Posted by: salamandercandy | July 17, 2007

Déjà vu

I’ve been cited… and then some. A group of researchers studying antimicrobial peptides (AMPs) from shrimp really liked my review paper on AMP evolution. In fact, they liked it a little too much. The following is a section of text from my paper, published in 2005:

Although individual tests of selection on AMPs are sometimes merely suggestive, taken together these studies present convincing evidence that positive selection on AMPs is common and taxonomically widespread…
…The specific pathogens driving selection undoubtedly vary among hosts, which could result in different patterns of evolution. Some hosts might be in a constant co-evolutionary arms race with pathogens that are under selection to resist their defenses. A variety of resistance mechanisms to AMPs are known in microbes, some of which involve a single gene product (Andreu & Rivas, 1998; Yeaman & Yount, 2003). In some cases, derived microbial strains are more resistant than the wild type (Fernandez & Weiss, 1996; Thevissen et al., 2004), which is consistent with the hypothesis that positive selection on microbial genomes can result in increased resistance to AMPs. Thus, it may be the case that resistance is easy to evolve and happens frequently. On the other hand, some AMPs might attack their targets in such a way that evolving resistance is not possible without coordinated changes at many microbial genes. Selection on these AMPs would primarily occur when hosts enter new niches and are forced to adapt to completely different pathogen species not previously encountered.

Compare that to the following section of text from this paper, published in 2007:

In consistent with the results of previous studies on the molecular evolution of AMPs in vertebrates and invertebrates (e.g. refs. Nicolas et al. 2003; Bulmer and Crozier 2004; Tennessen 2005; and Duda et al. 2002), the present study also present convincing evidence that positive selection on penaeidin, the AMP gene family of penaeid shrimps, is common and taxonomically widespread…
…The specific pathogens driving selection certainly vary among hosts, which could also result in different patterns of evolution (Tennessen 2005). Some hosts might also be co-evolving with pathogens that are under selection to resist their defenses. An array of resistance mechanisms to AMPs are known in pathogens, some of which are involved in a single gene product (Andreu & Rivas, 1998; and Yeaman & Yount, 2003). In some cases, derived microbial strains are more resistant than the wild type (Thevissen et al., 2004), which is consistent with the hypothesis that positive selection on microbial genomes can result in increased resistance to AMPs. However, it could be more likely that resistance is easy to evolve and happens frequently. On the other hand, penaeidin peptides might attack their targets in such a way that evolving resistance is not possible without synchronized changes at many microbial genes. Selection on the penaeidin mature peptides might also occur when hosts enter new habitats or environments and are forced to adapt to completely different pathogens not previously encountered (e.g. during species introduction).

Notice some similarities? Granted, only one sentence is completely identical, but there are also a lot of sentences that only differ by a few words. At this point, I think that best course of action is to simply be flattered and not register any kind of formal complaint. However, if I were teaching a class and a student handed in an assignment like this, it would be time for a discussion about plagiarism.

Posted by: salamandercandy | July 12, 2007

Scale in Biology

I’ve spent another week here at Vanderbilt, studying antimicrobial peptides from frogs and their effects on different microbes. A lot of biology lab work involves measuring out liquids, moving liquids between tubes, mixing them, heating them to particular temperatures for particular lengths of time, etc. You can’t actually see your tiny objects of study, so conducting very different types of research can look superficially the same. I’m used to working with DNA and enzymes, biological molecules that are too small to see even with a microscope, and in practice it just looks like I study small plastic tubes containing clear liquid. Similarly, the microbes I’m studying here can’t be seen with my naked eyes, so it’s just liquids in tubes all over again.

However, the volume of the liquids is different. In molecular biology, almost all of your time is spent manipulating volumes between a microliter (a cubic millimeter) and a milliliter (a cubic centimeter). Working with DNA, I never use a pipette tip that can hold more than a milliliter. Working with cells, though, I often measure out tens of milliliters. It’s because cells are so enormous compared to molecules; a microliter can easily hold billions of molecules, but to store billions of cells, you usually need many milliliters. And since cells actually can be seen under the microscope, that adds a whole new activity to my routine.

This got me thinking about biological scale in practice. Not the size of proteins versus cells versus organisms, but the scale at which scientists actually work when they study different levels of biology. Here’s a list of your basic options for the scale of your work:

Read More…

Posted by: salamandercandy | July 5, 2007

Adventures in peptide world

Greetings from the Department of Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, where I’m ensconced in the lab of Dr. Louise Rollins-Smith. After years of studying genes encoding antimicrobial peptides, as of a week ago I still had yet to handle an actual antimicrobial peptide, so I am here learning how to work with them. Today I learned how to extract peptides from frogs. You give the frog a shot of norepinephrine, a stressor hormone that induces the frog to release the contents of its skin glands. You place the frog in a beaker of buffer for about fifteen minutes, and the frog secretes its antimicrobial peptides into the buffer. You add some acid to denature any enzymes that might break down the peptides, and you’re good to go. Other researchers use electroshock methods to induce peptide secretion, but that sounds painful. Alternatively, if you know the sequence in advance, small peptides can be synthesized artificially.

I’m also learning how to assay the antimicrobial activities of a peptide. You add known concentrations of sterile peptide to known concentrations of bacterial or fungal cells (for fungi, you can actually count the cells under a microscope to calculate how many you have). You incubate them for a day or a week, depending on the microbe being tested. At the end, you assess microbial growth by how cloudy the solution is, since cells will block the light (using a spectrophotometer, of course, not just your naked eyes). Keeping everything sterile takes some effort (working under a hood whenever solutions are exposed to the air, passing solutions through filters, using lots of sealed and disposal tubes and tips, etc.). I’m accustomed to keeping an area free of PCR product, but keeping an area free of microorganisms is slightly different. It also turns out that antimicrobial peptides don’t always want to go into solution and stay there, which in practice can be a bigger issue than I ever would have imagined.

In general, there is still a sizeable gap between evolutionary geneticists and protein biochemists. The former group is good at identifying nucleotide substitutions that have been favored by natural selection, and the latter group is good at assessing the functional differences among protein isoforms, but only recently have the two fields started to merge. We still have a lot to learn about how non-neutral genetic differences identified by statistical tests of DNA sequence data translate into differences in protein function.

Posted by: salamandercandy | June 28, 2007

Molecular Evolution among the Bluenoses

SC has been quiet for a month, we know. It’s a busy summer us. This week, for the second year in a row, I attended the annual meeting of the Society for Molecular Biology and Evolution. This time the conference was in Halifax, Nova Scotia. I saw many outstanding talks and posters on a range of topics in evolutionary genetics: models of codon substitution that account for selection on synonymous sites or tertiary protein structure; evidence for adaptive evolution in mammalian globins, fish antifreeze proteins, and mollusk reproductive proteins; analyses suggesting that positive selective sweeps might be major drivers of genomic evolution; studies of adaptive variation maintained by natural selection in several different taxa; evolutionary forces governing gene duplication; etc. If you understood all of that, you might want to think about joining the Society.

One of the highlights of the meeting was getting to meet some of the other scientist bloggers, whose work so often provides a welcome distraction from whatever I am supposed to be doing. Photographic evidence of this historical encounter can be found here.

Now I’m at Vanderbilt University in Tennessee, where I’m about to spend a couple of weeks learning that there’s more to studying molecular evolution than just catching frogs and looking at their DNA sequences. Updates to follow, hopefully.

Meanwhile, Ivan is somewhere off in the wilderness catching frogs. Like I said, it’s a busy summer.

Posted by: salamandercandy | May 31, 2007

When the basal devour the derived

While the angels, all pallid and wan, / Uprising, unveiling, affirm / That the play is the tragedy, “Man,” / And its hero, the Conqueror Worm.
-Edgar Allan Poe

In the lay-evolutionist’s mind, the phylogenetic tree of life is often confused with the idea of a “great chain of being:” that living things occur in a series from “least evolved” to “most evolved,” with bacteria at the bottom and humans at the top. The chain of being is further mixed up with the food chain, such that “primitive” species are lower on the food chain, and “advanced” species are higher up the food chain, with humans again on the top. In reality, however, evolutionary relationships form a branching tree pattern, with all extant species on the tips of the terminal twigs, although some lineages have changed morphologically over time more than others, and humans are arguably the most different from the ancient common ancestor to all life. But what about this food chain business? The food chain and the tree of life are different metaphors explaining different relationship patterns, one ecological and the other evolutionary. But are they connected? Within the tree, are species that are more closely related to humans higher on the food chain?

In general, the truth of this trend is obvious; after all, most instances of heterotrophy involve animals eating plants. Similarly, think of all the examples of vertebrates eating invertebrates, amniotic vertebrates eating non-amniotic vertebrates, and humans eating other mammals. All of these acts of carnivory happen much more often than the reverse arrangement. But there are exceptions. Some plants eat animals; dragonfly nymphs eat tadpoles; spiders eat birds; squids eat fish; cane toads eat mice; and certain sharks and crocodiles will eat just about any mammal they can swallow, including humans. And even though ecologists like to separate decomposers and pathogens from herbivores and carnivores, that doesn’t change the fact that we will all eventually be “eaten” by tiny brainless microbes.

For some reason, the thought of a “primitive” creature eating a more “advanced” one appeals to me. It helps explode the myth that there is a consistent chain of command starting with humans and spreading to more distant and lowly portions of the tree. It makes the world appear less one-sided; when a Venus fly trap snaps up its prey, it seems to be striking a blow for justice against the near-totalitarian assault on plants by herbivorous insects. As a vegetarian, I am happy to occupy a lower trophic level than many other animals, and I like evidence that humans are not necessarily meant to be at the top of the food chain. Mostly, though, it humbles our species, and goodness knows we need it. While we claim to rule the world, who was just bitten by a mosquito?

Posted by: salamandercandy | May 23, 2007

Evolutionary Forecasting

Last week I attended the annual Peter Yodzis Colloquium in Fundamental Ecology in Guelph, Ontario. This year’s theme was “Applied Evolution: Understanding the Past, Predicting the Future.” There were several top-notch talks, mostly focusing on how adaptive evolution can be observed happening right now in extant species, and the discussion after each talk was particularly lively. But, despite the title of the conference, I didn’t learn much about specific events that are likely to occur in the future.

This isn’t really surprising; biologists are not soothsayers, after all. But at the same time, it seems like evolutionary theory should be able to help us better understand the consequences of our actions, with powerful applications in conservation, medicine, and agriculture. Someday, perhaps, predictions of future evolutionary trajectories might be somewhat accurate. However, maybe the more important role of evolutionary thinking is to remind us that we can’t predict the future as well as we’d like. Just when you think you understand a biological system well enough to say what it will do next, it might evolve on you and start obeying different rules. The presentation by Dr. Graham Bell at the conference illustrated this best: we can make predictions about how oceanic algae will absorb some of the excess carbon dioxide that we are pumping into the atmosphere, but if the algae evolve in response to the increased CO2 levels, as they do in lab experiments, all bets are off. Similarly, evolution can throw off our expectations about everything from the efficiency of antibiotics and pesticides to the number of pounds of fish we can harvest from the sea. Evolution adds some uncertainty to our predictive equations, which we ignore at our peril.

When I left Canada, I had to explain to the border guard what I had been doing in the county, including the name of the conference. “So where are we going?” he asked. I explained that I was going to spend that evening in Ann Arbor. “No, where are we as a species going?” he clarified.

“It turns out that it’s not so easy to predict the future, after all,” I replied, and drove into the U.S.

Posted by: salamandercandy | May 14, 2007

Catch Frogs, Release Toed: Part II

My pursuit of frog toes, originating in Illinois, has now continued across several Midwestern states. A tip from the Wisconsin DNR sent me to a muddy farmer’s field near a spring, where I easily captured two dozen pickerel frogs in broad daylight while curious cows looked over my shoulder. When collecting on private land I always feel the need to work as fast as possible, both to impress the landowners with my herpetological prowess and to promptly give them back their privacy. Luckily, these cheese-head frogs complied. In contrast, I only found a handful of plains leopard frogs in central Iowa, not enough to justify taking their toes, but I was on state land in the middle of nowhere and there was no one I needed to impress. In Michigan my field site was a military base. I might have been denied entry at the security gate but for the fact that I was accompanied by the president of the Michigan Society of Herpetologists, who had been there before and could convince the top brass to let me in. If I had accidentally wandered into the wrong section of the base, I could have been shot by practicing soldiers, so I made sure to read the map extra carefully. It was all worth it, as a riot of the world’s best-protected pickerel frogs were waiting in a seepage area to donate their toes to science.

All of these places were full of wildlife other than the frogs I was chasing, of course. Gray tree frogs and spring peepers called at night. These hylid frogs are much louder than the ranid frogs I sought, and it was often a challenge to listen for the call of leopard frogs over the deafening din of their smaller cousins. Waterfowl were everywhere; I even stumbled upon a Canada goose nest where three eggs were hatching, and I managed to observe the shells slowly crack and peep without being attacked by the irate parents. I won’t really miss the wood ticks, which I inadvertently collected even more prolifically than I did frogs.

The dried toes are now safely preserved in plastic tubes inside boxes, awaiting DNA extraction. Who knows what lessons might be gleaned from there genes? The remarkable thing is, I feel like I’ve learned so much already just by collecting them.

Posted by: salamandercandy | May 8, 2007

Paradise Lost all jacked up


I went to Hawaii a few weeks ago, for a good friend’s wedding (seems I only travel for weddings these days). I have been to Hawaii several times and I must say I love the place. I probably wouldn’t want to live there for very long because of the lack of seasons and because the sheer isolation and limited land area of the archipelago would probably drive me nuts. But it’s a lovely place to visit, no doubt.

Hawaii is superficially very beautiful, but with my biology goggles on I can’t help but see it for what it is: an environmental disaster. Specifically, Hawaii is a sad example of how human-mediated invasions of alien species can radically change natural ecosystems. Insane numbers of introduced organisms have been ferried over to Hawaii since the first Polynesians pushed their canoes ashore. These new species can outcompete and consume natives, introduce new diseases, and destroy habitat. Now the rate at which new species are arriving on these once isolated islands is millions of times higher than it was before humans were in the mix. We have introduced great numbers of weeds and other plants, invertebrates, fish, amphibians, reptiles, birds, and mammals. Hawaii’s native bird species have been decimated by disease and introduced predators; half of all the plant species now on Hawaii are non-native. Boo!

I was on Maui during my recent visit. I saw some exotic-looking birds that most tourists probably assume are Hawaiian endemics. Nope. I’ll bet that just about every bird I saw was an introduced species. And who knows how much of the lush plant life I saw while hiking in Iao Valley (see photo above) was composed of weeds and such from all corners of the world? I couldn’t even get excited when I found a cane toad hopping in the grass of a beach side resort one night– Hawaii has no native amphibians or reptiles.

Depressing…

Posted by: salamandercandy | April 25, 2007

Catch Frogs, Release Toed: Part I

I have just spent the past week collecting leopard frog toes in western Illinois, from which I plan to extract DNA for genetic analysis. I survived lightening storms, mosquitoes, snapping turtles, snakes, coyotes, encounters with local law enforcement, and the peculiarities of rural culture hundreds of miles from the part of the state that elected Barack Obama. Armed with a dip net, a headlamp, a pair of scissors, and a bottle of Everclear (to sterilize the scissors, not to consume), I stalked ponds and flooded roadside ditches at night looking and listening for specimens. Although toe-clipping is unpleasant, it is the least-invasive way to reliably get large quantities of DNA in the field, while simultaneously marking frogs so you know if you happen to catch a repeat victim (not possible with other methods like buccal swabbing). The locals were generally indifferent to my presence, since both fishing and bullfrog gigging are common regional activities, and I just looked like a normal guy with a net. When they found out what I was really up to, they were amazed that I would think to travel all the way to they neck of the woods for research, and they helped me herp and gave me beer.

Read More…

Posted by: salamandercandy | April 9, 2007

Back to Life

Yesterday was Easter. I celebrated in the standard Unitarian Universalist way, with a flower communion (yes, UUs are just a bunch of hippies). I do not believe that Jesus was the son of God, or that he rose from the dead, but Easter is very meaningful to me. Like most “Christian” holidays, is has its roots in the ancient animist religions of old Europe. You don’t need the bible to celebrate fertility, renewal, and the waking of the world after a long winter sleep. Though I live on the other side of the world from the home of the Bronze Age pagans, northern North America also experiences a re-greening at this time of year, so the holiday still fits (are whites in the tropics or the southern hemisphere less likely to embrace the rituals of their ancestors, I wonder?). Trees that were bare are now bursting with leaves and blossoms, and flowers are everywhere upon the land. The Willamette Valley receives very little snow, but in the surrounding mountains, ground that had been covered in several feet of dead ice crystals is now re-asserting its support of botany.

And thus we get to the real mystery of the Christian Easter: why are they so impressed? A man rose from the dead? That’s your miracle? Well forgive me for not really caring, but life rises from the dead at least once every year, if not more so. The tiny dry seed of the wilted annual, the withered brine shrimp egg in the desert, the spore, the cocoon, even the frozen frog… would you not call these dead if you didn’t know any better? Living organisms die, it is the fate of chromosomes to break and cells to suffer the assaults of free radicals, yet somehow, miraculously, the germ line stays alive and undamaged, and the next generation is just as spirited as the last. I myself am a collection of atoms that have spent time as trilobites, tree ferns, dinosaurs, dandelions, dragonflies, and slime molds. In me, they have re-assembled and re-discovered the wisdom generated by past beings, perhaps even to add to it.

Miracles are everywhere, right here, right now. It is time for religion to mature and embrace them, instead of putting too much stock in dusty old stories which, even if they were true, wouldn’t be all that interesting. The whole world is risen today. Alleluia.

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