Getting plant sex wrong (3)

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Continuing my tendency to be irritated by descriptions of botany in the popular literature, I’m now reading The Forest Unseen: A Year’s Watch in Nature. I’m not too impressed with the book in general, but here’s a bit that’s particularly irritating (end of the chapter “March 25th – Spring Ephemerals”):

This intricate web of dependency dates back one hundred and twenty-five million years to when the first flowers evolved. The oldest fossil flower, called Archaefructus, had no petals, but its pollen-bearing anthers had flags on their tips. The botanists who described the fossil believe that these extensions may have been used to attract pollinators. Other ancient flowers also appear to have been insect-pollinated, further supporting the idea that insects and flowers have been partners since the first flowers evolved. How this marriage came about is unknown, but it seems likely that flowering plants evolved from fernlike plants. These ancestors produced spores that attracted insects looking for an easy meal. The ancestors of the flowers turned the plague of insect predators into a blessing by producing conspicuous displays to attract these spore munchers, then producing so many spores that thee insects’ bodies would be coated. The predators inadvertently carried some of this sporey dust onto the next flower, increasing the fecundity of the spore producer. Eventually the spores got wrapped in a package, the pollen grain, and the true flower was born. The bees and spring beauties in the mandala reenact the main theme of the original relationship. The bees, or their larvae, eat most of the pollen they gather, transferring only a small number of pollen grains from flower to flower.

To say “it seems likely that flowering plants evolved from fernlike plants” is somewhat misleading and at least unhelpful. Flowering plants are not particularly closely related to ferns; various of the ancestors of flowering plants back around their common ancestor with the gymnosperms might have looked vaguely ferny, but not in any way that is relevant to the evolution of pollination. But that’s not really too big a deal, it’s just a minor annoyance. The big irritation is here: “Eventually the spores got wrapped in a package, the pollen grain, and the true flower was born.” First – a pollen grain is not a package of spores. Each pollen grain begins as a single spore. Then one or more (the details depending somewhat on which lineage we are talking about) cell divisions take place inside the spore wall, and you have a group of cells inside a single spore. If we’re doing academic botany, we call that an endosporic microgametophyte; in popular writing there are any number of less technical ways to say “several cells inside a spore” but “a package of spores” is just wrong. Second – pollen predates flowering plants, so identifying the origin of pollen with the origin of flowers is also wrong. All the gymnosperms, which do not produce flowers, do produce pollen. A few of them (Ephedra, for instance) even produce structures that look an awful lot like the stamens of flowering plants. The defining morphological feature of flowers, as compared to the cones of gymnosperms, is the carpel.

Getting plant sex wrong (2)

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I’ve been reading Horseshoe Crabs and Velvet Worms by Richard Fortey. Overall, I’ve been finding it enjoyable. However, portions of the book cause me to cringe. Here’s an example near the beginning of chapter two:

These Gondwanan coniferous trees, with their relatively large leaves and bright berries, do have a very special appearance, at least to a European accustomed to pines and firs with their dry-looking cones. A botanist would remind me I should really describe the berries as “fleshy peduncles” because they carry exposed seeds at their tips.

What’s wrong with that? Well, the trees (podocarps in New Zealand, specifically totara, Podocarpus totara and rimu, Dacrydium cupressinum) Fortey is talking about do not have berries. He is apparently aware of this, but the way he presents it suggests that these things really are berries and that describing them as “fleshy peduncles” is some kind of obscure scientific quibbling. It isn’t: “fleshy peduncle” is right, “berry” is wrong. This follows an irritatingly predictable tendency in science writing about plants: present a misleading description as though it were true, restrict the correct information to some kind of afterthought, and don’t explain it enough for readers to actually figure out what’s going on. This both misinforms readers and gives the impression that the situation is hopelessly complex and cannot be understood by anyone who doesn’t have a PhD and a labcoat.

So, OK, here’s what a fleshy peduncle is. In conifers, a peduncle is a stem that bears one or more cones. In this case we’re talking about seed cones, analogous to the seed cones you’d see on pine, spruce, Douglas fir, etc. You know, these things. In the podocarps Fortey is discussing, the seed cones are very small, having one or two small leaves each with a single exposed seed. In these species, the peduncles bearing the seed cones are swollen, fleshy, edible, and look somewhat like berries. Why aren’t they berries? A berry is a kind of fruit. Fruits are found only in flowering plants (not conifers) and instead of leaves with exposed seeds they have carpels. Carpels are leaves that have been folded and fused into little chambers with seeds inside of them, protected from the environment.

That is more complicated than just saying “these trees have berries; well, technically they’re fleshy peduncles”. However, it’s also informative. Authors writing about science should aim to inform readers about science rather than reinforcing misconceptions and presenting science in a dismissive and uninformative manner.

Here’s a similar example from near the end of chapter 3:

Despite their apparent simplicity, Porphyra and Bangia have quite complex life histories. Cells of the “weed” contain only one package of genetic information; they are described as haploid. A second phase in the life history of these seaweeds is called the Conchocelis stage, which makes miniature branching plants, some varieties of which inhabit the borings they make inside seashells. These plants are so different from their “parents” that they were once given the separate generic name, Conchocelis, which is now only retained as a label for one stage in the life cycle. Conchocelis plants are the diploid, or the sexual, stage of the red algae. The leafy stage releases gametes that mate with one another, thereby doubling up the genetic content; this produces spores that can germinate into Conchocelis.

Some of the basic ideas here are correct. However, the definitions of “haploid” and “diploid” are misleading, the processes of fertilization and sporulation are conflated, and describing Conchocelis as “the sexual stage” is incorrect.

First, what does “one package of genetic information” mean? A package of genetic information could refer to a few different things. It could possibly refer to a gene, or a chromosome, or a nucleus. When discussing haploidy and diploidy, we’re talking about chromosomes, which are long strands of DNA, each containing many genes as well as regulatory sequences and non-coding “junk” DNA, bound up with proteins. So why not just say “one chromosome”? This would be less ambiguous, but it would also be wrong. One vs. two chromosomes is not the distinction between haploid and diploid cells. Instead, the distinction is how many copies of each chromosome is present. In a haploid cell, each chromosome present as a single copy. In a diploid cell, chromosomes are present in pairs. We could easily reword the second sentence of this quote to say “Cells of the ‘weed’ contain only one copy of each chromosome; they are haploid.”

Second, Fortey says that “the leafy stage releases gametes that mate with one another, thereby doubling up the genetic content; this produces spores”, which conflates fertilization and spore production. The union of two gametes is fertilization, the process by which we move from haploid cells to diploid cells. The cell produced by fertilization is not a spore, it is a zygote. The diploid zygote then goes through several mitotic cell divisions to produce diploid spores. By suggesting that fertilization produces spores, Fortey is simply skipping this stage of the life cycle and implying that fertilization directly produces spores, which is incorrect.

Third, Fortey describes Conchocelis as “the diploid, or the sexual” stage of Porphyra and Bangia. Sex consists of the production of gametes and their subsequent union in fertilization. The Conchocelis stage is not directly involved in this process: it doesn’t produce gametes and it isn’t produced by fertilization. Instead, the diploid spores mentioned above can grow into the Conchocelis stage, and the Conchocelis stage produces haploid spores by meiosis (Porphyra and Bangia produce multiple types of spores, which is rather odd). The Conchocelis stage is part of the whole life cycle in these algae and the whole life cycle includes sex, but that’s as close as it gets. It’s like describing a human liver as “the sexual stage” in humans. A functional liver is a necessary component of the human life cycle and the human life cycle includes sex, but the liver doesn’t have any direct role in sex.

The life cycles of Porphyra and Bangia are fairly complex and difficult to describe clearly and accurately. Fortey had two good choices here: either don’t bother with it since it’s not really necessary for the narrative of the chapter or go into the detail needed to convey what’s going on. Instead he makes a third, bad choice: discuss the topic briefly, confusingly, and incorrectly. All readers are likely to get from this passage is that something weird and confusing is happening.

That said, Fortey is doing far better at botany than Bernd Heinrich, who in The Trees in My Forest repeatedly refers to “flowers” of conifers. This is just wrong. Pines do not have flowers. At least Fortey tells us that the “berries” of podocarps are in fact fleshy peduncles, even if he does so in a rather unhelpful fashion. And maybe we can cut him some slack, since his book isn’t primarily focused on plants, much less trees or conifers in particular. Heinrich, on the other hand, wrote a book about trees, with long discussions of conifers, and gets it completely wrong. He tells us that conifers have flowers and provides no explanation nor any indication that this might not be consistent with what we actually know about botany.

Misunderstanding group selection (1)

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I’m not sure why, but group selection seems to be a topic that inspires vociferous but poorly-considered critique. An example from Steven Pinker:

Human beings live in groups, are affected by the fortunes of their groups, and sometimes make sacrifices that benefit their groups. Does this mean that the human brain has been shaped by natural selection to promote the welfare of the group in competition with other groups, even when it damages the welfare of the person and his or her kin? If so, does the theory of natural selection have to be revamped to designate “groups” as units of selection, analogous to the role played in the theory by genes?

No, groups do not play a role analogous to genes. But that isn’t what group selection is about. Here’s the very short version:

Genes are the basic units of heritable information. Genotypes, however, are not directly exposed to natural selection. Genotypes are exposed to selection via the phenotypes to which they give rise. The question we are concerned with in the group selection debate boils down to “Phenotypes at which level?” Genes are expressed at varying levels of organization. Any particular cell has a phenotype. If we’re talking about multicellular organisms, we can talk about the phenotype of the organism. If we’re talking about multicellular organisms that occur in groups, we might also talk about the phenotype of the group. At which levels can natural selection apply, and, for any particular trait of interest, which level is most appropriate and enlightening? The “pro” argument on group selection boils down to: In some cases, discussing selection at the level of group phenotypes is both accurate and the best way of understanding what’s going on. The “con” side boils down to: It is never appropriate to talk about selection at the level of group phenotypes.

There’s a lot more nuance to it than that, of course, but the basic idea is that we’re talking about gene expression at different levels of organization. Steven Pinker gets it wrong in the third sentence of this article, and perpetuates that error throughout the article. As a result, I find Pinker’s criticisms largely unintelliglble. This is too bad, as in his other writings I’ve found him cogent and compelling.

Jerry Coyne has also been making criticisms of group selection that I find confused or poorly-expressed, but his errors are more sophisticated. I may get to them later.

The decline of field botany

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An article worth reading:

Profiling prolific plant hunters provides insight as to strategy for collecting undiscovered plant species.

The gist is: the current situation is dire.

“Plant collecting is a specific part of the three-step process of plant species discovery (collection, recognition and publication), and as the numbers of professional taxonomists who classify plants decline, there has been a massive increase in the utilization of non-professionals to aid in this work. This study suggests that as science pushes for more rapid documentation of the world’s flora, policy makers and funders must examine how best to develop the experience and skills of selected individuals to catalog undiscovered plants more efficiently.

“One way for institutions to encourage the development of these skills is in performance evaluations, rewarding effective field work on an equal footing with number of papers published and grants obtained,” notes Davidse.”

In other words, there’s no money to do field botany, institutions aren’t encouraging it, we aren’t training new field botanists, and we aren’t hiring them. And that’s why we need to do what we can quickly and on a shoe-string budget.

Problem of Induction

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A random thought–the problem of induction, popularized by Hume, is one of those long-standing issues in philosophy. The gist is roughly:

Inductive reasoning works by taking some set of observations and generalizing their characteristics to a larger set of phenomena. A typical example is this–How do we know the sun will rise again tomorrow? It has always done so in the past, so it will do so again tomorrow. We can take a step back and ask–How do we know that, just because something has always happened in a certain way in the past, that it will also happen that way in the future? Or, more generally, how do we know that we can take observations of some subset of a class of phenomena and then assume that the observed characteristics also hold for the whole class? Hume’s contention was that any answer to this question will, itself, rely on inductive reasoning (e.g.–Yesterday I predicted, on the basis of past events, that the sun would rise today, and it did! Therefore, the same reasoning will work again tomorrow.), and that’s circular, so we can’t get anywhere. Apparently, no one has found a way out of Hume’s problem of induction. We simply have to take inductive reasoning on faith, or give it up.

The alternative to inductive reasoning is deductive reasoning, in which we simply work in the opposite direction. We infer the characteristics of a particular individual from characteristics known to hold for the class of individuals to which it belongs. A typical example is this–All men are mortal; Socrates is a man; therefore, Socrates is mortal. Responses to Hume’s problem of induction focus on trying to provide a deductive proof for inductive reasoning. Nobody seems to have any qualms about deductive reasoning itself; there is no corresponding “problem of deduction” to complement the “problem of induction”. But we might ask:

So, OK, we can’t provide a deductive argument establishing that inductive reasoning works. What about the opposite? Can we provide an inductive argument establishing that deductive reasoning works? It is not intuitively obvious how we would go about this. For instance, we might pull out the old chestnut about Socrates and say, “Well, he died, so the deductive argument for his mortality works!” However, all this tells us is that the conclusion of that particular argument happens to be true, not that the reasoning works. If we followed that line, we’d end up having to say that any reasoning that happens to lead to a true conclusion is valid, and any reasoning that leads to a false conclusion is invalid… but that is in direct opposition to the operations of deductive reasoning. I can’t really think of a way around this problem. Maybe someone has done it, I don’t know. Maybe deductive reasoning just feels so right that we can’t imagine giving it up; but, then, we’re in no danger of giving up inductive reasoning, either, whether it can be justified or not.

Pointless trivia…

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A job application (for a botanical position with the state of Missouri) had a field for typing speed. Since I don’t know how quickly I type, I figured I’d take several of the various online tests. Over four of them I averaged about 85 words per minute, which I guess is respectable.

Geranium dodecatheoides

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My second new species from New Mexico is published, Geranium dodecatheoides P.J.Alexander & Aedo. Many thanks to Carlos Aedo, who knows far more about Geranium than I could ever hope to. Read the article here: http://www.bioone.org/toc/rhod/113/955. The location where I found it happens to be along one of the most readily accessible trails in the Sierra Blanca; it is surprising that it has not been collected before, but so far as I can tell it was completely overlooked. So, one more reason to keep your eyes open outside, even in areas where you wouldn’t really expect to find anything too exciting. I’m sure I’ve stumbled past at least as many undescribed species as I’ve happened to notice… with luck, perhaps I’ll find another that I can give a name with even more syllables!

NOAA

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I just stumbled across a lovely interface for tracking precipitation in the U.S.: http://water.weather.gov/precip/. Previously I’d been using this site: http://www.cpc.ncep.noaa.gov/products/precip/realtime/. Alas, NOAA has discontinued that page and replaced it with something that is, to me at least, not very useful; fortunately, water.weather.gov is a great improvement.

It is also worth mentioning that I’ve always found NOAA’s website hopelessly baffling. They seem to be improving that; water.weather.gov is surprisingly easy to navigate to from either weather.gov or noaa.gov, but the cpc.ncep.noaa.gov side is hopeless. Suppose you start at the CPC’s “Monitoring and Data” page. Then you click on “United States Climate Data and Maps”, then “Precipitation and Temperature”, then “Recent Precipitation Maps”… and that sends you to http://www.cpc.ncep.noaa.gov/products/precip/realtime/, where you are redirected to http://www.cpc.ncep.noaa.gov/products/Global_Monsoons/gl_obs.shtml, which is apparently intended for global monsoon monitoring. Huh?

Botany is hard

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So, in the post below, and probably in a number of posts that will follow, I criticize the results of or approaches to research that relies on field botany and plant identification. I should say now: it’s hard. None of us always get it right and mistakes will be made. A major target of my ire tends not to be that people aren’t perfect botanists, but that I think there is a systematic undervaluation of botanical expertise. Field personnel whose work requires them to be able to identify plants are often poorly trained and poorly paid, because the difficulty of the work is not appreciated. So far as I can tell, land management agencies and ecological research stations assume that someone who’s taken a couple of courses in plant taxonomy can be sent into the field and will bring back reliable data. Well, I’ve taken those courses, I’ve taught those courses, I’ve botanized extensively across much of the western United States, and I can tell you (assuming, hypothetically, a reader) now: this simply is not the case.

Someone who’s taken the courses available at NMSU (Rangeland Plants, Rangeland Grasses, Plant Taxonomy), done well and studied conscientiously, should be able to sight-ID a fair number of the common species (but few of those uncommon species that make up most of the biodiversity), and should be able to key out most plants assuming there is flowering and/or fruiting material available (and there often isn’t, but field crews don’t tend to have the luxury of waiting for good conditions). But that’s it. Don’t expect or rely on sight-IDs of most of the plants in the area, and don’t expect that any kind of identification will be possible for most species if the plants are in poor shape and many or most of the diagnostic characters are absent.

Suppose you want to answer a simple question: is plant diversity higher in grasslands or shrublands in southern New Mexico? Well, if you want reliable data, you need a field crew of people who already have several years of experience–probably voluntary / recreational since, AFAICT, no one will pay you to learn plants–botanizing in the area. Those people are scarce, and most of them have Masters or PhD degrees (and many are retired!); you probably can’t (and, ethically, shouldn’t) hire them for crappy minimum or near-minimum wage temporary positions. If, on the other hand, you hire a field crew of people fresh from their undergrad degrees whose experience is limited to two or three courses in plant ID or taxonomy, either that crew is going to be spending 90% of its time learning plant ID, or you’re going to get crappy, unreliable data. (As for the simple question, so far as I know there is no reliable answer! More on that some time later.)

One way to minimize the expertise required is to only focus on a few of the dominant plant species (as in the vegetation maps discussed in the post below). It is better to recognize one’s limitations and work within them, but this approach means you’re ignoring most of the botanical diversity in the area… not exactly ideal, in my opinion.

The gist is, if you try to fill botanical field crews on the cheap, rather than hiring highly trained botanists with extensive experience, you have a few options, none of them particularly good: deal with poor accuracy of identifications; get very little data back because your field crews are spending most of their time learning the plants; adopt a very myopic view of plant communities.

Vegetation mapping & confusion

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For a recent lecture in Rangeland Grasses, I was hoping to include a slide or two showing the decrease in grassland at the Jornada (Jornada Experimental Range and Chihuahuan Desert Rangeland Research Center). A recent paper documents this decrease:

Gibbens, R.P., R.P. McNeely, K.M. Havstad, R.F. Beck, and B. Nolen, 2005. Vegetation changes in the Jornada Basin from 1858 to 1998. Journal of Arid Environments 61: 651-668.

So, I thought, I’ll just pull the maps from there. Unfortunately, it is not that simple. One problem is common to almost all published vegetation maps: you can’t just look at the map and say, “OK, all this is grassland, and here it is quite extensive in 1918, and then there’s not much of it in 1998,” because the color system used is fairly confusing and you’d have to spend a minute pointing out that yellow, light pink, dark tan, etc., are grassland while light green, light blue, light tan, etc., are shrubland. There has to be a better way to do this! Here’s the figure (just for the JER; there’s a separate figure for the CDRRC), see how long it takes you to figure out the extent of grasslands at any point in time:

Looking at the map more closely I realized that, in this case, there are further difficulties. The map legend does not match the colors used. Here’s a comparison of the colors used in the legend and in each map:

That dark pink for “other grasses” never occurs in the maps; two different browns not in the legend are used. Presumably those browns mean “other grasses”, but I don’t know. It is odd that most, but not all of the areas of Scleropogon brevifolius (burrograss; light pink) in the 1918-19 map become brown in the 1928-29 and 1998 maps. It’s hard to tell if this is supposed to indicate a change in vegetation, or is simply an error in producing the map. I assume the latter, because similar maps were produced again, in:

Havstad, K.M, L.F. Huenneke, and W.H. Schlesinger (editors), 2006. Structure and Function of a Chihuahuan Desert Ecosystem. Oxford University Press, New York, NY.

Here, that difficulty seems to be solved. So far as I can tell, the legend matches the maps, and all those areas of Scleropogon brevifolius in 1918-19 are still Scleropogon brevifolius in 1928-29 and 1998 (as they continue to be today). However, this map is more precise about what the dominant species is (e.g., listing Sporobolus airoides, Sporobolus flexuosus, Sporobolus nealleyi and Sporobolus spp. instead of just “Sporobolus spp.”), which is good, but exacerbates the problem of colors that are difficult to distinguish to the point that much of the map is unusable. Worse, the maps are small and resolution is poor; and I have a physical copy of the map rather than a .pdf. There is no way, AFAICT, to use these as workable images in a powerpoint presentation. Luckily the GIS layers are available on the Jornada website, so I can make my own maps (which I may do as time goes by).

So, that’s frustrating. Here’s another difficulty: “Plant nomenclature follows Allred (2003).” Except, it doesn’t. For instance, Allred recognizes Gutierrezia microcephala and Gutierrezia sarothrae, while the Jornada literature uniformly lumps both as Gutierrezia sarothrae. And then there are the big questions that remain even if we leave this niggling behind us:

1) How exactly do we determine what the dominant species is in the first place? The standard has always been that you look out at a landscape and guess (and the methods of the 2005 paper are consistent with this). In clear cases, this should work. In other cases, it won’t, and you’ll get different answers depending on who’s doing the fieldwork (or, for that matter, what time of year, how wet the year is, etc.). An objective measure, and some account of seasonal / yearly variation as well, is needed.

2) How much does that tell you, anyways? If we want to understand the distribution of vegetation, don’t we want to know more than just one (or two–the 2006 book includes separate maps for the second most abundant species) of the species at a site? This is a constant frustration of mine with ecologists and land management agencies. Interest is almost always focused on the most abundant species and, due to the Endangered Species Act, the least abundant species. The other 95% of the biodiversity is uniformly overlooked.

Lest you think I am singling out the Jornada for criticism, I also searched for vegetation mapping information for the Sevilleta LTER. Results were worse. A vegetation map was created, but never published. At one point it was online, but at present it is not available through the Sevilleta website; you can find a fairly illegible jpeg through archive.org, but that’s it. Despite 25 years of research and three long-term NSF grants at the Sevilleta LTER, so far as I can tell there simply is no published account of the vegetation, nor one available online. This is disappointing. Poking around online also led me to this article:

Weiss, J.L., D.S. Gutzler, J.E. Allred Coonrod, C.N. Dahm, 2004. Long-term vegetation monitoring with NDVI in a diverse semi-arid setting, central New Mexico, USA. Journal of Arid Environments 58: 249-272.

From which I quote:

“The objective of this study is to examine 11 years (1990-2000) of seasonal and inter-annual variability of NDVI in a diverse semi-arid setting in central New Mexico, USA, that includes six different vegetation communities: Great Plains / desert grassland (GPGrslnd), Chihuahuan Desert (ChiDes), piñon-juniper woodland (PJWdlnd), juniper savanna (JunSav), Colorado Plateau shrub-steppe (CPShbStp), and Colorado Plateau grassland (CPGrslnd) (Moore, 1989-2001).”

OK, we have six different kinds of vegetation. You might ask: How are they different, exactly? How do we know that they’re different? And just how much of the variation in vegetation at these sites is captured by those designations (e.g., does “juniper savanna” mean just any kind of juniper with any kind of grass, or is it always Juniperus monosperma with Bouteloua gracilis; and what about the other 95% of the plants in that habitat)? In particular, I was curious what exactly the difference between Great Plains grassland and Colorado Plateau grassland is at the Sevilleta. However, in the paper there is no explanation of any of these points, nor any citation indicating how you could find that information (the Moore citation is for meteorological data). Near as I can tell, “Great Plains grassland” must refer to communities dominated by Bouteloua gracilis east of the Rio Grande, and “Colorado Plateau grassland” must refer to communities dominated by Bouteloua gracilis west of the Rio Grande, but is that a meaningful distinction? Are these actually distinct plant communities or just different names for the same thing? I don’t know, but it’s the kind of basic knowledge I can’t imagine conducting ecological research that relies on vegetation classifications (nevermind running an LTER site) without. And yet… well, maybe it’s all in that unpublished vegetation study.