Fossils of insect-damaged leaves reveal clues about how plants may respond to future global change

Sep 28 2012 Published by under Uncategorized

In my previous posts, I've discussed some of the impacts that very large, "mega-" herbivores have on plants. There are many microherbivores, however. While they may be small, insects have packed a large whallop in the evolutionary arms race with plants. We know a surprising amount about this, considering that the players are smaller and more fragile than the other organisms that make up the fossil record. While insects are rarely preserved in the fossil sediment record, signs of their presence survive in the fossils of leaves that they consumed. Can these fossils tell us anything about modern plant-insect relationships?

Let's start with what we do know. Carbon dioxide concentrations have probably not exceeded 280 ppm in the last 650,000 years; current values (>380 ppm) are predicted to be greater than 550 ppm by 2050. Temperatures are predicted to increase by as much as 6 degres C by the end of the century, according to our best estimates (IPCC 2007). It's well-known that plants that grow in high CO2 environments tend to be nutrient poorer than those that grow in low CO2 conditions, because the ratio of carbon to nitrogen (C:N) decreases as CO2 is more available. As a result of this lower-quality forage, herbivores of all kinds need to eat more leaves of high-CO2 plants in order to get the same amount of nitrogen. Given what we know about how plants respond to temperature and CO2, and what's likely to happen in the future, understanding how plants--especially plants we eat-- will respond to these changing conditions has been an area of extensive research.

The last 56 million years of Earth's climate history. The PETM was an abrupt blip in an otherwise smooth transition to warmer temperatures during the mid-Eocene. Courtesy of Wikimedia Commons.

In order, then, to understand how plants and insect herbivores have responded to a combination of warmer temperatures and elevated CO2 levels in the past, you have to go back more than fifty million years to find the best analog to the conditions we're predicted to be in in the next century. In the early Cenozoic, some ten million years after the extinction of the dinosaurs, temperatures had been gradually warming for some time. Around 55.8 million years ago, this gradual transition was interrupted by a 100,000-year "spike" of especially rapid, warm, and high-CO2 conditions. The partial pressure of CO2 in the atmosphere (pCO2) is thought to have tripled or quadrupled, as global mean surface temperatures warmed by 5°C over around 10,000 years (geologically speaking, a short period of time) (McInerney & Wing 2011).

Much of what we know about how plants and animals responded during the "Paleocene-Eocene Thermal Maximum," or PTEM, comes from a series of amazing fossil deposits in the Bighorn Basin of Wyoming, some of which can be seen here. Some responses, such as the movement of subtropical plants into Wyoming, are fascinating but not particularly surprising. One of the things that caught researchers by surprise, however, is that the leaves from the PETM have a greatly-increased rate of insect damage from herbivory than the fossil leaves above and below the PETM layer. One study of more than 5000 leaves from the Bighorn Basin found that 57% of PETM leaves were damaged, as opposed to 15-38% before or 33% after (Currano et a al., 2008). Additionally, more kinds of insect damage were recorded in the PETM fossils than those that came before or after, presumably because warm-loving insects invaded from the tropics to enjoy a broader range of plants. The scientists concluded that this increase in both the rate and extent of damage was due to the fact that insects would have had to have eaten more leaf material to get the nitrogen they needed.

A selection of the diversity of fossil insect damage from the PETM. Photo from Currano et al., 2008.

One prediction that comes out of this research is that with increasing pCO2 and temperature concentrations in the Anthropocene, we should expect increased activity from insect pests. This has been tested empirically in some cases, such as the increased insect damage to soybean crops grown with experimentally high levels of CO2 (Zavala et al., 2008). Such a conclusion comes with a few caveats, not the least of which is the fact that the response of plants and insects to changes in temperature and pCO2 his highly variable among species of plants and insects; some plants may produce more defensive chemicals and reduce herbivory (Knepp et al., 2005), and some insects may become more common in a high-CO2 world, even though the rate of their herbivory may decline (Stiling et al., 2009).  Another issue is that phenology (the timing of ecological events) plays an important role in plant and insect life cycles, and so the ability of an insect to consume a plant is going to depend a lot on the timing working out for all parties involved (DeLucia et al., 2008). Ultimately, the indirect effects of increased CO2 and warmer temperatures (not to mention moisture!) on plants' abilities to tolerate herbivory may be more important than the number of insects or the rate of insect herbivory (Lau & Tiffen 2009).

The concept that we have to look back more than 50 million years to find the closest analog to the Anthropocene when it comes to climate and the atmosphere is sobering, especially when you consider that the climate change recorded in our closest analog took place over 100,000 years, not 100. It's amazing to me that the damage created by insects on leaves is captured in the fossil record as something we can look to to see how plant-herbivore interactions have changed through time, under different environmental conditions. There are widespread insect outbreaks today that are having a devastating impact on North American forests, from the hemlock woody adelgid in the eastern United States to the mountain pine beetle in the American West. The paleorecord may reveal clues about how ecosystems responded to similar outbreaks in the past. There are a lot of unknowns about how insect herbivory will affect plants in the future, and generalizations should be avoided. Still, by looking at the evidence left behind in meals eaten 50 million years ago, we might just learn something about the next 50 years have in store.

Currano, Ellen D., et al. 2008. Sharply increased insect herbivory during the Paleocene–Eocene Thermal Maximum. PNAS 105: 1960-1964

DeLucia et al., 20008. Insects take a bigger bite out of plants in a warmer, higher carbon dioxide world. PNAS 105: 1781-1782

Intergovernmental Panel on Climate Change, 2007. Fourth Assessment Report of the Intergovernmental Panel on Climate Change

Knepp, Rachel G., et al. 2005. Elevated CO2 reduces leaf damage by insect herbivores in a forest community. New Phytologist 167: 207-218.

Lau, & Tiffen. 2009. Elevated carbon dioxide concentrations indirectly affect plant fitness by altering plant tolerance to herbivory. Oecologia 161: 401-410.

McInerney & Wing. 2008. The Paleocene-Eocene Thermal Maximum: A Perturbation of Carbon Cycle, Climate, and Biosphere with Implications for the Future. Annual Review of Earth & Planetary Science 39:489–516

Stiling, Peter, et al. 2009. Seeing the forest for the trees: long-term exposure to elevated CO2 increases some herbivore densities. Global Change Biology 15: 1895-1902.

Zavala, J. A., et al. 2008. Anthropogenic increase in carbon dioxide compromises plant defense against invasive insects. PNAS 105: 5129-5133

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Where the buffalo roam, wallows will follow.

Sep 19 2012 Published by under Uncategorized

American bison are one of the few species of megafauna to survive the late Quaternary extinctions in North America, only to be hunted to near extinction in the 19th century (though they're no longer considered endangered today). It's impossible to know for certain how many bison there were before the great buffalo hunts of the 19th century; early European anecdotes describe landscapes darkened by the giant animals as far as the eye could see (Krech 1999), though Charles Mann points out in 1491 that this may have been due to a population explosion following the devastation of Native American communities by European diseases.  Earnest Thompson Seton, the first to estimate the population densities based on carrying capacity in the early 20th century, suggested that there were "not less than sixty million" bison in North America in 1500 AD (Krech 1999); subsequent estimates have been lower, in part because researchers have learned that bison tend to be very unevenly distributed across the landscape through time (a factor that some have suggested is responsible for their survival into the Holocene). While the exact numbers of bison may be unknown (and disputed), what is less contentious is the role of bison as a keystone species of the North American tallgrass prairie, maintaining patches of different species as they ate, wallowed, and rubbed their way across the Plains (Knapp et al., 1999).

Bison are picky eaters; their diets are typically composed almost entirely of grass, and they usually avoid other common flowering prairie perennials, like ragweed and ironweed (Fahnestock & Knapp 1994). In addition to avoiding these “forbs” in their diets, the very presence of bison makes the prairie a more forb-friendly place. Forbs tend to be shorter than grasses in the tallgrass prairie, and also have shallower root systems. This means that forbs can’t outcompete grasses for light in the shadow of grasses, and aren’t as able to reach the moisture in prairie soils that sustains grasses through dry spells. In other words, by acting as ecological lawnmowers, bison basically keep the grasses in check, allowing forbs get a bigger slice of the resource pie. Understandably, the late Holocene near-extirpation of bison is thought to have significantly influenced the ecology of the modern Great Plains, and bison grazing is thought to be an important component of prairie restoration efforts.

Top: A bison wallow at Konza Prairie. Bottom: An ungrazed portion of Konza Prairie. Photos by the author.

Bison do more than just eat, however. Like many other large animals, bison roll around in the dust or mud in natural depressions on the landscape. As they roll and lay in these “wallows,” they compact the soil, enlarging the depression when they carry away the mud that sticks to their fur. It’s not entirely known why bison wallow (yep, it’s a verb, too). They may be seeking relief from insect bites or parasites, cooling off, grooming themselves during their moulting period, or even just having fun (MacMillan et al. 2000). Regardless, these patchy disturbances in the prairie landscape can persist for a century or more; some modern wallows have been found in places where bison have been absent for >120 years. It’s estimated that there may have been >100 million wallows over the 70,000 ha of the prairie prior to European settlement (McMillan et al 2011).

While the diversity of plants in wallows has been found to be lower than that of the surrounding prairie, those species found in the wallows are often different, particularly along the disturbed edges (Collins and Uno 1983). If you read the Little House books, you may remember that Laura’s little sister Grace wandered off and was later found in an old buffalo wallow full of violets in By the Shores of Silver Lake. One reason for the difference in composition is that bison compact the soils in the wallow as they roll around, and so wallows provide disturbed habitat where ragweed and other forbs are more readily able to out-compete deep-rooted grasses for water. Since wallows are formed in the spring and summer and tend not to drain very well, they hold more water (and for longer) than the surrounding undisturbed soils, which can provide good habitat for wetland species and is a source of water for prairie animals. At Konza Prairie, reintroduced bison both reactivated old wallows and made new ones, which were then used as breeding sites by frogs in the years when the climates were cool and wet enough that the depressions formed standing pools (Gerlanc & Kaufman 2003). Today, the absence of wallows has contributes to the prairie being a less diverse place than it was before European settlement, all else being equal.

Modern prairie remnants or restorations may be grazed by cattle, which don’t wallow, or may not support any megaherbivores at all. Bison wallow research, even as something of a niche field, points to the importance of non-trophic interactions between animals and plants; landscapes, it seems, experience much more of a megaherbivore than its digestive system. If the Holocene prairie was more like a patchwork quilt than a bedsheet in terms of landscape diversity, what are the ecological legacies of the loss of bison wallows? Do the frogs, birds, insects, and wetland plants of the modern prairie record a signature of the loss of these missing potholes of diversity?


Collins & Uno, 1983. The effect of early spring burning on vegetation in buffalo wallows. Bulletin of the Torrey Botanical Club 110: 474–481.

Fahnestock & Knapp, 1993.  Water relations and growth of tallgrass prairie forbs in response to selective herbivory by bison. International Journal of Plant Science 154: 432-440.

Gerlanc & Kaufman 2003. Use of Bison Wallows by Anurans on Konza Prairie. The American Midland Naturalist 150(1):158-168.

Knapp et al., The Keystone Role of Bison in North American Tallgrass Prairie. Bioscience 49: 39-50.

Krech, Shepard, III, 1999. The Ecological Indiana: Myth & History, W. W. Norton & Company, New York, NY.

MacMillan et al., 2000. Wallowing Behavior of American Bison (Bos bison) in Tallgrass Prairie: an Examination of Alternate Explanations. The American Midland Naturalist 144(1):159-167.

MacMillan et al., 2011.Vegetation Responses to an Animal-generated Disturbance (Bison Wallows) in Tallgrass Prairie. The American Midland Naturalist 165(1):60-73.

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Why does a cow have four legs?

Aug 01 2012 Published by under Uncategorized

I think that I have talked enough in these posts about variational and transformational evolution, and so today I will write something about how phylogenies affect the way biologists work as scientists.  Why is the concept of evolutionary history so important in biology?

In one sense, science is about problem solving. We set out to find the answer to a particular question, and in order to do so we have to solve the puzzle posed by that question. So, a relevant point is this: Is problem solving different in the biological sciences compared to the physical sciences (eg. physics and chemistry)? My answer is "yes and no".

To me, there is a way in which they are all the same, and this involves performing some sort of experiment to test any ideas we have that might solve the puzzle. So, as I noted in an earlier post, we all attempt to explain natural phenomena in terms of other natural phenomena.

However, in another way biology is different from physics. First, in biology we have to deal with the fact that organisms respond to their environment, which other physical objects do not do. If I drop a stone then it falls downward, and it will do so no matter where I am on earth. However, if I release a migrating bird it will adjust its flight depending on where it is released. This complicates the study of biology. Second, organisms pass information between generations, via their genes. There is no equivalent concept of inherited information in physics.

The consequence of these differences is that in biology unique historical events can have effects that last for millions of years. Something that happened to one of my ancestors thousands or millions of years ago can still affect me now, because the information about that event has been passed down to me in the genes that I have inherited from that ancestor. There may be no other evidence of that past event except in my genes. No physicist has to deal with this concept — in physics, those past events that have an effect now do so by leaving observable traces in the environment. The laws of physics that operated back then are still operating now, and we can therefore study them now.

This ultimately means that cause and effect can be separated in biology by a great deal of time. The explanation for the natural phenomena that I see now may be a long time in the past. For example, the cause may no longer be important in the modern world but it was in the past. How do I know about its importance back then? The cause may no longer be apparent in the modern world, so maybe I don't even know about its existence. Under these circumstances, even imagining the cause may be difficult. Perhaps most importantly, the cause may be an historical “accident” — a one-off event that has not happened since. We believe that modern biology is actually the result of a whole series of historically unique accidents!

How do I study natural phenomena under these circumstances? This is where a phylogeny comes into play. We use phylogenies as the framework for studying biodiversity, because they take into account the historical component of biological studies. In biology we use them to describe the natural phenomena, to explain them, and to predict them.

Consider the question posed in the title: Why does a cow have four legs? This is a question about explanation, not description or prediction. So, merely describing the legs of a cow is insufficient to answer it, and predicting how many legs the next cow will have is also irrelevant (although it may be interesting in its own right!).

A physicist might attempt to answer this question in terms of balance and stability, particularly while the cow is moving. The idea is that four legs are stable while allowing the animal to graze, walk or run. This tries to explain the presence of four legs in terms of what we know about the number of legs on other other objects in the modern world, and how stable they are while moving.

For example, we know that a 3-legged object can keep its balance while stationary, but three legs is very awkward for moving. (It is usually suggested that a 3-legged object would have to rotate itself to walk, alternately standing on each of its legs.)

Alternatively, we know that two legs is okay for walking and running, since we do that outselves; and if you are Swedish then you are well aware that at least one cow walks on two legs! We also know that insects have six legs and spiders have eight legs, so these are okay for balanced movement as well.

This is Mamma Mu (on the left) and Kråkan (on the right).

However, a biologist would not approach the question in this way. A biologist knows that a cow has four legs because it inherited that characteristic from its parents, both of whom also had four legs. Furthermore, those parents inherited the characteristic from their parents, and so on. Therefore, to a biologist the explanation for four legs may have little to do with cows in the modern world. The cows have a set of genes inherited from their ancestors, and it is those genes that cause them to have four legs (rather than some other number). There may be no particular relevance to having four legs (as opposed to two or six) in the modern world — modern organisms have characteristics because they inherited them, and not necessarily because they need them.

This starts a search backwards in time, through a series of ancestors in the phylogeny, searching for the one who first acquired four legs. The answer to the question about cows' legs then becomes a question about why that ancestor had four legs when its ancestors did not.

Thus, all cows have four legs, and so we conclude that the common ancestor of their species, Bos taurus, also had four legs. Indeed, all cow-like organisms have four legs, and so the common ancestor of the genus Bos had four legs. Furthermore,  all bovine organisms (cattle, bison, buffalo, yaks, etc) have four legs, and so the common ancestor of the subfamily Bovinae had four legs. Continuing, we work our way backwards through the common ancestors of (respectively) the Ruminantia, Cetartiodactyla, Laurasiatheria and Mammalia, all four of which we conclude had four legs.

Eventually we come to the common ancestor of the superclass Tetrapoda, which also had four legs. (After all, that is what the name says — tetra = four, pod = limb). Not all descendants of this ancestor still retain four legs in the modern world, of course. Primates have modified the front pair of legs into arms, birds and bats have modified them into wings, whales (and dolphins and porpoises) and seals (and sea lions and walruses) have modified their front legs into flippers and greatly reduced their hind legs, manatees and dugongs have front flippers but no hind legs at all, and snakes have lost all four legs almost entirely. Still, the common ancestor of all tetrapods had four legs.

The part of the phylogeny involving the origin of tetrapods is shown in the next diagram. There are four groups of organisms involved.

The part of the phylogeny involving the origin of tetrapods.

The main point about this phylogeny, for our question, is that modern lungfishes and modern tetrapods all have four limbs, while modern coelacanths  and other fish do not. The number of limbs is:

Tetrapod = 4 legs + 1 tail
Lungfish = 4 lobe-fins + unpaired tailfin
Coelacanth = 7 lobe-fins + paired tailfin
Ray-finned fish (most fish) = 7 ray-fins + paired tailfin.

Each fin on a fish is designed to perform a specific function, as shown in the next picture. (NB. MostSome fish also have a small adipose fin behind the dorsal fin, for stability.) Note that pectoral and pelvic fins come in pairs, one on each side of the body. The picture provides the physical explanation for why fish have so many fins,  in terms of balance and stability while moving in water.

So, modern lungfish all have fleshy, paired pectoral and pelvic fins and a single unpaired caudal fin. The other fins of most fishes are absent from lungfish. Modern tetrapods have muscular, paired pectoral and pelvic limbs and a single tail. So, lungfish and tetrapods have the same number of fins/limbs in the same places. We conclude that this arrangement has been inherited from their common ancestor, which is therefore the one we are looking for to answer our question. So, what did the common ancestor of these four-limbed lungfish and tetrapods look like?

We are sometimes incorrectly told that: "Scientists have long known that ancient lungfish species are the ancestors of the tetrapods." This idea is largely discredited today. Lungfish are the closest extant relatives of tetrapods, not their ancestors. That is, they are not primitive — they are well adapted to their natural environment. However, lungfish are one of many relict species of fish that share many ancestral characters.

So, did the common ancestor look something like this?


Or more like this?


Probably neither, because we think that both of these fossil species were descendants of the common ancestor in question. But it was presumably more similar to these than to either modern lungfish or modern tetrapods.

So, the initial question about cows' legs becomes: why did the common ancestor of the tetrapods and lungfish reduce their number of fins from seven to four (and no less)? The answer I was given, by the fish biologist W.J.R. (Pim) Lanzing, when I was a student, was that this is the minimum number of fins that can maintain stability and movement in an aquatic environment.

Most of you know roughly how fish move, and how agile they are in water, so I don't need to describe it. However, locomotion of coelacanths is unique to their kind. They have high maneuverability and can orient their bodies in almost any direction in the water. They have apparently been seen doing headstands and swimming belly up. Lungfish, on the other hand, are essentially sedentary. They are reputed to be sluggish and inactive, but still capable of rapid escape movements using their tail. They can can use their paired fins to "walk" underwater, with alternating movements — first one fin moves forward, then the other. They can also use the fins simultaneously to move forward with a lunging action. So, apparently one is not agile in water when one only has four fins, but one can still move around efficiently.

The first tetrapods are thought to have evolved in coastal and brackish marine environments, and in shallow and swampy freshwater habitats. They used their modified, limb-like fins to get around in the water, as do modern lungfish. That is, the origin of legs wasn’t a transformation that happened on land. Limbs were an aquatic innovation that just so happened to be advantageous when tetrapods began to venture out of the water.

So, why does a cow have four legs? Our phylogeny reveals that this is because one of its ancestors (c. 360 million years ago) was aquatic, and four fins is the minimum in liquid. Most descendants have never changed this number, but they did use it to leave the water and live on land. The first part of this answer is a biological one (about ancestry), although the second part is a physical one (about stability and movement).

This is not the sort of answer that can be determined by an experiment. So, scientific problem-solving in this situation is quite different, making biology distinct from physics.

It is sometimes said that physics lies at the heart of science because all explanations ultimately involve physics. That is, the physics explanation lies beyond the biological one — the biological explanation is a proximal one while the physics explanation is the ultimate explanation. This may be so to a physicist, but I do not see why it should be so to anyone else. The biological explanation (in terms of ancestry) is equal to the physical one (in terms of aquatic balance), rather than inferior to it. Moreover, there are explanations beyond the ones that the physicists consider, although that takes us outside science.

In finishing, you might like to try this physics question, instead: Why are tables generally made with four legs and scientific instruments with three?

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What Makes a Cell Alive? and a joke

Oct 26 2011 Published by under Uncategorized

OK, last post about this, I kinda promise.  I was thinking about this and reading Luisi's book and he asked another interesting question... one that reflects part of the discussion yesterday.  If you survive all the way to the end, then you will be rewarded with my favorite (and only) Halloween joke... just to show I can do stuff besides ask pointless question.

Let's put aside the question about the difference between an apple and its tree and whether a dead thing has live cells and get to the fundamentals.

Take the nucleus out of an oocyte, as in the cloning experiments, is the nucleus living? And is the cell, without a nucleus, alive?

Now we get even more fundamental. The cell itself. Can it be alive without some parts? If so, which parts? Venter and his colleagues made a cell with scratch assembled DNA.  There have also been various attempts to make a minimum cell by removing pieces until the cell no longer functions.  I don't think this tells us very much about what it takes to be alive though.  Even a minimal cell has all the functions that we normally think of a required for life.

On the other hand, we know that to continue living, a cell must have correct DNA.  Venter's team missed a single nucleotide and the entire organism died.  It must have been a critical function for life.

I think that a lesson we could take from this example is that life has to have instructions.  It there has to be some underlying component that can tell a living thing how to do all the things that it needs to do.  Again, we often think of a living thing as reproducing, metabolizing, responding, moving, and growing and developing.  So the cell has to have the instructions to do all those things.

But leads me to a very unsatisfying definition of life.  "The ability to do all the things that living things have to do."  A better circular argument hasn't been seen, I think.  But, I think we're on a good track.  What is the purpose of life?  If you go with the selfish gene concept, then the purpose of life is to spam the environment with as many copies of yourself as you can.  What do all the copies have in common?  The genes, the genetic information to create copies of itself and the ability to keep itself alive to make those copies.

Could we define life as “the existence of genetic information (enough to operate and reproduce the organism) AND the ability to maintain and/or propagate that information”?

That one sentence, after all of ten seconds reflection, really does a nice job of summing up the functions of life and still allows room for the existence of forms of life other than organic systems (e.g. computer based life or non-organic based life).

Since the horse, as a unit, cannot maintain or propagate the genetic information it contains, it is no longer alive. Same with the apple (which is still problematic to me). For a while, the dead organisms can use internal resources to maintain, but not propagate the genetic information. But it cannot continue the process for longer than the cells have resources.

A bacterium, on the other hand, does have genetic information and can maintain and propagate that information.

The cell without a nucleus is an interesting question, even with this definition. But a little thinking about my definition might reveal a new concept (one that human scientists don’t seem to like dealing with).

Alive may not be an all-or-nothing state. It may even be reversible in some situations. Perhaps the cell, without a nucleus, is dead. But by putting a new nucleus in, then the cell can become alive again.



A vampire bat returned to its cave.  It was covered in blood.

The other bats crowded around it.  "Where'd you get the blood?"  "Look at all the blood."  "Comon, don't hold out, where's the blood from?"

Finally, tired of the incessant whining of the other bats, he said, "Fine.  Follow me."

All other bats followed him out of the cave.  The flew across the field.  They flew over the river.  Finally, they flew into the forest and landed on a tree.

The other bats were so excited.  "Are we there yet?" they cried.

"Almost.  You see that big tree right over there, the really tall one?"

"Oh yes," they all replied.

"I didn't!"

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Why Are Dead Things Dead?

Oct 25 2011 Published by under Uncategorized

Here's another brain twister for the day.  I was kind of hoping for a particular response to yesterday's "Are Apples Alive?" post and I got it this morning (thanks Arthur).

Now, I'm not trying to be difficult I promise, but if an apple that is in the fruit bowl (we'll assume recently picked) is considered to be alive... then why is an animal considered to be dead, when many of its cells are still functioning after we declare it 'dead'?

Our organs can survive for a fairly prolonged time in the event of the whole body death.  Limbs can survive as long as 6 hours.  Bone and ligament, much longer.  Hair and fingernails continue to grow after  death.  The brain can survive for about 10 minutes under optimum conditions without major damage.  There is at least one case of a cat being completely revived after one hour of death.*

Now, I freely admit that we're moving beyond scope a bit.  We're talking about brain death and clinical death here and the prior conversations have been about living things.  But I think that this serves to emphasize a point that I made earlier.  Biology is squishy.  It is very difficult to objectively and completely define some parts of biological systems, because there are always exceptions and, thanks to 3 billion years of evolution, life is very, very tough.  To paraphrase Neil Stevenson, "We come from a long line of stupendous bad-asses... because every living thing in the history of the Earth that wasn't a stupendous bad-ass died quickly."

OK, let's get back to where we were... when considering a multi-celled organism, can we say that it is alive if all of its cells are alive as Arthur suggests?  Yes, of course, the cells in the apple are alive, but is that enough to be considered alive?  If it is, then why is our animal dead, when the majority of its cells are alive and will continue to be so for quite a while?

The direction I'm taking here, is that an apple fallen from the tree is not that different from a limb that has been severed from the body.  That part, whatever it is, can survive for a time, but it is no longer connected to the super-structure that makes the entire thing alive.  A living thing can reproduce itself in its entirety, a broken off portion probably cannot (let's not get into Planaria right now).  A living thing can intake material and energy, which is then used for maintenance, movement, response to the environment.  A broken off part cannot (again, in general, plant cuttings may work fine**).

BTW: In case you are wondering, I'm totally off my planned material at this point and thinking 'outloud'.

Can we say (should we say) that a multicellular organism is no more than it's component parts?  Or is a multicellular organism something like what we were previously talking about... is there something that makes it more than the parts.  Is there an emergent property that says we shouldn't treat single-celled and multi-celled organisms in the way (with respect to being defined as 'alive')?

But research seems to indicate that there is little difference between single-celled organisms and multi-celled organisms at some level of evolution.  This report basically describes the change from single-cell to multi-celled due to predation. (for for the Springerlink link, I thought I had the full article downloaded, but I've lost it).  So, again, life is squishy.  There's not a dividing line between single-cell and multi-celled, so it will be (probably) futile to discuss a difference between life and non-life from that angle (and thus we see an example of real science in which we take a shot and it didn't quite work how we intended).

Or do we go back to the multi-celled structure having specialized cells and all the parts can't function unless they are connected (however tenuously) to the other parts.  The whole organism can do all the functions of life, but pieces cannot.  The cells in my reproductive system, while vitally important to the whole and the species, just can't do their job without the lowly small intestine.

I very well may be obsessing about this too much and am being silly.  I don't think so, but what do I know.  I think this is very important thing to consider.  Not because we'll change the definition of life and biologists will stop studying prions or something silly like that.  I don't want biologists and computer scientists to get into turf wars over who gets to study some digital organisms and not others.

I do think, that at some point, probably in the near future, some scientists will go for it.  They will endeavor to create life in a large, complex simulation.  Maybe it will be a giant Uery-Miller set-up with clary substrates all over and pyrite chunks for catalyzing, put a wave machine in to create vesicles on the clay.  Will it work?  We won't know until someone tries.

But, if we aren't sure what life is, how will we know if they succeeded?

OK, I'll go away now, I'm just blathering.  The plan is to talk a little bit more about this concept of what is live, then get into some abiogensis research and see some of the really cool stuff that is being done to examine the questions of what is life and how did it get here?


* Hossmann KA et al., KA; Sato, K (1970). "Recovery of Neuronal Function after Prolonged Cerebral Ischemia". Science (American Association for the Advancement of Science) 168 (3929): 375–6. doi:10.1126/science.168.3929.375. PMID 4908037.

Hossmann KA et al., KA; Schmidt-Kastner, R; Grosse Ophoff, B (1987). "Recovery of integrative central nervous function after one hour global cerebro-circulatory arrest in normothermic cat". Journal of the Neurological Sciences (Elsevier) 77 (2–3): 305–20.

** Which brings up the whole issue of stem cells.

7 responses so far

Are Apples Alive?

Oct 25 2011 Published by under Uncategorized

Here's where we get to some interesting questions on what is life.

Chapter 2 - Question 3

Is an apple – hanging on a tree – living? When it falls to the ground – is it still living?

This isn't a silly question

Wow, now we get to the meat of it. And this is where I start to have fuzzy thoughts on the subject. It all depends on how you define ‘life’. If reproduction is a requirement for life, then the cell in the apple are probably alive, but the apple itself is not. The seeds are the result of reproduction in the parent tree, not in the apple it self.

This article relates an interesting story about that.

What is the definition of life? I remember a conference of the scientific elite that sought to answer that question. Is an enzyme alive? Is a virus alive? Is a cell alive? After many hours of launching promising balloons that defined life in a sentence, followed by equally conclusive punctures of these balloons, a solution seemed at hand: “The ability to reproduce—that is the essential characteristic of life,” said one statesman of science. Everyone nodded in agreement that the essential of a life was the ability to reproduce, until one small voice was heard. “Then one rabbit is dead. Two rabbits—a male and female—are alive but either one alone is dead.” At that point, we all became convinced that although everyone knows what life is there is no simple definition of life.

To use the classic definition of life that I was taught many, many moons ago. Life has these characters: Composed of cells, has metabolism, grows, adapts, responds to stimuli, reproduces, and maintains homeostasis.

I kind of like that definition, but an apple is not alive by this definition. The cells within it are, but the apple itself does not grow, reproduce, respond (except chemically), or has a metabolism.

Can we separate the living thing from the cells it is composed of? i.e. if the cells reproduce, does the organism? If the cells retain metabolism, does the organism?

I ask because a dead organism may have most of its cells function even after the organism itself dies… at least for a little while.

Which brings us to another question, that maybe we should consider first.

Chapter 2 - question 1

Do you believe in the utility attempting to give a definition of life?

I do think that there is utility in dealing with this question now. Avida organisms can already evolve complex logic functions. And computers are beginning to approach the computing power of the brain (cat brains first) and the human brains processing abilities.  (I will note that there is some skepticism on whether IBM has actually reached the equivalent computing power of a feline.) With that in mind, the question of what is alive will become very important… or maybe not. Humans have an unfortunate tendency to use resources and organisms regardless of the ethical considerations involved.

Life is like porn (you knew I was going there right?).  We might not be able to define it, but we know it when we see it... or do we.  Avida organisms are something that's pretty close to any reasonable definition of life, but they are definitely not made of cells.  Could there be other non-cellular life that we would just ignore because we don't see cells?

So what are the qualities that life must have to be considered life?

Honestly, I've been thinking about this for several months (in those 12 seconds between when I can finally lay down and when I actually go to sleep... otherwise known as 'spare time').  It is extraordinarily difficult to develop a definition of life that does not have some exception.  The apple above for example.  Combinations are even trickier.

I have placed an additional burden in that I think that digital organisms could eventually be alive.

11 responses so far

Determinism, Cotingency, and the Accident of Mankind

Oct 24 2011 Published by under Uncategorized

Well, we seem to be off to a good start.  I do have work tomorrow, so I'll just get this in now and let everyone stew over it all day.  The best sauce and all that...

Since we already kind of got started in this direction, I'll put in questions 2 and 3 from The Emergence of Life - Chapter 1.  This link is to my review of chapter 1.  Here's a link to the book on Amazon (I get no income from this).  But at the least you'll understand the thinking behind determinism and contingency.  [NOTE: You'll find I link to Wikipedia a lot.  It's a convenient location for much of the material that I think you might benefit from.  I do not consider it an authoritative source, but the references and further reading are often  peer-reviewed works that will describe material in detail, with authority.]

Chapter 1 - Question 2:

Do you accept the idea that biological evolution is mostly shaped by contingency? If not, what would you add to this picture?

First we need to talk about contingency and determinism. In the book, Luisi describes determinism (in this context) as the notion that life can develop purely by the interaction of chemical and physical processes. In other words, if the chemicals are available, life will develop. The opposite of this thought is NOT that there was an intelligent designer or something like that.

The other position is that of contingency. That is, the interaction of many factors (the majority of which may be deterministic) is required in an unlikely sequence of events to result in life. Contingency is something like chance, but not quite. Luisi describes it as this way. Contingency is getting hit on the head with a piece of tile roof. The deterministic factors (your walk to work, the poor condition of the roof, wind, gravity, etc) all combined to result in you getting hit with a piece of tile. Another way to look at it is what I call the “re-do” effect. If you reset everything back to the way it was before you walked to work, would you still get hit with the tile? If we reset the universe back 6 billion years and let it run again, would be in exactly the same place we are now?

In my mind contingency is the philosophical equivalent of chaos theory.

Now to answer the actual question. Is biological evolution mostly shaped by contingency?

First, this is a rather curious statement considering the focus of the book. Evolution really doesn’t have that much to do with abiogenesis… or does it. It can be shown that evolution occurs with any system that replicates imperfectly. Is a single RNA strand alive? If not, then we do have evolution on non-life and that evolution may drive replicators toward life. However, is evolution contingent anyway? I think so, if only because of the massive amount of potential influences on an organism. Mutations, environmental effects, what actually determines relative fitness, etc are all contingent things. A particular mutation might be great in an ice age, but if it's not an ice age, then it may be useless.

As far as abiogenesis is concerned, before reading this, I was squarely in the deterministic camp. However, contingency makes a lot of sense. It would explain why we haven’t heard from aliens (of course, there are lots of other reasons for that too).

At this point, I’m thinking that life is probably pretty common in the universe. However, I’m wondering how much life exists beyond slime molds (or alien equivalents)? Is multi-cellularity much more difficult to achieve than we might think? With a sample size of 1, it’s difficult to really examine this, but research seems to indicate that being multi-celled is useful and so may be likely once cellular organisms exist.

Intelligence may be less likely than multi-cellular organisms, but again, a small sample size has resulted in little ability to explore.

I can see the value in both positions.  I think the future research that will be done in space exploration may well give us evidence one way or another.  If the deterministic proposal is correct, then we should see a universe filled with life in all kinds of strange environments (more on this later).  If contingency is more correct, then we should rarely see life and even more rarely see intelligent life.  Which neatly segues into the third question...

Chapter 1 - Question 3:

Are you at peace with the idea that mankind might not have existed; and with the idea that we may be alone in the universe?

65 million years ago, dinosaurs were satisfied. They had existed on this planet for over 160 million years (almost a 1000 times longer than modern humans have existed). Mammals existed for much of that time, but they were rarely much larger than mice.

It took a freak accident to allow the rise of mammals, which has resulted in the development of modern humans. Without an asteroid crashing into and utterly devastating the planet, we would not be here. I have no problem with that.

I’m not so sure about ‘alone’. In the sense that humans may be unique as the only sentient species (i.e. capable of ad hominem arguments and recognizing the fact), I can live with it. I’ve read too much science fiction to be comfortable with the idea… I want to believe. But I can live with the idea that we are unique.  That doesn't imply special privilege or a designer or anthropocentrism in my book.  It just means we are lucky.

But in the sense that there are other living things, I don’t think I can be OK with that. I believe that there is too much energy in the universe (in the physics sense) and the likelihood of complex chemical reactions is too great to say with any confidence that Earth is the only planet with life. Since we find organic compounds in the most unlikely of places (nebula and comets) I think that life is not only possible, but likely to exist elsewhere in the universe, perhaps even elsewhere in the solar system. This life, like the dinosaurs may be satisfied at whatever level it has obtained to this point, but I doubt it. Life changes. Darwin and hundreds of years of observation have shown us that life changes and in ways we cannot imagine (reptiles developing a proto-uterus for example).

Again, this is my belief, but if life exists elsewhere in the universe, then intelligence also exists in the universe.

Your thoughts?

4 responses so far

Who is This Guy and Why is He Here?

Oct 23 2011 Published by under Uncategorized

Hi. I’m very excited to be guest blogging here. This is my first guest blogging spot, so please be gentle.

Cassandra’s Tears is where I normally hang out blogging. I attempt to make some really cool science accessible to the non-scientist. I also talk a bit about technology and the anti-science positions. Rarely, readers are treated to a bit of humor or a past attempts at short stories and poetry.

I have always enjoyed science. When I was three, I could shock anyone older than about 30 by telling them I wanted to be a paleontologist and name dozens of dinosaur genera. Over time (more than I’d care to actually think about), I learned a lot about myself.

I still love science, but I love the knowing. I’m not real big into the actual finding out. Basically, I suck at experiment and observation. I’m also easily distracted. I can’t stand to be fixed onto one subject. I’ve never gotten an advanced degree, because they don’t make advanced degrees in general science. Still, I’ve learned a lot on my own and am pretty comfortable with most areas of science.

This stood me in good stead while I was teaching. I taught, for a few years, at a tiny little school in Sabine Pass, Texas. You might remember it being run over by hurricanes Rita and Ike. I joined Sabine Pass School right after Rita and stayed until right after Ike. I taught; biology, chemistry, physics, IPC (physical science), oceanography, and TAKS prep courses… all in the same year. Suffice to say that I know a little about a lot.

I’m a huge fan of science fiction, even though there is little out there worth reading or watching nowadays.

Now, I’m still involved with both education and science. I’m a science content specialist for a company that works in publishing, education, and assessment. So, I get to read all the cool stuff and then try to incorporate that into our products. Yes, I live in a cube farm.

On Cassandra’s Tears, I’m engaged in a chapter review of The Emergence of Life by Pier Luigi Luisi. Abiogenesis is a fascinating topic and so much has been learned in just the last decade. What’s interesting about the book is that the author has included some chapter ending questions for the reader. These aren’t like ‘test’ questions, they are thinking questions.

Those are what I would like to talk about here. I think this would be a good place for discussion. I’m planning on taking a few of the questions about life and the generation thereof and giving you my thoughts about the matter. I would love to hear your thoughts on the matter as well.

“What is life?” and “Where did life come from?” are not simple subjects. I think it’s the nature of biology (being squishy rather than firmly defined).

If you think about chemistry, you can firmly declare a molecule to be of a given type. It isn’t water unless it’s 1 oxygen and 2 hydrogens in a covalently bound system. You can even talk about solutions with varying ratios of solute to water, but you can define them in very specific ways and have a standardized convention for stating how much solute, how much solvent, and the concentration of the solution. So, even if there’s a range, you still have a very specific definition.

You can't really do that for life and there are a lot of 'ifs', 'ands' and/or 'buts' involved.

So, that's what we'll discuss here. Totally new, totally fresh, so let's get the ball rolling. What do you think a good definition of life is?

7 responses so far

Evolving Ideas and Intelligent Design

Feb 19 2011 Published by under Uncategorized

Well, it seems that my earlier post on Darwin has ruffled some feathers in the Intelligent Design (ID) camp, so they've been trolling the comments section on my personal blog. This post started out as a response, but I decided to expand it to include some of the context surrounding Darwin's work.

A comment by VMartin

...One wonders why no one noticed “natural selection” before. And there were ingenous minds in the history! One answer might be this – it was never observed because it doesn’t exist. Darwin implanted this speculation there. And “On the origin of species” reads sometimes like comedy. One should try to count how many times Darwin used words like “which seems to me extremely perplexing” etc....

It's interesting how 'simple' natural mechanisms and systems can take longer to be acknowledged than one might have thought. Heliocentrism is another example of something that now seems very obvious, but was historically slow to be recognised (and is still not recognised or not known about by some). It's easy to blame organised religion for the suppression of such observational truths about the universe, since challenges to traditional belief were seen as heresy and dealt with accordingly, but there's far more to it than that.

One reason why some scientific theories have been slow to come to light

One reason why some scientific theories may have been slow to come to light

Let's set the scene - Darwin's formative years were tumultuous with regard to sociopolitical events. The Napoleonic wars drew to an end with the Battle of Waterloo when Darwin was six years old, the Peterloo Massacre occurred and the Six Acts were drawn up by the Tories to suppress radical reformers when he was ten - reflecting the ongoing social division between the establishment and the public.

Peterloo Massacre

When Darwin was in his twenties the power of the strongly traditional British establishment finally began to wane, when the Whigs came to government allowing the 1832 Reform Act and the 1833 Slavery Abolition Act to be passed. There was also the devastating Great Famine in Ireland when Darwin was in his thirties and all of this was set against a background of the Industrial Revolution, which was providing the impetus for science to play an increasingly important role in society.

This meant that Darwin's work was by no means formulated in intellectual isolation. Theories of evolution had been proposed 2,400 years previously, but they were poorly developed. Natural philosophers like Darwin's own grandfather Erasmus and Jean-Baptiste Lamarck raised the issue of evolution at around the time of Darwin's birth, but the mechanisms for evolution were either ignored or flawed. Evolution was an established topic of discussion and publication by the time Charles Darwin came onto the scene, with people like Robert Grant being more radical on the subject than Darwin found palatable in his early manhood. Despite this interest, the mechanism of evolution remained elusive - perhaps unsurprisingly, since the academic community addressing natural sciences was largely composed of members of the clergy and the natural theology of the time was seen as being mechanism enough.

But a literature base that was to inspire non-traditional hypotheses was also developing at the time - Vestiges of the Natural History of Creation in particular offered an alternative view that was seen as too radical by many - clearing a path for subsequent works that challenged orthodox views.  Given this context, it is perhaps unsurprising that Darwin and Alfred Russell Wallace converged on the same premise at the same time. In short, the ideas evolved to fit the intellectual and social environment. The same has been true of other discoveries and inventions where there was a requirement for the right intellectual groundwork to be laid in advance. This groundwork is required before a robust theory can take root - and Natural Selection is a component of the robust theory of Descent with Modification, or evolution.

The critiques I have seen of evolutionary theory  have come from people who quite clearly don't understand it - and such critiques tend to rely on statements of incredulity rather than a strong factual base. No well-supported alternative hypotheses have been constructed or presented and a lack of understanding hardly counts as a robust refutation of a well supported theory.

An accusation by IDers is that 'Darwinists' (N.B. I don't know anyone who would call themselves a Darwinists following the New Synthesis) stick with Natural Selection because they are atheist. I think I see the real agenda emerging here, particularly when you see evolution as a theory being conflated with just one of the mechanisms involved. After all, Natural Selection is not the only mechanism involved in evolutionary adaptation and speciation - there are also other factors like hybridisationhorizontal gene transfergenetic drift, perhaps some epigenetic influences and artefacts of EvoDevo processes. But these factors are still constrained by the simple fact that if they are selected against, they will not be perpetuated.

Intelligent Design

The Intelligent Design agenda

John A. Davison left this comment on a previous post:

Natural selection is a powerful force in nature. It has but one function which is to prevent change. That is why every chickadee looks like every other chickadee and sounds like every other chickadee – chickadee-dee- dee, chickadee-dee-dee. Sooner or later natural selection has always failed leading to the extinction of nearly all early forms of life. They were replaced by other more prefected forms over the millions of years that creative evolution ws in progress...

First and foremost, the suggestion that Natural Selection prevents change is erroneous - change will occur if there is a change in the environment and/or if beneficial mutations arise in a population (tell me that mutations don't happen - I dare you...). The obvious response to the next statement is that I can think of six different 'chickadee' species, with an additional three subspecies (and this is ignoring numerous other very similar members of the Paridae), all are similar, but all are different - so the statement makes no sense as it stands. Getting to the meat of what is being implied about the Creationist interpretation of species, another bird provides a good example to the contrary. The Greenish Warbler shows a distinct pattern of hybridising subspecies across their vast range, until they form reproductively isolated species at the extreme ends of their range, where they happen to overlap yet not hybridise (a classic ring species [pdf of Greenish Warbler paper]). This is a well-known example of how genetic variation can accrue and give rise to new species without any supernatural intercession.

Salamander ring species (picture from Thelander, 1994)

Salamander ring species

Another comment by VMartin

...But no wonder that Darwin considered “natural selection” for such a complicated force. Even nowadays Dawkins speculates that NS operates on genes, whereas E.O.Wilson has brushed up “group selection” recently (citing of course Darwin as debeatur est .

So may we “uncredulous” ask on which level “natural selection” operates?

As to this question about the level on which Natural Selection operates, I thought the answer was pretty obvious - it operates at every level. Change the focus of Natural Selection from passing on genes to the only alternative outcome - the inability to pass on genes. It doesn't really matter which level this occurs at or why - be it a reduction in reproductive success when not in a group, or a deleterious single point mutation - if it happens then Natural Selection can be said to have occurred. Being 'fit' simply means that an organism has not been selected against.

There's a lot more to modern evolutionary thought than Darwin's key early contribution, but Darwin is still respected because he was the first to provide a viable mechanism by which evolution is driven. This mechanism has helped make sense of an awful lot of observations that were previously unaccounted for and, moreover, evolution has been observed and documented on numerous occasions [here's a pdf summary of some good examples].

I fail to see why Intelligent Design has been taken seriously by some people - it relies on huge assumptions about supernatural interference (so it fails to be a science) and I have as yet never seen a single piece of evidence that actually supports ID claims. The only research I have seen mentioned by proponents of ID are old, cherry-picked studies that report a null result from an evolutionary study - this is not the same thing as support for ID, as anyone who can spot the logical fallacies of false dichotomy and Non sequitur (in particular the fallacy of denying a conjunct) will tell you.

I like to keep an open mind, but as soon as I see logical fallacies being wheeled out I lose interest in getting involved in the discussion. This may be a failing on my part, because I should probably challenge misinformation, but quite frankly I don't have the time or the patience - much as I hate to stoop to an ad hominem, my feelings on this are best summed up by the paraphrase:

when you argue with the ID lot, the best outcome you can hope for is to win an argument with the ID lot

and my time is far too precious to waste arguing with people who ignore the arguments of others and construct Straw man arguments based on cherry-picked and deliberately misrepresented information. I have no problem with other people believing in any of the numerous gods that are available, but please don't try to bring any god into science (and heaven-forbid the classroom) - since it is neither necessary nor appropriate.

Intelligent design as a scientific idea

Intelligent design as a scientific idea

54 responses so far

The rest of the iceberg

Feb 18 2011 Published by under Uncategorized

Working in a museum is an awesome experience. It's something I wanted to do since the age of four and I've been incredibly fortunate to get established in this highly competitive field. The role of a curator is particularly rewarding since we get to research collections and bring some hidden treasures out into the light of day (figuratively speaking of course, our head of Conservation would be very disapproving if we did that literally).

Unfortunately, no matter how much material we manage to put on display, the vast majority of collections are kept in storage since there is simply too little room to display everything. This means that what you see in showcases is very much the tip of the iceberg; at the Horniman Museum for instance it is estimated that 95% of the collections are in storage. Of course some people are critical of this and want to see more material on display, whilst others subscribe to the less-is-more philosophy in exhibitions (see point 8 ), but being in storage doesn't mean that the collections don't get used - far from it. Researchers, artists and members of the public use the stored collections for all sorts of projects - in fact, we even refer to our stored objects as our study collections.

Exhibition space limitations aside, much of what we have in storage wouldn't be considered to be particularly interesting if it did go on display. Some specimens are very small and plenty are by no means pretty. Many can't tell an interesting story without an awful lot of additional information and prior knowledge. As a curator I have a desire (and indeed a duty) to provide some of the information and knowledge needed to make objects relevant and interesting. As a technophile I think that the Internet provides a fantastic medium for doing this, which is why I started a blog back in 2009. This has provided an opportunity to show a tiny glimpse of the rest of the iceberg.

Damage by the ivory-eating squirrel, the odd object in storage that inspired the first Friday mystery object

So for 83 weeks in a row I have posted an image of an object and I've asked a simple question relating to it (usually I ask for an identification). The responses to my question gives me an opportunity to gauge how self-explanatory an object is and it also provides an insight into how objects are perceived by a varied audience. Then when I provide an answer to my question the following Monday I get the chance to provide a greater depth of information.

This Friday I've decided to use a particularly challenging object, that a few people will identify immediately because it is so distinctive, but anyone who hasn't seen one before is likely to struggle a bit. Can you work out what type of bone this is and which species it comes from?

(N.B. this is the same bone photographed from different sides - click for bigger)

For those few that are in the know perhaps you could drop hints rather than blurting out the answer and I hope that everyone else will feel free to ask for clues or make a note of their thoughts about this specimen in the comments section below. Good luck!

4 responses so far