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.

Another unnecessary tree failure

The end of August brought an unseasonable rain- and windstorm to the Puget Sound region. We had some spectacular tree failures which I missed seeing as I was out of town. But one of our Facebook group members, Grace Hensley, was on the ball and took some great photos of a fallen purple-leafed plum. The first thing you see is the complete lack of a stabilizing root system.

"Rootless" purple leafed plum
“Rootless” purple leafed plum

Now look at the base of the trunk, which is actually a massive circling root that has girdled the trunk over time.

A big wooden donut
A big wooden doughnut

By now you must be able to see the orange twine extending from the base of the tree to the soil. Yes, those are the remains of the balled-and-burlapped clay root ball that was planted many years ago. Commercial landscapers will assure you that tree roots can grow through the burlap and establish. And this is sometimes true, as in this case.

But what doesn’t happen when the whole B&B mass is plopped into the ground is that circling woody roots aren’t discovered and corrected. Over the decades what started as a small circling root grew bigger and bigger, slowly squeezing the trunk and preventing it from developing girth at that point. It’s kind of like a blood pressure cuff being pressurized but never released.

Trunk growth was prevented by the girdling root
Trunk growth was prevented by the girdling root. The broken part here used to be in middle of the wooden doughnut.

In time, the constricted point becomes so unstable that the tree breaks. Look are how small the trunk that’s still in the ground is compared to the trunk of the tree itself. Windstorms are often the final push these failing trees need.

How long before this neighboring tree fails, too?
How long before this neighboring tree fails, too?

Commercial landscapers say it’s too costly to remove the twine and burlap and clay surrounding the roots, not to mention doing any of the corrective root pruning that might be needed. It’s easier to just plant the whole thing and cross your fingers that the tree lives past the warranty date. This is what happens when you consider a tree as just another design element rather than a living organism.

As a homeowner, however, you can insist that your trees are planted correctly (if you have someone else do the work). Or you can do it yourself. The bare-root method (sometimes called root washing) is an emerging science and it requires thoughtfulness, but it’s certainly better than the conventional approach in terms of long term tree health.

Ray’s 2015 Tomatoes

I thought I’d share some of the new varieties of tomatoes I’m growing this year, along with some old favorites.

Garden Gem and Blush
Garden Gem and Blush

First up is a picture of a new variety from Dr. Harry Klee’s research at the U. of Florida called Garden Gem, along with Blush from Artisan Seeds.

Garden Gem is a new hybrid, poised to take the fresh market grocery store tomatoes on. Same disease resistance, same shipping quality, but with much improved flavor.  Dr. Klee describes the research at his site:

The first step in a flavor improvement program starts with a simple question: what do people like and what’s in the varieties that people do like? In order to answer this question, we took a giant step back to “heirloom” tomatoes.

Blush has been around for a few years, an open pollinated variety with a great history of breeding, since 8 year old Alex was instrumental in choosing its parent lines.

The year that the cross that created Blush was made, Alex participated in setting up crosses for our annual winter crossing list.  He chose 3 of the 19 crosses to be made that year, after the other 16 had been established (by a PhD-holding plant breeder with big plans).  The striking outcome is that about 90% of the value from that year came from Alex’s 3 crosses.  The progeny from his crosses continue to permeate most everything we are doing.  

Both have something in common in that one of the progenitors for each is a variety called Maglia Rosa.

Note also the meatiness of Garden Gem … I think it will make a great all-purpose variety for the home gardener for canning and sauces, as well as fresh eating.

Another aspect, which you can’t tell very well from the picture of Garden Gem, is the faint yellow striping in the skin, and some later fruits that have a hint of a nipple on the blossom end.

GardenGemGreenTiger
Top Garden Gem Next Maglia Rosa Bottom Green Tiger

Next up, another Garden Gem, followed by Maglia Rosa, and then Green Tiger. See hints of vestigal “nipple” alluded to earlier in the Garden Gem.

Currant
Currant Tomato Solanum pimpinellifolium

Cute little feller … a Currant Tomato. Actually, a different, but very close relative, and source of much research and study, since it still grows wild in the Andean mountains … PITA to pick, but great “conversation piece” when used as a garnish. Solanum pimpinellifolium 

We grew these as part of a variety trial a few years back … more for the novelty. But when we did a Brix test that year, it was the highest recorded.

A little odd, since the flavor is not in the least “sweet” … coulda been just more concentrated. Dunno, really.

AuntRubyGermanGreen
Aunt Ruby’s German Green Heirloom

Aunt Ruby’s German Green. One of my long term favorites.  It’s a more tangy than sweet heirloom variety that stays green when ripe.

Green Zebra
Green Zebra

Green Zebra … an open pollinated variety bred by Tom Wagner and introduced in 1983 according to Wikipedia.

Green when ripe, and with yellow striping.
Dunno why most of mine this year are exhibiting a lobed shape, rather than perfectly round.

I may have to buy new seeds next year.

Garden Treasure
Garden Treasure

Another hybrid from the research lab of Dr. Harry Klee of the University of Florida. This one is named Garden Treasure.

I don’t have any information about its progenitors, like its companion Garden Gem. 


Beautiful, baseball-sized fruit. Very slight indication of green shoulders, and with the same faint yellow stripe as Garden Gem. Also a heavy fruit, very meaty.

And very good flavor. Pretty good balance between tart and sweet. I can see these being popular with fresh market growers.

I sourced the seeds from Dr. Klee’s efforts by making a small donation to his research program at the University of Florida.  The idea was brought to my attention by his colleague, Dr. Kevin Folta in this blog post.

We can look forward to new, satisfying varieties that merge the best of production traits with the historical successes that delighted the senses. These are new heirlooms, and they open an exciting peek of what is coming in plant genetic improvement.

Here are more details of the story and the individual varieties! I hope you order some seeds and give your feedback to Dr. Klee so he can build your ideas into the future of tomatoes!

I often complained about the flavorless red things that you find in grocery stores, so here was a way to support researchers working to overcome that.

And Dr. Klee is not alone.  Rutgers University went about restoring the old fresh market hybrid varieties that gave “Jersey Tomatoes” their deserved reputation.

Read about Ramapo, Moreton, and a processing tomato at the Rutgers site Rediscovering the Jersey Tomato .

And there are other research programs at Purdue, University of Michigan and Israel conducting similar efforts.  No doubt there are others.

The future of good tasting grocery store, and fresh market tomatoes seems bright.

Don’t just stand there like a statue

Posted by Bert Cregg

 

Reading through Linda’s recent article in Arboriculture and Urban Forestry “Nonnative, Noninvasive Woody Species Can Enhance Urban Landscape Biodiversity” (Arb. & UF 41:173-186) reminded me of some thoughts I had while I sat through a talk by Doug Tallamy at the New England GROWS conference back in February.  As most GP blog readers are likely aware, Tallamy is the author of Bringing Nature Home.  The basic premise of the book is that native insects only feed on native plants and therefore the use of exotic landscape plants will cause ecological food webs to collapse and the end of the world as we know it.

 

Looking at things critically, there was certainly plenty to nitpick in the talk.  For example, to illustrate that insects feed more on native than non-native genera, Tallamy contrasted Quercus, a genus that includes hundreds of species distributed across the northern hemisphere, to Ginkgo, a monospecific genus (heck, a monospecific order) with a limited native range in China.  Tallamy also compared the food value for birds of seeds of five native shrubs with five Asian exotics.  The North American plants all had higher nutrition, which leads to one inescapable conclusion: If you’re a bird-lover in Asia you need to plant more exotics from North America.

 

But, as I said, those items are nitpicking.  In an apparent effort to appease critics, Tallamy addresses the question of whether it’s ever OK to plant exotics.  He says yes, but think of them as “statues” – nice to look at but devoid of any ecological value – and then put up a slide of a landscape with a bunch of statues photoshopped in.  All analogies break down eventually but the ‘exotics as statues’ model fell apart before the slide hit ever the screen.  First off, native insects, birds, and other wildlife do utilize nonnative plants and I’ll refer you to Linda’s review and her 100+ citations on that point.  But just as importantly, nonnatives can also provide many of the same environmental benefits as native plants.  Statues, on the other hand, don’t cool buildings, sequester carbon, reduce stormwater run-off, and create vertical structure and cover for wildlife – OK, statues provide perches for pigeons, but that’s about it.  Landscape plants, and trees in particular, can provide a myriad of ecological services – but they can only provide these functions if they are alive to do so. Despite the intuitive appeal of, “Native plants are adapted to our local environment”, in many urban, and even suburban, environments this is simply not true due to urban heat island effects, top-soil removal, compaction and other site disturbances.

 

In his talk, as in his book, Tallamy demonizes the typical suburban landscape showing a photo of an expansive lawn with a lone Bradford pear tree.  OK.  Is the problem here the pear? If we changed the pear to, say, a lone shagbark hickory would anything change dramatically?  No, but this does bring me to a point of agreement with Tallamy.  The fundamental problem we face in our landscapes is lack of diversity; not only species diversity but also structural diversity and age class diversity.  If we can build diversity and generate ecosystem services with natives; great, go for it. But we need to understand that our list of suitable native trees is shrinking (as an aside, ignore Tallamy’s recommendation to plant green or white ash if you live in eastern North America). Vilifying, or even banning, nonnatives will ultimately reduce diversity in urban and community forests and their ability provide ecosystems services, not enhance it.

Where double flowers come from (sometimes)

Doubling of flowers — the development of extra petals — is a common mutation, and often beloved by gardeners. Sometimes double forms of flowers become so popular that gardeners hardly recognize the single flowered, wild-type. Wild roses, for example, have just 5 (or, in once case, 4) petals and look totally different than the extra petal flaunting varieties familiar from gardens.

Rose rubrifolia, like other roses before human breeders got their hands on them, has only 5 petals
Rose glauca, like other roses before human breeders got their hands on them, has only 5 petals

Doubling usually happens when gene expression gets mixed up and bits of cells that were destined to develop into anthers develop into extra petals instead. Sometimes a single mutation makes a dramatic change all in a go, but more often, the path to a double flowered cultivar starts with something like this:

Iris x norrisii with three ugly little petaloids full of potential
Iris x norrisii with three ugly little petaloids full of potential

Here we have a flower of Iris xnorrisii (formerly known as x Pardancanda norrisii) with the usual six petals, and three “petaloids” — anthers that are stuck in an ugly transition between anther and petal. This is a seedling in my garden this year, and I’m going to grow out lots of seeds from it — hopefully some of them will get past the petaloid stage to full on extra petals and hey presto, a double flowered variety will be born!

Joseph Tychonievich