Thoughts on reproducibility and reliability in science

You’ve probably heard about a project that attempted the replicate 98 psychological studies and found that only a third of them were reproducible, the other two thirds produced different results – sometimes very different, more often only somewhat so.

Though psychology was the subject of this study, you shouldn’t assume the results were unique to that particular field. The are plenty of reports of similar failings and the so-called ‘Decline effect’ in other scientific disciplines.

So why is that? There are a lot of reasons. Research can be poorly designed, based on flawed assumptions, and sometimes an unlucky flukes can create false positives. It is also the sad fact that science is done by humans, and humans are complex things with a lot of motives besides the pure quest of knowledge.

I think the general public often fears that scientists are swayed by money from corporations and/or special interest groups, but my experience in academia is quite different. I’ve never heard anyone concerned they might loose a corporate grant. I have heard lots of people, more-or-less continuously, worrying that if their experiment doesn’t work out they won’t be able to get their PhD, land a job, or get tenure. There is enormous pressure to find something significant, to find an effect, and it matters not at all the political ramifications of that effect. So if you are worried about Monsanto buying off scientists to say GMO are safe to eat, don’t be. Convincing data that GMOs are somehow unsafe to eat would be of enormous significance, completely rewriting what we know about genetics, and would come with huge professional rewards. In my opinion, you should be more concerned that some new study showing that X, Y or Z makes plants grow bigger or yield more is actually the result of fervent, wishful thinking on the part of a grad student desperate for publishable data.

So what’s the solution? There has been a lot of talk in the academic community about making it possible to publish negative results and provide funding to regularly attempt to replicate previous studies. I hope these changes go into effect, as they could make an enormous improvement in the reliability of new findings.

In the mean time, you, as a concerned gardener, should take information supported by only a single, isolated study with a big grain of salt, particularly if it seems to contradict findings from other research. If you go to scholar.google.com and start searching around, make sure you read as much of the research on the topic as you can, so you can differentiate between the intriguing new research that may well be proved wrong and reliable findings that have been sustained by several independent researchers. And always remember that while the scientific process is far from perfect, it is still the best we’ve got.

It’s the Next Best Thing Since Draft Beer: New Plants and Their Proper Evaluation

'Graham Thomas' rose
‘Graham Thomas’ rose

With many new nursery catalogs arriving in my mailbox at work for 2016 introductions, I thought I would focus this blog on “new” plants. With all the publicity and marketing that goes on for new plant introductions, you would think that they are the next best thing since draft beer or even bread! I am a bit cynical and question whether these new plants really live up to their performance expectations and ornamental attributes. With so many new hydrangeas, coneflowers, coralbells, spireas, etc. released each year, you may ask why am I so cynical? Why would I not jump on the bandwagon and promote all of these new plants like so many garden centers are doing across America? Let me explain.

A decade ago, I conducted research trials evaluating 20 new or recently introduced cultivars of “hardy” shrub roses, many of which are not even on the market anymore. I chose three locations in the state of Wisconsin, each having their own unique soil types, pH, soil drainage and fertility, rain/snowfall and cold hardiness zones. I replicated each of the 20 cultivars ten times at each location and arranged them into blocks with each cultivar represented in each of the ten blocks. The roses were randomly selected for each block and planted, mulched, watered with an application of a slow-release fertilizer. Plants were watered for the first year only as needed. To properly analyze plants for various traits, I allowed the roses to establish for a year with evaluation initiated the following spring. The only care the roses received the remaining years were application of a slow-release fertilizer, weeding and pruning of dead wood following winter. I was trying to replicate conditions that are common in most landscape settings. I did not spray any insecticides or fungicides to any of the roses, regardless of how bad they may have looked due to pests.

After the first winter, I evaluated the roses for winter injury, which they all experienced. The roses were all on their own root systems so if they died back significantly, the new growth would come from the same root system and produce flowers that spring. To some extent, they all grew, though voles killed some of the roses. After the roses starting growing, I evaluated them monthly at all three locations for insects and diseases as well as flowering (amount, size, duration of bloom, etc.). I also measured the plant’s height and spread. A few roses had good fall color. The first year of the trial, the roses all bloomed prolifically. So, one would think that all 20 cultivars are ideal. Not so fast, or “but wait, there’s more” as the television salesman would say to viewers in TV land about a new product. The “real” evaluation started in year two.

In year two, amount of dieback and winter survivability was recorded. To my surprise, the roses in the zone 3 location (boy, that’s cold) had better winter survival than the roses in my zone 4 and 5 location! This is due to consistent and significant snowfall in the most northern location compared to sporadic snowfall and lower amounts in the other two locations. I also evaluated the roses during the summer and fall for flowering, pests, and hip production. Contrary to the catalogs, many of the roses had hips, but some of them never colored up before the cold temperatures arrived at the three locations. Flower production was cited as being continuous all summer by their introducers, however, this was not true for some of the cultivars evaluated. Disease resistance was the most alarming quality I evaluated with many of the so-called “disease resistant” roses being the exact opposite. I explain all these variables to demonstrate what is involved in proper plant evaluation. For a complete report of my rose research trial, see: Jull, L.G. 2004. Hardy Shrub Rose Research Trials. Combined Proceedings of the International Plant Propagators Society vol. 54:429-434.

Knockout® rose is very disease resistant with non-stop blooms, but not hardy in zones 3-5 without significant winter protection Photo credit: http://www.gardeningknowhow.com/wp-content/uploads/2011/08/knockout-rose-400x600.jpg
Knockout® rose is very disease resistant with non-stop blooms, but not hardy in zones 3-5 without significant winter protection Photo credit: http://www.gardeningknowhow.com/wp-content/uploads/2011/08/knockout-rose-400×600.jpg

Now, you may ask, “Why are these new plants, including roses, promoted by these large nurseries as being the best plant around when in effect, they are not?” Many new introductions are from nurseries that trial their plants in their location only. So a plant that performs well in the state of California might not perform the same in Michigan and vice versa. There isn’t the scientific rigor applied to these new plant evaluations that would occur by non-biased, university researchers who have no stake in selling or promoting plants to the public. This is where the beauty of applied, scientific, university-based studies can play a huge role.

Also, these new plants should be evaluated over numerous years, at various locations/soil types, climates, with appropriate replications of each new plant in a random arrangement (not all planted together). This type of quality research is done by a few large nurseries but it is seldom done this extensively by others anymore as demand for new plants is never satisfied and the cost of trialing over several years and locations is too costly.

Unfortunately with increased costs and significant budget/program cuts, most university research is now geared toward larger, basic science studies that have high indirect costs built into the grants. These funds, usually 50% or more of the grant total, go directly to the university to cover overhead. The researchers do not see or can use overhead funds. Ornamental plant evaluation research is now considered either non-fundable by granting agencies, not “scientific or scholarly” enough by their own departmental colleagues or provide significant overhead funds back to the university.

Some researchers rely on their various nursery and landscape associations for small amounts of research support, while others try to piece meal together small amounts of research funds. With the increasing costs of land (yes, we do have to pay for research space at university research stations), plants (not all are freely given to the researchers), labor, supplies, etc., it is becoming critically important to seek alternative funding sources as most federal and state granting agencies do not fund ornamental plant evaluation research. Many of the new initiatives for federal grants seek to fund food crop based research, especially in organic and sustainable food production. Applied ornamental horticulture plant evaluation research at universities has plummeted with most new plant evaluations conducted by the large nurseries that introduce these plants.

There is another source for evaluation of these new plants. Various arboreta and botanical gardens around the U.S. are conducting evaluation trials. I am a fan of these studies as these gardens and evaluators are also not in the business of selling plants and can provide some analysis, though it is usually only at one location. Richard Hawke, Chicago Botanic Gardens Plant Evaluator and Horticulturist, has done an excellent job of evaluating many species of herbaceous perennials and a few woody plants. He publishes Plant Evaluation Notes: (http://www.chicagobotanic.org/research/ornamental_plant_research/plant_evaluation), a series of wonderful publications that help both the amateur and professional gardener to choose appropriate plants for the Upper Midwest. There are other botanical gardens and arboreta that do the same, with evaluations based on their local climatic conditions. I often rely on Mr. Hawke’s recommendations when choosing herbaceous perennials in my Wisconsin garden and have yet to be disappointed.

Chicago Botanic Garden Plant Evaluation Notes Source: chicagobotanic.org
Chicago Botanic Garden Plant Evaluation Notes
Source: chicagobotanic.org

So the next time a new plant comes across your way, think twice before buying it. There is the philosophy “Buyer Beware”, and I do recommend people to buy plants, but instead of buying 10 of one cultivar, try one or two of the new plant and make a judgment call the following year or two after you planted it. This is especially important for landscapers who design and plant large amounts of plants. You might be surprised to see the “best thing since draft beer” plant being anything but that. As some of us know, there is nothing better than draft beer (or whatever beverage you really like).

Laura Jull, Ph.D. aka The Lorax

Scientific Beekeeping

Apis mellifera
Honey bee (Apis mellifera), Courtesy of Charles Sharp at Wikimedia Commons

When I first moved to the country in the late nineties, one of the first things I wanted to do (after establishing several vegetable gardens to indulge my tomato obsession) was to become a beekeeper.

So I took a six week course sponsored by West Virginia University, read the full documentation available from the University of Maryland and Penn State as well as back issues of beekeeping magazines, and checked with some hobby beekeepers in the area.

Unfortunately, at that time, honeybees were being devastated by an invasive species … the Varroa mite (Varroa destructor), and the amount of effort needed to keep colonies free from them discouraged me, and the message I was getting from experienced hobby beekeepers was one of “be prepared”, and “I’m, regretfully, giving it up because of the effort involved.”

Basically … too much work … not something I was willing to commit to.

But I never lost my fascination with them (and other bees and wasps, for that matter.)

Then in 2006, I started hearing about Colony Collapse Disorder, or CCD, and it was while researching it, that I found the site of Randy Oliver, a biologist who also made his living beekeeping.

The site is Scientific Beekeeping.

From his About tab.

I started keeping bees as a hobbyist around 1966, and then went on to get university degrees in biological sciences, specializing in entomology. In 1980 I began to build a migratory beekeeping operation in California, and currently run about 1000 hives with my two sons, from which we make our livings.

In 1993, the varroa mite arrived in California, and after it wiped out my operation for the second time in 1999, I decided to “hit the books” and use my scientific background to learn to fight back.

The site is not a beginner’s “how to”, but a way to share what he has learned with others:

What I try to do in my articles and blogs is to scour scientific papers for practical beekeeping applications, and to sort through the advice, opinion, and conjecture found in the bee magazines and on the Web, taking no positions other than to provide accurate information to Joe Beekeeper.

(If you’ve been following my blog posts here, then you’ll probably recognize the pattern of places that rise quickly in my judgment, as ones I like)

The site has become my “go to” source for all things related to honeybees, and I recommend it to others who want to stay abreast of the subject.

Scientific Beekeeping

FrankenFoodFacts

Sunset papaya cultivar
Public Domain Photo of GMO Papaya via Wikimedia Commons

 

The subject of Genetically Modified Organisms, or GMOs, first came to my attention sometime in the fall of 2009, not long after I started following the Garden Professors Blog.

I stumbled across a site called Biofortified, run (at the time) by a couple of grad students in the field, who were trying to accomplish the same thing that the GPs were, combatting myths and misconceptions about a subject, with research based information.

I spent about 2 years lurking there, because much of the information at the time was over my head, and seemed to be targeted to fellow scientists to help with getting the information out.

So I’m incredibly pleased to introduce you to the blog of Dr. Layla Katiraee, a scientist in a related field, but with little to no experience at all with the topic of GMOs, so spent time learning about it and sharing what she learned with the public.

She is now also a contributor to Biofortified.

One of the best things I like about the blog, is her continual checking with “the spouse” to see how her posts might be viewed from someone outside the field.

Here’s a great example:

So, the spouse has often complained that I don’t have a post with an overview of what transgenesis means and the transgenic (GMO) crops themselves. They’re scattered throughout the history of this blog, but not in a single place.

What does this mean? To explain, I have to go to the beginning: the working units within any cell are proteins. Proteins are made up by linking together amino acids in a given sequence. The exact amino acid sequence is defined in the cell’s DNA; the DNA blueprint for a specific protein is known as a gene for that protein. In general, one gene encodes for one protein (of course, there are exceptions). Since there are thousands of proteins, there are thousands of genes. We’re still figuring out what different genes/proteins accomplish.

Another great post on how the science of safety testing works …

The first thing to keep in mind is that there are many aspects to safety. In our example, we have to select an aspect of water safety that we want to examine: health impact, water transportation, water treatment, proper water storage, etc. For our example, we’re going to select “health impact”.

Then, we have to come up with a null hypothesis. Spouse, I know that it’s counter-intuitive and the double negatives in these statements suck, but unfortunately, it’s a key aspect of this whole article. The baseline for much of research is that there’s no impact or no difference. It’s the researcher’s responsibility to disprove that hypothesis, ie. to show that there is a difference or that there is an impact. So for our exercise, our hypothesis will be “Drinking water does not cause cancer”.

So follow her blog, FrankenFoodFacts, or follow her articles elsewhere on Biofortified, or her Twitter feed, and gain some better understanding about the science behind GMOs.

Out of the bottle and into the bag

Last week I was having lunch with my mom at our favorite nearby nursery/café. After failing to resist the grilled cheese sandwich (3 cheeses! And buttery panini bread!), we walked off lunch in the garden supply part of the nursery. Normally I’m on my best behavior when I’m shopping with my mom (i.e. I don’t take photos of things I’m going to take to task on the blog). But like the 3-cheese grilled sandwich I was unable to resist the bags of biodynamic compost.

Biodynamic compost is now available at garden centers
Biodynamic compost is now available at garden centers

Long-time readers of the blog may remember my earlier column and post on biodynamics. Since I wrote the original column over 10 years ago I’ve watched biodynamic marketing move from boutique wines to coffee, tea, tomato sauce…and now to garden products. Really expensive garden products, as in $19.99 for one cubic foot of compost.

An "untapped source of power and majesty" makes this compost different.
An “untapped source of power and majesty” makes this compost different.

What makes this bag of compost worth $19.99? One has to assume it’s the biodynamic preparations used to treat the compost. They’re referred to in the label under “concentrations of yarrow” and so on. Do these preparations make a difference? The label suggests it might be to restore the soil’s vitality. Is there validity to this claim?

It's doubtful that all of these ingredients are locally available. And why are so many materials needed?
It’s doubtful that all of these ingredients are locally available. And why are so many materials needed?

In 2013 I published a review of the scientific literature on biodynamics, specifically looking at whether biodynamic preparations have a measurable impact on anything they’re applied to. In a nutshell, the answer is no. (Though this article is behind a paywall, I can send a pdf to you by email if you’d like to read it.)

Don’t let packaging and magical words sway you. Compost made with local materials like bark or agricultural wastes and certified by the US Composting Council is reasonably priced and sustainable.

 

Show me the data!

One of my favorite bumper stickers from days gone by said simply “Stop Continental Drift”. Good luck with that.

stop_continental_drift_530

Today’s topic deals with another type of drift – a phenomenon one of my professors referred at ‘Bibliographic drift’.   This type of drift occurs when authors cite a paper without bothering to look up the original source.  Then a second author cites original source based on the first author’s paper; then a third author cites it based on the second paper and so on and so forth.  This is why grad students learn that second citing is a cardinal sin.

 

It’s an easy trap to fall into even in the age of access to electronic journals.  It can happen in all sorts of ways, especially if the point the author trying to support is something that is intuitively appealing and not likely to be questioned.  For example, I was recently reading through The Practical Science of Planting Trees by Gary Watson and E.B. Himelick.  It’s a good book with lots of great info and photos but under the section on digging the planting hole there is a subsection “wider is better”.  This is something we all ‘know’ but there is no data with any scientific rigor to support it; at least not that I’ve ever been able to find and I’ve looked repeatedly.  So I was intrigued to see Watson and Himelick cite four papers to support the notion that wider is better. Cool. So I went through the bibliography to look up the citations.

Can you dig it? My former research technician Dana Ellison installs a tree in Detroit.
Can you dig it? My former research technician Dana Ellison installs a tree in Detroit.

First up, Arnold and Welsh 1995. Effects of planting hole configuration and soil type on transplant establishment of container-grown live oak. J. of Arboriculture 24:213-218. This paper doesn’t even discus planting hole width, at least not directly.  The authors looked at various planting hole configurations (round, square, star-shaped) but made a point to keep the planting hole volume the same. Zero points for wider is better.

 

Next, Corley 1984. Soil amendments at planting J. Environ. Hort. 2:27-30. One of the experiments in this paper compared root and shoot growth of four shrub species transplanted from #1 containers into holes that were with 1.75x or 3.5x the width of the root-ball. The author measured root and shoot growth after two years and the results were a mixed bag.  They found the wider hole was better about half the time, the other half of the time it didn’t make a difference.  One point for wider is better (sort of).

Next, Montegue et al. 2007.  Influence of irrigation volume and mulch on establishment of select shrub species Arboriculture & Urban Forestry.  33:202–209.  The title of the paper says it all; the authors compared water relations and growth in response to mulch and irrigation but planting hole size wasn’t included as a variable. (Spoiler alert: mulch improved growth and water relations). Zero points.

Last and most interesting, Watson et al. 1992. The effect of backfill soil texture and planting hole shape on root regeneration of transplanted green ash. J. of Arboriculture 18:130-135. In this study the authors looked at new root growth and shoot and diameter growth for three years after transplanting green ash trees into planting holes that were 1.2x, 2x, or 3x the width of the root ball. And they found… nothing. Well, not nothing but they didn’t find any effects of planting hole size on root density, shoot growth or caliper growth. To help visualize the response I’ve summarized their growth data three years after transplanting below. One point for it doesn’t matter.

Cumulative growth response of green ash trees to planting hole width 3 years after transplanting. adapted from Watson wt al. 1992
Cumulative growth response of green ash trees to planting hole width 3 years after transplanting. adapted from Watson wt al. 1992

 

As a final note I include a photo from the Waston et al. paper 1992.  The photo is fuzzy but the caption should be clear.

watson et al 1992

So where does that leave us? Digging a wider hole doesn’t hurt, except maybe your back. And I think that’s part of the appeal of this advice:  If it’s more work it must be better. Dig a hole 2 times, 3 times, 10 times the width of the root-ball if you want. Just don’t say “Research shows wider is better…” because it’s ambiguous at best.

Nature’s Poisons

Nature's Poisons
An early 17th century “plague panel” from Augsburg. Public Domain picture courtesy of WikiCommons

It’s more than a little bit intimidating to be a part of the Garden Professors team, since I have no advanced degrees, and my undergraduate degree is in Mathematics, with no formal training in Botany, Horticulture or Plant Science at all.

I am, however, an avid and active hobby gardener; I read a lot; and I have a life-long love of learning and sharing what I’ve learned with others, which led to a nine-year stint as a county Extension Educator, implementing a county wide mosquito management program for West Nile, with additional responsibilities for pesticide education and consumer horticulture.

So, what I hope to do with my space here on the GP site, is share some of the other blogs that I read on a regular basis … ones I’ve learned to trust for either the expertise, or writing style, or some additional insight into plants or gardening, or issues that arise in gardening circles.

First up this week … Natures Poisons, a blog written by Dr. Justin Brower a forensic toxicologist – that’s someone who is employed CSI-like, to investigate possible crimes related to toxicology.

His blog isn’t directly related to his profession, however … as Dr. Brower explains:

I also like plants and gardening, and seeing how there are thousands of plant based poisons, there’s no shortage of material.

Some things I will write about:

•Nature’s Poisons – all types chemical and biological
•Interesting poisonings – recent and historical
•Old uses of Nature’s Poisons

So he’s a gardener, like me, and the rest of you folks who follow the GPs.

I like the blog, not only for the wit and wisdom, but also because it puts a realistic perspective around the idea of “natural” … something which we gardeners often mistakenly equate with benign.

Plants make chemicals to protect themselves from being eaten, and the science behind that, and our use, and avoidance of them, is fascinating.

To get you started exploring the blog, here’s one of my favorite posts there discussing Horseradish, or Armoracia rusticana

Not only do you learn a lot about glucosinolates, and other chemicals in horseradish, but also a peek into the mind of a scientist.

Back inside the warm confines of the house, I cut off the tops of the horseradish roots, rinse off the dirt under water, and scrub them clean with a wash rag.

The “typical” method of preparing horseradish is to grate or grind the horseradish with an equal amount of water, wait a few minutes for the allyl isothiocyanate to build up to the desired hotness, then quench the reaction with a tablespoon or two of vinegar. Throw in a pinch of salt, and you’re done.

You’re always cautioned to do this in a well ventilated area or outdoors.

But screw that.

One, it’s cold outside, and two, and most importantly, I’m a Scientist.

If you like the blog, you’ll likely also like this book by Amy Stewart … Wicked Plants.

Enjoy!

Spec errors mount

For years I subscribed to Consumer Reports. I appreciated their objective approach to product testing and lack of advertising. In their own words, their policy is to “maintain our independence and impartiality… [so that] CU has no agenda other than the interests of consumers.” But recently they’ve veered off the science-based trail – at least the one running through our gardens. Their approach to plant and soil sciences is more pseudo than science. And last year, after 30+ years of loyal membership, I quit my subscription when Consumer Reports began partnering with Dr. Oz (see here for instance ).

So until today I’ve been blissfully unaware of whatever CR has published on gardening and garden products. Then this post appeared on our Garden Professors blog group page ). I’ve included some of the article below along with my italicized comments in brackets.

“Lawn care without the chemicals: rid your yard of weeds and pests with these mostly organic solutions”
“…Here are 10 common weeds and pests that plague homeowners nationwide, along with chemical-free measures [“chemical-free?” Well, we shall see.] that should be effective in bringing them under control. For more information, go to the websites of Beyond Pesticides and the Great Healthy Yard Project. [Neither of these two sites is remotely scientific or objective.]

“Dandelion – what is it? A perennial weed whose common yellow flowers turn to windblown seed. Telltale signs. Though a handful of dandelions is no big deal, a lawn that’s ablaze in yellow has underlying problems that need to be addressed. How to treat. Like many broadleaf weeds, dandelions prefer compacted soil, so going over the lawn with a core aerator (available for rent at home centers) might eradicate them. [Like many broadleaf weeds, dandelions will grow anywhere. That’s why they’re called weeds.] It also helps to correct soil imbalances, especially low calcium.” [I’m curious how CR determined a “soil imbalance.” And did they test their hypothesis experimentally?]

Dandelions obviously suffering in a calcium rich soil

“Barberry – what is it? An invasive shrub with green leaves and yellow flowers, often found in yards near wooded areas. Telltale signs. Left unchecked, the shrub’s dense thickets will start to choke off native trees and plants. How to treat. Cut back the stems and paint their tips with horticultural vinegar or clove oil (repeated -applications may be needed). Burning the tips with a weed torch might also work.” [Yes! Chemical free vinegar and clove oil! By the way, clove oil has NO demonstrated efficacy for this application. And I’m sorry, but “burning the tips” of barberry is just going to stimulate lots of new growth below the damage. Just out of curiosity, how many people have problems with barberry in their lawn?]

I think you’d notice this in your lawn…

“Crabgrass – what is it? An annual weed with a spreading growth habit. It’s common in the Northeast, in lawns with poor soil conditions. Telltale signs. Lots of bald spots, especially after the first freeze, when crabgrass dies off. How to treat. Have your soil tested. Lime or sulfur may be needed to adjust the pH. Aeration is also recommended. Corn-gluten meal, applied in early spring, can be an effective natural pre-emergent herbicide. [Corn gluten meal, applied in early spring in climates where it rains, is an effective fertilizer for crab grass.]

Crabgrass with increasing levels of corn gluten meal.
Courtesy of Tom Cook, Oregon State University.

“Kudzu – what is it? An aggressive climbing vine that’s common in parts of the Southeast and the Midwest. Telltale signs. The thick vine forms a canopy over trees and shrubs, killing them by blocking out sunlight. How to treat. Pull out the vine and, if possible, its taproot. Be sure to bag and destroy the plant or its vines will regerminate. If the root is too thick, paint the stump with horticultural vinegar or clove oil repeatedly, or burn it with a weed torch.” [Ditto the comments for barberry.]

Have fun painting stumps. (Wikimedia)

“Canadian Thistle – what is it? An aggressive creeping perennial weed that’s found throughout the U.S. Telltale signs. Look for outbreaks in vegetable gardens, particularly those with peas and beans. [I have no idea where this little nugget of nonsense came from. It’s a weed! It will grow ANYWHERE! It doesn’t need peas and beans!] How to treat. Repeated hand weeding and tilling of the soil will weaken its extensive root system. [Because tilling the soil is such a great way of suppressing weed seed germination. And it’s really good for your lawn, too.] Planting competitive crops, such as alfalfa and forage grasses, will keep it from returning.” [Yes, do replace your lawn with alfalfa and forage grasses.]

Your new, improved lawn (Wikimedia)

“Fig Buttercup – what is it? A perennial weed with yellow flowers and shiny, dark green leaves. It’s common in many parts of the East, Midwest, and Pacific Northwest. Telltale signs. The weed will start to crowd out other spring-flowering plants. It can also spread rapidly over a lawn, forming a solid blanket in place of your turfgrass. How to treat. Remove small infestations by hand, taking up the entire plant and tubers. For larger outbreaks, apply lemongrass oil or horticultural vinegar once per week when the weeds first emerge. It might take up to six weeks to eradicate.” [Now in addition to pouring vinegar on your lawn, we’ll try lemongrass oil instead of clove oil. Another unsubstantiated application – maybe lemongrass because buttercups are yellow? Makes about as much sense as anything else. It smells nice though.]

Color coordinated weed control

“Phragmites – what is it? An invasive grass species found nationwide, especially in coastal wetlands [where so many of us have lawns]. Telltale signs. Dense weeds can crowd out other plant species without providing value to wildlife. How to treat. Cut back the stalks and cover the area with clear plastic tarps, a process known as solarizing. Then replant the area with native grasses.” [Solarizing pretty much nukes everything that’s covered – not just the weeds. In fact, the rhizomes of this weed are so pernicious I’m not sure that solarization would work. Am still waiting for CR to test their hypothesis in an objective and scientific manner.]

Phragmites rhizome (Wikimedia)

So, Consumer Reports, I’d love to come back to you. But until you start applying your own standard of objective rigor to everything you cover, I’ll have to pass.

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.

According 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.

Now, 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.