Archive for the 'Physiology' category

>Dinosaurs and the Mystery of Body Temperature III: Intertial Homeothermy

Jan 28 2007 Published by under Animals, Evolution, Links, Paleontology, Physiology

>Body size is an important factor in the debate over whether dinosaurs were cold or warm blooded (or something in between). When you have a land animal 42 feet long weighing nearly as much as a blue whale, temperature models tend to break down. If the dinosaurs were ectotherms, relying on the environment for heat, they may lack the surface area to sufficiently heat the blood pumping directly beneath the skin. If dinosaurs are endotherms, and internally heated by its own metabolism, it may not have enough surface area to expel excess heat from the depths of its massive body.

The following chart shows this principle a little more clearly.


As you can see, the second two cubes have the exact same volume (body size), but the surface areas are vastly different. Large animals like dinosaurs and blue whales are like the middle cube with the smaller ratio; it becomes difficult to use surface area to heat/cool its insides. Also, the more massive an animal is, the more heat it produces/requires, generally speaking.

The reason blue whales get away with being the most massive animal to ever live (so far) is that temperature exchange with their environment is rapid. The ambient temperature of the ocean is on average much lower than ambient temperatures on land, allowing the whale to circulate heat through the thinner parts of its body and allowing the cold water to carry away the excess. Plus, the whale's 100 tons is spread out along 100 feet of body as well.

You can see how a creature on land weighing as much as the blue whale, compacted into 40 or 50 feet and lacking the might present a particular problem for scientists to figure out, especially in the absence of direct evidence.

But, the creature did exist. We're just now picking up the pieces, so to speak.

And recently, scientists put those pieces to good use. By simulating the ontogenetic development of eight different dinos using data from recent bone analyses, they were able to determine that the internal temperature of dinos depended on size. Smaller dinosaurs maintained a lower body temperature and probably grew at a rate consistent with extant reptiles, while the larger dinos maintained a higher body temperature, like today's birds and mammals.

The largest animal studied, Sauroposeidon proteles, was estimated to have an internal temperature of 48 degrees Celsius (120 degrees Fahrenheit), a few degrees higher than what was thought to be the upper limit of temperature tolerance for animals. Because of this extremity, the authors believe that temperature may have been the ultimate cap on body size.

Ultimately, this study was transposing a state called "inertial homeothermy," which is observed in ectotherms like crocodiles and the Galapagos tortoise that can maintain their internal temperatures by adjusting their internal physiological conditions, much like endotherms. The researchers performed the same tests on crocodiles of similar size (when they could; there are no crocs alive today to compare with the larger dinos):


Perhaps, if time allows in the near future, I'll detail a bit more about all the thermies: poikilo, homeo, hetero, ecto and endo.

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>Dinosaurs and the Mystery of Body Temperature II: The Evolution of Endothermy

Jan 19 2007 Published by under Animals, Birds, Evolution, Links, Paleontology, Physiology

>There's a fairly significant problem with the evolution of endothermy from ectothermy, a paradox that has no satisfactory conclusion as of yet: How could well-insulated animals with high metabolic rates producing lots of heat from within their bodies evolve from animals with low metabolic rates and poor insulation, expertly absorbing heat from the surrounding environment?

If these characteristics evolved independently what purpose would they serve? An ectotherm has no use for insulation like feathers or hair since heat exchange needs to be rapid with its surroundings, just as it has no use for a heat producing high metabolism without the necessary insulation.

Raymond Cowles' experiment showed that by putting little fur coats on lizards wasn't keeping heat in, it was keeping heat out. The lizards couldn't warm up.

That's the paradox, the catch-22. The ticket out, however, is the exaptation: An adaptation of a structure that becomes useful for one biological purpose that originally evolved for another.

Feathers are are thought to be derived from the long scales of ancient archosaurs. These reptiles could lift their scales and expose their skin directly to the source of heat, or orient them so that they could block heat absorption. Just as the marine iguanas of the Galapagos Islands are able to trap a layer of air within their scales, these reptiles are thought to have done the same, retaining more metabolic heat, leading to a more active life.

Another theory concentrates on our reptilian ancestors from the synapsid lineage. The synapsids were steadily becoming more active (illustrated by changes in bone structure), and those morphological changes could have been accompanied by higher metabolic rates, leading to more heat in the body. The more hair on the body, the better heat retention.

So which came first, the dino or the egg?

It's apparent that endothermy evolved at least twice; once beginning with an exaptational insulator in the case of birds, and once beginning with exaptational skeletal changes and a needed increase in activity for foraging, in the case of mammals.

Largely, however, the jury is still out. (I heard that there is also evidence that pterosaurs might have been endothermic, leading to a third origin of endothermy; please link research if you know of any.)

Its important to realize that there are in-between states of thermoregulation, and the progression from ectothermy to endothermy (and back again, in some cases) took place in baby steps across millennia. Time and again we're shown that organisms tend not to fit our definitions and molds. It's not like flipping a switch.

More on dinos and thermoregulation for part III.

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>Dinosaurs and the Mystery of Body Temperature I: Endothermy vs. Ectothermy

Jan 19 2007 Published by under Evolution, Links, Paleontology, Physiology

>This is repost from September of '06. I never had the chance to finish the series because of school, so I will be finishing in three parts this week.

Why have the dinosaurs been relegated to little kid stuff? Why can't I find a purple triceratops t-shirt in XL?

Were the dinosaurs warm-blooded or cold?

I want to talk about dinosaurs and body temp for a couple of posts, but I think the best place to start is with a little discussion of why this issue is important and the evolutionary implications of endothermal/ectothermal states.

Ectothermy is the state of commonly referred to as "cold-bloodedness" (an inaccurate term; it's more about precise regulation) which is observed in most reptiles (though not all), most fish (not all) and basically every animal that is not a bird or a mammal (though not all). Ectotherms rely on heat from outside sources to maintain their body temperature. The sun is the main source of this heat energy (infrared), which can be transferred directly through absorbing the sun's rays, or indirectly through convection - movement of heat between objects (including organisms) and the air.


When a lizard suns itself, its blood vessels just below the skin open up, allowing more blood to flow next to the skin and the source of heat (the sun's radiation). The lizard's blood warms and transmits heat to the rest of the body.

Endotherms, on the other hands, are animals that regulate their own heat, like us. We don't need external sources because heat production is built in to our metabolic machinery. In fact, most endotherms spend more time trying to dissipate heat than acquire it. As you might expect, there is a formal range of classifications (lower lethal, lower critical, thermoneutral, upper critical, etc.) that biologists can use to determine the tolerances of certain endotherms.

The most important thing to remember is the necessity of temperature regulation in animals, the "why." Metabolism is all about burning calories, and the processes that burn those calories are driven by chemical reactions. Chemical reactions within the body are finicky; they depend on enzymes to catalyze which only work within a relatively narrow band of temperatures.

Endotherms have an advantage in this respect. A constant high body temperature increases the activity of the central nervous system, and subsequently neurotransmitter and enzymatic activity. Ectotherms do not have this advantage; on cool days/nights, they lose the ability to be as active. Keep in mind that this does not mean that endotherms are better, just different.

So what does this have to do with dinosaurs?

The main problem in assessing the body temperature of dinosaurs is that we have no direct evidence. There are no extant dinos, so scientists have to look to their descendents, birds and reptiles. But, as we covered earlier, temperature regulation is far from uniform in these animals.

There is one other problem: temp regulation is a special problem in the case of such huge animals.

Next time we'll look into the evolution of endothermy and how it might have arisen from the dinosaurs.

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>The Evolution of Crab Balls

Dec 21 2006 Published by under Animals, Environment, Evolution, Links, Physiology

>The University of Maryland Center for Environmental Science recently published an article discussing some progress in blue crab research and conservation, and mentioned a related report:

The Chesapeake Bay blue crab population has stabilized, but at historically low levels according to a recent report by the Chesapeake Bay Commission’s Bi-State Blue Crab Technical Advisory Committee.

Though the news isn’t quite heartening, it’s better than nothing.

Blue crab populations have been declining tremendously over the past few decades, not only threatening a population of the animals, but also endangering fishermen and families. So before everyone prepares their crab balls for Xmas (probably shipped in from Indonesia), I’d like to spend a couple of posts discussing the blue crab—its history and ecology.

Blue crabs (Calinectes sapidus) are part of a large order of crustaceans* called the decapods—literally ten foot, which refers to the number of thoracic legs (also called pereopods; legs on the thorax of the animal). The first three thoracic legs have been modified for feeding, while the back two are used for movement. In the case of the blue crab, a brachyuran or swimming crab, the last pair of pereopods is equipped with paddles to propel the animal through the water.

It is interesting to see adaptational trade offs in organisms so similar. The decapods have all evolved different means of protecting themselves. Lobsters have size and a thick exoskeleton on their side, while hermit crabs crawl into a snail shell to protect their relatively weak carapace. As a true crab, Calinectes has evolved a carapace well suited for swimming; escape is as good a defense as any.

We see the same evolutionary pathways in the cephalopods (squid, octopus, nautilus) although as an offensive solution rather than a defensive one. Ancient cephalopods were split into two groups, the ammonites and the nautili, both equipped with thick, tough shells. As bony fish became increasingly adept at hunting, cephalopods had to become faster and more efficient. Shell were reduced and exchanged for the swimming power of muscular siphons, propelling Today only one species of cephalopod retains its shell in any significance: the ancient Nautilus. The ammonites have been extinct for some time now.

Evolution has favored the quick in these cases. But in order for early decapods to become successfully streamlined, the abdomen, including the telson or tail, had to become less of a hindrance. For the past 100 million years, it has slowly curled inward, so to speak, contained entirely under the carapace of the crab, which itself had to expand, giving the crab its well-known shape. This process was theoretical until:

the 1930s [when] the missing link, Eocarinus, showed that [the origin of crabs] must lie among the Pempiphicidea, an extant group of lobsters.

Fossils are hard to come by, especially in the world of invertebrates, and crustaceans are no exception. Recently a man in North Carolina stumbled across a fossilized Pleistocene crab, rare and unknown until recently. He told the local paper of his visit to a fossil seminar at the local aquarium:

“I went over to the aquarium and stopped the show,” he said. “Right away [he snaps his fingers] she said it could be 3 millions years old. That’s when man started walking upright if you believe in that evolution stuff.”

Whether or not you believe in that “evolution stuff”, blue crab populations in the Chesapeake are at historical lows. Next time I’ll explain the life cycle, ecology and major environmental problems involved in the decline of the blue crab.

*As an aside, the crustaceans are an incredibly diverse group of invertebrates, especially when it comes to modes of reproduction. They reproduce sexually and asexually, can be spermatophoristic, gonochoristic or hermaphroditic and are fertilized both internally and externally.

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>Sensing the World Around Us

Oct 29 2006 Published by under Evolution, Links, Neurology, Physiology

>We've talked about the contemporaries of our ancestors, modern archaea and bacteria. They communicate, replicate and socially organize into tight societies much like our own.

That is a relatively fuzzy comparison, however. One cannot entirely equate the complexities of our society with the biochemical signaling of such a simple organism. There are interesting similarities, but the argument is hardly conclusive.

At a more fundamental level, however, the comparison can be correlated. Biologically, each one of us is a direct descendant of those bacterial colonies. The framework for communication and organization was already set up for our body plan; natural selection merely condensed and implemented it.

We are each a giant walking colony of organisms; each of our trillions of cells has its own role in the larger organism, much as Donovan stated last week, and has become specialized to perform distinct operations in the interest of the larger organism (not to mention the many species of bacteria that inhabit our skin, mouth and gut). This is essentially a compartmentalized, specialist version of the basic bacterial colony.

We have muscle cells that provide the framework of motion, blood cells for nutrient dispersal and defense, cells that regulate hormone levels in the body, cells that absorb and digest nutrients, etc. Perhaps the most important of these are the nerve cells.

Nerve cells help the larger organism sense the world by distributing sensory information along a fabric of neurons (nerve cells) woven through our entire body. Eventually this information is trapped in brain cells for later use (memory).

It is interesting to note that objects we encounter in the world-fruit, pavement, pencils-have no inherent scent, feel, taste, sound or even appearance; we assign the qualities of an object according to their usefulness to us. We are nauseated by feces and rotting garbage because it is dangerous for us to consume. The "scent" of garbage was contextualized in ancient times, and our brain is genetically wired to send waves of repulsion through our body, driving us to turn away in disgust or even vomit.

Similarly, we are attracted to certain foods. Our mouths water at the smell. We are compelled to eat more of a food because its taste and texture indicate that it is nutritiously viable. Our bodies love lots of high energy, fatty foods.

The funny thing is, most of the information about the world in which we live is never "consciously" processed.

I'm sitting in the spare bedroom of my apartment typing this article. Loads of sensory information is coming in through my five senses:

I see alternating images, the keyboard, the desk and the monitor.

I feel a faint wind through my open window, the pressure of my tongue on the roof of my mouth, the chair pressing on my back, my feet on the floor, fingers exacting the pressure required to press each key and a dull pain in my head from staring at a light source for too long.

I smell the carpet, my lunch, fumes from cars on the highway, my deodorant; I hear trucks gearing down, my girlfriend shuffling papers, the cats running the hallway, the stilted clicks of my fingers tapping keys. I taste the remnants of my cereal in my molars.

I sense all of it and I haven't even left my seat. In fact, if I wasn't consciously exploring what exactly I was sensing at one time, all of these things would not pass through my conscious mind, since it is much more focused on organizing separate letters into words (lexical arrangement) and separate words into sentences and paragraphs (syntactic arrangement) to match and represent the ideas floating about in the conscious portion of my brain. It's busy writing this article.

But what else am I missing?

A hell of a lot. Food is being metabolized, waste removed, individual cells die and others are replicated, your heart beats, electronic messages race along our neurons, dumping chemical messages of pleasure or pain, telling different parts of the brain to increase quantities of this chemical or decrease quantities of that.

We never even catch wind of these processes in our conscious mind. Can you tell me how much serotonin you need at certain times during the day or under certain environmental pressures? Of course not, that process is autonomous.

Just like our reaction to, pain, or the "fight or flight" response, or sexual attraction to a potential partner. These are all chemically driven responses to the environment for protection or procreation of self that never even make it to your conscious mind, hard wired from our ancestors, reaching back billions of years to the very analogs of the bacterial colonies we discussed last week.

I talk about the conscious mind as a separate entity, and it is in a way; there is a definite section of the physical brain that it occupies. However, it is but one piece of our entire central processing unit (the brain) that has evolved to oversee the conglomerate of separate organisms we call the human body.

Originally published here.

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>Listening in on Our Ancestors

Oct 18 2006 Published by under Evolution, Links, Physiology

>What if I told you that with all the structural complexity of our language-written and vocal-at its very base, is no different than communication between bacteria?

It is not too foreign of a concept, considering that the beginnings of life were in fact bacteria, which congregated into giant colonies, forming structures called stromatolites 3,500 million years ago. These stromatolites lined the salty, otherwise lifeless beaches of the planet, rising to heights of dozens of feet, monuments of a greater future under a new sun. Communication between these organisms was necessary for any attempt at joint effort.

Are we any different? Basically our bodies are nothing more than the result of the cooperation of tens of trillions cells passing information-genetic and chemical-to regulate the macro organism, the human being. Every cell is connected, streaming all sorts of vital information-regulation of nutrients, presence of outside stimuli, reaction measures and presence of alien substances.

Recent research exploring colonial bacteria has illustrated the level of linguistic complexity within these colonies. Modern theoretical linguistics has opened studies of communication in many fields, including biology, and given us a view of language as entirely structural; "words" (or chemical signals analogous to words) have no inherent meaning, only the meaning that one applies to them.

From an evolutionary perspective, this rings true. There are myriad examples of one structure becoming useful in another function (exaptations): lungs becoming useful as swim bladders, sturdy fins become useful as walking legs, insulating feathers become useful in staying aloft, etc.

The same goes for biochemical elements. A molecule by itself has no inherent function until it is contextualized, placed in a functioning system.

Communication among bacterial colonies is incredibly complex. They exhibit the same basic social intelligence observed in human beings. (Social intelligence is a term applied to the functions of the mind outside of academic pursuits, specifically the exchange of information to organize in groups, and therefore exhibit a group identity.)

Experiments have exhibited specific examples of such behavior. The phenomenon of antibacterial resistance (a looming, potentially catastrophic problem in the future) has provided scientists with a chance to observe colonial propagation in the face of destruction. The bacteria resistant to the agent are able to exchange chemical information among the survivors, relaying their dire situation. The individuals respond in concert, immediately initiating conjugation. The colony begins replacing the lost members with new, resistant ones.

They identify in this manner as one organism. Mass communication has allowed the United States and other information age nations to respond similarly to catastrophic events. September 11 comes to mind.

The complexity deepens. In starvation conditions, most bacteria are able to assume the form of spores (through sporulation). These spores are incredibly durable (many can survive the vacuum of space), and do not need to feed in order to persist. When conditions become favorable again, the bacteria can change back into a fully function individual. In colonial species, the bacteria can detect the nature of the environment (food or no food) and notify the rest of the colony by releasing biochemical messages. Each individual is able to receive the message, evaluate the circumstances and "vote" on whether or not the colony should sporulate.

Species-specific communication within the colony has to be fine tuned and complex since, in the natural world, colonies coexist with dozens of other colonies of other species, sending their own messages in their own languages.

Our mouths are a perfect example of this. At any given time, you have about 20 species of bacteria inhabiting the tissue of your gums, each trying to organize feeding and procreation (at least until the next time you brush). Their messages need to be clear and purposed-as scant molecules among trillions-to extend the life of the colony.

These are just a few examples among dozens (among hundreds as more research is done). The entire story, however, cuts deeper, closer to home.

In each one of these cells lies the secret to our success: energy producing structures called mitochondria.

Mitochondria generate the flow of energy that makes everything possible, gleaning ions from the constant stream of nutrients into our mouths, absorbed through our digestive tract. They have made our lives as multicellular, eukaryotic organisms possible.

Mitochondria have their own genetic information, their own blueprint for life, distinct from the blueprint for our own body, making them the odd structure out in the plan of the cell. So odd, in fact, that scientists think that this is enough evidence to posit the mitochondria as a benefactor from the ancient past; in essence, the mitochondria is a separate entity in the cell, a life giving, incorporated bacterium in each of our cells.

We have not left our past behind. Our lives depend on it.

Originally published here.

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>What's Reflected, What's Absorbed

Oct 14 2006 Published by under Evolution, Links, Microbiology, Physiology

>I've been on a serious pigment kick lately (reinforced by my little art excursion last night and my review of all of the fall leaf literature), and rhodopsin came to mind, a light absorbing pigment found in animal eyes, archaea and bacteria (often referred to as bacteriorhodopsin in the case of the archaea).

While chlorophyll is capable of absorbing red and blue light from the sun for much of the year (all year for evergreens), bacteriorhodopsin can absorb wavelengths that much of the plant world reflects, from 490 - 550 nm, or the color green (see chart below).


Bacteriorhodopsin is particularly widespread in the oceans. The depth of the photosynthesizing organism determines the wavelength of light most strongly absorbed; in shallow, churning waters, bacteria will absorb green wavelengths more readily, while blue wavelengths are favored in deeper waters.

When light strikes bacteriorhodopsin, it causes a change in the shape (conformation) of the protein complex, which in turn powers a biological cornerstone: the proton pump. Protons are moved between membranes, creating a gradient of pH and an energy potential. The energy created is in turn used to pluck phosphorus from a cell's cytoplasm to complete the most well-known energy transporting molecules, adenosine triphosphate, or ATP. ATP then can be transported from there for use as energy in any other system.

Photosynthesis runs on different organic systems in the archea, leading biologists to believe that photosynthetic machinery must have evolved twice: once in the archaea, and once in bacteria (cyano; the discrepancies lie in the ETC and in the fixation of CO2 into glucose).

Heather's had her first "core review" session this morning (a pass/fail panel review of her work and one of the reasons I've been delving into pigment), and it went extremely well. I'll post some pics of her paintings at some point today or tomorrow.

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>A Few Early Morning Links

Oct 10 2006 Published by under Evolution, Links, Paleontology, Physiology

>PLoS Bio: Looking into our biological future...

Seed: N. Korea's underground nuclear tests...

NY Times: Giraffe-sized camel fossil discovered in Syria...

The Loom: A short history of Homo floriensis (the "hobbit" hominid), including a review of recent research...

Science Daily: More on Homo floriensis (a new paper suggests that the hobbit was merely a modern human suffering from microcephaly)...

Darren Naish: Tetrapod Zoology: The origins of the domestic dog. Awesome post...

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>Flipping the Aging Switch

Oct 07 2006 Published by under Genetics, Links, Physiology

>Researchers at HU and NCU have found a gene in stem cells that actually "turns off" replication. They noticed a dramatic increase of expression from Ink4a in aging subjects - 10 to 100 times the expression of younger subjects.

Ink4a actively interferes with the ability of stem cells to divide in several different types of tissue, including the brain, the pancreas, and the blood-forming system of the bone marrow.

Under optimal circumstances, stem cells are able to copy themselves and differentiate into other cells, thus replenishing their numbers and acting as a repair system for the body. The Ink4a gene appears to be widely active in locations where stem cells regenerate new tissues.

Presumably as a regulator. Morrison, Sharpless and company suggest that synthesizing medicines to alter the expression of Ink4a could bolster our "defenses" (replication and neurotransmission) against aging.

One gene, one medicine?

Though mice with Ink4a deleted had more regenerative capacity in tissues like the brain and the pancreas as they aged, they started dying of a wide variety of cancers at one year of age. So it can’t really be said that losing the gene helped them live longer.

"If you had a drug that could inhibit Ink4a function, you’d potentially have a therapy against degenerative diseases," Morrison said. "But you’d have to watch patients carefully for cancers. By the same token, drugs that mimic Ink4a function could be used to fight cancer." Ink4a was known to be a tumor suppressor gene that becomes more highly expressed with age, eventually triggering the cell to shut down replication.

*shrug* Every time I have read a statement like that from a geneticist (about medicines inhibiting or increasing expression of one gene) they usually turn out to be largely optimistic. These issues always tend to become more complicated.

The stem cells have a built in balance between replication inhibitors (Ink4a) and promoters (Bmi-1). Disrupting that balance doesn't sound like the best idea. Push too far one way and your body's regenerative ability slows; push too far the other way and your body turns into a tumor machine.

It would, however, be advantageous if the balance and rate of expression at a young age could be maintained into adulthood and beyond (which is probably what Morrison is talking about; he just worded it strangely).

I am hoping that classes/homework/newspaper will lighten a bit this week so I can update here more frequently. Today I have a slightly-less-than-blank Quark template waiting for me in the office. The newspaper calls.

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>The Mythology/Biology of Fairy Rings

Oct 03 2006 Published by under Links, Physiology

>Fairy rings are regarded in legends across Europe and North America. In Wales and much of Britain, people thought the rings were leftover from the merriment of fairies. In Ireland they are associated with leprechauns. In Germany, witches gathered around the rings at night. In Scandinavian tales (from which, by the way, Tolkien borrowed heavily), elves danced among the mushrooms in meetings called älvdanser.

In reality, fairy rings are the result of the natural tendency of mycelium (the underground "spreading" portion of the organism) to spread out in a ring shape.

Think of the mycelium like a radar blip, slowly moving outwards in an ever-expanding circle. The only above ground signs of the movement are an early ring-shaped change in the color of the surrounding ground and grass (due to the decay of older mycelium, which releases nutrients into the soil) and a late "bloom" of the cap (basidiocarp) - the spore releasing fruiting body of the fungus.

These basidiocarps, which we call mushrooms, grow from the rings of mycelium, release spores in a circular fashion, perpetuating the fairy ring.


I stumbled on this fairy ring just a couple of weeks ago, just outside of the student union at FSU. I ran around campus (and back into the publications office) trying to find a camera while Heather waited patiently in the car.


I think it is Chlorophyllum molybdites, one of the species found in this area that tends to grow in rings. Chlorophyllum is poisonous, and causes much confusion [and indigestion] among its human and animal consumers:

Of the mushrooms generally considered poisonous, the one far most often consumed is Chlorophyllum molybdites. It is large and meaty; it resembles a generally choice edible, Lepiota (Chlorophylium) rachodes, it tastes good; and it grows in lawns and parks. Chlorophyllum molybdites quickly rewards the unwary with gastric distress, vomiting, and diarrhea lasting several hours.

Hopefully this week I'll be able to get back to the dinosaur/body temp discussion; it's been a crazy few weeks between the newspaper, tests, papers and labs.

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