biogeocoenosis

The Grandeur in this View of Life

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Are reviewers crazy? Or are they saints?

kerkhoffa:

As a way to get my own blog restarted, I thought I would post this great piece on peer reviewers from Scientist Sees Squirrel

Originally posted on Scientist Sees Squirrel:

Image: © Jason McDermott, with permission

Are reviewers crazy? Or are they saints? Both, of course, and neither; but I’ll try to do better than that.

I’m writing this post because last week, the peer-review comic (above) was wildly popular on Twitter – it must have come up in my feed several dozen times. Which is reasonable enough, because it’s pretty funny, and we all feel this way about peer review from time to time. Those reviewers are crazy, eh? And sometimes they are. Sometimes they’re really crazy (for instance when they suggest a paper needs some male coauthors and bring the internet down in flames around PLoS One’s writhingly apologetic leadership)*.

But, here’s the funny thing. Everybody furiously retweeting that comic missed the first two sentences of the blog post it originally decorated:

 “I’m a big fan of peer review. Most of the revisions that reviewers suggest…

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How Do Tall Trees Move Water (GREAT Video!)

A few weeks ago, my post touched on the amazing way that trees move water from the soil to their leaves, in long continuous strands pulled under tension between the soil and the atmosphere.

Well, the wonderful vlogging team at Veritasium have put together a FANTASTIC video describing the process in clear and entertaining terms. In particular, they do a great job of describing the concept of negative pressure in liquids, noting how the water is “super-sucked” (analogous to super-cooled) and that with the introduction of any gas-phase water, it will spontaneously boil inside the plant! In fact, this is what happens when lightning strikes a tree, causing it to blow off it’s entire outside layer! They also highlight how most of the water (90%) is simply lost to the atmosphere as part of the exchange process that brings CO2 into the leaves for photosynthesis, which is how trees help make rain.

The only fact they fail to mention is that all of that water is actually transporting essential nutrients from the soil (nitrogen, phosphorus, potassium, etc.) to all parts of the plant. Plants make their sugars, and even most of their woody bodies, from light and air, which never fails to amaze me. But they still need mineral nutrients from the soil or they cannot survive. The solutes in the xylem sap are also used to create concentration gradients that help move the sugary products of photosynthesis around to all of the plant’s cells.

Still a beautiful piece of scientific communication! Thanks Veritasium!


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Deextinction: Asking the Wrong Question

The phenomenal ecological success of humans and our cadre of partner species (livestock, crops, pets, parasites) has come at great cost to other species. Indeed, one of the hallmarks of the Anthropocene is the sixth mass extinction event, one that is shaping up to be on the order of the End-Cretaceous event that took out the non-avian dinosaurs. Our list of victims includes almost all of the non-dinosaur poster species for extinction: Wooly Mammoths*, Tasmanian “Tigers” (really marsupials), Dodos, Passenger Pigeons, maybe even our close cousins the Neanderthals*. And despite our conservation efforts and good intentions, the Anthopocene extinction event goes on, fueled by human population growth, our monopolization of natural resources (land, plant productivity, fisheries, etc.), and increasingly, anthropogenic climate change.

Dodo_1

This is tragic, but understandable. Earth is finite, the vanishingly thin skin of its Biosphere even more so. As we take more and more, there is less and less to go around. At a very coarse level, the math is remarkably simple, and sad.

Wouldn’t it be great if we could bring them back; if through human ingenuity, hard-won technical know-how, and forward-thinking venture capital investment, we could revivify extinct species? Imagine the crowds of conservationists, dabbing tears from their eyes as the first new flock of Passenger Pigeons is released. Imagine yourself on a Siberian safari, trekking over the remnants of soggy, melting tundra to observe a newly established herd of Wooly Mammoths. Wouldn’t that be great?

That is the vision of “deextinction,” and it is not science fiction. It is a very real endeavor being pursued by a collection of scientists and conservationists. The biotech basics of the process have already been worked out and several projects are up and running, including goals of producing a viable cloned Wooly Mammoth and a new Passenger Pigeon. Last week’s TEDxDeextinction Event was a debutante ball for the project. For a taste, you can watch Stewart Brand’s talk, entitled “The dawn of deextinction: are you ready?”

It may surprise you to know that as an ecologist I would say, emphatically, NO (and I am not alone). Don’t get me wrong, I would LOVE to see a flock of passenger pigeons or a herd of mammoths as much as the next nature geek. And I marvel at the scientific insights and creativity that go into the deextinction project. These people are visionary, brilliant. But Brand’s title asks the wrong question. It does not matter whether we, as individuals, are ready. Instead, I would argue that what really matters is that we, collectively, as the stumbling architects of a new geological epoch, are not ready for this responsibility. Moreover, Earth and its Biosphere are not ready. Developing my argument would go well beyond a blog post, but the summary is rather simple.

Every species is part of a larger ecosystem. This is the fundamental fact of ecology. Many, perhaps even most extinct species belonged to ecosystems that were either coopted by humans, or have changed irreversibly in their absence. The forest/grassland mosaic that was home to the Aurochs (another deextinction target) across Europe is now home to some of the densest human populations on Earth. The world of the Aurochs is gone. The glaciated home of the Mammoth is gone, and we are marching in the opposite direction, climate-wise. The world is not ready for them to come back. Every revived species would need to have a place, and yet, we cannot even seem to make room for the species that are still here. If we cannot responsibly manage the extant species, do we really want to take on reviving extinct ones? I argue that we are simply not ready, not competent enough as a species to handle this task.

I have no illusions. Some form of deextinction will occur, with sad solitary animals, maybe even small populations consigned to zoos and reserves. And I have no doubt that the projects that lead to these breakthroughs will yield tremendous insights, both technical and conceptual. Some of those insights might even help rescue extant threatened species.

And that would be great.

But my fear is that news of these big ideas, of this optimistic, technologically advanced project will be interpreted as a solution to the biodiversity crisis. No need to worry about Tarzan’s Chameleon, the Spoon-billed Sandpiper, the Pygmy Three-toed Sloth, or any of the other 100 most threatened species. Just freeze some DNA, and we’ll bring them back later.

Species need space and food, a functioning ecosystem, not just a genome and a zoo. Perhaps the visionaries of deextinction have fallen prey to the most common form of hubris in science, solving the problem of how they can do it without thinking deeply enough about the questions of why or whether they should do it.

What do you think?

*The role of humans in the extinction of Pleistocene megafauna and the nature of our interactions with Neanderthals are still subject to investigation. But while correlation is certainly not causation, extinction, particularly of large vertebrates, does seem to have followed in the wake of the migrations of evolutionarily modern humans, whether in Eurasia, Australia, Oceania, or the Americas.


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Of π Day, Plants, and Paleoclimates

Happy π Day! After not posting anything on Darwin Day, I decided that I could not let another geek holiday go by without a post. So let’s talk about the importance of π in the global biogeocoenosis.

Now you may say, “But π is just about geometry! That’s not biology!” Or maybe if you’ve blocked out 10th grade math, you may say, “But pie is just for dessert!” Allow me to retort:

WRONG!

Biology is all about structure and function and the mathematics of structure (and to some extent, function too, come to think of it….) is geometry. Much of evolutionary biology is concerned with the history, diversification, and development of biological form. On some level, most evolutionary biologists study changes in the geometry of organisms and why it matters. Also, pie makes an excellent breakfast.

So because π relates the diameter of a circle and its circumference, we need to think about the important circles of life. I like trees and the cross-section of a tree trunk is roughly circular, so that seems like a productive place to start! Imagine a beautiful sugar maple like the ones local farmers here in Knox County tap to make maple syrup early every spring. My checker at Wal-Mart told me that just last weekend her husband had really smoked up her house boiling down the last of their haul of sap for this season.

Maples.tapped

So where does that sap come from? The tree stores starch in its roots and early in the season, the roots start moving the starch into the sap to fuel the production of leaves way up in the canopy. The sap flows through little tiny tubes just under the bark of the tree, which is why we can tap into the sap. These tubes, collectively called the xylem system, stretch continuously through the body of the tree, from the tiniest tips of the roots to the veins of every leaf. But how does the sap flow? Are there little pumps down in the roots that push the fluid up? Does it simply “climb” up the little tubes by capillary action? For a long time, this was one of the major mysteries of botany: how do plants, which have nothing resembling a heart, get water from the soil to their leaves, fighting all the while against gravity?

The answer, which has only become fully established over the past few decades, turns out to be a little crazy. The water in the little tubes is not being pushed, but pulled up the tubes. The water molecules form long, continuous strands from the roots to the leaves, stuck together by the electrochemical force of cohesion. And all those tiny strands of water are under tension – they are being stretched like minuscule rubber bands. And the crazy part is that they are being stretched by the air! The underside of leaves are pocked by tiny pores called stomata, and as the water evaporates, it pulls just a bit on the strand of water behind it, all the way down to the roots. So simply because it is drier than the plant’s tissues, the air “sucks” water up from the soil, perfusing all of the plants cells along the way. Plant xylem is one of the wonders of engineering accomplished by evolution. In a single large tree, the xylem can move hundreds of gallons of water over large distances without any direct input of energy on the part of the organism. Talk about efficiency!

About now, you may be wondering, “What about the π?”

To find the importance of π here, we just need to consider the circles in the picture. Not just the big circle of the trunk, but all of the tiny circles that make up the tubes of the xylem. And how tiny they are matters, because the same forces that hold the water molecules together in strands also make it stick to the side of the tubes. In bigger tubes, less of the water is in contact with the wall, so it flows faster. Back in the mid 19th century, scientists figured out that the flow rate (Φ) through a pipe could be described by the following equation:

HP-LawSo there! There is my favorite pi in biology!

The πr4 term, where r is the radius, has to do with the cross sectional area of the pipe and how much fluid is in contact with the wall of the pipe. What is so important about it is not so much the π (sorry, but such is the life of a constant) but the fact that the radius is raised to the fourth power. That means that if you double the radius of a tube, all else equal, you actually increase the flow by a factor of 24 or 16-fold! So plants with bigger tubes can move more water, more quickly.

It turns out that this simple fact has terrific importance for both plant evolution and perhaps even for the history of Earth’s climate. Back in the Cretaceous, 65.5-145 million years ago, Earth’s vegetation was dominated by conifers and ferns. No Triceratops ever munched on a sugar maple. The lineage of flowering plants that are so common today were only just beginning to evolve, and evolutionary biologists have long marveled at their rather explosive (in geological/evolutionary terms, at least) diversification and rise to dominance. Darwin himself called it, “an abominable mystery.” What were the secrets to their success?

Almost certainly, some of them were physiological, and one of the most notable differences between flowering plants and their cousins was in the xylem. Flowering trees had not just discovered flowers and animal pollination (another of the secrets to their success), they had also found a way to make the tubes bigger than those of conifers. And not just a little bigger, a LOT bigger: up to fifty times wider! And because of the πr4 term, even though one of these humongous vessels takes up as much space as 2,500 smaller tubes, the flow rate increases more than 6 million fold! At the same time, the leaves of flowering plants were changing too. The density of leaf veins increased enormously during the Cretaceous, bringing more of the water and soil nutrients in the sap closer to the sites of photosynthesis, and releasing much more water vapor into the atmosphere. The evolutionary relationship between these innovations, their relative order and mutual influence, remain uncertain, but together they changed the world. In fact, they sped it up.

Provided with more water and nutrients, the photosynthetic machinery of the leaves went into overdrive. Vegetation became more productive, capturing more carbon from the atmosphere, though it released more through respiration as well. Those faster living leaves also died younger, speeding up the cycling of nutrients through decomposition. And after the cataclysmic transition from the Cretaceous to the Paleocene, whole forests of flowering trees became dominant over large swaths of the continents, and they even began to make their own rain. With their huge vessels and richly veined leaves, theses trees collectively accelerated the hydrological cycle, moving water into the atmosphere that eventually had to return to the ground as rain. Even erosion may have increased. Recent modeling studies suggest that if Amazon rainforests were constrained to more ancient conifer-style rates of water transport, the dry season would lengthen by up to 80 days, well beyond the tolerance of most rainforest species.

And in making their own world here on Earth, the flowering plants have made our world. No primate ever knew a world without them. Even our climate is a product of their evolution. And we could not understand it without understanding that the ratio of the circumference to the radius of a circle is a transcendental constant.

π for now.

Evolutionary research on the vascular innovations of flowering plants is incredibly exciting right now. Two recent interesting papers (which I drew on for this post) include:

C. Kevin Boyce and Maciej A. Zwieniecki. 2012. Leaf fossil record suggests limited influence of atmospheric CO2 on terrestrial productivity prior to angiosperm evolution. Proceedings of the National Academy of Sciences of the USA.

Taylor S. Feild, Timothy J. Brodribb, et al. 2011. Fossil evidence for Cretaceous escalation in angiosperm leaf vein evolution. Proceedings of the National Academy of Sciences of the USA.


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The Anthropocene gets its own journal!

My last post was on the dawning (and a bit about the conclusion) of our own geological epoch – the Anthropocene. Now a new open access journal launched that is dedicated to the science of the Anthropocene: Elementa Science. The journal is produced in collaboration with BioOne, Dartmouth, the Georgia Institute of Technology, the University of Colorado Boulder, the University of Michigan, and the University of Washington. They will begin accepting submissions in a wide variety of scientific disciplines this April, and best of all, all of their published papers will be freely available to all!

As a teaser, they posted this slick little video. To me, the most important part is the words at the end, which largely echo my last post – “Let’s make it count.”


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IBS, part 3: The Anthropocene: Biogeography from the Far Future

At a scientific meeting like the IBS, most of the presentations detail specific, narrowly focused studies, the bricks and mortar of the scientific edifice. But sometimes there are fora in which we get to explore BIG IDEAS. One of the Saturday sessions at the IBS meeting delved into an important recent big idea by examining The Biogeography of the Anthropocene.

So what’s the big idea? The Anthropocene.  It has been proposed as a new geological epoch reflecting the emergence of humanity as a global force of nature, on a par with the other phenomena that shape the planet, things like asteroid impacts, glacial cycles, massive volcanism, and plate tectonics. You get the idea if you take a look at our global transportation system. We are big.

gts

But what is the evidence for the dawning of the Anthropocene? That was the topic of the first talk of the session, by Tony Barnosky from UC Berkeley. For you see, the Anthropocene is an epoch that does not yet officially exist. It is being considered by the International Commission on Stratigraphy, which, after careful consideration, will deliver a verdict on the status of the Anthropocene in 2016. Barnosky is part of the working group doing that careful consideration.

What was most interesting for me was that Barnosky’s talk was not about the abundant current evidence for human impact, but about how those stalwart stratigraphers would go about delineating the boundary of the Anthropocene. He emphasized that while we think of epochs as periods of time, and thus ultimately intangible, they are in fact defined by the most tangible of earthly things: rocks. Each age in the geological time scale corresponds to specific rock strata deposited during that period in Earth’s vast history, and the boundaries of the period must be clearly defined by globally observable stratigraphic zones. In particular, biostratigraphic zones, delineating particular changes in fossil assemblages, have been instrumental in defining distinct geological epochs. And like any other epoch, the Anthropocene requires a stratigraphic definition.

Listening to Barnosky, I imagined a time far in the future, tens of millions of years after the last human passed away, our species extinct, a ghost glimpsed in fossils, artifacts, and fragmented, indecipherable texts and codes. If some newly sentient and scientific creature were to arise on Earth (or, if you prefer, arrive on a spaceship) equipped with rock hammers and microscopes, how would they recognize the fact that a single species of (at least semi-) intelligent primate had come to dominate the biosphere and change the planet?

According to Barnosky, ample fossil evidence will point to big biogeographic and biogeochemical changes centered around our present geological instant (mid to late 20th century). For example, one future paleontologist, a specialist in fossil seeds, will note not only a global proliferation of maize seeds out of what was once North America, but also a synchronous differentiation of many new forms in the lineage, like the super sweet varieties we enjoy every summer here in Ohio. Another paleobotanist will note that in the same strata, so many newly introduced plant species appear in Australian fossil assemblages that they come to outnumber the previously recorded native species in a geological instant. In a separate publication, an invertebrate paleontologist will observe over the same period a global homogenization of marine fossils, transported worldwide by our shipping fleets. Bivalves isolated to the western Pacific in earlier strata will appear in north Atlantic deposits or on the coasts of the Indian Ocean. The title of her paper might be “Suddenly, everything is everywhere.” Another rock hound will note that in many marine deposits, this change in the invertebrate assemblage is associated with another sort of biostratigraphic zone, a horizon of microscopic shards of plastic, as dazzling in its array of colors and chemical composition as it is notable for its depth. The flattened remnants of our settlements and road networks, even the radioactive traces of our flirtations with nuclear power and nuclear weapons, all of these stratigraphic features will coincide. Slowly, those strange and wonderful new scientists will piece together a story, chronicling the biological evolution, cultural emergence, and perhaps inevitable decline of our species, the authors of our own geological epoch.

But as I listened to Barnosky’s presentation, I started to wonder not about the strata at the base of the Anthropocene, which he seeks to define its beginning, but about those layers of rock yet to be laid down. What story will they tell of humanity after its global emergence? Will they document a cataclysm of geological upheaval and mass extinction, like those that followed the Great Oxygenation Event or the Chicxulub impact? Or will those layers tell a new story, one never before seen in the history of life on Earth, of a species that sought to mitigate its newfound global impact in order to maintain a sustainable planet? What will those future paleontologists read of our own future?

Recognizing the Anthropocene is a sort of coming-of-age for our species, an acknowledgement that we can no longer live as simple children of nature, grabbing what we need or desire and discharging our waste without regard for our impact on the rest of the planet. More than just a new box on the geologic time scale, it is a first step towards “putting away childish things” and taking responsibility for our collective actions. We have a choice, and the future is watching.


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kerkhoffa:

One of the realities of rapid climate change is that environmental conditions are changing so fast that many species cannot migrate or adapt quickly enough to keep up with them. This problem is especially present for some of my favorite organisms: trees. Trees, of course, can only move as seeds and their generally long generation times mean that evolution moves at the pace of, well, a tree.
This problem has many ecologists and conservation biologists considering rather extreme measures: helping organisms move around to keep up with climate change. Of course, this sort of action has risks involved, so there is a robust debate going on in scientific and management circles. This post, from the Early Career Ecologists blog, does a great job of laying out the basics of assisted migration.

Originally posted on Early Career Ecologists:

By Sarah Bisbing

Trees on the move?! I know you’re thinking, “Come on, Sarah. Trees can’t move.” And, generally, you would be correct in that statement. Tree species are now, however, in a position where movement may be necessary for survival under changing climatic conditions. How trees will move is under debate within the ecological community, but why trees will move is accepted as a survival strategy related to the adaptation of species.

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