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Nanomechanical oscillations…

This week one of our Facebook group members posted a link to a 2013 paper entitled “Love thy neighbour: facilitation through an alternative signalling modality in plants”. The premise in the paper is that plants are capable of acoustic communication and the experiment purported to demonstrate this. (I strongly encourage you to download the article from the link above so you can read it for yourself.)

chilisBriefly, chile seeds (Capsicum annuum) were placed into petri dishes, covered to ensure darkness, and then the dishes were placed in a circle. In the middle of the circle was either an empty acrylic box covered in black plastic (the control), an acrylic box covered in black plastic containing an adult basil plant (Ocimum basilicum) called the masked treatment, or an adult basil plant without a box (the open treatment). Seeds were watered and inspected daily for germination and the petri dishes were randomly rearranged.

basilAccording to the authors, “the presence of basil positively enhanced germination rates of chilli seeds, validating the claims of many gardeners who recognise the beneficial effect of basil on the growth of chilli plants.” Their reasoning is that the open and masked treatments induced more seed germination than the control. And since there was little difference between the masked and open treatments, they claim that the phenomenon is due to some signal other than light or gas (since the black plastic-covered acrylic container would prevent this).

How does this work? Well, according to the authors, this is evidence that acoustic signals are “generated in plants by biochemical processes within the cell, where nanomechanical oscillations of various components in the cytoskeleton can produce a spectrum of vibrations.” Never mind that the experimental design and methodology was laden with opportunities for experimental error. In particular, opening the petri dishes to water and count germinated seeds every day is deeply flawed. The easiest and least error-prone method would be to have the petri dishes sealed with parafilm to prevent water loss and inspected ONLY after the experiment was over. That is the standard method for testing for germination rates. Moreover, opening the dishes to count and water seeds every day really screws up the “covered to ensure darkness” part. In fact, chile seeds germinate better with light – which is what they got every day when they were opened. Was each dish exposed to light for exactly the same time every day? Exposure to light converts the seeds’ phytochrome to what’s called the active form, and phytochrome plays a crucial role in seed germination. The longer the light exposure, the more phytochrome is converted.

germinationNow, plant scientists would know these things when they were designing their experiments. But as neither of the authors have degrees in plant sciences, it’s understandable. What’s not understandable is how this article got through peer-review. Unless none of the reviewers were plant scientists, either.

For those of you that belong to a university journal club or some other science discussion group, I think this would be a great article to discuss.

Shooting Fish in a Barrel

Someone recently posted a scientific article on our Facebook page which purportedly demonstrates that Roundup can be damaging to earthworms at concentrations that would typically be used in a field situation. Wow. Scary. I mean really, if we’re damaging earthworms when we apply Roundup, then that lends fuel to the emotional fires that rage against this pesticide. But is that really what this article shows?

It’s unfortunate, but most of you will not be able to see the article that I’m writing about because you won’t have access to the journal in which it was published. Here’s the abstract though.

http://link.springer.com/article/10.1007/s11270-014-2207-3

Basically what the authors did was to place worms in small pots, expose the pots to different concentrations of a commercial formulation of Roundup, and measure how the worms fared over time (about a month and a half). Unsurprisingly, the worms not exposed to Roundup performed better than the worms exposed to the Roundup.

After reading the above paragraph you might think that this is an open and shut case. Roundup is bad for worms, potentially leading to “local extinction” of these animals in agricultural fields (that’s the authors’ wording).

It’s not that simple. The authors are stretching well beyond the data, and the research has some issues, most of which could be cleared up by better, more thorough reporting.

First, let’s take a look at some of the problems that this paper has in terms of reporting its materials and methods. You may think this is picky, but it’s not. It’s fundamental to figuring out how valid the reported results are. From the materials and methods as they were written it is impossible to figure out exactly what was done in terms of watering the pots (we know soil moisture was kept at 80%, but we don’t know how. Watering? With what?). We don’t know what the ground plant materials were that were added to the pots (Lima beans?). We know that pots were placed into 1m X 1m X 0.60 m containers, but we don’t know how many pots were placed into each container or whether pots were randomized by treatment within each container. Sure, we could make assumptions – but in a well written scientific paper we shouldn’t have to. Would knowing these things affect how the worms performed in the Roundup treatment versus the no Roundup treatment? In a word, yes. The watering regime in particular might very well alter the results of this study.

That’s enough of that. Now let’s take a look at my BIG PROBLEM with this study. Six worms were placed into small (28cm X 14cm), half-filled pots and treated, or not treated, with Roundup.

Let me offer an extreme analogy to explain why this is such a problem. Let’s say that you want to see whether shooting bullets into the ocean will kill all of the fish that live there. To test the theory you grab a 50 pound fish and you stick it in a 5 gallon bucket. The tail is hanging out, the fins are flapping, water is getting all over the place. Then you shoot the bucket. Dead fish. You do this 50 more times. Each time, dead fish. You conclude that shooting bullets into the ocean is indeed a threat to fish and may lead to local extinction. Right?

Wrong.

From this study you can conclude that bullets can kill fish. That’s an easy conclusion to make. You cannot conclude that shooting bullets into the ocean will kill all the fish there. Now, if we hired a swat team to fire bullets into the ocean and all the fish were killed, well then we could make that conclusion. Would that actually happen though? No way of knowing unless we try it. I suspect the ocean would retain its fish – but I’m just hypothesizing. (Quick FYI – high velocity bullets lose so much of their speed when they hit water that they wouldn’t be lethal to fish after traveling about 3-4 feet).

There are any number of studies out there that FORCE target organisms to be exposed to whatever chemical is being tested (that is basically what is being done here). These studies CAN show that the chemicals tested MAY affect the target organism. They CANNOT show that the target organism IS AFFECTED IN A GIVEN ENVIRONMENT. You need to test the chemical in that environment to figure that out.

To give an example of how you might test the effects of Roundup against worms in an agricultural environment: Take an acre of agricultural field, divide it into six sections. Treat three with Roundup and control weeds in the other three sections with hand weeding. Sample the sections every two or three weeks after Roundup application to see how the worms are doing.

Now, my final problems with this paper. Much of it is related to other, already published studies. This, in and of itself, is no problem. It is good that there are many studies on this topic. The problem is that most of these studies weren’t mentioned in this article. When I read a scientific article I count on its authors to put their study into context for me so that I can see where it belongs in the already existing collection of related literature. Without referencing these older papers the authors do us a disservice. I’m not going to list out all of the studies, but if you go to scholar.google.com and type in earthworm and glyphosate you’ll see what I mean.

I believe that any experiment from which data can be extracted should be published. I think that the authors of this article had every right to publish it. However, as a scientist, I think that there are enough problems with the reporting of this article, particularly the materials and methods, that, as it is currently presented, I can’t extract much of value. I certainly can’t reach the sweeping conclusions that its authors do.