Filthy dirt

Experimental work with plants takes some planning and some time.  Nothing magic about plant growth so you just have to wait, but time to get a glasshouse experiment going.  And so an energetic student ready to get underway with the next experiment asks, "Where do I find the dirt?"  Thus they innocently gave voice to a common misconception.  TPP answers, "You find dirt under your finger nails, and in certain kinds of books, movies, and websites."  "Perhaps you mean soil?"  Soil and dirt are not the same at all.  "Does that mean my research proposal has to be changed?"  "Yes."  Careful consideration has to be given to the soil used for experiments.  Sometimes you can use a commercial potting mix, or just make one, but a potting mix is not at all like the soil these plants naturally grow in.  Soil is more than just a whole bunch of eensie weensie rock particles and organic matter, it also contains microorganisms to the tune of about 8-10 million per cubic centimeter (for the non-metric, a volume about the size of a sugar cube).  Not only that, but the plants growing in a particular area can greatly alter the soil microflora to their benefit and perhaps the detriment of others, and in particular that includes invasive plants.  This produces some problems in the experimental design, but let's let that go for now.  Fortunately your mentors were thinking way ahead and soil (sod actually) was dug 2 months ago and set aside in anticipation of this experiment; soil from our research prairie, soil affected by an invasive plant, and soil from an adjacent grassy meadow, so a very practical consideration is next.  Those buckets with great big old chunks of sod need to be screened to remove rocks and root systems and in the process reducing the big old chunks into a much finer texture.  It's a great student activity for a cold winter afternoon.  So, no dirty thoughts, just become one with the soil.  Wonder how many hits this title will generate of people looking for real "dirt"?  We'll see if the data for click ins and outs, i.e., zero time spent reading the blog goes up.  Something like this happened a week ago when the daily traffic at TPP jumped up by a factor of 3 for no particular apparent reason producing quite a blip in the data.

Serious Stuff from Plant Scientists

Some time back quite a number of plant scientists around the world were asked about what they thought were the most important questions facing plant science. The responses were distilled down to one hundred important questions facing plant science research. As you might guess some of these questions are pretty heavy duty. Here's a sample. Q2. Which crops must be grown and which sacrificed to feed the billions? Here's a snippet of the answer: "we may be forced to choose between production of staple food crops to feed the world population and the production of luxury crops, such as tea, coffee, cocoa ..." Aaaaaaah! Who could face that without coffee? And this would be in addition to improving crop productivity and using more previously forested land for food production. This isn't a future you're going to want to see, but our children's children may well see it. At times it's hard not to be pessimistic. Some of you may want to comment about some of the other questions or the answers as we presently see them. HT to Botanical Garden and Conservation International.

Why don't students want to study plants?

Others have wondered the same thing? Why is it that plants capable of fascinating the Phactor for so many years are of so little interest to students? There is no one answer, but several factors do come into play, but before outlining these for you, some smallish percent of our biology students do like studying plants, about 10% on average.
Firstly, and most importantly, it takes a certain mental and emotional maturity and sophistication to apprectiate something a subtle as plants. This certainly explains the attitudes of many of my zoological colleagues. Flower children versus colleagues red in tooth and claw. They're just like most of our students, but grown up. Secondly, you have to know something about plants to appreciate them, and today's biology, especially in the USA, has a heavy human biomedical emphasis that even ignores non-vertebrate animals. A student complained about our animal behavior course as being about "insects" rather than animals. Wow! Unfortunately biology students who think biology is about baby zoo animals is all too are all too prevalent, and they become high school teachers. So thirdly, high school teachers educated in this system perpetuate the cycle by treating plants as uninteresting items forced into the curriculum. When the Phactor complained once to a chair that botanists weren't being considered for many jobs, he said, "You won't be happy until half the department are botanists (at the time it was 8 out of 34), but what will they all teach?" Genetics, cell biology, ecology, evolution, physiology, etc. was my answer, but of course, "real" biology is animal biology, so this could not be tolerated. He was dick about lots of other things too, so no big surprise in his attitude. To a great extent generally held preconceived notions about plants (and fungi) color people's attitudes, and even many gardeners revolt, or get revolting, when you try to learn them something about plants, sort of a don't muddle my poor head with knowledge, and never ever use a scientific name (which is why the Phactor blogs every now and them about knowing your genera; oh, it's been that long?). Fortunately the master garden programs are reversing this for many. Even worse, higher education, which should be a bastion of biological diversity, is run by pin-headed "bean" counters so if your area of expertise is on the short end of the stick, well, too bad. No one needs all of biology, just enough to get people into medical school, and so it goes with no real regard for the discipline. It''s like a conspiracy.

What is a botanist

This query (?) is asked many times a day (30+), and the web site ChaCha provides an answer. After the obvious omission of a question mark, which calls the ChaCha mission into question because after all how can you provide decent, reliable answers if you cannot properly pose the questions, this site provides dreary, lifeless, dictionary type of definitions, which while technically correct, are bereft of the soul and passion that drives botanists. You might as well define beer as a carbonated, fermented hops and malted barley beverage, which while perfectly correct hardly makes you want a cold one. Anyone interested enough in botany to ask this question deserves far better answers.

Clearly the one thing they didn’t do is ask a botanist. Our diversity is quite impressive, and while it is technically correct that we botanists study plants and other green organisms, and we are scientists, we are so much more, and some of the nicest people on Earth to boot. So click yourself on over to the Botanical Society of America and see what a bunch of real botanists say about themselves and what they do.

Everyone wants to be a botanist, it just takes some people longer to figure this out than others.

What's new in botany?

My colleagues have been very busy, and the things you can learn from them.

Horsetails may have been a favored food of sauropods, and cycads the least favorite.
Water clover ferns have been around unchanged for over 100 million years.
Somebody else got did a similar experiment to one of mine and got the same results!
One colleague began his talk with a summary and conclusions because of his penchant for going too far too fast and covering too much. There was applause.
Our scientific discipline has some really bright young people.
The newest molecular techniques are completely unknown to me, even the name was new.
At least two chapters in a book I'm writing have to be revised. Blast.
Evolutionary relationships among seed plants remain uncertain.
Hornworts are now considered the sister group to the rest of land plants, which are mostly vascular plants. Liverworts are now even more certainly the oldest lineage of land plants.
Termites were eating wood more than 100 million years ago.

OK, you get the flavor. Some of these and others deserve elaboration, so explanations will be forthcoming. What sounds most interesting?

Plants are dull and uninteresting!

OK, the Phytophactor is pissed. TV networks producers think programs about plants are dull and boring! What a bunch of simple-minded morons.

Plants do everything animals do, except crap and bite, but they do it with a great deal of dignity and grace. The bottom line is simple, it takes a sophisiticated intellect to appreciate something as subtle as a plant. A colleague of mine has pointed out on many occasions how people are "plant blind". To them plants are merely a passive backdrop against which animals move. Such people suffer from a simplistic perception, and they probably have difficulty appreciating fine food, classical music, and art too.

Like many other things, their inability to appreciate something is directly based on their ignorance of the subject. I suppose this isn't surprising because TV certainly appears to be aimed to the least common denominator of our society, so the people in charge must themselves operate at that level.

I am proud to say that I have wasted not one nanosecond on "reality shows". Exposure to Regis Philbin kills more brain cells than multiple head injuries. And the people who put such programming on TV think plants are uninteresting. Hmm, it does give you pause. No wonder scientists are considered elitists, real eggplant heads. Well, consider this, you would be naked, miserable, and hungry without plants, so cultivating an appreciation might be a wise thing to do.

Plant of the week (eon?) - Cooksonia

This picture of Cooksonia is pretty remarkable. Not so much for displaying this plant's simple beauty, not even because the picture is actually in focus, but because this plant has been extinct since the Devonian some 380 million years ago.

This fossil is looking particularly good because it is a model on display in the Darwin House at the Royal Botanical Garden at Kew.

Cooksonia is significant because this is the first land plant sporophyte to show apical branching. As the axes grew, the apex divides into two equal axes, a type of branching called dichotomous. Fossils show axes of Cooksonia branching thusly 1 to 4 times. Each axis then terminating with a sporangium. This appears to be a way of getting the maximum number of dispersable offspring from a single fertilization event.

Cooksonia is also significant because at the time this was the tallest plant of its day. These axes towered some 5 centimeters (nearly 2 inches) above the substrate. It is also the earliest appearing plant to have vascular tissue, xylem, although the oldest specimens found in Silurian sediments may not have possessed true xylem.

This plant is the first step on the way to trees, and it did not really take too long for the first trees and forests to appear (near the end of the Devonian).

Plant of the week - October 21, 2008

Azure beauty berry

Callicarpa dichotoma (Verbena family).

Generally when it comes of fall color you think of plants whose leaves turn a nice bright color. But the beauty berry has the neatest electric blue display of fruits in September and October. This particular one holds a cluster of fruits above each leaf axil on a gracefully arched branch. What could be nicer. This particular fruit color, bright blue, is pretty rare among temperate zone plants, but more common in tropical forests. This Chinese species has more cold hardiness than American beauty berry.

Small light purple flowers preceed the fruit, and while nice enough, are no match for the fruit display. Flowering and fruiting are on new wood, so the bush is cut back to 12-18" every spring, or you let the bunny rabbits do it for you over the winter. This low shrub grows fine in light to medium heavy shade. You might consider placing it where it could be viewed from above, so next to walkways or below windows.

Now that frugivorous birds are migrating through, the berries are beginning to disappear, so the display definitely attracts some species. This is one of the nearly 150 species growing in my personal arboretum.

Does botanical research offend the dignity of plants?

The Swiss ethics committee has declared that plant scientists are not allowed to do research that offends the dignity of plants. This initially struck me as hard to believe because I think of the Swiss as a pretty level-headed and practical people, but this is just goofy.

Maybe this was just a Swiss attempt at humor. But this is for real and my botanical colleagues must deal with this. Now I do think certain plants have a majesty, and they certainly can be violated, for example, by cutting down redwood trees to make somebody a porch deck. But is the dignity of a cabbage offended when it is converted into coleslaw? Does it regain any of its dignity when converted into sauerkraut? Are my prairie plants dignified? Does a fertilizer treatment offend them?

You really have to wonder about what kind of cuckoos are on the Swiss ethics committee because they are guilty of pure anthropomorphic thinking. Unfortunately until some level heads prevail, my botanical colleagues in Switzerland are stuck dealing with this.

What this is all about is a resistance to genetically modified crops. And we must presume that altering a plant’s genetics is an affront to its dignity. I guess a certain case can be made for that. Let’s face it, a toy poodle doesn’t have too much dignity. But humans have been altering the genetics of plants ever since their domestication began. Wonder if ethicists like seedless grapes? Have they ever had a fertile banana? Eating around all those big, hard seeds is something special. What could be a bigger offense to the biological dignity of an organism than to propagate sterile plants when their whole purpose was to reproduce?

So who will decide what offends the dignity of plants? To help out the Phytophactor will channel your research plants to determine if their dignity is offended, for a modest fee, payable in Swiss cheeses, of course.

Dealing with ecological rejection

I firmly believe in sabbatical leaves, and it is my great good fortune to have been allowed to take four of them. The academic world of science is difficult and it takes a concerted effort to try or explore new things, to learn new areas of science, and while taking a break from the week to week routine. As this is being written my fourth and last sabbatical leave is winding to a close. I'm taking a week to visit friends, a week to attend national scientific meetings, and that leaves two weeks to prepare for classes. Already I have people clamoring for a laboratory guide.

As part of this leave's exploration into new topics, I collaborated with an old friend and colleague. I dragged him to the rain forest to study insects that consume flowers, but aren't involved in pollination (my usual tropical topic). These insects had never been studied before, and in fact no one even knew these flowers were their brood substrate, or that they had two broods, a smaller one that produced bigger adults, and a larger one that produced smaller adults, or that they had a female biased population, and a number of other things. And we had fun doing it.

Oh, but science isn't science until its published, and our manuscript was just rejected. And the reason was it was too much natural history and not enough ecology. This means we didn't conduct an experiment aimed at determining some ecological principle, but just figured out a previously unknown biology. In the eyes of ecological snobs, ecological studies trump natural history. But ecological study is impossible until you know enough about the system to manipulate it.

Ecology is coming of age. It's getting snobby. Long treated as an inferior, less than demanding, descriptive field of science, barely divorced from Victorian natural history, ecology is now asserting itself by dumping on the very field that gave rise to ecology. This is because biology is done by people, and many people have need of a pecking order and having someone lower down to peck at to feel good about themselves. And this is nothing but someone inforcing their personal belief that ecology, as they define it, is better, more important, higher quality science than natural history.

Fortunately I know how to deal with such rejection. My lapsed membership in the organization will now be on permanent hold. Another publishing venue will be found, and our natural history will become part of biological knowledge, and then some stinking ecologist will use our study to do some "real science" that can get published in a top ranked journal, well, top ranked for ecology.

Most successful plant in the world

People call universities to find things out that aren't easily looked up, and for many years all the weird plant related questions have been forwarded to me. I'd like to think it was because of my success at answering such questions, as opposed my being weird. So it was not a surprise when my phone rang recently and someone wanted to know, for an article they were writing, what was the most successful plant in the world?

Now that's an interesting question because it can be answered from several different perspectives depending upon how you define success.

My first idea was that the most successful plant in the world was one of the domesticated grasses, a cereal grain. From its beginning as a wild middle eastern grass wheat has become the most commonly cultivated plant in the world. But rice provides the majority of calories to the majority of the world's people. And altogether cereal grains occupy something like 70% of all tillable land.

Now such plants are successful because they were useful and important to humans. Cereal grains have moved with us and native plant communities removed for the culture of these cereals, and in a manner of speaking cereal grains have become immensely successful. But without human intervention, they would not long persist in such vast areas.

And of course there are weeds. Weeds are adapted to disturbance, so they grow rapidly reproduce quickly, in great numbers, and then disperse widely. You probably didn't need to be told that, but now you know why. Nature produces disturbances, so weeds occur naturally to take advantage of these sites. But the thing that humans do best, and most frequently and thoroughly, is create disturbance, so weeds have greatly benefited by human activities. Agriculture can be defined as a systematic disturbance of natural communities for the purpose of growing domesticated plants and animals. So weeds have greatly prospered and gained great success as a result of human activities too, but they have done it on their own. No wonder such successful plants are so hard to eradicate.

Another concept of successful is longevity. Some aspen or sagebrush clones appear to be 10,000 years old, and that's a long time for one individual to exist. Some bristlecone pines are known to be over 7,000 years old. Such long-lived organisms are certainly successful. Osmunda cinnamomea, the cinnamon fern, certainly is a longevity contender too. 70 million year old fossils of this fern have been found that are virtually identical to the living species. This makes this fern the oldest known species, period, plant or otherwise. I have a fossil fern stem from the Carboniferous era over 300 million years ago that is anatomically identical with modern Osmunda ferns. So the group has been around for a long, long time. Selaginella, a clubmoss, is another genus with a very long history dating to the early Carboniferous, and that makes it the oldest living genus.

If you take a broad definition of plant, then perhaps a particular cyanobacterium (sometimes called blue-green algae), like this one pictured here on the right, might be considered the most successful and influential plant in the entire of Earth history. Sometime 2 to 2.5 or so billion years ago this cyanobacterium became a chloroplast giving rise to all of the other green organisms. When you look outside your window you see green because this incredibly tiny green cell, now functioning as a cellular component in all plants, has been duplicated in countless numbers. Cyanobacteria, including chloroplasts, are the only organisms that use water in photosynthesis for a hydrogen source, which leaves oxygen as a by-product. All of the oxygen that makes up 20% of Earth's atmosphere (and its ozone layer) is a by-product of photosynthesis. Talk about influential! This changed Earth history completely. Aerobic organisms such as ourselves were not possible until there was oxygen in the atmosphere. So in terms of sheer number, ubiquity, and influence, the cyanobacterium that became a chloroplast is probably the most successful green organism in the entire of Earth history. But we are probably wrong to call it a plant.

So there you have it. Depending upon the type of success you were looking for, those are the most successful plants.

Field work - snapshots in ecological time

Only other field biologists can appreciate and sympathize with this problem. Studies done in the field cannot control for all the variations in nature, in particular normal variations in weather patterns, and so each study is actually a snapshot in ecological time. The trouble is that we try to extrapolate from these snapshots, and sometimes that doesn't work. And even worse you worry that the effects of weather can overwhelm your treatments.

The effort involved in field work makes the situation even worse. The steadfast effort involved in maintaining long term field studies is beyond most of us. For this reason I really admire Deborah and David Clark whose quarter century survey of tropical forest tree growth in Costa Rica is laudable just for its longevity, its contribution to understanding changes that may accompany global warming notwithstanding (Tropical rain forest tree growth and atmospheric
carbon dynamics linked to interannual temperature variation during 1984–2000. D. A. Clark, S. C. Piper, C. D. Keeling, and D. B. Clark. 2003. PNAS 100:5852-5857.). If you haven't read this paper and want to see good evidence of changes that accompany increases in carbon dioxide and temperature, I recommend it.

In just the 3d year of our field study on the effects of hemiparasitic plants on the prairie community, and already the year to year variation seems destined to swamp any treatment effects. Last year our plots had so many hemiparasite seedlings that we wondered if eradication was a feasible treatment. They just kept sprouting, and we just kept weeding. Those seeds were the product of the 2006 season. The spring of 2008 was very different. It was cold and wet, and this affected the number and/or activities of bumblebees because seeds of our hemiparasite are scarce even though it flowered like crazy. Last year I could collect seeds in huge numbers, nearly 250,000 in about 20 mins. But this year a similar investment in collecting produced a very small volume in comparison. Guess we won't have so many seedlings to remove next year.

But that's not all. Last year produced a bumper crop of seeds, but so far they have not been germinating like last year at all. In 2007 we could find hundreds per square meter, and this year when we decide to monitor seedling mortality, seedlings are hard to find. It makes for easier eradication, but is messing with out demographic study.

That's just how field work goes. And it's why those rare long term studies are so valuable. If we monitored pollination, and seed production, and seed germination for 25 or so years, we would probably understand many of the variables. But when something gives you a significant result, well, dang, you just know it's important and real because everything was working against you getting any results at all.

Field work and blogging - incompatible?

April stands for so many things: spring begins, tax season ends (very significant if you're married to a CFP), the end of the semester is in sight, deadlines and events abound, and all of this pales because it is also the beginning of field season, that time of year when the natural cycle of your research organism requires that you begin spending significant amounts of time out of your office, out of your lab, and away from your university. There is a satisfying component to this work, especially if you are smart enough leave electronic communication devices turned off (or, if you are truly enlightened and have achieved oneness with creation, you do not own such things).

It is a good sign when you manage to find 107 out of 108 quadrats after your prairie has been burned. The 108th is still there, but it's location somewhat uncertain until the corner pin is found using a metal detector. And it is a good sign that the exposed bones do not belong to that graduate student who went missing last semester. It is always a surprise to see how many skeletons, both big and small (deer, beaver, fox, vole), are visible after a prairie burning. I wonder if my patch of prairie is something of an elephants' graveyard that all injured or terminally ill animals seek out.

But in spite of the fact that I am relieved of teaching and administrative duties this spring, I find it difficult to have the time to do field work and keep up with everything else. Two journals are waiting for me to review articles on floral biology. A doctoral research proposal is demanding my immediate attention. My own expansive estate is calling for attention. And I have a book manuscript and three research articles to complete.

And then there is the Phytophactor. In the middle of winter, when field work is out of sight and out of mind, starting a blog seemed like a good idea. I like the venting blogging allows. But I wonder about other bloggers, especially those in science. Apparently very few do field work. Maybe very few do science either judging by their attention to the pseudproductivity of blogging. Many seem rather young, and perhaps they have fewer responsibilities beyond their teaching and research. Or they have much smaller gardens, if any. Very few seem to be ecological or botanical. Does this say something about the temperment of botanical ecologists, or is this just a measure of how much time they have, or how little sleep they need? Dare I suggest field work and blogging may be incompatible? Nah!

Cellulose – Tough Old Stuff

Cellulose is best known as the cell wall material of land plants and algae, and some 100 billion metric tons of cellulose are synthesized each year. Good thing some fungi and bacteria have cellulases because otherwise we would soon be up to our bippies in cellulose.

Cellulose is widely known to be a very stable molecule. The herbarium I curate has 200 year old pressed, dried plant specimens that look no different from specimens collected last year. And since the primary material present is cellulose, unless these specimens get burned, flooded, eaten by insects, or discarded by some hopelessly stupid people, like the trustees of the University of Utrecht, who just closed down their famous herbarium, these specimens should last hundreds of years longer providing an invaluable scientific record.

But cellulose can last much, much longer. Cellulose fibrils recovered from ancient salt deposits have been aged to 253 million years old, the oldest known intact biological macromolecule (Griffith, Willcox, Powers, Nelson, and Baxter, 2008, Astrobiology). I’m not sure this is true because spores are older, and spore walls are made of sporopollenin. Nothing decomposes this macromolecule; it is forever.

Still cellulose is tough stuff. What’s funny about cellulose though is that it’s just a polymer of glucose, a plain old 6-carbon sugar, long chains of honey. Your primary source of calories is starch, amylose, and it too is just a polymer of glucose. So in basic terms both cellulose and amylose are pure glucose, but you can digest one not the other. You have an amylase, but not a cellulase. The difference between chewing on a cracker and a woody twig is largely based on the two different ways glucose monomers can be linked into a polymer.