Search This Blog

Friday, December 30, 2011

Tale of Two Skinks

There are two edges to the sword of change that is slicing through so much of the biological skin of our planet.  The first is the staggering loss of biological diversity, adding up one of the great waves of extinction in Earth's history.  Along the trailing edge, ecosystems and the species that evolved in them are under increasing pressure from species new to the system.  We pay a lot of attention to the problem of extinction, but much less to invasion, even though it can and does contribute to the former.  It is perhaps a bit easier to rally to save a charismatic species such as a panda rather than organize to fight the diffuse threat posed by signal crayfish or purple loosestrife or kudzu.  However, scientists have started asking why some species become so destructively overabundant even though close relatives may be on an endangered list. 

Behavior alone won't dictate success.  Species that establish in new places also tend to be introduced over and over,  increasing the odds that eventually, a few individuals will survive the initial colonization event.  This in turn may be dictated by who lives where the most common transport routes start.  However, individual behavior seems to play a larger role than we expected.

Kudzu consuming a barn in North Carolina. Photo: NASA

If you want to successfully colonize a distant planet, you might consider taking a close look at how this works right here at home.  First, you've got to get yourself on some kind of transport vehicle, whether in the gut of another animal or the hold of a trading vessel or cargo plane headed elsewhere.  Realize you're probably not a welcome passenger, so you've got to be discreet.  You have to survive the journey, which means somehow finding or maintaining conditions in which you can live, with enough water, warmth and energy to avoid death.  Once you arrive, you need to sneak out of the way lest you be caught in the act and exterminated.  Very few stowaways make it this far, but the journey isn't over yet.  You need to find appropriate food, water, and shelter in these new, unknown surroundings.  Eventually, you need to reproduce successfully, which means you need to find, recognize, and successfully interact with a mate.  Next, your children must also raise children.  The resulting little community must avoid being found and eradicated, and finally, new colonists must leave and establish more communities before the invasion can be considered a success.

The odds, in short, are heavily stacked against you.  However, even if animals don't get help (in the form of deliberate introductions by people, such as starlings in North America, cane toads in Hawaii and Australia, or possums in New Zealand), some species still manage to pull it off.  We've just started to think about how animal behavior influences the risk of successful invasion.

The delicate skink, Lampropholis delicata, and its cousin the garden skink (Lampropholis guichenoti), illustrate the point.  The delicate skink is native to eastern Australia, but has managed to colonize New Zealand, Hawaii, and Lord Howe Island.  The closely related garden skink, however, has stayed home even though it is quite similiar to its more adventurous cousin in many ways.  The two skinks are similar in size, have similar diets, and similar life histories.  Both species live together in urban areas in Australia, close to transport hubs such as major shipping ports and airports.  Both are common, and occur at high densities, suggesting no lack of individuals available for export.  What, then, is different?

Although both skinks like to explore new environments, the delicate skink was far more willing to move through a tube when it couldn't see the exit, enter a small black box in the test cage, and walk up a graveled ramp to reach a heat lamp suspended above the cage floor.  A greater willingness to explore, then hide, may explain a good part of why delicate skinks are called plague skinks while garden skinks have been at worst temporary tourists who never established outside their native range.  The opportunity to become a problem appears to be the same, but the behavior of the animals influences who takes advantage of that opportunity.

Garden skink.  Photo: Peter Robinson, Museum Victoria, Australia.

Not all delicate skinks successfully found the elevated basking site; animals, after all, are individuals.  Other research found that individual mosquitofish vary in their tendency to strike out for new horizons.  Interestingly, fish that chose to disperse also seemed less tolerant of other mosquito fish, and these personality traits were consistent in individuals over the study.  There may need to be a range of personalities and behavioral tendencies to support a successful invasion from start to establishment. 

We don't often think of the individuality of wild animals, or how much that might matter to the survival of a species.  If we were better at recognizing the individuality of non-domesticated animals, how might that change our view of them?

Chapple, D.G., S. M Simmonds, and B.B.M. Wong. 2012. Can behavioral and personality traits influence the success of unintentional species introductions? Trends in Ecology and Evolution 27:57-64.

Chapple, D.G., S. M. Simmonds, and B.B.M. Wong. 2011. Know when to run, know when to hide: can behavioral differences explain the divergent invasion success of two sympatric lizards? Ecology and Evolution 1:278-289.

Colautti, R.I., I.A. Grigorovich, and H.J. MacIsaac. 2006. Propagule pressure: a null model for biological invasions. Biological Invasions 8:1023-1037.

Cote, J., S. Fogarty, K. Weinersmith, T. Brodin, and A. Sih. 2010. Personality traits and dispersal tendency in the invasive mosquitofish (Gambusia affinis). Proceedings of the Royal Society B 277: 1571-1579.

Saturday, December 17, 2011

Driloleirus macelfreshi lives!

This week marked the third anniversary of a significant scientific discovery made by my dogs.  We were out on a walk on a messy afternoon marked by mud, driving rain, and wind, courtesy of a Pacific winter storm.  Young dogs still need their walks, and so do their owners.  I can't really say quite how it happened, other than as I bent down to discharge my responsibility as a dog walker after my old dog had finished her business, I glanced back and saw the young one standing with a long pinkish stringy thing hanging from his jaws.  He looked quite pleased with himself, and was an instant away from flinging up his head and consuming his prize.  I witnessed this in the split second between discovery and annihilation. And somehow I knew that he absolutely must not be allowed to eat this thing, not for any risk to himself, but because of what it was. 

I leaped at him, howling at him to drop it, which is absolutely not how you are supposed to train a six-month old pup to surrender highly desired objects.  Fortunately for science, he was so shocked at my behavior he did drop it, and in his moment of indecision I swooped on his find and scooped it into a spare plastic bag.  The dog was utterly unimpressed at my inexusable theft of what he regarded as rightfully his.  There are times when I wonder whether he still remembers this.

At that time, however, we went home, and I laid the dog's find out on the counter.  It was an earthworm, and it measured four feet four inches long.  It was flabby, pale pinkish-gray, impossibly thin, and quite dead.  It was also the first specimen of the Oregon giant earthwormDriloleirus macelfreshi, to be documented in twenty-seven years.  We know very little about this species, other than it seems to be endemic to the wooded bottomlands of the Willamette Valley.  It had been pretty much assumed to be extinct.

There are many little pieces to this discovery, each of which made that sudden, instinctive recognition on my part possible.  Over a decade ago, I had the great fortune to meet two of the last earthworm taxonomists in the world, Dorothy McKey-Fender and her son, Bill Fender.  This in itself was a culmination of improbable circumstances, but the crux was a workshop, conducted by Dorothy who was then in her eighties, on how to identify native earthworms.  The workshop was followed by a search for native worms in 2000.

Bill Fender and Dorothy McKey-Fender with a specimen of Driloeirus macelfreshi in their laboratory in 2000.  Photo: D. K. Rosenberg

I know a little about earthworms, as much probably as any average gardener or curious naturalist knows.  Native worms have been largely replaced by exotic species, and most of the worms we see as we go about our daily lives are descendants of recent immigrants to this continent as most of us are.  Ecologically speaking, we do not even know what we've lost, because the native worm fauna has been very poorly studied and described.  We do know that different families of worms behave differently, and affect nutrient turnover and soil humus in different ways.  We do not understand all the implications, although they include reducing the humus layer, which is itself a vital habitat for many organisms, and allowing exotic weeds to establish on the surface of soil no longer protected by that deep blanket.  For the most part, though, we just don't know what we've broken or what pieces remain somewhat intact.

There are earthworms out there, native worms, very different from the nightcrawlers we all immediately identify as the ultimate worm.  Even more amazing, there happens to be a gigantic native worm called the Oregon giant earthworm, Driloleirus macelfreshi.  Dorothy McKey-Fender herself had studied most of the specimens that have ever been collected- a scant few dozen in all.  They were far too rare to allow the workshop participants to examine, but Dorothy moved around the lab room set up with dissecting scopes and trays filled with other worms pinned to the black wax, delighted to share some of the knowledge accumulated over a lifetime.  Her love and respect for these animals was palpable, and her excitement contagious.  I've been more aware of worms since then, for their own sake, not just for what they do.

So there we were, in a wet riparian forest at the tail end of a storm dumping heavy rains, swelling the Willamette River until it licked and curled at the bases of the cottonwood trees along its banks.  A party of several people and several dogs ahead of us had walked right by the corpse of the giant worm lying on a bed of fallen leaves, not far from the floodwater's edge.  I would not have noticed it either, if my young dog hadn't loved to eat dead things.  But at least in that instant of seeing it, I was open to the existence of giant native worms.  Without that, the discovery would not have been possible, even if I had still looked straight at my dog in that instant before he snatched and swallowed.

Looking for another giant worm- the last one was right around here somewhere...

The worm is now among those in the McKey-Fender collection, although a small segment of the tail sits in a vial on my desk for possible genetic analysis.  More importantly, we know we can still look along the rivers and woods and hope for more than we recently dared hope for, that one of the unique forms of life on this planet may still be with us.  If we can be open to those possibilities, I hope we can also be open to more creative visions of how to live more gently and equitably among all of our fellow species.

Monday, November 28, 2011

Leaves in Grass

Our neighbors have gone south for the winter, seeking climates where it does not rain six days out of seven.  They leave by Halloween each year, before the rains have really set in, and return when spring is still early enough that wet cold days are the norm even as the Indian plum sends out graceful arcs of cream-colored flowers.

I've been thinking about communities lately, both ecological and human.  We take it as a given that the natural world is made up of many interconnected pieces, so that no single organism stands by itself.  For some reason, we have a much harder time accepting this view of our own communities, even though it is every bit as true.  This matters, as how we manage the coming enormous upheaval on a planet in rapid climatic transition will depend on how we see each other, and our relationship to both the rest of humanity and to the larger biological community of which we are an indivisible part.

The leaves have fallen in the neighbors' garden, thick enough to smother the grass if they remain there until spring.  I took the dogs and a rake and wheelbarrow and went to work, sweeping up the remnants of last summer's photosynthesis and depositing them in the garden plot.  Leaves are extraordinary.  They do all the work of taking sunlight, which in itself is simply energy, and transforming that energy into actual food- both for the plants, and for nearly all the rest of the non-plant life forms on the planet.  It is a very cool trick.  An even more amazing part of the trick is to shed the biomass when it becomes more of a liability than an asset, first salvaging the good stuff before letting the depleted leaf fall free.  The rest of us get a blaze of colorful glory before the curtain falls and winter takes the stage.

We have an understanding with these neighbors.  In the summer, they allow us to pasture our ewes and lambs on their five-acre pasture, and keep an eye on the water trough.  They've helped us build fences, taught us how to deliver lambs that are too tangled to come out on their own, and loaned us innumerable tools.  They've shared vegetables, gardening knowledge, tips on livestock care, small gifts, and great stories.  They are the sort of neighbors most people only know of through a culture of yesterday. 

In return, we help as we can, share lamb and blueberries and fresh bread, and keep an eye on their place when they go away for the winter.  I rake leaves and I can never quite believe that the summer is really gone, our neighbors are gone, and now there is the winter to be gotten through before we look down the hill and see their lights shining, breaking the darkness with a friendly light that says the neighborhood is as it should be.  The leaves have got to be gathered up first, and given a chance to move through the next stage of the cycle.

Shed leaves are a major component of soil humus, providing food and shelter for all manner of soil organisms.  I leave a fair number of scattered leaves as I rake, so they will provide fodder for the earthworms and enrich the soil that in turn supports the tree.  They'll be long gone by spring, and they are scattered enough so they will not impact the grass.  I use a bamboo rake and a wheelbarrow, because they get the job done while leaving me with the peaceful late fall afternoon, broken by the happy huffing of my dog in hot pursuit of his tennis ball, which I throw between sweeps of the rake, the calls of small flocks of juncos and chickadees, and once the sound of a tree falling in the woods by the creek.  It was wet and windy the day before, and the cycle of renewal incorporates more than just leaves.

I finish before dark, but not before the cold of evening flows in along the creekbed next to the garden, and the sheep start looking expectantly for some alfalfa pellets in their feeder.  Properly done, the afternoon's work will nourish both the human community and the wild one, with no loss to either.  Surely we can find a way forward that truly honors that which we value most.

Friday, November 18, 2011


One of the reasons I love living in western Oregon is that winter brings another season of life rather than a frozen dead spell, when most organisms either flee or hibernate until spring.  A few mammals and birds tough it out where winter brings snow and ice, but the woods are pretty quiet besides the sound of bare branches scraping in the wind.

Here, the tree branches are free of leaves now thanks to some Pacific storms ranting across the coastal mountains.  The branches aren't bare, however.  The forest is turning a new shade of green, one with delicate pale-gray hues, as the lichens unfurl on every small branch and twig of the oaks and maples.  Thick rugs of newly revived liverworts and mosses embrace the trunks and larger branches.  The snakes and lizards have disappeared, but the rough-skinned newts are out, marching along on their rubbery legs as they begin to move toward their breeding pools.

Photo by Miguel Viera, Flickr Creative Commons

The rough-skinned newts, Taricha granulosa, appear when late fall finally eases the harsh seasonal drought with the misty rain.  The newts are both numerous and active during daylight, unlike any of their kin.  They are encountered more often than they are noticed, judging by the number of flattened corpses on the road leading to the forest gate, and sadly, even in the woods where vehicular traffic is replaced by bicycles and walkers.  It isn't always adaptive to look like a somewhat rotten stick when viewed from above.

Rough-skinned newts tend to freeze in place if startled, although they can move along at a good clip if they decide they need to.  They are patient, and will stand motionless in mid-stride for many minutes if disturbed.  Their second line of defense is to curl in a distinctive ring, head thrown back, tail arched toward their throats, exposing their undersides in bright warning.  This dance to avoid being eaten is called the unken reflex, and it is shared among salamanders, toads, and frogs who defend themselves using chemical warfare as a last resort.

Unken reflex.  Photo by Ap2il, Flickr Creative Commons.

In the case of the newt, the bright orange color is backed up by tetrodotoxin, a potent neurotoxin, one shared with the blue-ringed octopus, a few toads, and some fish, most famously the puffer fish.  The Japanese serve a dish called fugu, which ideally offers the adventurous diner tingling lips but if not expertly prepared, leaves the victim paralyzed then dead through respiratory failure.  The Seattle Audubon Society's book Amphibians of the Pacific Northwest(1) reports that people have died from eating newts in the genus Taricha, although they do not reveal the circumstances.

How exactly such a diverse group of organisms have hit upon the same defense strategy is still unclear, although some researchers have suggested that symbiotic relationships with bacteria who synthesize the tetrodotoxin may explain the pattern(2).  Not everyone agrees, however, that this is how the newts acquire their chemical weaponry(3).  All stages of the newt are toxic, and mothers seem to pass on the poison to their eggs.(4)  Individual newts have variable levels of the toxin(5); presumably it is biochemically expensive to manufacture, and you might get by with a less stringent defense if your enemies expect all members of your species are equally bad for the digestion.  The predators, however, are on to the game.  Common garter snakes (Thamnophis sirtalis) have immunity to the poison(6), although they may become toxic themselves from the tetrodotoxin that builds up in their livers after eating several newts(7).  Larval dragonflies will snack on larval newts, and seem able to discriminate the palatable individuals from those best left alone(8).  Ultimately, any strategy is a gamble, and staying alive means playing the odds.

The chemical-defense strategy may not be the best option in this new world dominated by humans.  Cars do not notice unken reflexes, nor do fast-moving bicycles respond to poison.  Newts can live a long time if they avoid tetrodotoxin-resistant snakes and savvy dragonflies.  Like many long-lived species, they reproduce slowly, with few offspring reaching adulthood.  Their populations are poorly equipped to lose many members to novel death traps.  When I find a newt on a road or a popular path, I promptly give it a lift to the other side, hoping it will keep moving away from the ribbon of danger it cannot hope to comprehend. 

In December, we'll begin looking in the drainage ditches and small ponds in our area, hoping to see the graceful, slow dance of the swimming newts as they gather to mate, then lay eggs long before the first buds appear on the trees.

References (for the terminally curious)
(1).Jones, L.L.C., W.P. Leonard, and D.H. Olson, editors.  2005.  Amphibians of the Pacific Northwest.  Seattle Audubon Society, Seattle, WA.
(2). Chau, R., J.A. Kalaitzis, and B.A. Neilan. 2011. On the origins and biosynthesis of tetrodotoxin. Aquatic Toxicology 21(3):131-141.
(3). Lehman, E.M., E.D. Brodie, and E.D. Brodie. 2004. No evidence for an endosymbiotic bacterial origin of the tetrodotoxin in the newt Taricha granulosa. Toxicon 44(3):243-249.
(4). Lehman, E.M. 2005. Tetrodotoxin as a maternally-endowed defense against egg predation in the rough-skinned newt, Taricha granulosa.  Integrative and Comparative Biology 45(6):1032.
(5). Hanifin, C.T., M. Yotsu-Yamashita, T. Yasumoto, E.D. Brodie, and E.D. Brodie.  1999. Toxicity of dangerous prey: variation of tetrodotoxin levels witin and among populations of the newt Taricha granulosa. Journal of Chemical Ecology 25(9):2161-2175.
(6). Brodie, E.D. III, and E.D. Brodie, Jr. 1990. Tetrodotoxin resistance in garter snakes: an evolutionary response of predators to dangerous prey. Evolution 44:651-659.
(7). Williams, B.L., E.D. Brodie, and E.D. Brodie. 2004. A resistant predator and its toxic prey: persistence of newt toxin leads to poisonous (not venemous) snakes. Journal of Chemical Ecology 30(10):1901-1919.
(8).  Gall, B.G., A.N. Stokes, S.S. French, E.A. Schlepphorst, E.D. Brodie, and E.D. Brodie.  2011.  Tetrodotoxin levels in larval and metamorphosed newts (Taricha granulosa) and palatability to predatory dragonflies.  Toxicon 57(7-8):978-983.

Sunday, October 30, 2011

Live Burial

There are still some glorious sunny afternoons as October draws down, but the warmth of the sun is noticeably less than just a few weeks ago.  The turkey vultures have wobbled south on their wise wings, leaving the red-tailed hawks and the chickadees in charge.

In the ground, along with the seeds the chickadees miss, the hatchling turtles are waiting.  They've been out  of their eggs for as much as two months now, paddling free of the one shell they'll shed in this life, to voluntarily wait in the womb of earth their mother shaped until spring brings them a second birth.

Western pond turtles lay their eggs in summer, coming out of the water in long evenings or short nights to find the right dimple in the soil, with the right texture, to dig a flask-shaped hole.  Into this vessel they pour a half-dozen or so fragile eggs.  The mother turtle tamps a plug of earth into the vessel's neck, and then abandons the chamber and its developing contents to fate.  Motherhood as we think of it is not a turtle's strongest suit.

The development of the embryos inside the eggs unfolds to the warmth of the earth surrounding them.  Even the mix of males and females that emerges from the nest is set by the sun, as solar radiation heating the earth triggers cascades of biochemical reactions during a few critical days of development.  In that short time, the power of the distant sun determines each turtle's future role in the propagation of the species.  The eggs will hatch twelve to seventeen weeks after laying.

Sometimes the newly hatched turtles will leave their sanctuary  before winter, but most often they remain inside unless flooding or some other catastrophe forces an evacuation.  Instead, they shelter in place, encircling each other on tiptoe, heads pointing up, and waiting as the short winter days spin past.  They wait, while water percolates through their sometime shelter, and frost makes iron of the earth around them.  Their tissues may freeze, and some of them die from the cold.  The rest of them stand still, embracing both living and dead in the darkness.

What does a turtle think, in the blank black cold, unmoving?  Where are the lines between death and life and consciousness, through the long night?  The gift of golden yolk their mother gave them must sustain their metabolic fires until the little turtles finally venture forth from cold bleak safety.  What is it like for them, to feel the warmth of the sun directly for the very first time, when they are already almost a year old?

Even then, they wait and do not eat.  Newly minted pond turtles in western Oregon may not venture toward water until mid-May, although they emerge as early as March.  The size of quarters, the hatchlings are cheap snacks for herons or raccoons or wandering mink, and they take shelter in either the narrow hole that protected them all winter, or they move a few scant feet away and use moss or leaves as frail shields against large appetites.

They don't make the abrupt journey to water's edge for another two months.  Maybe they are waiting for the spring sun to chase the last of winter from the pond water, so it is warm enough for a little turtle to digest food and grow without having to rely too much on the deadly risky business of basking.  We do not understand much about this.  Once the young turtles grown enough to escape the mouths of many of their enemies, they'll join their bigger kin on logs or rocks.  That may happen next summer, or the year after.  Until then, they will shelter in mats of floating algae, bits of pond weed with eyes.  Next winter, they'll choose a living burial either in muck at the bottom of some pond or in the leaf litter and soil on the forest floor, but they may get up and move around on good days.  They’ll take with them the memory of the sun, felt and seen, rather than only its echo in yolk.  

I think of this, as I toss the last of the season's apple windfalls over the fence for the sheep, as the sun swings lower and the old year shuts down.  I think of how the earth shelters both our past in the bodies and bones of our ancestors, and the substance of our future.  Pond turtles are only one more expression of that understanding, and we owe them thanks for that.

Friday, October 7, 2011

Hope in a White Plastic Box

Among all the bad news about the environment, you don't hear so much about the success stories.  There really are some, and they are very useful not only in what we can learn from them, but also for the hope they can inspire.  Hope is a great motivator for human behavior, probably far greater than we typically realize.  It also generally makes us feel better, and although that observation could naturally lead to a discussion of how we may be hard wired to respond to hope, to a kind of innate optimism, I'd rather discuss a specific event for now.

The subject: Oregon spotted frogs, Rana pretiosa.  These animals might not seem a likely source of hope.  They're a candidate species for listing under the Endangered Species Act.  Candidate species are those that the U. S. Fish and Wildlife Service has determined to be worthy of listing, but the agency just hasn't quite got around to getting the paperwork all done.  There's no regulatory muscle behind the designation.  It just formally states that Oregon spotted frogs might be in some pretty serious trouble.  Unfortunately, it is a common story especially for a species of amphibian.

Oregon spotted frog, Rana pretiosa.  Photograph by Dan Rosenberg.

All is not gloom and doom, however.  A group of people, including biologists with the Washington (state) Department of Fish and Wildlife, NorthwesTrek Wildlife Park, the Woodland Park Zoo, the Oregon Zoo, and other organizations has been working to reintroduce populations of frogs into areas where they've been driven out.  It is a complex process, involving a several-year-long evaluation of site hydrology, presence of exotic species like bullfrogs, and potential for disease.  It isn't easy to find sites that pass muster for biological reasons, and the candidate sites are also subject to more human considerations, such as land ownership and other land uses.

Then there's the issue of where you get your frogs.  The animals released on October 6 were collected as egg masses from two sites whose populations were robust enough to handle some baby-snatching.  Egg masses from both sites were then distributed to the zoos and other organizations who reared the frogs. 

This is an even more formidable task than finding a place to release any frogs you might raise.  A suitable wetland doesn't look all that spectacular, but it provides the right water temperatures, nutrition, and shelter to turn an egg into a frog.  Mimicking that is actually very, very difficult.  Every species is different.  Will  Oregon spotted frogs thrive on one of the pre-formulated tadpole chows (yes, there are such things), or some new recipe?  Are conditions optimal for proper development?  How do you clean the rearing pens without accidentally throwing out the babies with the tank water?  When you're dealing with a rare species, failure to raise healthy young individuals really isn't an option.

Thankfully, much of the needed husbandry has been worked out, and the project collaborators brought over a thousand young frogs for release into the site.  Frogs were first introduced several years ago, but each year the population is augmented to ensure it gets established and begins to grow on its own.  Although it wasn't the first time, the people involved clearly viewed the release as sweet reward for the arduous care they'd given the thousands of eggs, tadpoles, and little frogs over the last seven months.

Rana pretiosa just before release.  Photo by J. A. Gervais

Plastic containers were lugged down to the muddy shoreline, lids removed, and the young frogs burst out like popcorn.  Some animals dove right down, seeking shelter.  Others hit the water and bounced right back onto the land, and a few even leaped for the containers.  I had to wonder what passes through the mind of a frog at a moment like this.  "This water is COLD!"  "Where's the frog chow?"  "Whoa!  This isn't what I signed up for, where's that plastic box?" 

More serious questions include how exactly an animal raised in a tank is going to know how to find wild food and life-saving shelter, recognize danger in time to escape, and learn to deal with an environment staggeringly more complex and changeable than the conditions it has experienced since hatching.  Incredibly, a large proportion of young frogs seem to figure it out.  I was told that the six-week survival rate is actually quite high.  Not the sort of release strategy that would work for an animal that depends on parental guidance to learn how to survive, but frogs don't look after their young, and they seem to start life with all they fundamentally need to know already programmed into their neurons.  Frogs are much easier to deal with than, say, condors or elephants.  Humans may have invented formal schools, but plenty of other species believe in education.  Not frogs, fortunately, which simplifies things like reintroductions.

Releasing 300 young frogs into the wild.  Photo by J. A. Gervais

It was all over at each release site in a matter of minutes, at least from our perspective.  We plodded back through the muck, put the now-empty containers back into vehicles, and went our separate ways. 

Back in the pond, the new arrivals were dealing with amphibian-centered immigration issues, determining who will get what space with access to which resources.  They were learning how to navigate a new world much bigger than a rearing tank, and populated with river otters, herons, kingfishers, and raccoons.  The long-term payoff that justifies all the work will be the number of egg masses that these animals will eventually lay, and the persistence of this population of the species.  The short-term payoff may be equally significant to the humans involved, a rush of hope, of empowerment, a sense that the situation hasn't completely gotten away from us after all.  There is a chance we can still fix some of the things we've broken. 

There's a trick to this hiding thing.  Newly released R. pretiosa not quite "getting it".  Photo by J. A. Gervais

It's a brave new world we must face, one full of unimaginable threats.  Recognizing our vulnerability is a crucial first step to survival.  Hope will be equally necessary to motivate us to move forward into the future with strong hearts and open hands, oriented to find solutions to save what we love.  It is good to know that redemption can be found in something as simple as a white plastic box.

Tuesday, September 27, 2011

How many scientists does it take to change a light bulb?

Q: How many scientists does it take to change a light bulb?
A: They won't change it.  It's not their problem.

I noted something in the news a few weeks ago.  Presidential candidate Michelle Bachmann made a statement about the potential side effects of a vaccine for cervical cancer.  The response from the medical and public health communities was swift: the statement had no supporting evidence behind it.  Vaccines may carry some risks and cost money, but they save lives.  The benefits clearly outweigh the risks in most cases (although not all doctors agree whether teenage girls should get the vaccine for various reasons).  The rebuke got plenty of coverage, and the misinformation was effectively countered.

Contrast that with the blatantly false statement by Texas governor Rick Perry recently, that global warming is a hoax.  I heard it repeated over and over on the radio news briefs, with no countering view presented whatsoever.  Maybe some of that stems from the media's own reticence to acknowledge that there really isn't any debate at all in the world of science over the reality of human-induced climate change.  But no news outlet I follow, not even the "liberal" ones, reported on any response at all from the scientific community.  It's possible I missed it.  It's also possible that there was an outcry, but the media didn't report it.  Unfortunately, there is abundant evidence that the media tend to overplay any climate change deniers' claims compared to the overwhelming scientific consensus on the issue.  However, I really don't think that's what happened either, and an example of what makes me feel that way can be found in Hawaii in early November.

The Wildlife Society, the venerable professional society for wildlife ecologists and natural resource managers, is holding its annual meeting on the Big Island of Hawaii.  On their conference web site, the Society states that of all states, Hawaii "spotlights the most-pressing challenges that natural resource managers and conservationists face today—including the rapid spread of invasive species and the impacts of a changing climate."

The plight of the polar bear is probably the most widely publicized outcomes of global climate change.  Photo by Kathy Crane, NOAA Arctic Research Program.

Conference attendees won't be out solving those problems on the ground, they'll be attending paper sessions, networking, discussing the various topics of particular focus, and going on field trips.  The vast majority of them are going to have to fly to get there.  That adds up to a tremendous blast of carbon into the atmosphere, another blow to the goal of stabilizing emissions to try to limit the damage already underway.  That won't do much to help the highly endangered native Hawaiian ecosystems. The Wildlife Society meeting in Hawaii doesn't have a session on climate change. Presumably that will be discussed on the side.

Does The Wildlife Society really take climate science seriously?  One has to wonder.  Maybe this is why politicians and other leaders in our society go unchallenged far too often when they make blatantly ignorant statements about climate change.

Yellowstone fire. Photo by NOAA.

Unfortunately, this blind behavior isn't limited to wildlife biologists.  Virtually all of the scientific societies dealing with the biological sciences and even conservation biology hold national meetings and encourage their membership to attend.  Sometimes you can view presentations after the fact on the website, but no society to my knowledge allows members to attend remotely, or to view presentations in real time through skype, webinars, or other streaming technology.  Even the National Science Foundation expects the panelists charged with reviewing grant proposals for funding to fly in for a three-day meeting.  I found this out when I was invited to participate on a review panel.  When I asked if I could attend remotely, because the climate change science is very clear regarding the danger of carbon emissions, my email went unanswered.  Apparently not.

Individuals often do little better.  Most of us have changed our light bulbs, carry reusable grocery bags and coffee mugs, and occasionally carpool or use alternative transportation.  Very few of us have even begun to think about how we need to change the fundamental way we've begun to do business in the last few decades.  When I bring up climate change to another scientist, most often the answer is a shrug and a comment that the public is stupid, politicians are stupid, or we can't do anything about it anyway.  In short, it isn't our problem, we just do the science.

For people who profess to care about ecology and conservation, this is a travesty.  All of us need to recognize that we can either start planning how we are willing to be inconvenienced to limit the damage already in the works, or have far greater inconveniences forced on us without choice.  Not going to scientific meetings or networking in person is inconvenient.  There is a potential cost to a person's career.  But climate change and the horrendous damage that will follow from increased violence of storms, droughts, fires, and the fundamental chemical changes in the ocean and atmosphere will be far worse.

Wreckage of Hurricane Irene. Photo by Christopher Mardoff, FEMA

If we scientists, trained to evaluate evidence and respond accordingly, are unwilling or unable to take climate change seriously enough to alter how we do business, why should the reporter, the member of the general public, or the politician?

First, we have to own the problem, and be willing to recognize that we, too, are responsible both for the problem and its solution.  That is the necessary first step to being able to tackle the serious misinformation being presented by our society's leaders.  Changing a light bulb or restructuring a scientific society's annual meeting to encourage remote attendance won't save the planet all by themselves.  But if you walk your talk, people notice.  And when you also feel strongly enough about your science to call out those who would twist it to their own ends, people are much more likely to take you seriously. 

The Hawaiian honey creepers are counting on us.

'I'iwi, Vestiaria coccinea.  Photo by Jack Jeffry

Monday, September 12, 2011

Food Web

Buying a bag of dog food isn’t a big deal, if you’ve got a dog and a budget that allows you to look after your friend without making harsh choices about who’s going to get to eat in your household this week.  From the sales figures, most pet owners don’t have that misfortune, pet product sales being one of the most recession-proof industries in the last few years.  The figures aren’t all about dog food, either.  They include all the accessories you can possibly imagine, and unless you’re a dog owner, quite a few that you possibly can’t.  For many of us, our dogs are a major focus of our discretionary spending.

I never thought much about dog food until my young dog threw us a curve ball with his first grand mal seizure in the middle of a long night last winter.  After tests, our vet concluded that Raven has idiopathic epilepsy. At least he’s just a dog, as much as we love him, and not another human being.  For one thing, he only falls over from a height of two feet, not far enough to risk serious injury, and his thick fur helps pad the impact.  His life will not suddenly become much more difficult because he can’t drive a car, and he seems unburdened by the knowledge that he could unpredictably suffer another episode, something human epileptics must accept.  He’s still the same happy-go-lucky sweet goofball he’s always been, most of the time.  But each seizure is still a scary mess, and not something anyone would care to deal with if they don’t have to. 

I did some research, quickly learning that there is no consensus on how to best manage this condition other than with medication, which often doesn’t work.  Among the many tips unsubstantiated by any scientific research was the suggestion that feeding a high-protein diet without preservatives might alleveiate the seizures.  Diet changes had reportedly helped reduce seizures in children.  The lack of consensus in managing this disease may stem from the fact that lots of malfunctions in the brain lead to seizures; not knowing the exact cause, some cautious experimentation seemed in order.

This led to a trip to the local high-quality pet store.  I faced an entire wall of dog kibble, nothing compared to what I’d face at PetsMart but enough to be overwhelming.  After squinting at a half-dozen ingredients labels printed in size-three font, I sought the help of one of the store personnel, who in my experience have been pretty knowledgeable about what they sell.  I explained what I needed to an earnest young woman wearing round wire-rim glasses.

She pointed me to a bag of kibble that not only contained the requisite high protein content and no preservatives, it was made with regional meats including salmon, wild boar, and bison.  It cost $80 for a 30-pound bag.  They’re human-grade ingredients, the young woman at the store told me proudly.  Your dog will love it, she said. 

I’m sure he would.

We choose to share our lives with animals, and the benefits can be legion.  Part of the compact we make in return for their love is food, water and shelter.  Dogs happen to be carnivores, and although it is possible to feed a generalist carnivore like the domestic dog a diet made up of protein that is not meat-based, it is not easy and mostly not recommended.  My dog may eat more meat in a month than I have in my entire adult life. 

I struggled to explain that even without the sticker shock, I couldn’t feed my dog this food in a world that is rapidly becoming ever more crowded with people, with fewer resources to go around.  A lot of pet food is made from the scraps that those of us who can afford to be picky would prefer not to eat; in any case, the industrial food system pretty much renders them inedible to people and marginally edible for pets.  Feeding a dog is not necessarily synonymous with starving a person.  A bag of dog food doesn’t represent much against world hunger in any real sense.  Reformulating the entire company’s line of dog food into something not only human grade but human palatable wouldn’t make much of a dent.  However, even very small acts can build to major consequences.  And something within me balked at feeding my dog the flesh of a fish swimming against extinction in much of the Pacific Northwest.

Let the fish stay wild in the rivers.  I don’t like my dog eating the waste from the slaughterhouse floor and a staggering list of preservatives whose chemical names I can barely pronounce, but there has to be a middle ground, somewhere.  There has to be a way to restore some sanity to a world where the affordable food may not be safe or nutritious, and the safe food is the prerogative mostly of the obsessed or the wealthy.  Unfortunately the problem isn’t just limited to pet food, or pet ownership.

That led to a second dilemma for me, as I had to ask myself how much of my income I was willing to spend on my dog, and therefore not on helping other people.  The bills associated with owning my dog have soared, with twice-daily medications, regular blood tests, a somewhat less fancy but high-quality kibble, and other expenses.  There’s less money to donate to the food bank, the animal shelter, or to conservation.

Raven is not aware of issues of social justice, let alone concerned about them.  That’s not why we invite dogs into our households.  They’re there to give love, make us laugh, and maybe to offer us the opportunity to express the best parts of ourselves now and then.  These needs fall right behind the basic need of being fed.  Hopefully the people around us meet these needs, but it doesn’t always work that way, and many of us just find great joy in our relationships with our animals.  Those relationships are clearly worth a great deal, but how do we balance the choices with the obligations we hold to each other, let alone the other beings on this planet?

How will we navigate a world where increasing scarcity may force even more choices between who eats and who does not, where the shortages are not just political?  What exactly should go into a bag of dog food?

Wednesday, August 31, 2011

Manipulative Bounty

It is late summer in western Oregon, meaning the wild blackberries are just ripening, dangling tantalizingly between the wicked thorns of canes that can arch up over fifteen feet in the air.  The canes form thickets impenetrable to animals larger than rabbits.  Come and get it- just don't forget your machete and a willingness to make a small blood sacrifice.

We don't give plants much credit for intelligence, at least not as we typically define it, but the dark, sweet fruit is all about making up for the one thing plants sorely lack once they've put down their roots: mobility on a time scale relevant to getting your kids out from underfoot.  Trouble is, if you dump your offspring right around your knees, you're liable to kill them by outcompeting them, for space, water, and especially light. You are also a magnet for seed predators, waiting for the bounty to fall.  So, somehow, plants have to get their seeds away from them.

Some plants have gone the engineering route, and over time natural selection has outfitted them with pods that burst open, giving their seeds the equivalent of a blast from a cannon, or lightweight parachutes to help them drift away.  These plants don't ask for help from another living organism.  Some plants produce seeds that float to new locations, like coconuts.  Other plants have done some modified engineering, covering their seeds with sticky coatings or grapple hooks to catch a ride on any passing animal.  They are the freeloaders, getting a lift on the sly and offering no compensation for the service.

Jewelweed, Impatiens capsensis, has exploding pods, earning it a second name, touch-me-not.  Photo by Catherine Khalar

But plants with fruits definitely do ask for help from organisms that are capable of quick movement.  They pay a fee up front, and hope the agent delivers the goods as planned.  In short, fruits are a biological bribe.

The intended agents are those animals whose guts digest the fruit but leave the seeds unharmed.  The time it takes to process the meal helps guarantee a final deposit away from the parent plant, protecting the seeds both from infanticide and from the usual buildup of seed-eating insects or fungi that prey on the fruit that drops to the ground from the parent plant.  Think of an untended feral apple tree.

Some plants have evolved to rely primarily on birds to disperse their seeds.  Bird fruits are typically fairly small so they can be swallowed whole, and are often black, blue, or red and placed out on the ends of slender branches.  Other fruits appeal more to mammals, with big green or pale yellow fruits, often with an odor.  Many other plants outfit their seeds with small fleshy bodies called eliasomes, that appeal to ants.  The ants take both the seed and the eliasome back to their nests, where the elaisomes are consumed and the seeds are discarded, often in a safe underground spot perfect for germination.  Even fish eat fruit.

The fruits of salal, Gautheria shallon.  Photo by J. A. Gervais
Some fruits are simply weird, such as the osage orange.  If you've never seen one, it is a fruit the size of a softball and about as appetizing.  You need a hammer to crack one open.  The Missouri Department of Conservation considers the fruits hazardous and advises wearing hard hats in their vicinity.  In her engaging book The Ghosts of Evolution, author Connie Barlow makes a compelling case that such fruits actually are anachronisms, whose main seed dispersers were now-extinct large mammals and possibly even dinosaurs.  These fruits now "disperse" by crashing to the ground and possibly rolling away a little, sometimes helped along by flowing water.  Seed dispersal isn't an exact match of goods for services.

There are plenty of cheats, too, animals or other organisms that take the payment without delivering the goods.  My goats eat blackberries with gusto, but no seed will survive the ghastly conditions of their rumens.  Fungi readily infest fruit, and usually also destroy the seeds.  I've found that banana slugs eat fruit, but they damage a percentage of the seeds they eat, taking a higher payment than planned for their services.  The plant has to offer enough fruit to ensure that some of it falls into the right mouths- the first step, but only the first step, in the chain of events that will ultimately lead to a new plant that will someday produce its own seed.

Animal delivery may also come with a secondary benefit.  Tapirs in South America use latrines, small areas of communal relief.  Along with the rest of the waste, they deposit the seeds of the palm, Maximiliana maripa. Over time, these turn into stands of fruit-producing trees.  Tapir poop, too, seems to discourage the beetles that eat the seeds.  Ant garbage dumps are excellent germination sites for many plants.  Bear poop contains thousands of seeds which later germinate in the clumps of calling cards the bears leave behind.

Black bear fattening up on blueberries, Sol Duc wilderness, Olympic National Park. Photo: J. A. Gervais

Hot peppers are my favorite example of botanical craftiness.  Hot peppers get their kick from a compounds called capsaicinoids, which includes capsaicin.  The capsaicin triggers a specific receptor in mammals that is infamous for its response.  It is used in many different cuisines around the world, and also mace (something to think about when contemplating how spicy-hot you want your meal).  Turns out that peppers use birds as seed dispersers.  Birds can't taste capsaicinoids because they don't have the receptors- no tear-gas effect for them.  The compounds do, however, affect how quickly the birds' guts process the meal, shaping the rain of seeds over the landscape, and preventing a huge pile of seeds  from being deposited all in one place.  When that happens, most of them die from the competition.  The capsaicinoids also protect the fruit from attack by fungi, which would destroy the seeds.

The blackberries that are so common locally involve another twist.  They are an exotic species, Rubus armeniacus, originally from the Himalayas.  In open areas with plenty of sun, they can overgrow small buildings, abandoned cars, and nearly any other plant.  They also produce prodigious quantities of very tasty fruit, which feed nearly every wildlife species in the area judging by the bright purple bird droppings deposited on the car and mammal scat along trails in the woods.  Those seeds really get around.  The plant is a pernicious challenge to people trying to restore meadows, pastures, or stream forests. 

The blackberry thickets provide shelter and food to small mammals, birds, and reptiles in the forgotten wastelands that have been badly disturbed, but never rehabilitated or fully claimed by people.  At least the thickets are a good fortress against free-roaming cats, and offer a terrific late-summer energy boost to birds about to migrate.  They also provide us with an abundant supply of local fruit for the freezer, and blackberry jam in midwinter is one of the finest wild gifts we receive from the woods and fields around us.

Blackberry thicket overgrowing a roadside.  Local bunnies taunt the dogs from under this natural razor wire. 
Photo: J. A. Gervais

Tuesday, August 9, 2011

Unintended Consequences

She kicked hard, flailing her sturdy legs madly, just missing my restraining hands.  She didn't have much of a range of motion because of her shell, but that didn't stop her from trying, stretching her neck around to snap at my fingers.  Once her hind leg kicked my wrist, and I was startled by how strong she was.  I had a good grip, however, and what happened next was my decision, not hers.

The turtle in my hands was a red-eared slider.  Like me, she was a native of the eastern half of the country.  I had come west a quarter-century ago, seeking broader horizons, while she had arrived here thanks to the pet trade. Whether she had once been released by a well-meaning but misguided pet owner who no longer wanted her, or had been born wild herself, I couldn't tell.

Red-eared slider, Trachemys scripta, basking in non-native waters.

It's against the law in many states to release non-native pets, and red-eared sliders are not even legally sold in Oregon in the first place.  But they're here, and they have found Oregon's waters to be enough like home to settle down and raise large families.  We don't really know all the potential consequences of this, although there is evidence that the native turtles don't do well once they're forced to share their space with this new arrival. 

My scientific permits specify that I cannot release any non-native turtles if I catch them.  This is meant to help remove the invaders, and give the native species a better chance of survival.  It isn't about just the individuals, or even individual species, but the sum of all the plants and animals, and the unique communities they form.  These communities can affect how water flows, how frequently and severe wild fires will burn, and whether soil will be swept away before the wind.  These processes are of fundamental importance to our well-being, if not our very survival.

I hold another set of permits, this set from the university.  These specify how I must handle individual animals in order to reduce any pain or suffering.  I have stated exactly how I'll keep any sliders I catch, and for how long, before delivering them to the state veterinarian for what amounts to their execution.  Under those conditions, the Institutional Animal Care and Use Committee gave me permission to proceed.  This set of permits is not at all concerned about ecological processes, but it is deeply concerned with the welfare of individuals.

There are very good reasons for both permits.

Turtle trap with red-eared slider inside.

Personally, I happen to really like animals.  I happily share my house with two dogs and a geriatric cat and there would be more if it didn't mean serious strife with my husband.  We raise sheep and goats, and the fact we slaughter our own meat makes us acutely aware that living beings are individuals, each with their own perspective and purpose.  I do not take killing lightly.

As a professional, I am only too aware to how careless introductions have changed everything from the composition of trees in the forests in much of the country to the soil dynamics beneath my feet.  I don't know if red-eared sliders will end up being the biological equivalents of neutron bombs in Oregon's aquatic systems, although they will have impacts.  I suspect probably not, although other invasive species may deserve the comparison.  However, I am not a policy maker, and it is not my call.  The law, and my permits, are clear.

Yet it is amazing how the ancient instructions for life have adapted these turtles to an utterly new place, one dominated by humans.  Sliders are doing fine here, and may do better still as the Pacific Northwest climate shifts to warmer and drier weather.  At some point, we may need to choose based on what can exist in the future, rather than what existed in the past.  The changes we're bringing about on our planet are so great that asking these questions is no longer only the business of theoreticians.  What do we want our future world to look like, given our past actions, and the choices we now have?

That is the big picture.  The small picture is me, holding this turtle, next to a drainage ditch near the airport, on a cool overcast windy day.

It isn't the turtle's fault.  She was only following the instincts that have carried her kind forward for millions of years before she swam into the trap baited with overripe sardines.  I personally didn't bring her here.  All that matters now, however, is that I have caught her, and what happens next is solely my decision.

I do what I must, based on what I know and what I have agreed to do, and she goes in a plastic bin filled with an inch of ditch water.  I wish her a quick and painless death as I look out over the landscape she won't see again.  I lug the sloshing bin to the truck.  It is a good deal heavier than a five-pound turtle, a gallon or so of water, and the container.  I am also weighed down with the ethical costs of undoing what never should have been done in the first place.

Thursday, July 28, 2011

How Science Works

National Public Radio ran a brief story on Friday, July 22, about an article in the prestigious journal Science.  It was originally published in 2010, and claimed that the likelihood that someone lives to be 100 years old could be predicted with 77% accuracy based on 150 genetic markers.  The study was subsequently retracted last week.  The authors had apparently realized there were mistakes made in how the data were collected.  The error was not caught during the peer-review process.

What, you might ask, is the peer-review process?

The final, critical step in research is publishing the results in a scientific journal to add this small piece of knowledge to the collective whole.  The researcher writes up the paper and submits it to a journal, whose editor decides whether the paper fits the journal and is good enough to be worth further review.  If the manuscript passes first muster, it gets sent out to two or three people who are thought to be competent in the subject area, scientific peers of the manuscript's author.  These people are asked to review the paper and decide whether the methods are defensible, the conclusions reasonable, and the overall manuscript worthy of publication.  The editor makes the final decision based on the reviewers' recommendations and the editor's own review.

NPR zeroed in on the fact that this paper had come under criticism for its methods, and they interviewed one person in the field who felt the paper's flaws should have earned it a double thumbs down during the review process.  They didn't interview the original reviewers or the editor who originally decided the paper should be published.  NPR also didn't tell their listeners that a small percentage of papers in the scientific literature are retracted every year, as flaws in experimental design or data analysis are discovered that negate the results. 

Even scientists make mistakes.

The major story here was missed entirely: the system works, more or less, which is about as good as any other human endeavor.  Science is an iterative process, and although redoing someone else's work never earns the accolades that the original work received, the repeated testing is crucial.  This often gets overlooked, as Science (the journal, not the discipline) and other top-ranked publications vie to publish the most cutting-edge, and therefore the least-tested, results.  This tendency inevitably leads to the occasional retraction.

Science (the discipline, not the journal) advances as people come up with ideas, and then disprove them or fail to do so.  Bad ideas may arise from mistakes in data collection, data analysis, or simply from lack of sufficient knowledge to describe a system or pinpoint an underlying process.  The crucial part is not that someone got it wrong, but that the mistake was found and ultimately corrected, thus advancing what we know.

An example can be found in the early efforts to describe the structure of an atom.  This is a pretty weird idea, one that currently involves mostly empty space, a tiny and impossibly dense nucleus, and electrons whizzing around in set orbits of very specific shapes, moving so quickly they are equally likely at any point in time to be anywhere within this orbital shell.  It is such a weird idea that chemists resort to ball and stick models to describe structures made up of multiple atoms even though we know that is not at all what an atom or molecule actually looks like. 
P orbitals, or where one series of electrons in an atom exist. 

Ball and stick model of the sugar glucose.  Image from NASA.

This wasn't always the accepted view.  The physicist J.J. Thomson suggested based on his early experiments that the atom was more like a plum pudding, with the plums representing the electrons that were embedded in the atom.  A decade later, physicists had to admit that this idea was wrong based on work conducted both by Thomson himself and by Ernest Rutherford, who had been Thomson's student.  It seems rather silly in hindsight, but Thompson's early experimental data supported his pudding model.  It provided crucial insight along the way even though it wound up in the "bad idea" heap in the end.  Thomson, incidentally, won the Nobel Prize in 1906 and Rutherford won it in 1908, both for their work on describing the structure of the atom.  In short, they got it right more than they got it wrong.

Plum pudding, which we know now is not at all like an atom.
Photo by Jules:stonesoup, flickr creative commons

Science, the discipline not the journal, is all about looking for patterns and determining the processes that create them.  An occasional misstep along the way should be expected.  No idea or study should be accepted with full confidence until it is corroborated by other researchers conducting other tests.  In hindsight, it is always possible to say that someone should have known better.  That isn't terribly useful, however. 

As our grasp of science and use of technology grow ever more complex, it is even more important to understand how the process of gaining that knowledge actually works.  The terminus of a glacier is a broken, dangerous mess of calving chunks of ice and stone that continually fall as the ice moves.  The anarchy at the front fails to reflect the cohesion of the massive river of ice that flows inexorably behind.  We should focus as much of our attention on the mass of knowledge behind the advancing front if we are interested in trying to use what we know to our best advantage.

Our survival is going to depend on it.

Johns Hopkins glacier face, Alaska Photo: USGS

Tuesday, July 12, 2011

Life in a Sandwich Board

Imagine living in a sandwich board.  Not one you could remove, like an advertisement people parade at busy intersections, but one that is made of your own bones and will be with you for your entire life.  No bending to touch your toes.  In fact, forget about touching your toes.  Forget about curling up, sitting down, even rolling over.  You can't breathe by expanding your rib cage, instead you have to pump air into your lungs using the muscles in your throat.  Now imagine that you need to swim around in order to survive.

Red-eared slider, Trachemys scripta. Photo: J. A. Gervais

This improbable body plan is actually a pretty ancient idea, because turtles have been using it, without major changes, since the Triassic.  In other words, over 200 million years.  Good ideas simply don't go out of style, and this good idea has endured ice ages, drifting continents, the disappearance of the dinosaurs, the appearance of mammals, and the arrival of the ape with the big brain and opposable thumbs.

The shell is an extraordinary piece of biological architecture.  Formed from the ribs and the spine, it incorporates the the carapace, or top shell, the plastron, or lower shell, and the bridge, the plates that hold the two together. The hips and shoulder blades are encompassed inside the rib cage.  Ultimately, nearly half a turtle's mass is bone.
Red-eared slider, Trachemys scripta.  Photo: J. A. Gervais

Life inside the shell has its advantages, in that you carry your fortress with you.  Although the shell offers some protection, determined otters and other predators have been known to pry legs or the tail free and gnaw them off.  There are no fast getaways, and if the fortress is breached, there isn't much that the turtle can do about it.

There are other drawbacks.  Reproduction is challenging, to say the least, when both participants are dancing in suits of their own unremovable armor.  The distinctly domed carapace of the female makes things more difficult, as does the fact that most female turtles are larger than the males.  The male turtles' plastrons are slightly dished, and their front claws are extra long, to help them hang on to get the deed done.  It's an awkward affair, but one that has worked well enough for a long time.

The shell has to grow with the turtle.  Each bony plate must grow in synchrony to keep the shell in its proper shape.  Turtles lay eggs, and unlike birds, they form a clutch and lay it all at once.  All those eggs have to fit in there somewhere, which is why females have taller, more domed carapaces than males.  Too big a shell wastes energy, both in its growth and in the effort needed to haul it around.  Too small, and turtles cannot gain weight to form their eggs, carry them til laying, or get fat to survive the winter- not to mention draw deep enough inside to be safe from their more nimble, agile enemies.

Turtle shells have worked so well they've not only been around for millions of years but turtles and tortoises also occupy all continents except Antarctica, in habitats ranging from the deep ocean to deserts.  They can survive in some pretty degraded environments, appearing to be much more robust than many other vertebrates to pollution, reduced water quality, and other challenges thrown at them in recent times. 

This pond supported turtles...  Photo: J. A. Gervais

However, the ape with the big brain and opposable thumbs may be too much for them, as wetlands disappear and turtles fall victim to roadways, over harvesting, the pet trade, and other human activities.  With a little care, however, at least a few may survive for another few million years, moving through time in that same cautious, patient manner that has served them so well for so long.