Archive for the Science Category

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…

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

Plant Genetic engineering: Current gene insertion technologies

Posted in Crop science, History, musings, pedantry, Science, Uncategorized with tags , , , , , on 03/01/2011 by sangomasmith

The long-awaited part duex:


The technology of gene insertion in plants is around 30 years old now, the product of a wave of research in the 1980s. Eventually, two main technologies came to dominate the field: Biolistic and agrobacterium-based insertion. They are, with a few tweaks and upgrades, the same technologies we use today.

Biolistics, as the name implies, use ballistic particles (usually microscopic grains of tungsten or gold) to punch through the tough cell walls of plants and deposit DNA (which is carried as an outer coating) into the nucleus. This process is fairly inefficient, with only a small fraction of cells being hit in the right manner to transfer a functional copy of the construct into the genome. Even in these few cases, the insertion is often fragmented, or else contains multiple copies of the construct. This inefficiency, in addition to the rather limited types of plant matter that can be used (almost always embryogenic cultures of cells rather than intact plants or whole tissues) means that biolistic insertion has slowly lost ground to its long-time rival: agrobacterium. Its great advantage, however: the fact that the process is not limited in terms of what species it can transform, will keep it on the front lines as a niche system for the foreseeable future.


Agrobacterium-based methods make use of an engineered version of the gall-forming bacterium: Agrobacterium tumafaciens. This clever little bug is able to use a special DNA carrier (the T-plasmid) to introduce DNA into its host. Normally, this DNA would contain genes to make the plant cells form galls and produce food for the bugs, but engineered versions have had this cut out and replaced with cloning sites to insert other genes. The result is a simple system that produces transformed plants with high efficiency. Unfortunately, the little guys are sort of finicky when it comes to what species of plants they will play with. This has been especially problematic for the cereals (wheat, rice, barley and the like), which are all grasses that Agrobacterium is normally not interested in. Recent advances have thankfully overcome this somewhat, so the future of this little bug is bright.


Of course, the field of gene insertion is not static. Both systems, good though they may be, have significant limitations in terms of their ability to target genes to specific places on the genome and also have trouble when being used to insert multiple genes. As these abilities are both going to be very important for the next wave of plant genetic engineering, a lot of research has been done to find something better. I’ll cover these future gene insertion techs in the next segment.

Nothing ever changes

Posted in medicine, rant, Science with tags , , , , , on 03/01/2011 by sangomasmith

Except the buzz-words