Sunday, January 11, 2009

The effect of dams on the survival of Pacific salmon smolts

A tiny salmon smolt, on its treacherous journey of a hundred miles or more to the sea, faces many dangers—-but new research suggests that the dams blocking its way may no longer be among them. A multi-year study using new tracking technology has demonstrated no survivorship difference between smolts in a dammed river and its undammed neighbor.

The study took place in the Snake-Columbia river system of Idaho and Washington, which has eight dams, and its dam-less neighbor to the north, the Thompson-Fraser river system of British Columbia. The dams in the Snake and Columbia rivers have often been blamed for killing the small salmon that swim through them, and ultimately for the decline in salmon stocks. Although dams were historically responsible for killing large numbers of salmon, in recent decades billions of dollars of investments have made dams much more salmon-friendly. The effect of the improved dams on salmon has not been compared with that of a damless river until now.

No matter how they analyzed the data or adjusted their detection methods, the scientists behind this study did not find a higher death toll among the salmon smolts in the dammed Snake-Columbia river than in salmon of the same species in the undammed river nearby.

“This result is surprising,” wrote the researchers in their October 2008 paper in Public Library of Science: Biology. “Dams are often implicated as major barriers to [salmon] recovery in the Columbia.”

With only two river systems included in the study, it cannot be proven that the results found were caused only by the difference in the number of dams, or if they resulted from some other dissimilarity between the two rivers. For example, it is possible that the salmon in the Snake-Columbia river system were of a stronger strain that was better able to survive the rough ride through eight dams en route to the sea.

However, if larger-scale studies confirm the result found by this study, the implications could be great for management of critically endangered salmon populations in the Northwest.

Salmon supply $1 billion dollars in income to fishermen on the Pacific coast and employ 60,000 people there. As a keystone species, they also provide valuable ecosystem services on which the survival of many other species hinges.

With those kinds of numbers at stake, and with billions of dollars available to spend, studies like this one are necessary to prevent taxpayer money from being wasted on expensive projects that have no effect on salmon populations, while more important conservation strategies remain undiscovered.

As the authors of the paper point out, their tracking showed smolt survivorship of as high as 20-30 percent from headwaters to ocean, but other studies have shown that the percent of salmon that survive long enough to turn back around and leave the ocean hovers around 0.5. This implies that the real focus for salmon conservation efforts should be the ocean, where the most salmon death may be occurring.

It is possible, however, that the dams were killing the smolts slowly rather than quickly, which would have not been detected by this study’s methodology.

“Our data do not address whether the possible delayed effects of hydropower system passage subsequently affects mortality after the fish leave the river for the ocean, currently a contentious issue,” wrote the authors. “We suggest that conservation efforts in the Columbia may be better directed towards understanding the effects of hydropower system passage on ocean survival.”

This study, and the larger-scale studies it will surely trigger, only became possible with the recent development of a massive acoustic tracking system permanently installed along 1,500 miles of western North America’s continental shelf. The Pacific Ocean Shelf Tracking (POST) Array uses an acoustic frequency that penetrates both salt and fresh water, and is powerful enough to detect a fairly small chip implanted in a fish hidden in a large body of water.

Before the POST Array was constructed, the only technology available to track the movements of small fish was a very short-range radio tagging system. This radio system is so weak that it only records fish two or three feet from the detector. While this works fine for dammed rivers-—the radio detectors can be installed in the fish channels through the dams—-it offers no reliable way record fish survivorship in wide-open, undammed rivers.

With this more powerful detection method in place, it should become easier for scientists to tell where and when salmon are dying. If it is confirmed by further study that hydroelectric dams should no longer be a point of concern for salmon conservation, all of those who rely on salmon for a salary or for a meal can breathe a small sigh of relief—-and turn their attention to the host of remaining dangers faced by these delicious, important fish.
postscript. The paper is publicly available at

update on my life

So, I haven't posted since late September. Since I try to write meaty posts that explore research papers and other topics not talked about elsewhere, rather than writing fluffy chatter on something someone else has gotten to first, the result is that these things take me a long time to write. Hours. So what I'm trying to say is that fall semester turned out to be killer, I decided to spend my time writing for my science journalism course assignments and doing a million other things required for academic survival, rather than writing for the denizens of the internet. So, for my three fans, I apologize. As we speak, I'm seriously pursuing a career in science journalism, working as an intern at the Kojo Nnamdi Show, a daily talk show on Washington D.C.'s local NPR station, and applying for a couple science writing internships. I just finished a mock-news article for my AAAS Mass Media Fellows Program application on a recent journal article of my choice, and I thought it might be interesting for people to read. It follows.

Sunday, September 28, 2008

“God likes matter. He invented it” (C.S. Lewis): A talk by Kenneth Miller at the University of Maryland

On Thursday I came back to my office to find a ripped-down poster haphazardly taped to my door, announcing a talk Friday by Ken Miller--the author of popular books about evolution, such as this year’s Only a Theory. The culprits, a couple friends of mine in the department, had misunderstood Miller’s stand on evolution due to vague wording in the poster, and stuck it on my door to piss me off.

They didn’t know of course, that I just finished Only a Theory last week, loved it, had no idea Miller was coming to speak, and was overjoyed to be informed of it. Needless to say, they were annoyed that the guy wasn’t in fact a creationist, and I wasn’t in fact pissed off. The talk was wonderful though. He is as good of a speaker as he is a writer. I think he fills a very needed role in the evolution/creationist debates—as a Christian himself, he is able to speak directly to fears that evolution and theism are fundamentally incompatible. As Miller points out, people’s beef with evolution is not really scientific, it’s philosophical—the fear that evolution takes away our ability to be moral human beings with purpose in our lives.

His talk was basically a summary of OAT, but for those who haven’t had a chance to read it yet, I’ll outline the talk for you here.

He started off with an overview of all the legal challenges to evolution that have been cropping up within only the last four years: there have been two federal trials (outlined below) and two state elections (OH and KS) that hinged on questions of evolution. Anti-evolution measures were passed in six state legislatures during this period, and 44 states had local measures passed in counties or in individual communities.

At the federal level, there was the 2004 case in Cobb County, Georgia, where the school board decided to put warning labels on the inside of the local high school biology textbook (written by Miller, incidentally). The stickers read, “This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered." Miller pointed out that the scientific definition of “theory” is not “we don’t really know,” and really a theory is of a higher order than a fact, since theories explain sets of facts. Additionally, he protested that the sticker conveys a false sense of certainty about all other fields of biology, and implies that, for instance, ecology and cell biology should not “be approached with an open mind, studied carefully [or] critically considered.” Kind of insulting to all biologists, really.

And then of course there was the famous Dover trial in 2005, for which he served as an expert witness for the side of science. In this case, the local school board was guided by the Discovery Institute’s booklet, “Intelligent Design in Public School Science Curricula: A Legal Guidebook,” and bought two sets of the Intelligent Design textbooks “Of Pandas and People” for the school library, as recommended by the booklet. The board also demanded that the biology teachers re-write their curricula to include intelligent design. They refused. The school board pushed back, demanding then that the teachers at least use an intelligent design lesson plan that the school board wrote for them. They refused. The school board finally asked the teachers to just read a statement to the class about the “weaknesses” of evolutionary theory and the teachers once more refused, forcing the school superintendent to come in and read the statement to the classes while the teachers stood outside. There was immediate protest from the community, of course, and a first amendment lawsuit was quickly filed against the Dover Area School District.

A group of scientists, including Miller, volunteered to serve as expert witnesses. Miller noted in his talk that despite ID proponents’ eagerness to subpoena “evolutionists” for a courtroom trial and force them to speak under oath, 5 of 8 ID witness volunteers dropped out of the case (including William Dembski, who wrote the document linked to in this paragraph).

The details of the ruling and the evidence is really quite fascinating, and you can find a thorough summary at Wikipedia along with a link to the judge’s decision. (The judge ruled, by the way, on the side of evolution.)

Miller then went on to outline just some of the purported evidence for Intelligent Design. In his talk on Friday, he just went over one major piece of the ID case—the “irreducible complexity” of the bacterial flagellum, but his book has many more, all of which he carefully considers and thoroughly destroys.

Michael Behe, one of the major ID theorists, defines irreducible complexity basically as the inability to produce a complex structure piece by piece while maintaining one function. For example, you couldn’t evolve a mousetrap because a mousetrap with only a couple of its parts is no longer a mousetrap—all of the parts are necessary for its mouse-catching function. The IDers say that the bacterial flagellum is an example of such an irreducibly complex structure, as it would not be able to function as a flagellum without any of its parts.

As Miller described in his talk and in OAT, the major problem with this argument is that it assumes that modern-day biological structures have evolved from earlier structures with similar functions. The fact is, as structures evolve, they often acquire radically new functions. (See my earlier post on the tryptophan operon for a biochemical example of this.) The same goes for the bacterial flagellum. It turns out that the base of the flagellum has incredible homology with another bacterial structure called a Type III Secretory System, used by bacteria to pump poisons. Additionally, other parts of the flagellum are made of a number of other proteins that exist elsewhere in the cell, performing other functions. So, unlike the predictions of the Irreducible Complexity argument, it is in fact possible to “take away” parts of a complex biological machine and have it still function—it’s just a different function.

At this point in the talk, Miller switched gears. He asked: well, if the best arguments the IDers can come up with don’t hold water, why is there such popular support for ID? He put a lot of emphasis on a quote from an NPR interview about evolution with former Sen. Rick Santorum, which I think is significant enough to reproduce here in its entirety:

"It has huge consequences for society. It's where we come from. Does man have a purpose? Is there a purpose for our lives? Or are we just simply the result of chance? If we are the result of chance, if we're simply a mistake of nature, then that puts a different moral demand on us. In fact, it doesn't put a moral demand on us."

Miller’s point was that Santorum--and approximately half of Americans--reject evolution because they see it as materialistic to a fault: denying souls, denying order, purpose, and meaning. Essentially, Miller argued, the design movement has forced science into a corner: out of opposition to the ID movement, scientists find themselves having to take the exact opposite position—that there is no design in the universe.

Miller argued the opposite: the universe has a design; it is the design of evolution. Basically, he said that evolution is an inherent, predictable property of life. It explores adaptive space in a predictable way, filling the same ecological niches with similar types of organisms. All organisms and biological structures do have a function, but it is a function that is driven by evolution. Miller went through several examples--such as the elegance of the genetic code, the specificity of proteins, the homology between different sorts of animals—-to illustrate this evolutionary “design.” He would probably note that the fact that I just put the word “design” in quotes in that last sentence is a sign that I am a scientist who has become afraid of the word because of its attachment to the anti-science ID movement. We, as the science-loving public, must reclaim that word, he argued. Regardless of our own beliefs about religion, we must show that the design of evolution does not mean our species and our lives are ruled only by chance and accident--we can still have purpose in our lives, and we are not "mistakes." Science’s derided materialism is its virtue, not its downfall, because it allows science to find natural explanations for natural phenomena. The ID movement was founded on an opposition to this materialism but Miller (like C.S. Lewis in the title of this post) argued that materialism shouldn’t frighten us, as a society, away from science. The scientific process cannot make claims about good and evil; this is society’s job as a whole. Science, and specifically evolution, Miller argued, will not make us immoral. It will only teach us about our place amongst the life on Earth, a place uniquely suited for us and our lives, each with its own unique purpose for the greater good.

Miller deftly answered the questions from the audience after his talk. This is obviously a man who has given many, many talks to diverse audiences, has heard every possible question, and has thought about all of them. His answers were eloquent and well-considered. If there were any IDers in the audience, they did not speak up in the Q&A period. As a friend and I discussed afterwards, they really wouldn’t have much to protest in the talk. Miller really covered all of the bases, and as a practicing Roman Catholic, could hardly be told that evolution is threatening to religion. If you haven’t yet read Only a Theory I suggest you pick it up at your local library. Not only does it thoroughly annihilate the ID position from every angle (useful reading for when you are forced to argue with a creationist) and discuss the larger anti-science implications of the anti-evolution movement, but it also provides a useful and much-needed perspective on the relationship between evolution and philosophical questions of morality and purpose. Read the book, and if you are lucky enough to see an announcement of a talk by Ken Miller, go and see him--and bring your friends.

Sunday, September 21, 2008

Increase in Measles Cases

The CDC has issued a press release on an increase in the number of measles cases in the U.S. this year, with 131 cases reported so far. Of those measles patients, 95 were eligible for vaccination but 63 of them were not vaccinated because of their--or most likely their parents'--belief that vaccines are "dangerous."
I'm not sure how much evidence there need to be to convince parents that the MMR vaccine, and/or the preservative in it, do not cause autism. Obviously, piles of evidence accrued from gigantic longitudinal studies of thousands of children over many years are not enough. (see here, here, here, here, and here, for starters.) Will an epidemic of preventable, deadly infections be the only thing that will change some people's minds?
If people want to put themselves in harm's way because of their willingness to believe a bunch of pseudoscientific wackaloons, that's their problem. It's a terrible shame that they're putting their kids at risk too.

Trickery and Sex in the Firefly World

This is not news in the scientific world, but it’s news to me—I ran across this in some reading I have to do for a seminar tomorrow. Further evidence that bugs are awesome:

Fireflies, lightning bugs, or Lampyrids (if you were the nerdy type). Who didn’t spend innumerable summer evenings in childhood chasing after these beetles, empty pickle jar in hand? But you might not have known of the high drama and Shakespearian trickery that was going on among these insects right there in your own childhood backyard.

There’s multiple species and genera of Lampyrids in North America, each with its own characteristic flashing pattern. Males and females of the same species locate each other for mating using these unique signals. However, females of the genus Photuris have evolved a deadly trap: they lure males of other genera by imitating their own females’ flashes. When the males come a-courtin’, the Photuris females pounce, and devour them with gusto.

You may wonder how the Photuris females ever mate, if they’re always on the prowl for dinner during mating time. Turns out that male Photuris capitalize on their female’s predilection for firefly meat by imitating the flashing patterns of males of other genera—the very insects that the female is trying to lure to their death! Some Photuris males go even farther in their imitation, by flashing not only the right pattern, but also at the right time of night, in the right location, to be even more convincing as the potential prey.

In some species of Photuris this imitative behavior has gone so far that the species has completely lost the ability to produce its own unique flashing pattern, instead conducting all its business using signals stolen from others.

I’m unaware of any papers that detail what happens next, after the flash exchange—how does the male Photuris end up as the mate, and not the dinner of the female? I’ll do some more searching because this has piqued my interest, and let you know if I find an answer.

Thursday, September 11, 2008

The Darwin Particle

My father works with the particle accelerator at Fermilab in Illinois. As a child, when I would visit him at work and we would walk through the underground tunnels where the beam-control equipment was kept, the towering machines on each side of the walkway would terrify me: they thundered, blinked, screamed "Warning: Radiation" to me at every turn.

Now CERN has built an even bigger, scarier accelerator. And all I have in my lab is jars of termites.

Fortunately, we biologists now have our own accelerator to terrify our progeny with. At last, the final secrets of evolution are within our reach.

The Black Widow Spins Her Deadly Web... Well, Sometimes.

I always get disproportionately excited when I read about a new discovery showing behavioral complexity in invertebrates. Of course, now that we understand the incredible intricacy of honeybees' language, these sorts of things shouldn’t surprise me too much. But I still love this stuff, wherever it pops up.

Black widows alter their web architecture to be better insect traps as they get hungrier. A neat little paper in this month’s issue of Animal Behavior [76(3):823-829] describes how this happens.

When a black widow spider is well-fed, it uses that energy with gusto—spinning out lots of thread, but making a chaotic, disordered cloud of a web near the opening to its hideout. This kind of web is called a ‘tangle-based’ web, and for all that thread, isn’t really that sticky.

However, take a spider who hasn’t been fed for a week, and watch her spin a web. That jumble becomes a well-engineered, efficient killing machine. Instead of making a jumble of undifferentiated, generic thread, the spider uses three different kinds of silk structures to spin a very specific trap (using less thread overall):
(This image is taken from the original paper)

SH is the silk sheet, a flat plane on which the spider can easily maneuver, supported by a network of threads (ST). Anchoring the web to the substrate are the very sticky gumfooted threads (GF), which are kept under constant tension.

The researchers set up homes for 112 juvenile black widow females, fed half of them every day for a week, and the other half nothing for a week. After the members of each group spun their characteristic webs, the webs were imaged to quantify the structural differences between them. Then the researchers saw what happened when half of each group was then moved to the other group’s webs, and then fed.

Under most metrics used, the researchers found that it was indeed much easier for black widows of both types to catch prey when the spider was using a hungry spider’s three-thread design, rather than the chaotic mass of thread of a fed spider. It seemed that the silk sheet made it easier for the spider to sprint out towards its prey. The prey may have alerted the spider to its presence by touching the gumfooted threads and sending out vibrations, and perhaps was slowed down by those threads’ especial stickiness.

Why would black widows switch between a poor web and a good web, though? Wouldn’t it be better to just maintain the efficient functionality of the three-thread design whether the spider was hungry or satiated? This is especially head-scratching when you consider that it uses up more silk to make the jumbled webs of the full spiders. The spider would be using up energy both to modify the web as well as to make the loads of silk needed to the tangle-based web.

Consider this though: the authors point out that many spiders are prone to killing more prey than they can eat, and just leaving the extra prey rolled up in silk on their webs. It’s also been documented that some spiders may just eat themselves to death if able to catch too many prey. Perhaps the switch to the poorly-trapping tangle-based web is a smart move by the black widows, at the very least saving them the energy of pursuing and killing more prey than they can use, at the most sparing them a fate like Monty Python’s Mr. Creosote. The authors also suggest that the tangle of web of a fed spider might serve as a predator defense in those times in which it doesn’t need the web to serve as a food trap.

I think the behavioral plasticity that can be built into such a small animal is really fascinating, and the adaptability of the webs of these spiders is just another example of that. So three cheers for the black widow (one for each part of her web)!

And one more that we aren’t one of the flies who get caught by her web when she’s hungry…