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February 25, 2008

Reversing evolution: conspicuous mimicry vs. camoflage

Two papers this week on the type of mimicry named for Henry Bates, whose book on exploring the Amazon was published shortly after The Origin of Species. Batesian mimic species resemble foul-tasting or dangerous species, thereby avoiding being eaten, even though they are not actually dangerous themselves. Bates worked on butterflies whose wing patterns resembled those of other species. Butterflies are still the best-known examples of mimicry, but there are also examples of mimicry (involving behavior) in snakes and octopi.

The two papers are:
Once a Batesian mimic, not always a Batesian mimic: mimic reverts back to ancestral phenotype when the model is absent
by Kathleen Prudic and Jeffrey Oliver, of the University of Arizona, and
Colour pattern specification in the Mocker swallowtail Papilio dardanus: the transcription factor invected is a candidate for the mimicry locus H
by Rebecca Clark and colleagues in the UK, Australia, Kenya, and Germany. Both were published in Proceedings of the Royal Society.

The first paper asks how mimicry evolves when the distasteful “model� species is absent. Model species are usually brightly and distinctively colored, so the mimics are, too. But what happens if the model becomes too rare to “train� predators to avoid that pattern, or if the mimic moves into an area where the model isn’t found? The mimic could, perhaps, die out under these conditions.

Prudic and Oliver used molecular methods to develop a family tree for admiral butterfly species. Based on this tree, they concluded that the common ancestor of the admirals was inconspicuous, black with a white band that apparently makes it hard to see. Some admiral species have evolved to mimic different model species. But some of these evolved further, reversing this evolutionary path and becoming inconspicuous again. These species are found, as you might expect, in areas where the model is absent. So, in this case, reverse evolution was fast enough to avoid extinction. The reversal itself could have been rapid, if only a small genetic change was needed. Or the conditions that increased predation on the conspicuous mimics could have developed slowly.

Evolutionary reversals are not necessarily rare. Peter and Rosemary Grant found that the populations of Galapagos finches (made famous by Darwin) can evolve rapidly in response to dry years, but the effects are reversed in wet years, so there may be little long-term trend.

When natural selection favors a phenotype (such as wing pattern) that it previously eliminated, restoration of the old phenotype may not involve an exact return to the original genotype. The second paper identifies an actual gene responsible for the appearance of another butterfly mimic, the Mocker swallowtail. The gene identified was previously found to be involved in wing patterns (“eyespots�) in another butterfly species.

Both papers make heavy use of molecular tools that would have astounded Bates or Darwin, but they would perhaps be pleased that questions they raised are still of interest.

February 22, 2008

Looking for junk DNA?

Looking for my review of an article on "junk DNA"? It's here.

Science Fair Secrets 2: Repeat Your Experiment

This is part of a series (copyright R Ford Denison) on the secrets of winning science fair projects. Click "science fairs" under Categories (at right) for more.

Like the first secret, this one is spelled out in the instructions to judges, but it seems to be a secret from the students. Don't tell anyone I let it out!

Here it is: do your experiment more than once. Two of the projects I judged last week had surprising and interesting results, but both got low scores because they only did the experiment once. Getting an interesting result once is almost meaningless. You think you're comparing apples and oranges, but you're really only comparing this apple to that orange. Maybe one had been in storage longer than the other, or something. Comparing three apples with three oranges is a little better, but if one apple was in storage longer, maybe they all were. So it would be better to come back to the store a month later, when you can be pretty sure they've gotten a new batch of each fruit.

Of course, this means you can't start your project the day before the fair. One guy complained that doing his experiment a second time would have taken a whole extra day. Poor baby! One of the winners worked on her project several hours a week all summer and into the fall. I know because she did the work in our lab.

Some experiments take months, because you're waiting for plants to grow or disposable diapers to decompose or something. In such cases, it may be very difficult to repeat the experiment, even if you start early. To some extent, you can substitute replication for repetition. For example, you could compare six organically grown apples to six conventional apples. But, as explained above, just comparing this batch (which happens to be organic) to that batch (which happens to be conventional) doesn't let you draw any general conclusions about organic vs. conventional apples, much less organic vs. conventional fruit in general. Ideally, you should compare organic Honeycrisp apples from farm A with conventional Honeycrisp apples from farm A, and also compare organic Keepsake apples from farm B with conventional Keepsake apples from farm B (or at least a neighboring farm), and so on. Then, if you get consistent results, you can be more confident there's a real difference between conventional and organic apples, not just a difference between specific farms or batches.

And what if there is no consistent difference? For example, what if organic Honeycrisp tasted better than conventional Honeycrisp, but conventional Keepsake tasted better than organic Keepsake? That's a perfectly valid and interesting result: there may or may not be a difference between conventional and organic apples, but other factors are also important. The important thing is to make sure your conclusions agree with your data. It doesn't matter whether they agree with your starting hypothesis.

February 19, 2008

Career vs. beer?

If you get a position where promotion (or even continued employment) depends on how much research you publish, how hard should you work? Morgan Giddings writes in PLoS Computational Biology that:

Enough work is exactly the amount at which one can maintain enjoyment of the process of work, without burning out (which is not enjoyable) or becoming socially isolated (which is not enjoyable). If that amount of work is not enough to maintain a scientific career, then a different career may need to be considered, where such enjoyment can be found.

But there may be a negative correlation between drinking beer and publishing.

February 18, 2008

Natural enemies complicate reproductive tradeoffs

Semelparous plants and animals are those that reproduce only once, whether after a few months of growth (annual plants, like wheat) or after years (“century plant� or most salmon). Iteroparous species iterate. That is, they reproduce repeatedly. For example, perennial grasses may produce seeds every year for a decade or more.

One reason this difference matters is that perennial crops may have some environmental benefits, relative to annual crops. Plowing, traditionally more common with annual than perennial crops, can greatly increase soil erosion, especially on steep slopes. So there is increasing interest in developing perennial grain crops as an alternative to wheat.

However, perennial plants have lower seed yield than their annual relatives, so we would need to devote more land to agriculture to get the same amount of grain. One reason for the yield difference is that an annual plant can transfer most of the carbon (energy) and nitrogen (needed for protein) from its leaves, stem, and roots into its seeds. It’s going to die anyway, so the next generation gets its accumulated wealth. A perennial plant needs to hold back some carbon and nitrogen for winter survival and spring regrowth. The more resources it puts into this year’s seed production, the less it can carry forward to support reproduction next year.

This week’s paper shows that iteroparous plants face additional costs when they reproduce, namely, ecological costs. “Herbivore-mediated ecological costs of reproduction shape the life history of an iteroparous plant� was written by Tom Miller and colleagues at the University of Nebraska (where I’ll be speaking on Darwinian Agriculture in April) and published in American Naturalist.

They studied the tree cholla cactus, Opuntia, which is eaten by the cactus bug, Narnia. This species produces new meristems (growing tips) each year, which become either seed-producing flowers or cladodes like very thick leaves, which contribute to future growth and reproduction by photosynthesizing. Thus, one simple measure of investment in current reproduction, perhaps at the expense of future reproduction, is the fraction of meristems that flower.

To measure the tradeoff between current and future reproduction, they injected a plant hormone, gibberellin into some Opuntia meristems, to prevent them from flowering. Control plants (injected too late to stop flowering) produced more flowers, as expected. They also attracted more bugs, which attacked the flowers. The more bugs, the more flowers aborted without producing seeds. They showed that this flower abortion was caused by the bugs, rather than being a side-effect of hormone treatment, because insecticide-sprayed plants had little flower abortion.

If the Opuntias make more flowers this year, they are trading potential seed production this year for future seed production. If, instead, they made more cladodes and fewer flowers, they would have higher photosynthetic rates next year to support more flower production. So far, this is similar to the tradeoff argument made previously against perennial grain crops. But this week’s paper shows that more flowers attract more bugs, so they don’t even achieve the potential benefit of greater seed production this year.

When they analyzed the tradeoffs between current and future reproduction based just on photosynthesis, they predicted that small plants should wait to flower until they are big enough to have a high photosynthetic rate, but big plants should have most of their new meristems flower. But when they included increasing bug damage with increased flowering, their model predicted that even large plants should have only about 60% of their meristems flower each year. This matches field observations for real plants. So apparently Optuntias (or rather the “blind watchmaker� of natural selection) have come to the same conclusion.
N. pallidicornis on flower bud.jpg
Narnia on Opuntia (photo from Tom Miller)

February 16, 2008

Science Fair Secrets 1: Use Scientific Sources

This blog is usually about the latest research on evolution, but this is the first in a planned series on the secrets of winning science fair projects. Click "science fairs" under Categories (at right) for more on science fairs.

This week's "secret" isn't secret from the judges -- it's right in the judging instructions -- but students don't seem to know about it. The secret is to use scientific magazines and books (not just web pages) in designing and explaining your project. This will automatically raise your score a few points, in addition to improving the project itself.

Here's a list of sources of information, starting with those that are more likely to lower your score than raise it, and ending with those that will impress judges most:

0) WORST: tabloid newspapers (sold mostly in grocery stores, with stories mostly about the sex lives of movie stars etc.) or crackpot videos (claiming scientists are lying about global warming to further their plans for World Domination, etc.)

1) Risky: Wikipedia and most other web sites. These are mixtures of "facts" (only some of which are actually true) and opinions of people who may or may not know what they're talking about. They can be OK as a source of background and ideas; just remember that some of the information is wrong and you can't tell which.

2) OK: David Attenborough videos, major newspapers (The New York Times has a major science section every Tuesday). These may not win you any points, but they won't lose you any points either.

3) Better: Scientific American or Science News (both written for an intelligent but nonexpert audience -- that's you, right?) or science books (if they're shelved near books that have Conspiracy or UFO in the title, they're probably not science books).

4) BEST: peer-reviewed scientific journals. "Peer-reviewed" means that each article has been checked by 2-3 experts in the field, so most (not necessarily all!) mistakes have been corrected.

The two best-known scientific journals are Science and Nature. Both are written for scientists, but an article on X doesn't assume the readers are already experts on X. So with a little work, maybe looking up a few words (even in Wikipedia!), a high school student should be able to get the main point. And that's important. If you claim to have read a scientific paper, but are clueless about what it said, that will hurt your score rather than help it.

Beyond Science and Nature, how can you tell if something is a real scientific journal? One clue is the references at the end of an article. If they're mostly web sites or references to the same "journal", that's a bad sign.

Scientific journal articles come in two main flavors: reviews and original research papers. If you read, mostly understand, and reference one of each, that will put you way ahead of other students. Review articles summarize lots of other papers, often with a good dose of expert opinion. Original research papers will have graphs or tables of results from observations or experiments. The Introduction of a research paper summarizes what was known about the topic before the research was done and explains how they came up with their questions and hypotheses. The Methods section may use equipment you don't have access to, but can still be a useful guide. For example, how many times did they do the experiment? How many plants (or whatever) did they use each time? More than once, and more than one, right? The Results and Conclusions sections of research papers can be a useful guide as you think about how to present your own results, even if they were counting stars and you counted flowers!

Aside from automatically impressing judges with your bibliography or list of references, how will reading scientific papers improve your project?
1) Ideally, you would like to answer a question that hasn't already been answered. Reading even one or two recent scientific papers on a topic will give you some idea of what questions have been answered already. as well as what questions scientists think are important.
2) As suggested in the previous paragraph, you may also get ideas for methods and for how to analyze and present your results.

Where can a high school student find scientific journal articles?
1) Your nearest college or university library. If you act serious, they'll assume you're one of those geniuses that start college at age 16, or maybe some professor's kid. Most university libraries allow the public to read or photocopy journal articles, anyway, just not check them out.
2) You may find Nature or Science in a good public or school library.
3) Journals often make abstracts of their papers available on their web sites. Even reading just the abstract can be a lot better than nothing. They're pretty condensed, but they are often written for nonexperts.
4) If you email the "corresponding author" (usually listed below the abstract), he or she will often email you a PDF of the paper. Use "reprint request" in the subject line of your email.
5) Some journal articles are "open access", available to anyone on the web. This is true of all articles in PLoS (Public Library of Science) journals, for example.

Next time: start early, so you have time to do your experiment at least twice.

February 11, 2008

Ancient temperatures inferred from DNA

"Where was you hid to see all that?" he cried. "It seems to me that you knows a great deal more than you should."? - The Complete Sherlock Holmes
"Our DNA is a coded description of the worlds in which our ancestors survived. And isn't it an arresting thought? We are digital archives of the African Pliocene, even of Devonian seas; walking repositories of wisdom out of the old days. You could spend a lifetime reading in this ancient library and die unsated by the wonder of it."? -- Richard Dawkins, Unweaving the Rainbow

Like many of the characters baffled by Sherlock Holmes, I am repeatedly amazed by the detailed inferences my fellow scientists are able to draw about events in the distant past. This week's paper:
Palaeotemperature trend for Precambrian life inferred from resurrected proteins
is a good example. Eric Gaucher and colleagues at the University of Florida and DNA2.0 Inc. used protein sequences from a variety of modern bacteria species to infer the protein sequences of their distant and more recent ancestors...

They then synthesized copies of those ancestral proteins and measured their stability at different temperatures. Based on the reasonable assumption that the ancestral proteins were most stable at the temperatures to which the ancestral bacteria were usually exposed, they calculated the average temperature of the environment where ancestral bacteria lived at various times in the past. They inferred that, about 3.5 billion years ago, bacteria were exposed to temperatures similar to hot springs, about 70 degrees Celsius (160 Fahrenheit). Similarly, they inferred that more recent bacteria, only (!) one billion years ago, saw lower temperatures,: about 40 C (100 F).

Every method has possible sources of error. For example, there is some disagreement on the details of the family tree of the bacteria, a key input to this sort of analysis. Therefore, the authors compared two alternative family trees. This gave only small differences in the temperature optimum of the earliest bacteria (65 vs. 73 C). Comparing two methods that are unlikely to have the same type of error, because they are based on unrelated assumptions, is even better. So they also compared their protein-based temperature estimates with estimates from stable isotope ratios -- relative amounts of two nonradioactive isotopes whose values in sediments are thought to depend on the temperature at the time the sediments settled out of the ocean. The rough agreement between the two different methods is much more convincing than either method alone.
FIg. 3 from Gaucher EA, Govindarajan S, Ganesh OK. (2008) Palaeotemperature trend for precambrian life inferred from resurrected proteins. Nature 451: 704-708 (Copyright NPG; noncommercial reproduction under Fair Use rule.)

February 3, 2008

Natural ecosystems as a source of ideas

This week I want to share some thoughts on “ecosystem services�, starting with this recent paper:
Proximity to forest edge does not affect crop production despite pollen limitation
They found that the closer grapefruit trees were to forest edges, the more visits they got from pollinating bees, but this trend had no effect on fruit production. There’s more to the paper than that, but I want to commend the authors for actually measuring effects on yield. It’s surprisingly common to measure variables that are hypothesized to have some effect on yield, without measuring yield itself. For example, Risch et al. noted that, out of 150 studies on how intercropping affects insect pests, only 19 bothered to measure yield, and only one study determined how much the pests actually affected yield (Environ. Entomol. 12:625). This would be like medical researchers measuring the effect of some treatment on cholesterol but not checking whether there was any effect on the frequency of heart attacks.

“Ecosystem services� have been a hot topic since Constanza et al. published a paper on the topic ten years ago (Nature 387:253). They estimated that nature provides services (pollination, purifying water, etc.) worth $33 trillion per year, exceeding the value of human economic activity. As an argument for conserving nature, it made me wonder how many of those services are or could be provided by managed ecosystems (including properly managed farms), and how many are provided by species that we couldn’t get rid of if we tried (microbes that break down crop residues, for example). Since then, the ecosystem services meme has spread so much that we rarely hear about all the other reasons to preserve wild species and natural ecosystems. One notable exception is a recent paper by D.J. McCauley titled “Selling out nature� (Nature 443:27).

McCauley illustrated the risks of tying nature conservation so closely to ecosystem services by updating an earlier story about the value of wild pollinators to coffee production. The earlier story had valued that service at $60,000 per year (PNAS 101:12579) -- but then the farm in question replaced coffee with pineapple, which doesn’t need pollinators. By the logic of ecosystem services, “the monetary value of the pollinators in forest fragments around Finca Santa Fe dropped from $60,000 per year to zero.� But, McCauley pointed out, that’s only if we assume that ecosystem services are the only reason to conserve nature.

Here’s something to think about: how does the value of a wild species depend on its rarity? The last 100 orchids clinging to a cliff on Kauai aren’t producing much oxygen. Should we concentrate on protecting spruce trees and oceanic plankton instead? From an ecological perspective, this might make sense. Sure, the spruce trees and plankton are less endangered, but their contribution to ecosystem services is so much greater. Maybe the orchids are essential to some rare insect, but what is that insect doing for the ozone layer?

An evolutionary perspective leads to a different conclusion. Even a rare species may have the solution to important problems. It certainly has the solution to many of its own problems, but perhaps to some of ours as well. For example, certain wild potatoes release insect alarm pheromones when wounded (Nature 302:608), scaring pests away rather than killing them with toxins. Any insect that evolves “resistance� to that signal will also evolve resistance to mating. Some fish see in muddy water by comparing light polarized in different directions, a technique since copied by human engineers (Optics Letters 20:608). Similarly, conch shells have inspired new fracture-resistant materials (Nature 405:1036). A search for “biomimetics� will find other examples.

Would humans have thought of these ideas, eventually? Maybe. But if I were in charge of an “industrial espionage� program, I would spy on nature rather than on my competitors. Many of evolution's "inventions", coded in the DNA of wild species, would be difficult or impossible to decipher outside of their biological context. Common species are not usually endangered and rare species usually contribute less to ecosystem services essential to humans. But even rare species, and the ecosystems where they live, may be a source of ideas useful in agriculture, engineering, or medicine – ideas whose economic value may vastly exceed that from turning a bit of rainforest into a soybean farm.

Here are some additional papers of note this week:

The Evolution of Quorum Sensing in Bacterial Biofilms

Selection for Social Signalling Drives the Evolution of Chameleon Colour Change

Widespread Genetic Incompatibility in C. Elegans Maintained by Balancing Selection

The adaptive significance of temperature-dependent sex determination in a reptile

Strong Purifying Selection in Transmission of Mammalian Mitochondrial DNA