Mendel’s Garden #4: A genetic journey through an organic garden

Welcome to the fourth edition of Mendel’s Garden. It is a belated edition, and I apologize to those waiting to read about the latest for this new blog carnival, which should hopefully become the place to go for the latest and greatest in blogging about genetics. Something happened last week, and all of my time was sucked away like nectar forage for a honeybee. In fact, it had to do with honeybees, local politics, science, human disease, and now the local paper! I’ll fill everyone in on those details later this week.

I have hosted the Tangled Bank before, with over 40 submissions, the real challenge was how to sift through all the excellent posts and figure out how to organize them without making it look like the reference section of a scientific research paper. Mendel’s Garden seems to be in its infancy, as there have only been six submissions. So rather than scour the net for anything related to genetics to include, I thought I would fill this edition of the Garden with a tour through a real garden. The EC Garden at UC Davis, where I keep my bees, grow plants, and stir up a little controversy. Genetic controversy.

Nestled between a highway, dome-shaped houses, an organic farm, a highway and some birghtly-colored student housing, lay the Experimental College Community Garden. It is a place where students, townies, professors and children can rent a plot of land to grow a garden. They can grow flowers, herbs, fruits (face it, most “veggies” are fruits), and vegetables. Tools are shared, wood chips are dropped off from the campus’s groundskeeping division, and gardeners can collaborate on projects. Just recently, gardeners came together to build a set of cobb benches to relax outdoors.

Work parties are also a common occurrance. With reggae music booming across the fields, gardeners have come together to clear brush, prepare new plots for potential renters, and share in the wonderful weather. It is amazing sometimes how much can be accomplished in so short a time.

So let’s take a little tour, shall we? The EC Garden is run by the Experimental College, which offers courses on everything from learning magic tricks, (guess who taught that course?) to podcasting, home crafts, dancing, and martial arts. They also offer some organic gardening lessons through the garden, organized by the garden coordinators. The EC Garden is a resource for education as much as it is soil & sun for your veggies.

So let’s see what people have grown. Here we have a plot that seems to prefer an arrangement of flowers rather than veggies. Usually, I see gardeners go for the edibles first, but these new arrivals have opted for a plant of beauty instead.

Tulips are interesting plants. Michael Pollan wrote a book called The Botany of Desire, and he chose to write about tulips as a representative of plants that we breed according to our standards of beauty. He’s coming to UC Davis this fall, and will give a talk based on his most recent book, The Omnivore’s Dilemma. You can read about the appearance here, but if you stick around, I’ll let you know more about it. That’s because I’ve been asked to be a panelist and I’ll get to ask him a couple questions. Maybe I’ll be able to grab him for my show!

Anyway, let’s move on just a few steps to the right, and take a look at one of the other functions of the garden. Garden coordinators and volunteers have painstakingly sprouted and planted some native grasses of California. When American Settlers arrived in the valley, they dramatically changed the landscape with respect to the flora in the valley. Their cattle preferred other plants as forage, so the humans dutifully did away with much of it. The sign here tells more about the native grasses. Click here for a closer look.

Conservation is important. And in order to more effectively practice conservation we need to have the kinds of tools that can help us do it right. This brings us to Jacob’s submission at Salamander Candy. In How Useful are Neutral Genetic Markers in Conservation?, Jacob explores the strengths and shortcomings of using microsatellite and mitochondrial DNA markers to study genetically distinct groups of organisms. Are they giving us an accurate picture of what’s going on in the field?
Let’s continue down the path to the left. There we find another sign educating people about the ecosystem at work in the garden. There are more signs to educate people about the way things work out here. It may look like just grass, trees, and shrubs, but many plants are here for a purpose.

For example, there are Elderberry trees growing around here, and a former gardener and colleague of mine at The California Aggie, Wolfgang Rougle, made a special sign to tell the story of the Elderberry Beetle, Desmoceros californicus dimorphus. A threatened species, in part because of the loss of habitat, but curiously, it seems, also because we seem to think that we can just plant elderberry trees anywhere and they’ll be ok.

Joe Kissell, at Interesting Thing of the Day, submitted a piece on the plight of the Spotted Handfish. This small fish that lives off the coast of Tasmania has fins that look and act like legs. It can swim, but it prefers to walk along the sea floor. But it’s an endangered species, and might soon take its final walk. Read all about it and then join me again to continue around and back into the garden.

Here are some more grape vines. Now you’re thinking, wait, didn’t I just see grape vines in full greenery, and what’s with these suddenly dormant grapes? Well, not all these pictures were taken at the same time. You probably also didn’t notice the pink almond blossoms, which flower in the early spring, as well as the tulips. But there are many pathogens facing grapes, noticably Pierce’s Disease, or Xylella fastidiosa, which UC Davis researchers are working fast to understand. Douglass Cook, a recent guest on my show, and a former professor and boss of mine, is one of several working to understand this disease. Currently, vineyards spray to kill the vectors, and tear up infected vines. Without a solution to this disease, the lush greenery you saw before might instead look like these.
There is another interesting aspect to these grapes – that of grafting. These and other cultivated grapes are actually two genetically distinct plants attached to one another. One makes up the root system, the other the shoots (and fruits!). Grafting has allowed us to combine the best of two different plants, sometimes those that we cannot breed together. There is even a tree in this garden that has three completely different fruit tree scions grafted onto it! Even stranger, fruits such as apples are not possible without grafting. You get a completely different tree grown from seed, one that is not too fun to eat. Sometimes the genetics of the rootstock can influence the shoot system, so there’s a whole area of science devoted to this rootstock-shoot interaction in the Pomology department at UC Davis. Organic is defined around what is “natural” and what is not, but grafted grapes seem to fit in somehow, no matter how unnatural the practice of grafting is. You’ll never look at table grapes the same way again.

An interesting idea being worked on here at UC Davis is to engineer the rootstocks of grapes to be resistant to the diseases in question. Because the eventual grapes that you consume in one form or another come from a plant that is grafted onto the rootstock, you will never actually eat a GMO if they do this. So here’s the question, could you grow an organic vineyard that has genetically-engineered rootstocks protecting the grape scions? If you think that you can’t involve genetically-engineered plants in an organic farm, think again.

In Hawaii, there was a a huge problem with papaya ringspot virus decimating the papayas. The University of Hawaii and others put together a project that resulted in genetically-engineered papayas that were resistant to the disease. Farmers welcomed it, and now, most of the papayas you probably eat from Hawaii are genetically engineered. But these papayas can’t be considered organic under current standards. Instead, organic papaya farms on Hawaii surround their organic papaya stands with a wall of genetically-engineered papayas, preventing the ringspot virus from spreading to the interior. What you are eating is not a GMO, but its existence depends on one. Let’s get back to the garden.
The EC Garden is home to many creatures. Although I could not get a good shot of any, we have plenty of orb spiders. you know them from the beautiful circular webs that they spin. Sadly, many people refer to these creatures as “bugs.” Although the “true bugs” belong to the insect order Hemiptera, the term generally refers to insects. And spiders aren’t insects. But why? Jbruno at The Voltage Gate answers the question with Why Spiders aren’t Insects IV: Adventures in Homology. He has already continued on to the fifth post in the series. Who knew that we could know so much about the evolutionary genetics of spiders?

Moving on, here is a nice planting of roses, another example of mingling with the genetics of plants over a long period of time (in human terms) to conform to the idea of beauty. Let me tell you, these blossoms are doing a good job. I came from Sonoma County, home of Luther Burbank, a well-known plant breeder who worked on varieties of crops, as well as roses. Currently, I can think of no one with the kind of visibility in crop genetics today that Luther Burbank had then. In my opinion, geneticists (and other scientists) should be rockstars, and Hsien-Hsien Lei at Genetics and Health agrees with me, with her piece, Rockstar Geneticists. Find out who are the rockstars today!

Let’s get into the meat of the garden, now. Some of the plots have had an impressive amount of work done on them. Take, for example, this mega-plot. We’re not supposed to sell what we grow here, but there ain’t no way one person needs this many herbs! Hehe, herbs full of scores of uncharacterized chemicals. Why do they have them? Are they for us? Was peppermint (foreground) put here on this Earth for humans to consume? Actually, peppermint is a sterile hybrid of spearmint and water mint. So we’ve been messing around, crossing species, and there are plots and plots of this plant growing all over the place in this organic garden. Amongst some of the most ardent adherents to organic food, there is an underlying philosophy that often paints crops as gifts from nature, not unlike a sort of creationist belief. I once heard a professor of integrated pest management refer to it as that. The fact is, humans had their hands deep in the creation of every food we eat, and mint is no exception. But if you are interested in real Creationist Genetics, PZ Myers will give you more than your fill of their shill. Or is it swill?
One of the garden coordinators tends this plot. And I thought that my rows were precise – this rivals GPS-aided planting. Garlic, onions, potatoes, and corn, laid out in an almost perfect grid of plants. The soil has been dug up, mixed with compost and carbon, and sprinkled with rice hulls. Basically, tilled to perfection. Or is it? Intensive tilling reduces the earthworm count, and releases methane into the air – a greenhouse gas more potent than carbon dioxide. Organic farms often employ excessive tilling to control pests, which not only reduces soil quality in the long run, but also requires energy – from fossil fuels. One of the ways that we can address this is to adopt no-till farming practices. Interestingly, one of the tools that has enabled some farmers to drastically reduce their tilling is genetic engineering. Crops engineered to be tolerant to an herbicide can be sprayed for weeds, the crop left behind, and the soil left un-tilled. Obviously, spraying an herbicide such as Roundup would make it non-organic, but is there some way we could engineer a trait such as this into crops without requiring the use of such a spray? Wait, I forgot, genetic engineering isn’t allowed in organic agriculture. Nevermind, it was just a thought…
Here we have some volunteer flowers growing between a cactus and a tuft of grass. The gardener seems to have welcomed the arrivals and kept them watered and happy. Although they may seem alike, genetic diversity lies beneath those blossoms. Alan Eshleman at Genes & Drugs found out some about his own genetic diversity in My Visit to a DNA lab II. Apparently, his own son, who runs the lab, has found out that his father is different at nucleotide position 16224 in his Mitochondria. The haplotype that contains this SNiP is shared by 8% of maternal Ashkenazi Jews. Soon we may all be able to learn the histories of our chromosomes through DNA testing. Let’s keep moving – see that tree in the middle background? That’s where my garden is, one that is sure to stand out, not because it grows particularly awesome or varied stuff, but because of the contrary opinion expressed by it, which by now you might have guessed.

MOGEL ENGINEERING, Genetic Engineering And Organic Gardening. (PRO GMO) By Karl J. Mogel and Ariela Haro. What a shocker. No really, what a shocker. My mother’s old civil engineering business had a couple leftover signs, and I peeled off a few letters, painted a couple new ones one, and voila! Two years ago, I decided that I wanted to express my opinion about genetic engineering and its exclusion from organic gardening. At first, it felt weird having such a big sign, and I was worried that it might get damaged. Thankfully, no one has wrecked it, although there has been some damage done to the garden, which I will talk about another time. For a while, no one said anything about the sign, except to ask in passing if I was growing any GMOs in the garden, to which I responded, oh no, but if you’d like to know why I have the sign, I’ll tell you. One person kept right on walking, uninterested, but many people have stopped to talk to me about it. One person jumped for joy when they saw it. One interesting thing did happen the summer I put it up – the garden contract was updated, and lo and behold – they changed it to make the exclusion of GMOs explicit! Check it out here.

There has been one “negative review” of my garden sign, which I received by email early 2005. A gardener called for the removal of my sign on the grounds that it was causing “unnecessary suffering,” which I contested. Tolerance of a point of view is a necessary thing, and the first amendment doesn’t stop when people get riled up. But he was the only person who reacted in such a way. Negative reviews can help you point out your deficiencies, as this reviewer pointed out that as a ‘teaser’ sign, it doesn’t explain everything nor go in much depth. But a presentation is better than a perfect presentation, or is it? Nature Genetics published an article on genetics blogging, which RPM at Evolgen dices up in his negative review of it. They even got the founder of Mendel’s Garden wrong! Read about it in Bad Article on Genetics Blogging. (Paul Decelles started Mendel’s Garden) Read a text file of the article here.
Neatly weeded by hand, here are my onion rows and chard during the winter, early 2006. In the background, you can see some spearmint growing in a patch next to my built-in pond. The chard grew so strong and vigorously that I dubbed it The Chard Row of Supreme Jealousy – due to the expressions on the faces of passing gardeners. Other species of animals on this planet ought to be jealous of us too, for there has been vigorous growth and change in some human genes since we split evolutionary paths with our closest relatives. Carl Zimmer at The Loom has the scoop on an RNA gene of interest with And the award for the fastest-evolving piece of human DNA goes to…

As I was saying, weeding in our gardens is done by hand, as with many organic farms. California banned hand-weeding in agriculture due to humanitarian reasons, except in organic agriculture, which argued that it needed hand-weeding to survive. For anyone who has stooped to yank a few interlopers in their lawns, weeding by hand is no joke. Is there some way to address the issue of weeding without resorting to chemical sprays, breaking one’s back, or shredding with relentless plowing? Yes there is.

Geneticists at UC Davis and elsewhere have been studying a gene that gives flood tolerance to rice plants. I know one of the scientists involved, Pamela Ronald. I interviewed her last December, and she told me that they were working on engineering this gene into rice cultivars that grow in specific regions. As it turns out, the genetically-engineered rice grows well, and gives the plants tolerance to being flooded, as reported by Ruth Shaeffer of the Biotech Weblog. Now, farmers can grow rice, and kill off the weeds through flooding, and not ever have to plow them up or spray them. Sounds like a fantastic new development, read about it at Genetically-Engineered Flood-Tolerant Rice.

Pamela Ronald is also a proponent of the combination of genetic engineering and organic agriculture, and I credit it her with opening my eyes to its exclusion, and the potential benefits of combining the two approaches.
Winter crops aren’t all that I planted in my garden. As you can see, I planted corn, squash, eggplants, petunias, and tomatoes. You can just get a glimpse of each of these in this picture to the left. Corn is a fascinating plant, a grotesquely enlarged grass that thanks to humans now dominates millions of acres. It is made all the more interesting as it was the plant that mobile genetic elements were discovered in. The varied colors in “indian corn” are caused by transposons, nicknamed “jumping genes,” which move themselves around in genomes with the help of an enzyme called transposase. This natural means of genetic modification moves DNA around from chromosome to chromosome, turning on and off different pigment genes in the process. The result are colors in corn kernels that seem to disappear and reappear all around the cobb. Makes our more precise methods of inserting genes look a whole lot better.

The tomato plant you see in the top right, is a tomato that has been bred to have high quanities of lycopene, an antioxidant that is gaining interest amongst consumers. One of the potential long-term benefits of better plant breeding and engineering is the improvement of the healthful content of our foods. Besides that, there’s an interesting fact about tomatoes that you probably didn’t know. The tomatoes that we eat have been bred with poisonous, wild relative species of tomatoes, and selectively bred to remove the poison. However, who knows what other genes have slipped in during the process? I’m not trying to raise alarm, in fact the risks are very low, but it is in a higher risk category than engineering one or two genes from the same species. Think about that when people argue for GMOs to be labeled, but not plants that have been outcrossed. (Another issue, which I hope to address later.) Take a closer look at my harvest from this week – someone’s going to have to make room for eggplant parmesan!

Strawberries are bizarre fruits. In fact, they aren’t even fruits! The red, sweet flesh of the strawberry is actually an enlarged Receptacle, which is at the base of the flower. Fruits, in contrast, are ovaries that enlarge and are filled with seeds. The actual fruits of the strawberry are the little dots on the surface of the red flesh, which are achenes with a seed inside each. But the strawberry itself is a False Fruit. An interesting bit of nerdy trivia that you can use to alienate you from your friends and family! 🙂

Anyway, strawberries are also odd because of their chromosome numbers. They can be diploid, hexaploid, and octoploid, with 2, 6, and 8 copies of each chromosome, respectively. Most of the strawberries we encounter are octoploid, however, a very fragrant strawberry known as the musk strawberry has six of each chromosome. There was a recent article in the Smithsonian Magazine about a plant breeder who is trying to resurrect this old variety, and is hoping to be able to put them in your hands in the near future. Have a look at some Berried Treasure.

Now it’s time for me to wrap this up. I hope that you have enjoyed this tour of the EC Garden at UC Davis, and what I have to say about the plants growing here, and the intermingling of the latest genetics blogging (and articles) in the fourth edition of Mendel’s Garden. Next to this image of a DNA sculpture I put up in my garden, I want to talk about ignorance of genetics. During this multi-season romp through small garden plots, I’ve talked about a few things I have learned about the genetics of the plants we grow for various purposes. We’ve touched on creationist genetics, a critical review of a paltry article on genetics blogging, genetically-engineered rice, and genetics in conservation.

Finally, I would like to present the idea that the public does not know enough about what goes on with those double-helixes in our nuclei. As reported in Nature, presented here at the Panda’s Thumb, the U.S. lags behind the developed nations on acceptance of evolution, and also, understanding of genetics. Well, at least we beat Turkey.

This is not acceptable. Genetics is an incredibly important field, it is important in medicine, human history, evolution, the food we eat, and the future of other species on this planet. I believe that if more people understood the genetic evidence for evolution, it would gain some more acceptance. I also believe that if people understood the genetics of crops to a greater extent, they would be more open to genetic engineering, and someday, we may see nutritious foods grown in healthy, integrated farms, that would make everyone proud. From the consumer to the farmer, farm hands to the grocers, and finally, the geneticists and other scientists that made it happen.

Unfortunately, I will have to abandon my garden when I leave Davis, but that’s not the end of this cause, just a relocation of it. When I go, I will leave a special sign for them, like Wolgang did for the Elderberry beetles. Growing a garden is like meditative therapy, it carried me through my stresses while I got my Bachelor’s in genetics. If you want to read about what I did in one of the genetics labs I helped out in juxtaposed against what an Intelligent Design research assistant does, then take a look at Monday Madness: What would an ID research assistant do?
The question was raised in Nature Genetics – Would Mendel Blog? Of course he would. Mendel’s work was forgotton and ignored, and the exposure that a blog could give him would have been phenomenal. This world is full of budding Mendels, and let’s hope that more of them become interested in communicating genetics and improving the public’s understanding of the stuff of life. We need more scientists who want to communicate what they are working on. Submit your stuff for the next Mendel’s Garden!

We know he would blog, but if Mendel knew what we know today about genetics, a better question might be, what would he grow in his garden?