What's with microbiologists and ecology?

As a member of a biological sciences faculty, I regularly get to interact with colleagues with very different expertises. What a joy! Among this biological diversity, no greater rift in understanding and mutual appreciation exists than between microbiologists and organimal biologists. Even worse is that it's a very one-sided bigotry born of a narrow, biomedical, reductionist approach to the study of bacteria.

Twenty years ago our microbiologists complained about biological diversity and evolution as required courses. Apparently systematics and evolution where not subjects with any apparent importance to microbiology. The same was said about educating pre-medical students who had no need to understand the basic concepts of biology.

Well, thanks to Carl Woese enough progress has been made in the study of prokaryote phylogeny that these objections became pretty ridiculous. Now they object to the inclusion of ecology in the core curriculum of biology. Wow! Another subject without any relevance to microorganisms.

However, more than anything this simply demonstrates the remarkably narrow perspective of my microbial colleagues who cannot see beyond their reductionist approach to biomedicine. This is particularly amusing, or dismaying, because the worst offender studies resistance to antibiotics. What does he think is happening when antibiotics are used? Apparently he thinks antibiotics do not exert a selective force on bacteria and that the community structure of microorganisms is unaffected. More and more studies are finding that interactions among bacteria form communities that can be disturbed and cause severe health problems. My own daughter was given the wrong antibiotic for a C-diff infection (test gave a false negative) and it made matters much worse! C-diff is a natural part of our gut's bacterial flora and is held in check by interactions with other members of this community.

Fortunately not all members of this field are so narrow in their perspective. Microbiologists exist who have discovered evolution and ecology, and their relevance to research, even biomedicine. A google search on "bacterial ecology" generated 2,600,000 hits, and a great many of these were journal articles. A similar result was obtained by googling "microbial ecology" (3,480,000 hits), and of course there are journals that specialize in these fields.

Such ignorance would be quite amusing except that the education of our students suffers from these narrow-minded views.

The real meaning of Baccalaureate

As part of a totally bizarre rant about masonic conspiracy and the control of higher education by the occult elite, David Flynn demonstrates a level of scholarship and understanding that makes the rest of his conclusions more understandable. In other words he’s so wrong about these simple things that you can readily understand how he made a hash out of more complex issues.

“This accomplishment [completion of a bachelor’s degree] earns the student a Bacchus laurel, for this is really what “bachelor” means. Bacchus is the Roman version of Dionysus, Greek god of wine revelry and facades, lies, and drunkenness.”

Correcting this in reverse order the baccalaureate degree was nicknamed the “bachelor’s degree” because at that time virtually all university students were unmarried men, bachelors, and of course, many people still think the B in B.A. or B.S. stands for bachelor’s, but of course, b stands for baccalaureate, the fruit of the laurel. Some college catalogues even make this mistake, all the more shameful for a scholarly institution. It was the custom in ancient Greece to crown champions with wreaths of laurel leaves, the noble laurel, Laurus nobilis, which is also found in your cupboard as bay leaves. And this custom gave rise to titles such as poet laureate. So you receive a degree as the fruits of your academic labors, and the fruit of the laurel, unlike the fruit of the grape, has no connection Dionysus. But then this author was intent on taking something traditional and noble and casting it as tawdry, but in the process Flynn reveals himself to be either a poor scholar and/or one who deliberately misleads. Me, a member of the occult educational elite, I’m betting on the combination of the two.

Letting foxes run the hen house - the Republican war on science and the environment continues

On Monday last the AP reported on new draft rules being proposed by the Bush administration to gut the Endangered Species Act. This would be the biggest change to the groundbreaking legislation since 1988, and would not require the approval of Congress. Currently, federal agencies are required to consult with an independent agency — the Fish and Wildlife Service (FWS) or the National Marine Fisheries Service — to determine whether a project would harm an endangered species. The AP reports that under the new rules, agencies would simply be able to “decide for themselves”.

Wow! Let's not drag any inconvenient scientific data into the discussion, let's just let government agencies, run by political appointees acting under super, double secret orders to make sure everything conforms to official ideological policy. More than any previous administration, the Bush administration has tried to create their own reality. And woe be to anything that stands in their way. If you don't like the results of studies by government sciences, well, just edit the final report to reflect your wishes.

The way the Bush administration has operated in other arenas, I'm surprised they didn't just define species out of existence. All of this shows the contempt this adminstration has for the American public, a majority of which actually support environmental protections. Congress won't pass such legislation, then find a way to change things such that congressinal approval is not needed.

Until Sen. McCain condems the Bush approach to governing this country, he doesn't stand of chance of getting my vote.

Do you teach here at the university?

It's that time of year when lots of strangers, all very conspicuous, are appearing around the campus here in Lincolnland. They mostly readily identify me as a campus native probably because I'm usually reading a book, manuscript, or paper, which isn't seen that often off campus, and they often want to ask some questions. Also I always offer to assist anyone who looks like they are a bit lost. In either instance, they often ask "Do you teach here at the university?"

I usually answer, "Yes, teaching is among the many duties of my job as a professor." I do not find teaching demeaning, but I do get annoyed by how many people fail to understand that university faculty are far more than teachers. We're experts and scholars, learned intellectuals, authors and researchers; we're more student (in a professional sense) than teacher.

I try to tell myself that many of our students are still first generation college students, but many of the people who ask are clearly college graduates if not alumni. The problem is that many of these people, as well as current students, attend and graduate from college without ever doing anything scholarly themselves. Their only interaction with faculty was the usual classroom student-teacher dichotomy. If they weren't worried about an exam or pissed at a grade, they never sought out a faculty member.

Since we (the university, which is us) allow this to happen, in a way, I am responsible for creating the very situation that annoys me. As best I can judge, we in the sciences do a fairly good job of engaging and involving our students in our scholarly enterprises, but then we work in our offices and laboratories so we are accessible. Many of my colleagues in the humanities are only in their offices for office hours; they work at home. I understand the problem of interruptions, but at home they are inaccessible to students. So I wonder about the level of interaction on a day to day basis. Maybe science just has more low level things for students to do that provide them with regular contact with faculty.

So I'm not a teacher like your high school teachers. I'm the guy who teaches the high school teachers, and writes their textbooks, and does the research they should occasionally teach about.

Bad line karma

I'm not an overly impatient person. I'm not pushy, impolite, or discourteous when waiting in lines. I don't cut in, jump ahead, cut off, or act to someone else's disadvantage. So where did my bad line karma come from?

I ask this after 1 hour of waiting at the Canadian-USA border. The official border is right there, I can almost touch it, but the customs booth is still a couple of hundred yard, and probably close to another hour ahead. Across the expanse of carefully groomed grass and gardens in the median, the backup for entering Canada is barely 10 minutes. Five days ago the line to enter Canada stretched back a kilometer or more and I was an hour and 10 minutes in line, and of the two lanes, the slowest one (right) to boot. So today I decided to stay in the left lane, and the right lane is outpacing the left by a factor of about 1.5 even with merging cars from the duty free shop.

If I pick a grocery store checkout lane, no matter how short it looks, it will immediately bog down. That one little lady buying a single can of food for her little dog will take forever looking for two loose pennies in the bottom of her handbag to make exact change. And then the register will run out of paper tape and have to be replaced before printing her receipt, and then a new checkout person will come with their drawer before it is my turn.

Over and over this happens. If a hell exists, something I think remarkably unlikely, but if mind you it does, it will consist of endless lines, a cue from hell so to speak, an exquisite form of torment.

Even worse I can think of no way to improve my karma. The guy in front of me just changed lanes by cutting off another car that was a tad slow to inch forward. And now he is already 3 cars ahead. My wife says that if I'm so annoyed to do the same thing, but that would require rapt attention and quick reflexes, so I stay resigned to my fate. I hope they strip search the bastard.

Green side up

Language is a funny thing, especially English as it is a linguistic conglomerate which makes for lots of potential fun. And for botanists and horticulturalists, nothing is more fun that when someone tries to make sense out of soil versus dirt.

Here I will pass along neither dictionary nor professorial opinion, but the New England yankee wisdom dispensed by my Father, the gardener. If anyone referred to the material in his garden as dirt, he'd reply, "It's soil." "Dirt is something you find under your finger nails and in certain kinds of books and movies." No one ever has been accused of using soily language, so this distinction always made a certain sense to me.

Of course as a biologist I know that soil is a complex substance, part inorganic and part organic. A cubic centimeter of soil, a volume about the size of a sugar cube for those of you somewhat metrically challenged, could harbor some 8-20 million organisms. Even the smell of soil, that earthy odor, comes from the metabolic activities of certain bacteria.

So something might start out as dirt, but if composted correctly, it can become soil. And in this I note that for years I have used two layers of newspaper covered with straw to mulch my kitchen garden. Although the data is not publishable, I'm quite certain that the opinion pages of our local newspaper compost the most quickly and thoroughly.

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.

A rose, is a rose, so how does I knows?

Our woody plant horticulturalist stopped by yesterday with a piece of leafy twig. "What do you think this is?" he asked. Hmm, after assessing the specimen, I said, "Well, it's in the rose family." He already had guessed that, but beyond that it wasn't obvious. Now this particular specimen turned out to be a bit unusual, a species I had never seen before, and if that were not the case, he wouldn't have needed my input at all. This particular specimen proved to be a tree quite uncommon in this area (Sorbus aria, whitebeam). After visiting several references, several possibilities were eliminated, and it wasn't until I tried an old woody plant identification key, one that includes ornamental species, that things began to make sense. This species has a simple leaf and most species of Sorbus have pinnately compound leaves, a single axis with two rows of leaflets. Well and good, between the two of us, we nailed the ID and felt pretty good about ourselves.

But here's the thing. Neither one of us ever considered any other possibility after initially deciding this plant was a member of the rose family, instead of one of the other 700 or so families. Now the rose family is a pretty big group of plants, 100-120 genera and 3000 to 3500 species. What made us decide rose family?

It's strange but I don't actually know. Of course I can recite a list of characters, but most of them were not present because there were no flowers or fruit. Yet this twig, with its dozen and a half leaves and buds somehow just looked "rosy". My first thought was a pear, but this specimen's leaves had a double saw toothed margin (pear's are mostly smooth edged), wooly white hairs on the back side of the leaves (never seen a pear like that), and rounded buds (pears are usually more pointy). OK so not pear, more cherry like, but the bark was very un-Prunus, no horizontal lenticels and shiny buds. And finally by a process of elimination I ended up at Sorbus, even though the leaf seemed all wrong (simple leaf rather than pinnately compound). Once this hurdle was cleared, the details fell into place. Score one for the botanist.

This is the hard thing about plant identification. At a certain point, you have enough experience, that you can simply use a gestalt. Some sort of search image is triggered that shoves you in the right direction. And even though I have been teaching such courses for years, I just don't know how to teach this. You simply must work at identifying plants long enough and if you are good, this sense comes to you.

I play a dirty trick on students learning plant ID by giving them two very closely related plants sequentially, sometimes the same species, but just with different colored flowers or leaves. Some few look upon the 2nd specimen with a puzzled look, and then ask, didn't we just do this? Some are even more certain, and toss it aside as knowing I tried a lame trick. Others without an iota of recognition labor through another step by step slog through an identification key, and act surprised when the same species comes up again. Interestingly this exercise has proven to be a great predictor of their over all performance in the course. And I wonder if this skill, this perception, is tied to the ability to conceptualize, to go past the details and grasp the essential underlying idea. Because that's how this works with plant ID. The species ID is in the details, but the broader classification, in particular the family level taxonomic grouping is in the conceptualizing of the commonalities.

That's one good thing about experience. You do get better in doing some things with age. And you can't hold a specimen up to your computer monitor and get any closer to an ID. Technology isn't making any serious inroads into such skills at all. You can scan it, or digitally photograph it, and put it on the internet, but sooner or later, it's someone like me who tells you what it is.

A long time colleague of mine once expressed his concern and apparent inability to teach such skill. "Maybe we can just rip their heads off and pour it in," he said. Sounds like fun.

2008's Botanical Geek Tour

The question was how best to stimulate the economy with those tax rebates provided by the USA? Well, our idea was to organize a 2nd botanical geek tour whose purpose is to visit botanical gardens and other places of botanical interest, and along the way to eat and drink well. So we stimulated the economy by travelling to London for a long weekend in late May to visit the Royal Botanical Garden at Kew, the Chelsea Flower Show, and the Chelsea Physic Garden. You might argue that this did little to stimulate the USA's economy, but this is an international form of the trickle down effect, so I'm sure the USA understands if the impact is a bit indirect.

Kew Gardens were not disappointing, although I have visited other more attractive gardens, but few with such grand vistas. Here is the largest, oldest Victorian glasshouse still in use, and the collection it houses is quite impressive. One of the cycads inside is probably the oldest potted plant in the world. The plant in the foreground is Gunnera, which is a basal lineage of the true dicots, and it's sort of strange seeing it so far from its Central and South American rainforest home.

The Chelsea flower show was quite amazing, the displays quite often provoking the question, "how did they do that?" However, although the daily attendance is capped, the crowds were equally amazing. Still all other garden/flower shows pale by comparison. My favorite was a small garden where everything, roof, walls, table, etc. were covered in moss.

The Chelsea physic garden is rather small and tucked away in a corner, but they have over 4000 labelled species arranged both medically and taxonomically in its 4 acres. The garden has been around for over 350 years, but has only been open to the public in recent decades.

Now you can get a bit foot-sore and tired with so much tramping about in the name of botanical edification, and the remedy for that is to sit yourself down at a local pub for a bit of refreshment. The Coach & Horses is right outside the main gate to Kew Gardens and it came recommended by a British colleague. A fine pub but this is as close to botany as he ever got. I wish I knew why pubs in Britain have so much more atmosphere than most bars in the USA, which seem fixated on the number of TVs screens they can cram in.

The next botanical geek tour may take us to Sweden, the home of Linnaeus. But it will have to wait until the next stimulus check appears, or when Lincolnland comes across with a decent pay raise, or hell freezes over.

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.