This Week in Evolution

I liked this essay comparing areas in evolutionary biology where there is genuine controversy -- i.e., where people who are actually collecting data and publishing on a topic disagree -- vs. the phony controversies imagined by creationists. Group selection may still almost qualify as a controversy, a question I may address in a later post, but age of the earth, common ancestry of all species (at least those studied so far!), and the power of natural selection to solve difficult problems are not at all controversial among those actively publishing on related topics.

The question of how much exposure high school students should have to genuine scientific controversies seems a bit more complex to me. I agree that helping students get enough of the basics to understand active controversies in any depth is a big challenge. On the other hand, I've been amazed how many high school students (and their parents) think that the only definition of "research" is looking up information in a library or on the web. If we want students to understand that scientific research is an exciting, ongoing activity, some kind of exposure to areas where scientists disagree seems essential. Areas of research that are easier to understand, like the mindless screening of drugs, don't convey the intellectual excitement of real science.

Here's a seminar class I've thought about for either high school seniors or first-year college students. First, let's set the minimum standard for a scientific controversy as: at least two conflicting points of view, each represented by data-containing papers from at least two nonoverlapping groups, in journals with an impact factor of at least 1.0. Each week we consider one question, such as:
1) What causes AIDS?
2) What is killing amphibians around the world?
3) How old is the earth (within 10%, say)?
4) What living species is the closest relative of chimpanzees?
Students get points for showing that each topic was controversial, at least at one time, with a big bonus for whoever shows controversy most recently. Then we could make a time-line, showing when each question was settled (pending new data, of course!).

Posted by R. Ford Denison at 11:21 PM | Permalink | Comments (0)

Not enough people voted on the Reader’s Choice, so this week’s paper is “Phylogeny and geography predict pathogen community similarity in wild primates and humans” by Jonathan Davies and Amy Pedersen, published in Proceedings of the Royal Society.

Many humans diseases, from flu to AIDS, come from other species. Similarly, diseases from dogs are an increasing threat to lions, while cat diseases kill sea otters. Are there general rules that predict how likely two species are to share diseases?

To find out, the authors analyzed several large data sets on diseases of humans and 117 other species of primate (apes, monkeys, etc.). They hypothesized that species are more likely to share diseases if they live near each other and/or if they are more closely related, that is if they share a more recent common ancestor. This is similar to how we define relatedness in humans: brothers and sisters have more recent common ancestors (parents) than cousins do (grandparents). Fortunately, the family tree for primates is relatively uncontroversial, at least among scientists.

Continue reading "Sharing diseases with relatives and neighbors" »

Posted by R. Ford Denison at 06:53 PM | Permalink | Comments (0)

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.

It is quite possible to do good experimental science fair projects using only everyday materials (rulers, paper cups, etc.). However, a small investment in inexpensive scientific apparatus can greatly expand the range of feasible experiments. For a fraction of the cost of a desktop computer, you can measure weight (mass), volume, temperature, acidity (pH), and light, all with sufficient accuracy to generate useful data. Unlike a computer, this equipment won't be obsolete in two years, or in twenty. These prices are old, so it might be a $275 science lab by now. On the other hand, these are all new prices; used would be cheaper. Items earlier on the list are most widely useful. Add an inexpensive microscope and you'll be about as well-equipped as Darwin. Aside from the boat, gun, greenhouse, and assistants, of course.

Compare with this much more ambitious home lab. Before spending that kind of money, I would wait and see what direction my research was going.

Item.................................................................Price

Triple beam pan balance (600 g x 0.1 g).......$ 93.00
Graduated cylinders (100 mL).................2 for 11.00
Multitester (use with sensors below)..............24.99
Mini-hook adaptors for above.............................2.59
Thermistors, for temperature (2 @ 1.99)...........3.98
Photocell assortment, for light............................1.98
Red-fluid thermometers (2 @ $6.50)................13.00
Acid/base pH indicator paper...........................13.30
Range extension set for balance (2 kg) ........24.95
Stopwatch.......................................................10.00

Continue reading "Science fair secrets 3: The $250 science lab" »

Posted by R. Ford Denison at 11:59 PM | Permalink | Comments (0)

This week’s paper, “Evolvability and hierarchy in rewired bacterial gene networks”, was suggested by Joel Lopez.

Randomly changing parts in a machine often breaks it. “Intelligent design” nuts claim this is also true of living things and that this is somehow evidence for design. The argument is nonsense – just because we had distant ancestors small enough that they didn’t need lungs doesn’t mean we can survive without them -- but is the claim even true? If a genetic change is big enough to have some effect, is it likely to be lethal? Or do many mutations preserve basic functions, just increasing or decreasing fitness (survival and reproduction) under particular circumstances?

Continue reading "Gene networks: evolved not designed" »

Posted by R. Ford Denison at 02:48 PM | Permalink | Comments (2)

Today or tomorrow I'll be reviewing a paper suggested by a reader last week, but meanwhile there are lots of other recent papers that look interesting, at least to me....

Continue reading "Readers' Choice!" »

Posted by R. Ford Denison at 05:57 PM | Permalink | Comments (5)

Three recent papers in Proceedings of the Royal Society discuss differences between males and females or, in one case, among males.

“The costs of risky male behaviour: sex differences in seasonal survival in a small sexually monomorphic primate” by Cornelia Kraus and others, is based on a 10-year study of differences between male and female behavior in grey mouse lemurs. During the breeding season, males had lower survival than females, despite any possible risks associated with pregnancy or raising young. The higher risk for males apparently resulted from their tendency to travel more, looking for females.

The sexes also differ in winter behavior: females hibernate, while males remain active. Is there something about female physiology that makes hibernation healthier for them than it would be for males? Maybe, but there was no difference in winter survival between the sexes, which don’t differ much in size in this lemur species. The authors suggest that hibernation might have longer-term benefits in females, such as increased lifespan, whereas males need to stay active to bulk up in preparation for the breeding season.

This paper reminded me of an earlier paper on albatrosses, in which "in each pair, the male spent the winter just north of the pack ice in Antarctic waters whereas the female stayed south of Madagascar." It’s not hard to understand why males and females might differ in various ways (size, color, etc.) but differences in behavior outside of the breeding season are more interesting.

The second paper addresses an old argument between Charles Darwin and Alfred Russel Wallace, who developed similar explanations of evolution by natural selection at about the same time.

Continue reading "Separate vacations and other sexual differences" »

Posted by R. Ford Denison at 11:02 PM | Permalink | Comments (2)

'No practical biologist interested in sexual reproduction would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should he do if he wishes to understand why sexes are, in fact always two?' -- R. A. Fisher (1930).

The scientific definition of "theory" is very different from its popular meaning of "wild speculation." The Theory of Evolution, like the Germ Theory of Disease, or the Atomic Theory that forms the foundation of chemistry, is solidly based in observations and experiments. The "theoretical" part, in each case, is a collection of well-tested principles that make sense of the masses of data and let us make predictions. For example, Germ Theory led to measures to limit the spread of AIDS, where the Divine Punishment Theory failed. The Theory of Evolution has been equally successful, with slowing the spread of insecticide resistance in insect pests among its recent contributions.

But is there a place for speculation in biology? I think there is, so long as we don't confuse it with fact or well-grounded theory. For example, life as we know it uses nucleic acids for heredity and makes much of its cellular machinery from proteins, but can we think of other possibilities? If so, can we design experiments that would detect such alien lifeforms, if they exist, on Mars or perhaps even on Earth?

Similarly, what if some alien life-form -- any sufficiently advanced life-form is indistinguishable from a god -- has intervened in evolution here on earth? Could we develop quantitative methods to measure this effect, as we now do for natural selection and gene flow? Or, suppose we had an old bloodstain purported to be from a demigod; could we extract DNA, look for alleles that don't match anything in the human genome, and (if we found any) clone them into E. coli? A gene for smiting might have military applications. Perhaps others could be reverse-engineered for flood control. (Hey, mixing religion and science was their idea, not mine!)

The topics in the last paragraph may be too speculative to be competitive for tax-supported research grants -- success rates for many NSF programs are around 10% -- but private foundations could certainly fund such research, if they chose. To be taken seriously, however, researchers looking for evidence of intelligent design would need, as in all of science, to design experiments that have the potential to disprove their hypotheses, if those hypotheses turn out to be wrong. And they would need to publish their results in peer-reviewed journals, so that other scientists have a chance to catch any logical fallacies or methodological problems they may have missed.

This is what the advocates of intelligent design have failed to do. Put all the intelligent design papers ever published in a pile and you don't match the productivity of one good graduate student. Whining, as in the much-discussed film, Expelled, is no substitute for science.

Posted by R. Ford Denison at 10:58 PM | Permalink | Comments (9)

“Every one is familiar with the difference between the ray and central florets of, for instance, the daisy… But with respect to the [two types of] seeds, it seems impossible that their differences in shape…can be in any way beneficial”—Charles Darwin

The theory of evolution is famously linked to the Galapagos Islands, but this week’s paper “Rapid evolution of seed dispersal in an urban environment in the weed Crepis sancta,” published in Proceedings of the National Academy of Science, studied much smaller “islands.” In an urban environment dominated by concrete, patches of soil around sidewalk trees (below left) are among the few places where plants can grow.

Photo credits: Gilles Przetak and Eric Imbert.

Members of the daisy or sunflower family (Asteraceae) often produce two types of seeds (above right) on the same disk-shaped composite flower head. Seeds from the center of the disk are light in weight and plumed, so they are easily dispersed by wind. Those from the outer edge of the disk are heavier and not plumed, so they tend to fall near the mother plant. Although Darwin apparently failed to see the benefit of having two types of seeds, this kind of diversity acts as a form of bet-hedging. Wind dispersal of seeds over a wide area decreases the chances that all of a plant’s offspring will be killed.

Then why not disperse all of the seeds? Because, given that the mother plant managed to reproduce -- many plants don't -- conditions near the mother plant may be better than where most wind-blown seeds might land. This was particularly true in the study discussed here. Earlier, Jonathan Silvertown pointed out, in an essay titled “When plants play the field," that the ratio of the two seed types changes in beneficial ways with changes in flower head diameter. The area of a disk increases four-fold as the circumference doubles, giving proportionally more of the wind-dispersed central seeds. So the plant will always drop some seeds in the same place that it managed to reproduce. But if favorable conditions lead to larger flower heads, more seeds will be dispersed by wind over a larger area, where they can compete with other plant's seedlings rather than with each other.

So, without any genetic change, this disk-size dependence adjusts the ratio of dispersing to nondispersing seeds to match current conditions. But what if conditions consistently favor more or less seed dispersal? Can this ratio also evolve, with a genetic change over generations?

Continue reading "Fear of flying -- in plants" »

Posted by R. Ford Denison at 03:02 AM | Permalink | Comments (0)

Olivia Judson's latest column includes a good summary of work in my lab on cooperation between soybean plants and the rhizobium bacteria that (typically) provide them with nitrogen. As she points out, "cheating" is less likely to evolve in symbiont populations if they are transmitted in eggs or seeds, relative to symbionts that are acquired from the environment. In the former, if the host dies before reproducing, the symbiont dies, too. Symbionts without brains (bacteria, say) can't anticipate the effects of their actions; it's just that those whose genetically programmed behavior increases host survival become more common over generations.

Similarly, low symbiont diversity within an individual host may favor symbiont investment in costly activities that benefit the host. If each host has many different symbionts, on the other hand, then helping the host indirectly benefits competing symbionts sharing that host.

Rhizobium bacteria reach new host plants through soil, not via seeds, and they can do so even if the host dies without reproducing. Furthermore, each individual plant has multiple strains of rhizobia, which should undermine cooperation. Why then, do most rhizobia use their limited energy supply to fix nitrogen, giving most of it to the host plant? Why not use that energy for their own reproduction, instead?

Although there are several rhizobium strains per plant, they are typically segregated into individual root nodules. So, Toby Kiers and I reasoned, if plants monitor individual nodules and do something nasty to those that provide less nitrogen, that would act as a form of natural selection against cheating rhizobia. A computer model by Stuart West came to similar conclusions. To test this hypothesis, we forced some nodules to cheat, by surrounding them with an argon-oxygen atmosphere lacking nitrogen gas. Control nodules on the same plant got normal air, which is 80% nitrogen. Would rhizobia freed from the burden of fixing nitrogen redirect resources into their own reproduction? Would the plant impose sanctions on nonfixing nodules? If the answers to these questions are yes and yes, what would be the overall effect of cheating on rhizobium reproductive success?

Continue reading "Welcome, fellow Dr. Tatiana fans!" »

Posted by R. Ford Denison at 06:09 PM | Permalink | Comments (0)

This week's paper is "Rapid evolution towards heavy metal resistance by mountain birch around two subarctic copper–nickel smelters", published in the Journal of Evolutionary BIology by J.K. Eranen.

Evolution is a change over generations, so evolution is typically faster (more change per year) in species with short generation times. Signficant evolutionary change in bacterial populations, therefore, can take only a day or two, under ideal conditions. Long-lived species like humans and trees evolve, too, but it takes much longer. So, for example, are trees likely to evolve fast enough to survive climate change?

Continue reading "Evolutionary trees" »

Posted by R. Ford Denison at 12:20 AM | Permalink | Comments (0)

For my first 100 posts, I’ve ignored journals with “evolution” in their names, to make the point that evolution is at the heart of biology, rather than an “appendix.” Much of our DNA can be deleted without obvious ill effect, but taking evolution out of biology would kill it as an explanatory, hypothesis-driven science. Point made? This week I untie my hands and discuss a paper from one of the 30+ scientific journals that focus on evolutionary biology.

“Learning ability and longevity: a symmetrical evolutionary tradeoff in Drosophila” by Joep Burger, Munjong Koss, and others, will appear soon in the journal, Evolution.

The ability to learn is useful under a wide range of conditions, but is it always beneficial? If so, why do most species have limited learning ability? Is there some evolutionary constraint, such as head size, that prevents evolving greater learning ability? Apparently not. Artificial selection for learning ability has been successful in several species. When artificial selection imposed by humans achieves something in months that natural selection has failed to do in millions of years, that suggests that the “improvement” has some cost that exceeds its benefits, at least in nature. But could the ability to learn really have a cost that exceeds its benefits?

Continue reading "Learning vs. lifespan?" »

Posted by R. Ford Denison at 01:18 AM | Permalink | Comments (1)

That was one of the questions in a recent poll by The Economist. People in the US and the UK were asked to choose among these answers:
1) the theory of evolution
2) The Bible
3) "Intelligent design"

That's easy. Of the three choices, only The Bible even attempts to explain the origin of the earth. A broad definition of the theory of evolution may include possible explanations for the origin of life -- narrower definitions are limited to explaining how life has changed since its origin -- but "the origin of the earth" is the province of astronomy or geology, not biology. What I've seen of "intelligent design" is mostly whining about alleged gaps in the theory of evolution, rather than attempts to develop scientifically testable explanations of the origin of the earth or anything else, so that's out.

Continue reading "Which explains the origin of the earth?" »

Posted by R. Ford Denison at 10:12 PM | Permalink | Comments (5)

"A struggle for existence inevitably follows from the high rate at which all organic beings tend to increase... It is the doctrine of Malthus applied with manifold force to the whole animal and vegetable kingdoms" -- Charles Darwin, Chapter 3, The Origin of Species

Although this paper focuses on Easter Island, it also discusses many of the same societies in Jared Diamond's 2005 book "Collapse." The book includes much that is not in the paper, but the paper has the advantage of being shorter and of supporting specific points with specific citations, in contrast to the diffuse "Further Reading" approach used in Collapse.

Continue reading "Oestrus Island" »

Posted by R. Ford Denison at 10:34 PM | Permalink | Comments (0)

This is a kilometerstone of sorts: my 100th post! Also, cumulative visits passed 10,000 this week. I know some blogs get more hits than that in only one day, but I used to spend hours preparing a lecture for 25 students, so I guess it's worthwhile to write a blog post for 10,000/100=100 readers. My readership trend over months seems to be slightly downward, however; I hope that's due to other blogs are getting better and readers having limited time, rather than my posts getting worse. Maybe I should be spending the time on my research or my Darwinian Agriculture book instead.

I recently wrote about mimicry in butterflies, then saw an interesting paper on how natural selection and migration affect mimicry in snakes. Selection and migration ("gene flow") are two of the four main processes responsible for evolutionary changes in the frequency of alternative genes in populations; the other two are the random ("drift") processes that can have a big effect in small populations but get smoothed out in large populations and, of course, mutation.

Selection and gene flow often act in opposite directions, because animals migrating into an area (or seeds or pollen blowing in) tend to be less well adapted to their new home, relative to animals or plants that have been evolving there. This general rule held up in this week's paper, as evident from the title: "Selection overrides gene flow to break down maladaptive mimicry", written by George Harper and David Pfenning and published in Nature.

Continue reading "100th post: reversing evolution II: mimicry in snakes" »

Posted by R. Ford Denison at 06:37 PM | Permalink | Comments (10)

Most scientists also volunteer their time as "peer reviewers" for scientific journals, checking submitted papers for serious flaws, such as lack of appropriate controls. Reviewers also make good papers better by, for example, suggesting alternative interpretations of results. My own papers have been greatly improved by this process, which makes up for the few times I've thought a paper was rejected unfairly. (Fortunately, there are plenty of good journals, and the odds are against getting the same incompetent or biased reviewer twice.)

As a minimum, reviewers try to make sure that the paper describes what was done and what the results were, clearly and unambiguously. Which brings me to two recent sentences from the New York Times that probably wouldn't have made it through peer review:

And now add to the lengthening list Gov. Eliot Spitzer, husband, father of three teenage daughters, who authorities on Monday said had been involved with a ring of prostitutes.

Police found the soldier, who was still in the vicinity, shortly after 11 p.m., using a helicopter with a thermal camera.

Posted by R. Ford Denison at 10:32 PM | Permalink | Comments (0)