than the reappraisal that I think he was hoping for. He’s still sticking to his guns, but then the man is nothing if not committed to his principles (whatever they may be at any given moment). Elsewhere, destruction of trial fields in the European Union has become so pervasive that research there has all but stopped. Elsewhere, Golden rice suffered another setback when a large field trial in the Philippines was destroyed.

Look at any article on the subject and you will see a slew of comments from conspiracy theorists, anti-corporate crusaders and nature-anthropomorphising pseudo-environmentalists all repeating the same tired myths about GMOs*. It reminds one of the climate change denialists – folks who have decided that their worldview is more important than facts and will fight tooth and nail to stay in their little bubble.


We will see if this year is any better than the last. But I’m not getting my hopes up.


*For people who wish to play anti-GMO bingo:

anti GMO Bingo


With thanks to this guy