Month: August 2012

Why Didn’t the EPA Ban Clothianidin?

~ raludwick

The EPA recently rejected an emergency petition to ban clothianidin due to colony collapse disorder (CCD). The tone of posts and stories about this are that it’s just amazing that the EPA wouldn’t ban clothianidin — it’s a bee-killing pesticide after all! There’s even a petition to ask the EPA to reconsider. An excerpt to give an idea of tone:

Last month, for the second time, the EPA refused to intervene to stop the use of the pesticide clothianidin, which scientists believe is at least partially to blame for the alarming rise in bee colony collapse — the sudden bee die-off which has claimed about 30% of the U.S. honey bee population each year since 2006.

To read this, you would think the EPA are just arbitrarily rejecting good science and public policy, but as usual there’s a bit more to it. I’ll be posting more on this as I read more, but I think a few excerpts from the actual documents the EPA released in the most recent petition rejection are useful. The main response letter is readable, even by non-experts, and makes it clear why an emergency petition was inappropriate.

When can the EPA ban a pesticide before going thru normal cancellation and review procedures?

The EPA response gives their authority here as being an imminent hazard:

The EPA may commence proceedings to suspend the registration of a pesticide during the period necessary to complete cancellation proceedings if it determines that an “imminent hazard” exists from the use of the pesticide.

But what really is an imminent hazard?

Courts addressing the suspension provisions have held that an imminent hazard exists if there is “a substantial likelihood that serious harm will be experienced during the year or two required in any realistic projection of the administrative process”.

Thus, to show imminent hazard, the petitioners would have to show that the harm would very likely occur within two years. The letter goes on to note that other courts have said the harm would have to occur within three or four months.

Why does the EPA reject the petitioners finding of imminent hazard?

The EPA response goes on to note that they do not believe imminent hazard has been demonstrated, saying:

As set forth in the legal background section of this response, and as explained by the federal courts, the imminent hazard standard includes the concept that the harm is imminent; that is, that it must be occurring or likely to occur within the one to two years necessary to complete cancellation proceedings — or in the case of an emergency suspension, within the three to four months necessary to complete suspension proceedings. However, nowhere in the petition do the petitioners explain whether the serious agriculture and ecological harm alleged on page 36 of the petition is likely to occur during these time periods.

So the petitioners failed to provide evidence for one of the conditions the EPA must follow to grant their petition. Worse:

Further the imminent hazard standard also incorporates FIFRA‘s unreasonable adverse effects standard, which is a “risk-benefit” standard. Because petitioners only address the potential harm from the use of clothianidin without addressing whether the harm is unreasonable when weighed against clothianidin’s benefits, the petition also fails to address this threshold matter as well.

The petitioners basically failed to give the EPA what they needed to even try to grant their request. That said, the EPA says they are going to look at it anyway:

Despite the facial inadequacy of petitioners’ imminent hazard claim, given the nature of the harm asserted, the EPA examined the evidence cited by petitioners to determine whether that information demonstrates that there is nonetheless a substantial likelihood of serious imminent harm. Based on the data, literature, and incidents cited in the petition and otherwise available to the Office of Pesticide Programs, the EPA does not find there currently is evidence adequate to demonstrate an imminent and substantial likelihood of serious harm occurring to bees and other pollinators from the use of clothianidin.

The paragraph continues noting:

  • Scientific literature clearly shows clothianidin is acutely toxic
  • Literature shows foraging bees are occasionally harmed by clothianidin
  • Evidence does not suggest severe economic or ecological harm from clothianidin in the next two years.
  • The adverse reactions from clothianidin that do exist should be mitigated.

But is clothianidin strongly linked with bee deaths?

This is a much harder question than it seems. As noted in a previous post there are a lot of questions we have to answer. We can’t just say “kills bees, therefore ban” because by that standard we’d have to ban pretty much all insecticides. The question is whether clothianidin specifically is more harmful or excessively harmful compared to its benefits to human beings. I don’t want to try to answer that here (I have an incredibly long list of posts I want to do if only I have the energy) but let’s see what the EPA said in their response letter1.

The petitioners claim that research indicates that honey bee colonies are in decline recently and that this decline appears to correlate with the registration of clothianidin and other neonicotinoid pesticides.

The EPA then continues noting:

  • Bee colonies have been registered for 20 years but a steady decline has existed for 60 years. In other words, if pesticides are implicated, neonics and clothianidin don’t seem to be uniquely harmful (and pesticides likely are involved in bee declines — as are bee diseases and pests, climate change and habitat loss).
  • More recently, colony losses have declined even though neonics continue to be used at levels at or above how they were used when CCD began in the United States. The EPA notes that this doesn’t mean neonics aren’t involved, just that it suggests it isn’t the primary cause.
  • Much of the literature petitioners cite have unaccounted confounding effects in their experiments, are actually for imidacloprid (also a neonicotinoid) or show effects on individual bees more than effects on colonies.

A major issue that should be determined is how widespread clothianidin use is and whether that itself increases its harmful effects. The EPA discusses this and notes that 90% of corn seed is treated with some neonicotinoid pesticide (I had no idea it was that high!) The petitioners note that clothianidin is persistent, however the EPA counters there is no evidence it persists more than year following planting and that more studies are being done.

While clothianidin is clearly acutely toxic to bees, it is not generally used in a way that causes acute issues. The more relevant question is whether the levels in corn plants and in the environment, as consumed by bees, are similar to those show in sub-lethal dose studies to affect bees. The EPA states:

The levels of clothianidin in pollen and nectar typically seen in the field are, however, generally below the levels at which sublethal effects reportedly happen, and lethal effects occur. Thus, the data do not suggest that bees are being regularly exposed to levels of clothianidin in pollen and nectar that could result in the sort of imminent, population level impacts necessary to support an imminent hazard finding.

But is clothianidin causing colony collapse disorder? That is the fear that many have and if you search the internet, you would think the case is certain. The EPA notes that the cited studies show that in a lab setting imidacloprid seems to show the effects needed for CCD. But the EPA notes:

However, the studies cited do not address whether these effects are permanent or transitory or whether such effects would be likely for other neoniotinoid insecticides. Additionally, the petitioners did not provide any evidence that the laboratory results are reflective of what would occur in the field and if so, whether the degree to which they occur would occur would effect populations of honey bees. For example, the minimum concentrations at which significant biological effects occurred in the majority of the cited studies are not typically present in the field or in chronic concentrations present in nectar and pollen from the most widespread use patterns of clothianidin. In addition, the pesticide residue analyses from national surveys of commercial honey bee colonies indicate that colonies that were eventually determined to have succumbed to CCD did not contain elevated levels of neonicotinoids including clothianidin, nor do colonies in the areas of the U.S. where the most treated corn seed is planted apppear to succumb to CCD at a higher rate than other colonies.

The EPA’s response continues answering various concerns including synergistic effects (the most likely in my mind, but apparently not that cut and dry), specific poisoning incidents (these are almost all acute cases and only total 20 in the united states and weirdly 120 in Canada), and general agricultural losses and ecologic effects. I really recommend reading it. It will only take you twenty minutes and provides good perspective on the limits of action for a regulatory body and how scientific evidence is used by regulators.

So now what?

The EPA has denied this emergency petition, but they are continuing to investigate. Senator Gillibrand has called for an expedited review. All registered pesticides are required to undergo regular re-review to determine if they have excess negative effects as compared to benefits. Obviously there are a lot of pesticides registered, so the EPA does this on a schedule. Since clothianidin isn’t up for re-review until 2018, Senator Gillibrand’s request for an expedited review seems reasonable to me. In fact, the EPA is already doing this review as you’ll note on the EPA’s webpage in the section “Next Regulatory Steps for Clothianidin:

Given the concern about clothianidin and other neonicotinoid pesticides and the EPA’s dedication to pollinator protection, the agency has accelerated the comprehensive re-evaluation of these pesticides in the registration review program. We are coordinating this re-evaluation with California’s Department of Pesticide Regulation and Canada’s Pest Management Regulatory Authority. This extensive review will determine if any restrictions are necessary to protect people, the environment, or pollinators. The EPA’s registration review docket for clothianidin opened in December 2011 (Docket ID: EPA EPA-HQ-OPP-2011-0865). In September 2012, the agency will seek independent scientific peer review on how to better assess the risks of pesticides to pollinators. This effort will improve our understanding and strengthen the scientific and regulatory process to protect honey bees and other pollinators.

Given how much attention is being given to clothianidin and bees, it doesn’t seem like the EPA is acting in a corrupt or incorrect manner. The EPA is obligated by law to make certain determinations based on best evidence before they can act. Asking or requiring them to do otherwise would not be good governance.

  1. Despite the belief of some, regulators working in organizations like the EPA are in general trying to do the right thing. They make mistakes and are sometimes subject to undue pressures, but it’s not like they are cackling viciously in their chairs in Washington thinking up new ways to screw over the environment to the benefit of pesticide makers. ↩

Positions, Science and Values

~ raludwick

I’ve recently finished reading The Geek Manifesto by Mark Henderson. While there’s a lot more to it than what I’m going to talk about here, it did give me better words for describing why I find certain political positions (and ways of advocating for them) frustrating. Many people are holding a belief for values-based reasons but claim evidence (usually scientific) for why they do. This avoids discussing the real underlying issues and so nothing can be resolved.

An early point Henderson makes in The Geek Manifesto is blindingly obvious but seeing it written out is helpful. Values are different than science. Science can’t tell us what to do, only what the possible effects might be. However, evidence, especially “scientific evidence”, has a halo. If the “science says” something, then how can we argue against it? This halo is so strong that politicians, lobbyists, even a person individually will seek out scientific justification for a particular position. And we do this even if that scientific justification doesn’t really exist or we have to cherry pick the one study out of hundreds that “proves” our point. Henderson calls this looking for “policy-based evidence” rather than making “evidence-based policy”. I would extend this to using “position-based evidence” to support one’s beliefs.

His point isn’t that we shouldn’t make decisions unless we have proper scientific evidence. It’s that we should be honest when we are making a decision (or believing something) without or in contradiction to what scientific evidence tells us will happen. One of his examples is somewhat extreme but illuminating. Science might tell us that an early curfew would reduce crime. However, most of us probably value freedom of movement and limitations on government power more than we value the reduction in crime. If a politician proposed a curfew and supported it with a good review of scientific evidence, most of us would rightly say that the science doesn’t matter in this case.

But on other topics, politicians feel the need to find some evidence — whether it’s representative or fair is irrelevant — because the values-based reasons to support the policy aren’t as clear (or as widely shared). Using “science” makes the argument more convincing to disinterested people and avoids making trickier arguments about values that might interest them. I might just recommend you read the book (and I do!) but I think a few examples might be helpful.

The GM Debate

This is painfully common in the current GM food debate. I’ve touched on this before when talking about GM labeling being a poor proxy for other worries regarding our agricultural system. If you get into any kind of argument about GM foods, the litany of reasons why GM food is bad will include a large number that are problems with conventional agriculture (and even organic). Some worry about safety and long-term health effects will be thrown in (generally justified with cherry-picked evidence), but much of it is related to things like over-use of pesticides, monocultures, farmers being beholden to seed companies, people not really understanding how their food system works, etc. None of these are peculiar to transgenic technology and all pre-date adoption of transgenic crops. I’m not sure why the technology became a poster-demon for the green movement but today it serves as a convenient boogeyman for many other concerns about agriculture that are largely about values. Large monoculture fields growing commodity corn or soy primarily to feed animals or make biofuels doesn’t fit with our conception of a “family farm”. But facing the those challenges is a lot harder than getting GM foods pulled off the market — and the decisions we will have to make are a lot more contentious. Given how much I’ve written, I’ll not bore you with more here.

Organic Food Marketing

Another example is organic marketing and foods (and I’m going to write a bit more on this than the above). I personally eat a lot of organic food. My reason for doing so is that without further information about how conventional food is grown (pesticide use, attempts to reduce runoff, etc.), organic is the best proxy I have for finding food grown with “less impact”. I put that in quotes because it’s a really hard thing to judge — for example, current organic practices generally require more land to produce the same yields (for most crops — as always, there is variability). That said, I don’t sweat not buying organic either. It’s only an inadequate proxy after all. Eating less meat probably has a far greater impact. But that’s a lot of complexity in reasons that aren’t really going to be convincing in marketing materials. “It’s probably a little better (sometimes) than the conventionally grown alternative!” does not make a convincing advertisement. Instead, inadequacies in modern organic (see above about land use) are ignored and many activists and companies make claims that are far more about values than evidence.

It’s widely believed, for example, that organic food is literally more nutritious than conventionally grown food. The evidence for that is pretty uncertain. Some studies see a difference, many don’t and many that do see a difference show very small differences (or insignificant ones in the context of a full human diet). But many of us value the idea of eating more nutritiously. A claim that organic is more nutritious provides an easy way to support that value — even if just eating more vegetables (organically grown or not) would work just as well.

Another common idea is that organic foods are grown “without chemical pesticides or fertilizers”1. Of course organic methods do use chemical pesticides and fertilizers (copper fungicide, Bt sprays, manure and compost all are made of chemicals). Sometimes the common organically permitted pesticide is even more harmful than the conventional alternative. There are two main values being sold here. First, the idea that we can have agriculture and not impact the environment. Second, the idea that “chemicals” are dangerous and organic lets you avoid them.

For the first, human agriculture absolutely requires inputs. Our food crops are bred for yields and quality and often not good resistance to pests or tolerance of resource limitation. Thus, we fertilize them and apply pesticides to ward off pests and competitors — even organic farming must or suffer commercially infeasible yields. The second is implying that food that isn’t grown with organic is somehow dangerous to eat and yet there’s very little (broad, repeated) evidence that we’re getting dangerous levels of the pesticides used in conventional agriculture — the USDA measures produce every year and almost uniformly finds levels undetectable or well below regulatory limits (which are set well below levels where effects have been seen).

But let’s leave it at that. In general, I think organic agriculture has a lot going for it. But it’s currently being sold in a way that exaggerates its benefits while demonizing agriculture seen as being in opposition. Meanwhile, evidence and the scientific process is ignored or misused.

The Geek Manifesto is about a lot more than just this idea of evidence-based policy decisions. There are chapters applying it to education policy, health, law and order, environmentalism and more. Each showing how evidence is ignored or manipulated and how “the geeks” can change policy for the better. Most examples are directly taken from UK politics but most of it is very relevant to the United States (and at least in part most modern democracies) so don’t be put off by the UK-centrism. It’s got me thinking a lot about how to communicate ideas in a way that is actually effective and it’s well worth reading.

  1. If this phrase seems like a strawman and organic advocates wouldn’t literally say that, google the literal phrase “without chemical pesticides or fertilizers” (in quotes). ↩

How to Use S3 as a Private Git Repository

~ raludwick

The files that generate the content for this website are stored in a git repository (for those that aren’t software people, “git” is a version control system that lets you keep a history of files in a logical way, including all changes over time). When I first started, I just kept it locally on my personal laptop (backed up to an external hard drive occasionally).

But what if I didn’t have my personal laptop and wanted to edit or create a post? Obviously I needed to keep the master copy of the source files on a server somewhere (“in the cloud”). This post is about what options I considered and the absurdly simple version of just keeping a private git repository in S3. This has been written up elsewhere, but given how ridiculously useful this is, it deserves more than just a tweet.

Finding a Solution

My first thought was actually GitHub. This is a hosted, social collaboration site for all kinds of software. While it would have worked, I would have to pay if I wanted to keep content private (for drafts and such). Public (and free) didn’t make much sense either: this is a personal blog site and not really collaborative (yet).

Next up, I considered just putting a git repository on a server that I have access to from Sonic.net, my old ISP that I still have an account at. The issue there is that the shell account I have isn’t necessarily always available. I discovered I would have to install git itself which suggests they weren’t really expecting me to do something like this. In any case, that account isn’t really meant for reliable and available backup.

Then I realized: I have a massive and cheap place to store data in a very reliable place of known as “S3”. The only sticking point is I needed to “push” my local git repository to one hosted in an S3 bucket. I googled and found Jgit and a couple blog posts on the subject.

Note: I do work for Amazon and since I was already using S3 to host the website itself, it was an obvious choice. However, I suspect this might work for other forms of “cloud storage” assuming Jgit supports it or you can modify it to support your hosted store.

Using S3 as a Private Git Repository

Create an S3 bucket

First, you do need an AWS account and an S3 bucket. Since my website was originally named “r343l.com”, I named my git repository bucket “r343l.gitrepos”. S3 buckets have to have globally unique names so most of my buckets are prefixed this way. Steps:

  1. Login into your AWS account.
  2. Go to the AWS management console and choose S3
  3. Click “Create bucket” and give it a name. By default the bucket should only grant credentials to you, but I would double check.

Setup local credentials to access S3

This step is to get the AWS access ID and secret key you need to access the repository. For this example, we’re just using the “main” one for the account. If you were sharing the bucket with someone else, you might create some other principals and grant permissions on the bucket to those. But let’s assume we’re doing this the simple way. Note that once you have this file on your local machine, you should treat them like SSH private key credentials.

  1. Pull the drop-down for Security Credentials from the My Account / Console menu at the top-right.
  2. Create a file in your home directory (I’m on Mac and not sure where exactly this goes on Windows) called “.jgit_s3_public”. Make sure it’s only readable by you (permissions 600). The commands on a unix-ish system are touch ~/.jgit_s3_public; chmod 600 ~/.jgit_s3_public.
  3. In the AWS credentials page, scroll down until you see “Your access keys”. Click the “Show” part to get the secret key. Copy both into the created file as follows:
accesskey: [access ID for AWS]
secretkey: [secret key for AWS]
acl: private

Everything between and including the square brackets are the values you copied from the AWS credentials page. The “acl” line ensures that newly uploaded files stay private.

Install Jgit

Download the software. I chose the self-contained shell script version that contains both a script to run Jgit (it’s a Java application) and the Java code itself. It sits in my home “bin” directory and is aliased to the command “jgit”.

Make a git repository and upload to S3!

Let’s pretend your bucket is foo.gitrepos where all your personal git repositories will be stored. In my case, I have my website master in here, but another use might be for blog posts that get hosted at another site. You know how everyone says to edit outside of the blog software because your browser might crash? Well, even better than editing outside the blog software is saving those files to a separate place in case the hosted blog loses stuff! For this example, let’s pretend you have a tumblr.

cd ~/
mkdir myrants-tumblr
cd myrants-tumblr
... create some files 
git init
git add *
git commit -m "my new files yay!"
git remote add s3 amazon-s3://.jgit_s3_public@foo.gitrepos/projects/myrants-tumblr
jgit push s3 refs/heads/master  ### NOTE: jgit not git!

You now have your files in S3!

Getting your files out of S3

What if you’re on another computer and desperately want at these files? Well, all you have to do is install jgit and setup the client credentials as before. Then clone down the git repository:

jgit clone amazon-s3://.jgit_s3_public@foo.gitrepos/projects/myrants-tumblr

Then you can edit or add files as needed. Pushing it back up to S3 is the same as the initial push. Note that once you have a local repository setup in multiple places, you’ll probably at some point need to update them. With jgit the commands are:

jgit fetch               ## gets updates from the S3 master
git merge s3/master

Basically, use git for local commands that manipulate the local repository (adding, committing, merging) and jgit for any interactions that involve sending or receiving data from the S3 bucket.

That’s it! I hope this was helpful.

Fukushima Mutant Butterfly Followup

~ raludwick

It’s been a few days since I posted about the media coverage of the study on mutation in butterflies around Fukushima. I’ve been following a few stories on it since then and I think the most important take-away from this kind of study is that science is complicated and hard to report on. I realize this is obvious and I thought it was obvious before. I also chose to primarily criticize an article that fits the Robbins’ spoof format pretty well which is perhaps unfair.

But by looking over coverage and discussions on this study, I’ve wavered from “this is crap” to “huh, this part is pretty good and kind of compelling (but of course we need more research” to “huh, that part that good part has some problems (but of course we need more research”). This is shorthand and leaves out a few stages but I think it gives an idea just how hard it is to really understand a new science paper well enough to be fair both to the process of science (I can’t dismiss a paper just because parts of it aren’t very good) and tell a comprehensible story to the public (I didn’t even really try with my previous post). This is of course why so much science reporting is formulaic and perhaps I understand a bit more why it’s so easy to do that.

In any case, I want to call out media that has been a bit more skeptical of the results.

First, there’s the Nuclear Diner post. While I think the original post may have gone a bit far (and missed a few important points), the comment thread has been good. Contrary voices (including mine) have been heard and others have added more to the analysis. One commenter points out that even the feeding trial has issues: what if the leaves were contaminated with other toxins released during the disaster or some had pesticides recently applied? He even recommends a more controlled study that would be very interesting (but presumably still hard to directly apply to the Fukushima disaster).

The Wall Street Journal published on Saturday a long essay making the point that people (especially those outside Japan who aren’t generally affected except indirectly) are panicking about Fukushima. The article mentions the new study in passing (without enough context really). The main thread of the essay is however a comparison about natural radiation exposure from radon in the Denver area with Fukushima area exposures. He then goes on to do various estimates on additional cancers and so on. While the author is quite right that radon exposure in the Denver area greatly exceeds most of the Fukushima area in straight rem doses, it’s not clear to me that exposure to radon is the same as exposure to iodine-131 or caesium-137. However the idea of the essay seems sound. Most estimates of additional harm specifically from radioactive releases from the Fukushima power plants are very low. Harm caused by the earthquake, tsunami and evacuation greatly exceed any harm directly from the damaged power plants themselves. Despite this, most people in the United States seem to worry most about the radiation.

The Metafilter discussion of the story started out fairly poorly, but some skeptical voices chimed in and the discussion got more interesting. Particularly the comment by pseudonick adds some useful context. The most recent parts of the thread are about some interesting alternatives to nuclear power.

But, I find that this is all I have. I’ve done some google searches for more, but nothing that I find worth passing on. If you find anything, I’d love to add it to the list.