The secret of a long life

There may be a cure for cancer lurking in the genes of an ancient fish.  At least, that’s the hope of University of Kentucky genetic biologist Jeremiah Smith.  With a $1.5 million-dollar, five-year grant from the National Institutes of Health, Smith is working to understand how the lamprey—a fish that is virtually unchanged in the last 450million years—can discard troublesome parts of its genome, and thus, seemingly escape cancers and other genetically-related disease.

Jeremiah Smith became a biologist because he fell in love with fossils.  On his parent’s South Dakota ranch, there were dinosaurs in the hills, fish in the prairie, and more life in the ancient rocks than anywhere else. While he liked everything biological, Smith, now a professor of biology at the University of Kentucky, understood that life has a long history, and that some species of fish, amphibians, and reptiles have remained unchanged for very long time.  That history, Smith noted, was expressed in each organism’s genetic code. And the longer in time that a species has persisted, the more its genome could tell us about its tricks for survival.

Pacific lamprey are among many species of lamprey that discard a portion of their genes as a way of avoiding disease.

Pacific lamprey are among many species of lamprey that discard a portion of their genes as a way of avoiding disease.

Two fish are the undisputed champions of species longevity: the coelacanth and the lamprey. Coelacanths– a lobe-finned fish ancestral to land animals–were thought to be extinct for at least 70 million years.  But in 1938, they were discovered in the ocean depths off East Africa.  Lamprey, an eel-like parasitic fish that lacks jaws, is even older. Lampreys have persisted for at least 450 million years virtually unchanged from their fossilized ancestors.

Smith began his career studying the coelacanth’s ancient genome. Coelacanths– a lobe-finned fish ancestral to land animals–were thought to be extinct for at least 70 million years.  But in 1938, they were discovered in the ocean depths off East Africa.  In 2013, Smith was part of the team that unraveled its genetic code. Surprisingly, results demonstrated that genes involved in immunity and nitrogen excretion were important in adapting to life on land, as well as the more anticipated development of  tail, ear, eye, brain and smell.

Jeremiah Smith and two graduate students are exploring the lamprey genome for clues to curing many human genetic diseases.

Jeremiah Smith and two graduate students are exploring the lamprey genome for clues to curing many human genetic diseases.

Then Smith turned his attention to an even more ancient fish—the lamprey. Smith is working to understand how the lamprey—a fish that is almost unchanged in the last 450 million years—can discard troublesome parts of its genome, and thus, seemingly escape cancers and other genetically-related disease. Decoded, this may contribute to prevention or cures for human cancers immune-system disorders, and other maladies..

Every cell in the human body contains the same DNA.  Lampreys harbor two different sets of DNA.  As embryos, they archive a complete set of genes in their reproductive cells, but then discard about 20% of the DNA from the cells that will become their body and tissues. These are genes that, if damaged or inaccurately reproduced as a cell grows or divides leave lamprey vulnerable to run-away cell division, or to inaccuracies in the cell’s genetic materials–resulting in probable cancer, aging, and other gene-related maladies. While these genes are essential to keep in the reproducive cells, having them in the rest of the body is a liability. “The fact that lamprey are getting rid of these genes suggest they know something we don’t.” Smith noted.

With a 1.5 million-dollar grant from the National Institute of Health, Smith will determine exactly what the discarded lamprey genes control, and, importantly, whether the human equivalent genes behave in the same way.  In the genes of an ancient fish, may lie secrets to curing and preventing much human disease.

And such a mechanism for preventing disease may explain why some species persist unchanged for so long. Another venerable animal, the hagfish, has been unchanged for at lease 500 million years, and may date to the original Cambrian explosion of life.  Like the lamprey, it discards a portion of its genes.  There is, says Smith, some evidence that perhaps the coelacanth does the same.  A valuable lesson, perhaps for leading an uncluttered life, right down to the very basics.

The Future according to the Class of 2017.

Lone treeXxxxwebIf you’ve ever wondered what life will be like in the year 2065, I have some ideas, fresh from the people (Whitman students) who will be guiding us there.
Based upon my observation that when riding a motorcycle, you go where you are looking, I asked the 18-20 year-olds in my Environmental Studies 120 class to write about the world in 2065. They gazed into their crystal balls. Here’s what they saw.
Although most of it is not a pretty picture, they think there’s hope.
IMG_1102Let’s begin with what we fear might be true: “The world is an environmental mess, spiraling downwards towards environmental disaster.” one paper began pessimistically. The issues of 2065 enumerated by students include sediment piling up behind dams, groundwater resources polluted by fracking, and an ocean bereft of life and replete with dead zones. “The world is full of talkers and not enough doers” observes one. Another student, who may have read too much Cormack McCarty in other classes, wrote “In the boy’s drawing, the sky was yellow, the tree was gray with no leaves, and when the teacher asked the boy why there were no birds in his drawing of the tree he responded that he had never seen one.” Then the student notes that this is NOT how she thinks 2065 will be, but how it is liable to be if we continue the way we are.
haboob approachesAMost of these college freshmen are more optimistic. “A move to more local styles of living will reduce future energy needs.” one predicted.. “Because we are focused on preserving many natural landscapes, I would like to think there will still be beautiful landscapes in 2065” said another. Other ideas include cars that derive energy from solar panels embedded in road surfaces, solar-powered trains that provide most of our cross-country transportation, and a world in which we “first-world” humans have learned to live simple lives that require few resources or energy (The Great Simplification.) Another student passed a law that forbade hydrocarbon production of use. One paper suggested, tongue –in-cheek, that with rising sea levels, Manhattan had become “the Venice of the Americas” with Miami following suit, (and filing suit over New York’s trademarked slogan.)
13 mt baker sunset 1BXWho knows whether any of this will happen. (I especially enjoy imagining Manhattan–as-Venice.) We do face daunting problems of climate change, resource depletion, and population growth. Taken at face value, the future looks gloomy. But the freshmen– people who will be elders in 2065–have different ideas. They envision solving global problems.
I know from experience that you go where you look. Or, put another way, by a voice from a different wisdom philosophy that I don’t often quote: “Believe it is possible to solve your problem. Tremendous things happen to the believer. Believe the answer will come. It will.” (Norman Vincent Peale.)

Seven Generations: The long reach of climate change.

IMG_1102Every month, the highly regarded journal Nature: Climate Change refines our understanding of global warming. This month’s revelation is more jaw-dropping than most. Its ominous title: Continued global warming after CO2 emissions stop.
We have naively assumed that if we just Stopped Adding Greenhouse Gases to the Atmosphere, global warming would slow, and then stop. This is a reasonable assumption. Within a year of banning ozone-destroying CFCs, the Hole in the Ozone stopped growing and started shrinking. Voile!
But that is NOT what is going to happen. Instead, the globe will cool – perhaps for a century. Then, after lulling us into complacency, the Earth will begin to warm again, as heat stored in the oceans radiates into the atmosphere. And this second warming episode may persist for hundreds of years. “….surface temperature may actually increase on multi-century timescales after an initial century-long decrease.” In other words: If we stop lacing the air with CO2, it will cool for about a century. But then all the extra heat stored in the oceans will radiate into the atmosphere, heating the Earth even more than before. So it is not just our children who face more desperate lives, but seven generations of humans after us.
This week there is a hopeful sign that maybe we are taking this climate thing more seriously. Less than a month ago, William Nordhouse’s book The Climate Casino was published. It’s the latest climate disaster book. The American economy looms large as a casualty. I’d planned to use The Climate Casino as one of several readings in my environmental studies class Spring term. But the Whitman bookstore can’t get it. It is sold out of the distributor, sold out at Amazon, Barnes and Noble online, The Bookloft in Enterprise, Book and Games in Walla Walla, and even a bookseller in London that I tried to order from. Perhaps Yale University Press only printed 100 copies or so, thinking that climate made dull reading. Evidently they were wrong.
But, while awareness of climate problems rises, we remain reluctant to act. After-all, nothing really bad will happen until long after we are gone. The US has no carbon tax, (17 other nations do, including Sweden, India, Japan, and Norway, and Costa Rica.) and no national cap and trade scheme. We remain conveniently wedded to fossil fuels. But shrugging our shoulders and getting on with life as “normal” is the ultimate cop out. The quality of life for our progeny—for all life—in the next two centuries is in our hands today. Bearing responsibility for the future should be no less a concern than that voiced eloquently by Iroquois tribal leader Oren Lyons: “In our way of life, in our government, with every decision we make, we always keep in mind the Seventh Generation to come. It’s our job to see that the people coming ahead, the generations still unborn, have a world no worse than ours and hopefully better. When we walk upon Mother Earth we always plant our feet carefully because we know the faces of our future generations are looking up at us from beneath the ground. We never forget them.

Nature Climate Change: Continued Global Warming after CO2 Stoppage. Froelicher, et al, 2013:

NY Times review of The Climate Casino:

Long Creek: Bringing Science Home

Long CreekA-1It is almost dawn in one of Oregon’s tiniest towns. Long Creek is 40 miles from anywhere. There is a Post Office, a school with 34 students (counting foreign boarding students, who must think they have been sent to the moon) and a watershed council office for the North Fork of the John Day River. Also a restaurant. And three churches. This is rural, conservative, Grant County, Oregon at its finest.
Last night I gave a talk about Oregon’s Oligocene calderas to pretty much the entire town. There’s not much to do on a Friday evening in Long Creek, and so when anyone comes to town to talk about anything, it’s a grand social event. The Watershed Council invited me. They provided a pot-luck dinner, and a raffle to win several Patagonia jackets, all donated to the watershed, which then donated to the Historical Society to help pay for some of the fixin’s.
Why drive a total of six hours and 300 miles to talk to 50 or so ranchers, loggers, rock-hounds, teachers, and an assortment of elderly ladies and kids about the rocks that rim their valley? Because these are people who incorporate the backcountry, the forests and grasslands, rivers and meadows, and all their wild inhabitants into the intimate fabrics of their lives. Because this generally conservative community represents the soft underbelly of resistance to science, global warming, and a host of other misperceptions based upon misinformation and fear. And because few of the residents of Long Creek have ever met, let-alone know, trust, and have shared meat-loaf, apple pie, and conversation, with a scientist.
In 2005, journalist Chris Mooney suggested that conservatives have become much less trusting of science from the 1970s to the present. This observation was tested—and confirmed — in subsequent studies, most notably by Gordon Gachet (2012). He noted: “….conservatives were far more likely to define science as knowledge that should conform to common sense and religious tradition.” He also noted that conservative audiences are under-served by scientific presentations.
So, what better place than Long creek, in Grant County, to connect landscape and community, as well as provide a portrait of how new discoveries are made, and why they matter to people in eastern Oregon?
Long Creek antelope-x1For a presentation, I chose the story of the discovery of the Crooked River caldera. Until 2005, geologists considered Smith Rock, Powell Butte, and other Central Oregon landmarks as separate volcanic peaks. But then, when a real estate developer could not find adequate water, and state geologists were called in to solve the problem, they found that the structures of a giant, Yellowstone-sized caldera, 29 million years in age, restricted ground water flow—and also connected the multiple, disparate peaks into a single 25-mile-wide supervolcano. Furthermore, there are indications that Tower Mountain, not far from Long Creek, is (or was) a very similar creature that might exert control over more local ground water.
In the 24-slide, 25 minute presentation, there was not a graph to be found. Just nice photographs and (I hope) engaging information, and plenty of good questions at the end. I left with the warm thank-you-s and firm handshakes of 50 new friends, a memory of some of the best questions I’ve been asked, and the tastiest meatloaf and apple pie in memory.
As academic scientists, we too often neglect this kind of American-roots experience. On resumes, a presentation to the American Geophysical Union glistens more brightly than a talk at the Long Creek Community Hall.
N Fork JD River-1But it shouldn’t. After all, the people who live in Long Creek are among those who have funded this research. They are more directly its beneficiaries than anyone at AGU. And they should be counted at least as equals in importance to learn about what they have paid for, and how science fits into their daily lives.
NSF has a requirement now for providing public outreach for most funded projects. Too often (but certainly, not always) this amounts to either a presentation in the school, or a graph and statistic-rich, jargon-laced, talk presented at the investigators behest, or perhaps a press release.
Science needs to refocus at least some of its outreach efforts. After all, loggers, ranchers, and urban and rural conservatives of all stripes are its bread and butter. And its meat-loaf and apple pie, too.


Weather or Not

George SteinmetzSmithsonian
(Dear reader– If you are tired of news (mostly bad) about climate, this is (mostly) not about climate, so you can skip to the third paragraph……)

The tempests seem unremitting. Just as the awful news of Typhoon Haiyan’s devastation fades from the headlines, leaving millions destitute and desperate, tornadoes eviscerate Midwestern towns. In November. November??? The powerful tornado that struck Washington, Illinois is the only November EF-4 in Illinois history; there have been only 20 EF-4′s in recorded history in November for the United States (records began in 1950).
For climate –change deniers, these are unfortunate perturbations in the planet’s normal, chaotic cycle. For climate-change believers they are evidence of yet more horrendous events to come. For Kerry Emanual, a hurricane researcher at M.I.T., computer models predict that as climate warms, tropical cyclones will increase in number and intensity everywhere — except the western Pacific. Go figure.
But whether you are a climate denier, believer, or researcher, there is a new cause for concern. The Antarctic ice sheet may be doomed. Not from warming atmospheric temperatures above, but from volcanic heat below.
The Antarctic continent is infested with volcanoes. They include Mount Erebus (12,500 ft.) and Mount Siple (10, 200 ft.) which are active, and Mount Sidley (13,712 ft.). Stuck in the Earth’s freezer, the volcanoes are quiet and well-behaved. The chain, known as the Executive Range, may represent a mantle plume and possibly a rift zone that is slowly tearing East an West Antarctic apart. Its burbling, basaltic volcanoes are progressively younger from one end to the other.
AntarcticVolcanoes2Now, Doug Weins of Washington University has discovered the onset of new volcanic activity, just south of the youngest volcano, Waesche, and a half-mile beneath the surface of the Antarctic Ice Sheet. Weins expects this rising plume of hot basalt to erupt, though it’s unlikely to breach the surface of the ice.
The more imminent threat, when the 2000 F lava nears the surface, and likely erupts, is it that it will melt millions of tons of subsurface ice. And lubricate the bottom of an already warming ice sheet with millions of gallons of tepid water. The MacAveal Ice Stream is the likely recipient of this watery largess. And it is a major contributor to the Ross Ice Shelf—which has already demonstrated a suicidal talent for heaving vast chunks of itself into the Ross Sea.
The threat of rising seas that come with global warming is solemn enough. When coupled with storms it is hideous. But when geology gets into the act, it begins to seem like a planetary plot. Or maybe an urgent warning.

We still have time before this new and un-named volcano erupts beneath the Antarctic ice cap. The duration and volume are yet unknown. But it seems certain, climate change or not, that we are going to loose more ice, that sea levels will rise, and that , consequently, storms like Haiyon, or Sandy, or Katrina will be more devastating, regardless of their cause.

For the original paper:

Seeking nature in Denver: thoughts on nature writing in the 21st century.

IYellow trees 1 TMXxx
In downtown Denver last week, enveloped in civilized concrete canyons, I grew lonesome for wild places. So on a Saturday evening, I decided to go looking for nature. Not in the great out of doors, but just around the corner from the Grand Hyatt, in Barnes and Noble—perhaps the most iconic and popular of national brick-and-mortar booksellers.

Nature is not easy to find in Barnes and Noble. There were shelves full of Romance Novels, Gothic Romance Novels, Young Adult Gothic Romance Novels Thrillers, books on how to grow your business, become a happier person, travel to London or Madagascar. Automobiles, History, Biography. An astronauts guide to living on Earth. Dan Brown. Stephen King. Anne Rice.
Nature in B&NxxIt took persistent wandering, but finally, in an obscure corner of the first floor, a lone, 30-inch-wide section of a bookshelf bore the label “Nature.” It was right next to two sections of books on dogs, and one section of books on “Pets”, and around the corner from five sections of “Photography”. We won’t enumerate the “Cooking” sections.
Twenty years ago Bill McKibben warned us that the End of Nature was neigh. Here was undeniable proof that, at least, in Barnes and Noble, he was right. The featured “nature book”? “Sagebrush Rebel: Reagan’s Battle with Environmental Extremists, and Why it Matters Today.” Sagebrush+Rebel+July+8
I looked for familiar writers and titles: Carson’s Silent Spring. Anything by Barry Lopez. Aldo Leopold. Terry Tempest Williams. Eaarth. The Monkey Wrench Gang. Instead, the shelf was inhabited by “The Wonderful World of Nature (Disney Press), “Savage Nature”, and Nature Bible. (“Kids can head out into the woods or off to camp with a full-text International Children’s Bible® translation that helps them enjoy the wonder of God’s creation.”) There were Michael Pollan books. Several tomes on how to write about nature. An anthology or two. A few stalwarts –Barbara Kingsolver, Emerson, Thoreau, and, yes, Bill McKibben spiced the shelves. They seemed almost embarrassed by their company.
For “Nature” to be banished to the distant corner of this iconic bookseller reflects our collective disenchantment with the subject. We fret about the global economy. Syria. Hunger. The rise of Swine Flu and the return of Polio. How much dog hair is there on the sofa? And has anyone hacked into my American Express account. Nature seems remote and irrelevant..
How did we get to this point?
There is the now-dogmatic recognition that children don’t get out much anymore. Legions of books and essays address “Nature Deficit Disorder” and warn of its dire consequences. There is considerable truth to this. Students (mostly First-years) in my ES 120 class at Whitman enjoy our excursions not only because they learn about water supply, the sins of dams, and the advantages of wind turbines, but also because each foray into the out of doors provides physical, if not mental, contact with dogs, cats, sheep, goats, horses, and cattle—all of which are pet-able. Yesterday, at a visit to Upper Dry Creek Ranch – a local raiser of grass-fed beef, lamb, and goat–all 24 students flocked to the animals when they should have been listening to a talk by our hosts, ranchers Robert and Cheryl Cosner. I really should have castigated my crew, but to be honest, they needed the contact with fur more than the lecture.
This deficit of contact with Nature, and its writing, might lead to a greater demand for books, or even videos, about “Nature.” But that’s not what I found back there in the far corner of Barnes and Noble.
While we have an instinctive hunger for contact with nature, we are also highly conflicted about the inherent dangers posed by The Wild, and hyper aware that humans are at fault for the loss of too many species, and the cause of to much pain.
There is also the fear of letting one’s children play in the woods, or marshes, or tall prairie grass. It arises not so much from concern about an ambush by cougars or wolves, or even Lyme-disease-bearing deer ticks, but from fear that some passing human predator will snatch our children. From this concern, which is not truly about nature, children absorb the sense that Outside is a Dangerous Place, without understanding the true basis of concern, in much the same way that my horse knows when I am afraid or unsure, without really knowing why.
This produces, I think, a sort of approach-avoidance conundrum. Yes, nature is beautiful. But it is dangerous, too. Maybe better not to go there.
And like everyone, I am unlikely to read about subjects that cause personal emotional pain. Nothing does this better than reading about Nature’s plight. Any book or article about elephants will either remind me that they are being poached and that their lives are full of pain and suffering. Because I already know this, if I read about happy lives of elephants, I tend to think of the piece as a Pollyanna-ish and inaccurate. If I read about wolves, there are often ranchers stalking them, or the return of hunting to excessive levels. Better to stick with stories of dogs (two sections). Or sink into the storied, fictional oblivion of The Road, since we seem to be inexorably moving in that direction, or Twilight, where the threats are mythic, and wolves are, too.
As Bill McKibben observed in The End of Nature, the true Wild has vanished, as mythic now as the Twilight wolves. The planet is no longer in charge. We are.
So what to do about that destitute shelf titled “Nature”?
When I was a child, my mother took me on long “walks in the woods” where we shared a happy sense of wonder and aesthetics, and she kept me safe. We can all do this, and the more one-on-one the time spent, the more enriching the experience. Taking a whole class on a hike, or a whole boy scout troupe, or a gaggle of 20 campers is preferable to no outside time at all, but it is hard to focus everyone’s attention on just one thing, hard to avoid the siren call of the iPhone and text messages (If only frogs and dung beetles and mergansers could text!) and learn to Just Listen, and to make that a practice.
photo-2Traditional “Nature Writing”, from Aldo Leopold to Terry Tempest Williams, generally presents descriptions of lovely places and charismatic animals – which seem curiously irrelevant–or foreboding tales of loss. Drowning polar bears. Dying bees. Orcas ridden with PCBs. One student in my ES 120 class, wrestling with depression over the state of the planet and everything on it, asked to substitute something more cheerful in place of the remorseless reading list of How Awful Things Are and Will Become.
It is very hard to find readings that work. Information relevant to us, now, on the brink of the perilous 21st century. But I believe there is a future for nature and nature writing. Not to find only the cheery. But instead, to tell relevant stories about resilience and connections. Restoration” and resilience are comparatively new. Only in the last two decades have we been serious about restoring what we have torn up for two centuries. And the idea of grooming fields and forests to encourage a resilient, adaptable natural world is newer still.
The reality is that the very nature of nature has changed. To write about the old world of wild nature is nostalgic; at best only tattered remnants remain, and those are shrinking fast. It is critical to save, restore, and expand what we can of Wild Nature But to survive, Nature Writing, as well as nature, needs to adapt. This need not be the apocryphal, or even the apocalyptical era, of the End of Nature. It can be the beginning of a nature-human partnership. Perhaps a harnessed nature. Or a wild adapted to humans, rather than overwhelmed by it. A resilient, adapted nature, which may be the only nature that can survive the next millennium.
Is this a loss? In my mind, yes. But not as much in my students minds, who tend to se nature as an extension of their social selves, and a continuum rather that the frontier mindset of humans and wild, Us and Them.
What might this new, more uplifting, literature look like?
We might build it upon E.O. Wilson’s concept of Biophilia–the need for humans to connect with nature. We could express our thoughts in sustainable woodlands, and forests that are adapting, however awkwardly, to a shifting climate. We could accept, to some degree, the idea proposed by students in my Environmental Studies class that invasive species are really “neo-natives” that WE have to adapt to. (Are zebra mussels clogging your dam? We, then, just take the dam OUT, and they won’t be a problem, and then, voila, you are managing for the neo-native population…. (I think zebra mussels are telling us something that perhaps we don’t want to hear.)
This idea of writing about resilience and adapting species is not native to my own perceptions of Nature. But it is native to the coming generations. If we are to save the Nature section in Barnes and Noble from extinction, the time for action is now!

The Season of Fog

Most people call it Winter. Here in Walla Walla, we call it The Fog. We live in a topographic bowl, huddled against the Blue Mountains to the east, the Horse Heaven Hills to the south, and the Palouse to the north. As with most things that are over-protected, this works to our disadvantage. Cold air sinks. It ponds in Walla Walla, where there is really no exit from the basin. Meteorologists speak of The Inversion. We have other names.
This morning was the first time this fall that I’ve found The Fog lurking outside my bedroom window. Our fog comes not on little cat feet, but more like a cat burglar, testing its entry points silently at night, checking to see if there are any valuables in sight, and robbing you of your morning sun. The Fog does provide some advantages. You focus on things that are close. You see details because you really can’t see much else. You hear sounds because they offer the best access to the world beyond about 100 feet. It is an entirely different sort of existence, and one that is valid and valuable in its own right.
Ultimately, today, it will clear. Already the sun has won the battle. If I look straight up, there is blue sky. To the east, a welcome golden glow warms the sky. These are visions I’ll have to remember as the fog thickens in the coming months. Today, it’s like a Fog Drill. Remember to look up. Remember the sun is there. Remember that some day, despite congressional inaction, April will come, which here is not the cruelest month, but the Month When The Sun Returns.
It’s a good life-lesson for all those days when I feel slightly overwhelmed, when the responsibilities, memories, and fears that rim my life trap too much stagnant air, too many heavy emotions. Look up. April will come.
Of course, there’s another, more immediate, way out of the fog. This is why so many people in Walla Walla have taken up skiing. Mountaintops rise from The Fog like little islands of normality in a sea of gloom. For the price of a two hour drive, and the inconvenience of applying chains to your car, you can escape the chilly oppressive grayness and bask in a carefree, sunny landscape where glistening white offers respite from murky gray. Up is good. Of course, sooner of later, you’ve got to come down.
So, we have to remember that The Season of Fog is just that, a season. The sun will come back. By July, we’ll be wishing for a little of fog’s humid coolness. But today, The Season of Fog has arrived. Here in Walla Walla, we are hoping it’s a short one.