Thursday, December 25, 2008

Christmas Tree Biology

I'm not a particularly big fan of Christmas insanity, and I have never intentionally purchased a Christmas tree greater than 10 inches tall, but this is the best "Christmas" themed topic I could imagine while trying to deal with sick kid and wife.

To start with...what is a Christmas tree (not going to assume anything here)?  The typical
 Christmas tree is an evergreen tree (Pinophyta or Conifera), typically a fir, brought inside and
 decorated with all kinds of shiny bright objects.  According to the, actually the U. of Illinois Extension Office, there are 36 million Christmas trees sold every year, and 73 million planted yearly.  That's a lot of Christmas trees, and they are planted at an initial density of over 2,000 per acre.  For comparison, in the state of Kansas, tree mitigation plantings are typically
 done at 640 trees per acre.  So we are talking some really high initial densities.  Of course anything sold by the millions will have government oversight.  Feel free to peruse the absolutely tedious USDA Christmas Tree Grades. (pdf warning...not that anyone's going to read that!)  Wow.  

About 95% of the real trees purchased come from farms.  According to the National Christmas Tree Growers Association, a few are allowed to be harvested from National Forests.  And let's take a moment here to appreciate that yes, there is a National Christmas Tree Growers Association and yes their 'Mythbusting' article is just as ridiculously snarky as anything I've ever read by a glorified PR firm.   The article is actually about the "Great De-Myth-ification Campaign".  I'll offer a quick summary:  Fake trees suck.  Although I'd prefer this message
 wasn't coated in a thin vaneer of hazy logic and silly attacks at the fake tree industry, I tend to think that environmentally, a real tree is probably a lot better.  

Why?  Well...As stated above, the real trees are grown on farms, and although it sounds like there are a lot of pesticides and other petroleum products used in their management, at least we're not talking about a completely manufactured product.  Of course, this is all a straw
 man...the real question is why have one in the first place?  Oh, you know, lots of culture and stuff.  Didn't I say I was going to talk biology?

I usually refer to conifer trees as evergreen trees.  Can anyone in the class tell me why that's not really a good term?  Yeah, that's right, because not all 'evergreen' trees are conifers.  Consider plants in the tropics:  None of them drop their leaves seasonally.   So let's stick with conifers.  

Conifers are typically distinguished by their leaves and reproductive organs.  The leaves are usually thin and waxy, allthough some are more like scales (see examples).  These leaves minimize water loss and maximize light absorption (especially in cold and dry climates).  As expected, almost all of them keep their leaves year-round even in temperate or northern climates, but a few do not.  Conifers tend to do better in cold or arid climates (i.e., northern or high altitudes) and can get really really big (Giant Sequoia).  I don't know anything about the evolutionary history of conifers, and nobody on the web is really giving me a lot of info on this.
  The best I can say is that conifer-like plants emerged around 300 million years ago.  There are currently ~700 species of conifers, which is actually a really small number for such an
 ecologically important group of plants.  By comparison, there are estimated to be 250-400,000 species of angiosperms.  Wow.

A typical Christmas tree takes about 7-10 years to grow.  Out of the 2,000 per acre planted, only between 750 and 1000 per acre will survive, which is still a heck of a lot.  Keep in mind that just because a plant is chopped off at the base and stuck in your living room it is still alive.  That tray at the bottom of the tree isn't just for the dog and cat to drink out of, its to keep your tree living.  Firs tend to not lose their needles easily even after dying and drying, but other species will, and keeping the trees well-watered will reduce that.  You'll also get more of the 'tree smell' that so many people (myself included) find awesome.  

I know that was a sorta non-sciency post, but I've been busy and its Christmas.  Merry Christmas!

Thursday, December 18, 2008

Species Profiles: The Bald Eagle

The process of listing and de-listing a species in the state of Kansas is both confusing and simple.  If a species is listed by the feds, it is automatically added to the Kansas list (if it is an animal).  On the other hand, if a species is de-listed by the feds, the species must be petitioned to be delisted in Kansas.  For most people I talk to, their reaction to this is that's stupid.  As I've discussed elsewhere, often there are very good reasons to continue to protect a species in one area that may be far from threatened elsewhere.   

However, the most recent round of petitions for listing or delisting species in the state of Kansas is now up for review, and the Bald Eagle (Haliaeetus leucocephalus) has been the subject of delisting petition (along with the Peregrine Falcon and the Broadhead Skink).  In my professional duties for KDWP I am not a part of the
 committee that determines listing or delisting of species, but I have heard that the Bald Eagle is likely to be delisted.  So I figure I better get a species profile of this popular bird up before it is out of my realm of interest.

How much introduction does a bird like this need?  Americans are well aware that the bird serves as a (perhaps the) national icon.  Less may be aware of Benjamin Franklin's scathing criticism of t
he bird (sources here and here):
I wish that the bald eagle had not been chosen as the representative of our country, he is a bird of bad moral character, he does not get his living honestly, you may have seen him perched on some
 dead tree, where, too lazy to fish for himself, he watches the labor of the fishing-hawk [osprey], and when that diligent bird has at length taken a fish, and is bearing it to its nest for the support of his mate and young ones, the bald eagle pursues him and takes it from him.... Besides he is a rank coward; the little kingbird, not bigger than a sparrow attacks him boldly and drives him out of the district. He is therefore by no means a proper emblem for the brave and honest. . . of America.. . . For a truth, the turkey is in comparison a much more respectable bird, and withal a true original
 native of America . . . a bird of courage, and would not hesitate to attack a grenadier of the British guards, who should presume to invade his farmyard with a red coat on.
That bit about the turkey, it doesn't necessarily come from Franklin's support of the turkey as a national bird, but 
rather from the poorly drawn seal from the early continental congress (shown below).  The Eagle was also an important bird for Native American Mythology, although the Golden Eagle (Aquila chrysaetos) was probably much more abundant throughout the continent.  

All eagles fall into the Accipitridae family, although where they fall is a matter of some dispute.  As befits one of the most well-studied species in North America, relatively more is known about the bald eagle than some other eagles.  Bald eagles fall into the Sea Eagle category, and are almost morphologically indistinguishable from their nearest living relative the White-tailed Eagle (or just Sea Eagle).  That species pair diverged from other eagles ~10-20 million years ago. 

This bald eagle killed a whale!  Or found one dead on the beach...Same difference.

I tend to get very bored when talking about birds because I have poor eyesight and don't really see them very well out in the field.  So let's talk about why I and many other people have no problem seeing lots of small birds (e.g., sparrows, swallows, cowbirds, etc.) and hardly ever get to see a bald eagle or heron from close up.  Surprisingly enough, it probably has a lot to do with energy kinetics.  

See, smaller birds, mammals and lizards tend to contract their skeletal muscles faster than larger birds, mammals and lizards.  In the case of birds, this means faster (and more powerful) wingbeats per unit muscle in a sparrow than a bald eagle, so a bald eagle has to pack on a lot more muscle to get the same amount of acceleration.  All that extra muscle means that big flying birds exist right at the limit of being able to fly at all.  So those big birds end up using a lot of 'runway' to get off the ground.  I'm sure everyone has seen a duck or goose running across a pond or lake before taking off.  Those birds are not only big, but they are heavy, and built for long migratory flights across continents.  

As a result of all that, the proximity that triggers a flight response from a bird varies tremendously.  Small, mobile birds can get off the ground and out of danger very quickly, whereas a bald eagle takes a few moments, and a goose takes even longer.  So a sparrow will let you get a lot closer than a bald eagle.  This is also why you occasionally see a few small birds harrassing a large hawk.  The hawk is simply incapable of manuvering its bulk around in the air fast enough to deal with the smaller birds.  

Back to Bald Eagles?  Ok, sure.  The Bald Eagles are top predators, and primarily fish eaters (as the whole Sea Eagles thing implies).  They tend to stick to major river corridors in continental interiors and congregate along coastlines.  Alaska has the largest population of existing Bald Eagles, despite a concerted effort by salmon harvestors to kill them off in the early 1900s.  In general, the eagle was the subject of human harassment and competition, and dramatically declined from pre-Columbian levels as the United States became more populus through the 1800s and into the early 1900s.  Protection for the Bald Eagle was first enacted long before Federal Threatened and Endangered Species laws, by the Migratory Bird Treaty and the Bald Eagle Act.  

Those laws might have worked to restore Bald Eagles if not for the Greatest Generation's plan to kill everything on the planet.  What am I talking about?  DDT.  DDT is arguably a huge boom to mankind, since it basically eliminated malaria from large portions of the globe, but it also caused dramatic and unanticipated impacts on human and environmental health.  The overuse of DDT and similar pesticides essentially created the modern environmental movement (see Carson, Rachel), and lead to the passing of the federal Endangered Species Act.  

Unfortunately, since its passage, the ESA has been more-or-less continually gutted in favor of economic conerns, and only a few species have ever been successfully removed from the Endangered Species list.  (I could go on and on about why the ESA isn't a great idea, but the reality is that it isn't a terrible idea either).  On June 28th, 2007 the Department of the Interior announced the Bald Eagle was going to be delisted, which came as little surprise.  The Eagle's numbers have been rising dramatically in recent years.  I've personally seen over 20 in the last year despite living in Kansas, where they are very scarce.  

I even saw one today.

Thursday, December 11, 2008

Reptiles: Because I'm out of good ideas

I've got some projects in the pipeline, but none of that is ready yet. So let's talk about does that sound?

Reptiles are air-breathing, four-legged, cold-blooded amniotes that live everywhere but the polar regions. Everyone knows what a reptile is, but oddly enough, the taxonomy is a little more confusing that we might otherwise think. To understand why, I'm going to introduce two terms: Monophyletic and paraphyletic. Basically a group is considered monophyletic if it includes all the animals desended from a common ancestor. If you take a monophyletic group, and remove one of the decendents of that common ancestor, then you get a paraphyletic group.

Full of confusion? Ok, let's put it another way. Below are all the vertebrates. If we highlight a group that includes reptiles and birds, we've got a monophyletic group (sometimes called a clade).

This figure shows our best understanding of evolutionary connections. The earliest common ancestor was some kind of vertebrate, which split into tetrapods and pisces (fish). You can see tetrapods split into amphibians and amniotes.

On the other hand, the group 'reptiles' as we commonly understand it, isn't a monophyletic group. Take a look:

The term reptiles doesn't include all descendents from a common ancestor because the are believed to be part of that lineage as well. The reason this is a little weird has to do with the way humans percieve these groups of animals. Birds and mammals are 'good' animals. Reptiles and amphibians are "slimy", creepy or scary. Yet these are very different types of animals. As you can see in the figures above, they aren't even that closely related.

This perception problem is pervasive in the sciences as well. Take herpetologists. Herpetologists study reptiles and amphibians. The only real commonalities are that they are cold-blooded and generally smallish. Is this really a meaningful basis on which to lump these otherwise very different groups together? (

Ok, but let's get back to reptiles. I've repeatedly used the term amniote without really explaining it. Maybe I should fix that? Amniotes are animals who's embryo is surrounded by protective membranes: They lay eggs that could survive on dry land! This improvement on eggs was the big development that separated the earliest reptiles and proto-mammals from the amphibians. At the time, amphibians were the masters of the terretrial terrain. However, amniotes were able to exploit a lot more land, and eventually began to displace amphibians as large, dominant herbivores and predators.

Reptiles, or at least, creatures that we would look at and think "reptile" predate mammals, and therefore you can safely consider mammals and birds specialized reptiles, if you feel like it. Those of you who think I'm crazy: Its right there in the family tree!

What did an early proto-reptile look like? Well, according to Wikipedia, Hylonomus is a good guess for one of the first reptiles:

Oh my gosh! It looks like a lizard!

Yeah, that was predictable huh? There are only 4 classes of reptiles left today (if you don't count mammals or birds). The crocodiles and the turtles are two of those classes. The third one is everything else you think of as a reptile: Snakes, lizards, mosasaurs (these are squamates). Unless you're amazing or a herpetologist, you probably have never even heard of the 4th group of reptiles. Why? Because (this is going to be a huge shock) even if you saw it, you'd just think it was a lizard.

I'm talking of course about the order Sphenodontia, a once hugely diverse order that now contains just a single species: Tuatara. And if you know anything at all about how the world works, you know this single remaining species of a once-great order is on the verge of extinction thanks to something mankind did. Fantastic. In this case, we brought rats to New Zealand.

Tuatara is a pretty ridiculously interesting animal. Like the last surviving member of any ancient lineage, people tend to refer to this species as a 'living fossil'. However, this has always been a hopelessly stupid thing to say. The implication is that the animal hasn't changed in the thousands or millions or tens of millions of years since our first fossil record. The likelihood of this being the case is incredibly small. Animals evolve to survive changing conditions, and there is basically no-where in the world that hasn't had changing conditions over the last 220 million years. Hence, this species had to have evolved. In fact, these guys (whose work I can't get anywhere) apparently found that tuatara is changing more rapidly than any other species tested.

Ok, aside from that tuatara has a third eye, incredibly primitive ears, and a fish-like spine (all unique or rare among reptiles). And now let's go back to reptiles.

There's a lot about reptiles is amazing, but I'm just going to talk about one more thing and leave it at that. Basically: How do they breath?

This seems like an obvious question. After all, we all instinctively know how mammals breath, and if you dig around the medical literature, you'll find talk about a diaphram and muscles causing your lungs to expand and contract.

Of course, this is how reptiles do it too, but in the case of the squamates, those muscles are also locomotion muscles. So when a lizard starts running, it isn't breathing. I haven't found anyone who says this, but I imagine this is why you see lizards making short bursts from hiding place to hiding place. The crocodilians breath differently. Like mammals, crocs have a diaphram (although it works a little differently). Turtles are where it gets really interesting. I don't know how many of you have seen a turtle, but they have a hard shell. Exactly how do you get your lungs to inflate and deflate if they are attached to a hard shell?

Turns out, different turtles do it differently. For the most part, there are two sets of muscles: One that pushes everything inside the shell out, and another set that pulls everything outside the shell in. Expand-contract. You get the idea. These muscles might interfere with locomotion, or they might not, depending on the species. You may also think: Aren't there a lot of aquatic turtles? Why yes, yes there are. And since you asked, some of them appear to breath from the butt.

Don't worry though. They aren't drinking from that oriface.

Well, that turned into a sufficiently bizarre post. Hope everyone enjoyed!

Anonymous Rattlerjen said...

Fantastic post on reptiles, and fund to read.
Turtles and tortoises do drink from their cloaca (yes, the bottom or aka anus). Many turtle species cannot "drink" unless they are sitting in water!
As for the breathing part, many aquatic turtles are able to hold their breath for a long time because they are able to absorb oxygen through their skin or cloaca. How weird is that!

As Rattlerjen points out, yes, its really the cloaca that turtles are able to respire from (butt is a non-technical term in this case :), although this is limited to side-neck turtles. However, I can't find any actual evidence to back up Rattlerjen's other claims. The paper I linked to previously (the link doesn't seem to be working, so the citation is below) actually demonstrates that cloacal drinking does not occur in a species that is able to breath that way. Anyone have any citations to share on other species?

Charles C. Peterson and David Greenshields. 2001. Negative test for cloacal drinking in a semi-aquatic turtle (Trachemys scripta), with comments on the functions of cloacal bursae. Comparative Physiology and Biochemistry DOI:10.1002/jez.1055

Thursday, December 4, 2008

Species Profiles: The Flathead Chub

Threatened and Endangered species tend to fall into one of the following categories: Rare to the point where they are never seen, abundant in certain locations, or just damned hard to find. The Flathead Chub (Platygobio gracilis) falls into that first category. For example, some researchers at K-State have been sampling the Kansas River for most of the last three years. In 2007, they pulled out >36,000 fish, but didn’t find a single flathead chub (Eitzmann and Paukert 2007). Needless to say, this one is on the list of Kansas T&E species that I haven’t seen.

The flathead chub is a member of the minnow family (Cyprinidae), otherwise known as the largest family of freshwater fishes in the world (~286 species in N. America alone). Like most members of this family, flathead chubs are small (typically 9-16 cm). This species has a relatively broad, wedge-shaped head with long, sickle-shaped pectoral fins. Coloration is greenish or brown on top, with plain, silvery sides. The species was first described way back in 1836 (McPhail and Lindsey 1970), although the name has changed a lot (the genus flipped back and forth from Hybopsis to Platygobio a few times from 1950-1989, so you will see some references to H. gracilis here and there).

This species has occasionally been broken up into two subspecies: A large-river variety (H. gracilis gracilis; primarily the Missouri) and a smaller stream variety (H. gracilis gulonellus; primarily in the Ark River drainages). The transition zone between these two subspecies was Kansas, and the possibility of distinct genetic lineages was disputed (some people disagree with designating these as subspecies). That question will probably never be resolved due to the species’ afore-mentioned “rare to the point where they are never seen” status in Kansas.

The absence of this species isn’t terribly surprising, although that doesn’t make it somewhat depressing. Like the Pallid Sturgeon, the Paddlefish, the Chestnut Lamprey, and a ridiculous number of other fishes, the flathead chub has been eviscerated as a part of the natural community in large portions of its range by the construction of impoundments. The species occurs widely throughout North America, but is only endangered in the southern extent of its range (see the pretty map from Natureserve). The large rivers in the Missouri/Mississippi Drainage have been extensively regulated, thus wiping out avenues for upstream migration, and also reducing the productivity associated with flood events and backwater areas.

Meanwhile, less regulated areas of the flathead chub’s range continue to support viable populations. In Wyoming, the occurrence of the chub may be declining (Patton et al. 1998), but at least it is still out there. NatureServe actually lists them as being ‘secure’ throughout Colorado, Nebraska, Wyoming, Montana, South Dakota and much of Canada.

Little is known about the spawning habits of this species, although in Kansas most spawning occurs between July 1st and August 15th. As an agency, Kansas Department of Wildlife and Parks is supposed to have a recovery plan for this species, but as yet none has been written. I have a hard time imagining such a recover plan that didn’t include propagation efforts, and KDWP currently does not propagate any fish species for non-game purposes. At this point, the agency primarily protects this species by restricting activities in waters where the species potentially occurs (the Kansas and Arkansas Rivers) during the spawning period.

Want to read more about this species? I recommend this conservation assessment by Rahel and Thel (2007; pdf).

Lit cited:

Eitzmann, J.L. and C. Paukert. 2007. Annual performance report: Distribution and Abundance of fishes in the Kansas River.

McPhail, J.D. and C.D. Lindsey. 1970. Freshwater Fishes of Northwestern Canada and Alaska. Fisheries Research Board of Canada, Bulletin 173. Ottawa, Ontario, Canada.

Patton, T.M., F.J. Rahel, and W.A. Hubert. 1998. Using historical data to assess changes in Wyoming’s fish fauna. Conservation Biology 12:1120-1128.

Rahel, F.J. and L. A. Thel. 2004. Flathead Chub (Platygobio grcilis): A technical Conservation Assessment. Rocky Mountain Region, USDA Forest Service.

Thursday, November 27, 2008

The Wisdom Teeth Edition

An adult human typically has 32 teeth. All but 4 of those teeth typically arrive during childhood, before the age of 10. The remaining 4 teeth are the mandibular third molars, more commonly known in English as "Wisdom Teeth". Wisdom teeth typically erupt from the gumline approximately between 18-20 years of age. The etymology of the name revolves around the idea that people get their wisdom teeth after they have gained some wisdom.

Where I grew up, and across much of the 'westernized' world, Wisdom teeth are removed during early adolescence or early adulthood as a purely preventative measure. Wisdom teeth that come in wrong in some way can lead to the crowding of other teeth, infection, impaction, and other problems. However, more recently, several studies have been attempting to determine whether preventative removal of wisdom teeth is appropriate. This summary in the Cochrane Library suggests that there is no reason to remove wisdom teeth until they are causing problems, although the data is apparently very limited.

In my case, the early prognosis from my dentists when I was in high school and college was that my wisdom teeth would come in with no problems. Considering both my parents had wisdom teeth problems, my sister did, and all my relatives on my mom's side did, I should have expected that these teeth would need to be removed eventually. Six years ago I had a wisdom tooth come in Mesioangular impacted, which means it came in facing the front of my mouth (see images on the Wikipedia article for reference). This is apparently the most common orientation of impacted wisdom teeth, and has the potential to crowd or damage the other molars. In my case, since I basically did nothing for 6 years, so I probably have some damage on my 2nd molar. Here's to hoping that's minimal.

I've been unable to find good data on what proportion of individuals have wisdom teeth that are impacted or the proportion that just have them removed (impacted or not). Some recent studies have suggested that even if they aren't causing obvious problems, they may be detrimental. WebMD suggests not removing them at all if you are over 30 and haven't had any problems. Partly this is because not all wisdom teeth pose problems, and partly it is because the older you are, the more the bones around your wisdom teeth have hardened and the longer and more painful the recovery is. Past a certain age, I imagine wisdom teeth are simply not removed.

A huge amount of variation exists among different human populations in the occurance of wisdom teeth (and in the number and arrangement of teeth in general). Citations in this PNAS study (which is really talking about the genetic controls over tooth formation) indicate a range from 0.2 % occurrence for Bantu speakers of Angola to virtually 100% in Mexican Indians.

The whole idea of wisdom teeth is a strong bit of evidence for the continued adaptation of humans to their environment. The exact mechanism for the changes in human jawbones is not clear, but it definitely seems to be related to diet (short discussions here and here). As humans began eating less coarse foods, the jaws began getting smaller, and the teeth (controlled by a different gene) did not have enough room to all fit in the jaw without problems.

I've actually known a number of people who've had their wisdom teeth function perfectly normally. When I was getting a blood test last week in preparation for my wisdom teeth removal, the lady who was taking my blood said that she lost her 2nd molar, and the 3rd molar (wisdom tooth) filled the opening this created and she got good use out of it for 20 years (eventually she had to have it removed...maybe she doesn't brush?). I've heard a few people whose wisdom teeth came in just fine, no problems at all. I'm not really sure how frequently any of these things happen, and I don't have access to very good medical journals.

I was fairly terrified about the prospect of getting my wisdom teeth removed. I've never been under general anesthetic before, and both my sister and dad have had some problems coming out of general anesthetic in surgeries they've had. Plus, there are a number of painful and annoying impacts of the surgery: Swelling, bleeding, and possible nerve or sinus damage. Problems which are more likely the older you are, and I've been feeling very old lately (I just turned 30).

I'm writing this on Tuesday, and I had the surgery on Monday, and I can tell you that my fears were vastly overblown. The surgery itself was brief, painless, and even though I was partially aware during the procedure (turns out it is not a true general anesthetic), I felt no pain or nervousness once sedated. Yesterday I felt great when I got home, and have have very little lingering pain. Today, especially this afternoon and evening, have been a lot more painful, but I think part of that has had to do with me wanting to avoid the pain meds as much as possible. I've also not eaten much, simply because I'm already sick of ice cream, yogurt, smoothies, etc.

Overall, if you're considering this surgery at the advice of a dentist or doctor, I recommend you do it immediately. I've had several painful experiences in my life (ulcer, concussion, foot surgery) and this is no-where near that level of pain and discomfort. Its more like 'persistent headache' than 'injured'. I think that if you need it done, its probably better to get it over with as soon as practical instead of waiting (yes, I'm talking to you!).

Some other references and guides to the whole wisdom tooth removal process:

Thursday, November 20, 2008

So I went to a Mexican restaurant yesterday...

...And finally lost my mind with the menu. You probably have seen this menu. The menu is the same at almost every Mexican restaurant I go to. The specific item that has made me realize this is the Vegetarian Combo D: A bean burrito, a chalupa, and a quesadilla.

I know of 5 restaurants in Kansas, 1 in Texas, 1 in Oklahoma, 2 in Indiana, and 1 in Missouri that all have the same, exact, menu. The combinations are all the same, the lunch specials are all the same ("The Speedy Gonzales"), the appetizers are all the same.

Why are all these menus the same? (and yes, I realize this is a different topic for the blog but this is analyze EVERYTHING, not just "Analyze Animals")

My co-worker Eric Johnson and I came up with several hypotheses in our 9+ hours driving the last two days:

1. The restaurants are all owned or financed by the same firm.
2. Random chance (we'll call this the null hypothesis).
3. The food supply firms are selling/promoting this menu.
4. This is the menu all restaurants have in mexico. (which just pushes the question into mexico)
5. There was some 'immigrant worker' promotion years ago which started this and it has just been passed down.

I'm skeptical that this many restaurants all decided to label that particular combination of food items the "Veggie D". Mexican restaurants that don't have this menu (I know of several) generally don't have any Veggie menu at all.

Possibility 4 is one I can't get at, because I haven't spent any real time in Mexico. Anyone got any clues?

I am skeptical that a single entity finances all these restaurants across the country. Maybe something like this is happening, but how would these random guys who start the small town restaurants all over find the investors?

So I really think it comes down to 3 and 5.

The food service industry is the possibility I deem most likely. This thread on Chowhound seems to suggest this possibility, without having any direct evidence. There are only a handful of large-scale food suppliers in the country though: Dot Foods, Sysco, Keith, Hawkeye. I've been unable to find anything online that looks like this kind of menu being sold, but I'm sure they don't have everything online.

Quick Aside Here: The industry group that represents food suppliers (the International Foodservice Distributors Association) has an article on their website that is accompanied by pictures which, for reasons I can't even articulate, I find incredibly humorous ("Look at how serious I am"). Some of the quotes are equally priceless: "We are now insisting that they begin to bring their logistics people to our top to tops that we have with them throughout the year." That quote is repeated twice, so I doubt it is a typo, but seriously, does that mean something?

At any rate, I'm totally stumped. I asked reddit and got back a bunch of irrelevant gibberish. Anyone got any clues?

Thursday, November 13, 2008

Mosasaurs: Ancient Kansas Wildlife

There are few animals in real life that can capture our imagination the way some fossilized animals are able. Take for instance, the Tyrannosaurus rex, which has been fictionalized again and again to represent our more primal understanding of 'monster'. Take also, the beast that once roamed Kansas as the unquestioned top predator: The Mosasaur.

What? You've never heard of a Mosasaur? Imagine a crocodile with flippers and you're superficially there. See, way back around 100 million years ago the North American continent was split by a vast epeiric sea (a shallow, salty, inland sea) called the Western Interior Seaway (really creative science people).

The whole physics and biology of the Western Interior Seaway and other epeiric seas is pretty amazing, and we'll get into that later. For now, let's just focus on what is known: The sea was shallow (for a sea), probably extremely productive, and was fed by mini-continents on either side. In limnology we tend to think of shallow waters as being the most productive, because of the ability of rooted plants to grow. I think the same is true of shallow seas, but I don't think it is for the same reasons (any oceanographers care to enlighten me on this?).

Anyway! The top predator of this inland sea and the ocean at large became the mosasaur (pictured below). Although this is a reptile, this isn't a dinosaur, and it isn't a crocodile. Think lizard. In fact, think monitor lizard (Family Varanidae), which includes the still living and awesome Komodo dragons and the recently extinct Megalania (the feared giant lizard of Australia). Many modern monitor lizards are highly adapted for living in and around water (e.g., water monitors), and so it isn't hard to imagine a scenario wherein these amphibious lizards took the next evolutionary step and became aquatic.

And become aquatic they did! Unlike turtles, crocodiles, walruses, and quite like whales and dolphins, the Mosasaurs gave birth at sea, to live offspring. The arms and hands of this species developed into flippers and became somewhat detached from the backbone (meaning they could not support their own weight on land). Pull this lizard out of the water and it would asphixiate.

One of the many interesting things about this invasion of the seas by lizards is that they weren't exactly getting themselves into an unoccupied niche. The first real mosasaurs occurred in the Cretaceous, and by 90 million years ago (MYA), we had three big subfamilies with lots of known species. However, way back in the Jurassic reptiles had already colonized the oceans with the famous plesiosaurs (think the mythical Loch Ness Monster) and of course the everpresent sharks had managed to come up with a particularly devastating breed (the Ginsu sharks) and you had other random nastiness lurking out there (just don't go swimming in the Cretaceous). Nevertheless, the Mosasaurs got really big and are generally thought to have been the top predator.

The reason I started getting interested again in Mosasaurs was an interesting paper by Mike Everhart published in the latest issue of the Kansas Academy of Science. The paper explores the occurence of mosasaur on mosasaur violence. And for something that happened 90 MYA, we can actually figure out quite a bit. Everhart was able to, fairly convincingly, estimate the size and mass of the attacker and the way in which it bit down on the victim.

A plate depicting the first Mosasaur discovery. The name is from Latin Mosa meaning the 'Meuse river' in the Netherlands, and Greek sauros meaning 'lizard'. The first specimen was found in a Meuse limestone quarry.

The way Mosasaurs ate is interesting, and has lead to some debate about the origin of snakes. Mosasaurs, unlike sharks or dolphins or most other big predators we're familar with, didn't have teeth that cut, just teeth that crushed. As a result, Mosasaurs either had to bite their prey in half (although this might have been possible, the family lacks the heavy skull that is common in crocodilians, making this somewhat unlikely) or swallow it whole. In order to maximize the food consumption, the Mosasaurs apparently had a somewhat hinged jaw that has lead many people to think: SNAKES!

Indeed, the theory of a shared snake and mosasaur marine ancestory has recently been in vogue, although it was first proposed in the 1890s (it's called Pythonomorpha if you're curious). The idea of snakes evolving from water lizards sounds inherently unlikely to me (why evolve flippers if you are just as good off just getting rid of limbs altogether?). Luckily, I don't need to push my uninformed logic, because apparently more recent fossils have shoved this theory to the wayside (read the link on the Phythonomorpha to get a better understanding). You can rest comfortably, however, knowing that this issue will continue to be fought bitterly by individuals committed to one side or the other until they die, at which point the next generation of paleontologists will find some other issue to argue about. And you thought politics lasted forever.

Mosasaurs have been found with a variety of food items in their stomaches: Mostly fish, but also a plesiosaur, other mosasaurs, turtles, birds, and sharks. I know sharks are fish too, but at least some species of sharks appear to have gone extinct as the mosasaurs became more prominent, suggesting they might have out-competed them (via direct predation?). Some species appeared to specialize on clams, and at least one late evolving species (Leiodon) managed to evolve teeth that cut. All of this evolutionary achievement probably put the Mosasaurs at the top of the oceanic food chain for around 20 million years before the K-T event happened and the entire family was wiped out. According to Everhart:

"Mosasaurs ruled the oceans of the Late Cretaceous and were beginning to invade fresh water environments such as estuaries, swamps and rivers when the Age of Dinosaurs ended. Did they die suddenly due the catastrophic effects of an asteroid impact in the Yucatan, or was their extinction more gradual following the general collapse of the marine ecosystem? We may never know."

Everhart doesn't mention a third possibility, which is that they are still out there and we just don't know it. Seriously, don't go swimming in the ocean.

Thursday, November 6, 2008

Is it (energetically) cheaper to can or freeze?

I know some of you had a garden this summer. And you were probably thinking to yourself “Man, what the hell am I going to do with all these zucchini?” I’m grateful that so many people overplant, because lots of people gave me excess zucchini. However, I was eventually faced with a quandary about the best method of preservation.

I was thinking about the carbon footprint of different foods, and how the processing affects that carbon footprint.

For instance, if I walk out to my garden and pluck two tomatoes, and just slice one up and eat it, I’m not really increasing the carbon footprint of the tomato. If I take the other one and fry it, I’m obviously using more energy to cook it, and therefore I’m increasing the carbon footprint of my food just by the way I process it.

Thinking about this is actually pretty huge, and I’m going to focus in on one particular aspect of processing: Preservation.

I’m going to focus on peaches, because I preserved 25 lbs of them this summer using a variety of methods. Peaches can be canned relatively easily (without a pressure boiler), and can be frozen equally easily (adding a little anti-browning agent keeps them from turning dark). Figuring out the carbon footprint between different energy sources can be difficult, so to simplify things, I’m just going to compare electrical usage.

The equation should be pretty simple really. We want to estimate the energy used per day of storage via these different methods: The electricity used divided by the duration of storage. For canning, almost all of the energy use will be up-front, and the longer you store the cans, the better overall energy use rate you get. On the other hand, foods stored in the freezer will continue to cost energy as long as you preserve them, so long storage times will lead to bad energy efficiency.

So here's the data I collected for this little exercise. Basically, I needed to figure out the energy cost to keep a pint of peaches frozen. I used dedicated freezers because A) its a hell of a lot easier and B) I've been thinking about getting one. I've cut some of the significant digits off to make this a little more legible, and I'm not going to give you the brands of the freezers, because I don't think it really matters much.

chest chest upright upright

Energy per year 274 279 442 582
Energy per day 0.731 0.744 1.179 1.552
Capacity in cubic feet 6.8 7.2 14.2 15.8
Peach pints per cubic foot 59 59 59 59
Peach pint capacity 401.2 424.8 837.8 932.2
energy per day per peach pint 0.0018 0.0017 0.0014 0.0016

Ok, so now we've got an estimate of the energy used per day to store peaches in these freezers. Now we've got to figure out what the energy costs of canning the peaches are on a per-pint basis. This becomes a little bit of a problem. The cooking phase has a limited capacity: My boiler only holds 5 pints at a time (for instance). So really, I'm going to assume you're canning in the appropriate increments. I had a hard time actually finding data on my stove, so I just used the data from a 2600 watt replacement burner. Remember, for most canned foods you have to first sterilize the jars and lids (for ten minutes), then heat the food, then process the cans.
So I opted against figuring out the units of energy that would actually be required to do this work, because I've found that I usually just have to crank my burner on high or close to high for the entire time I'm doing the sterilizing, cooking or processing. Therefore, I'm making a worst case scenario here for the canning. Although I'm making a best case scenario in terms of getting 'even' numbers of cans per process. Regardless, here are my estimates of the energy used to can:
Burners 8-inch burner
Energy consumption 2.6
Sterilizing jars 0.166
boiling peaches 0.333
processing jars 0.333
kilowatt hours 2.1632
Peach pints per process 5
kW/h per pint 0.43264
# of Pints 15
Total energy for canning 6.4896

Ok? So what does this mean? Like I said, the critical part here is how long you actually store the food. Let's take a look at a graph demonstrating this:

What we're seeing here is the estimate of energy use through time. Obviously, the canning doesn't change. Once you've done the canning, you're done. On the other hand, the freezer gets progressively worse through time. However, it takes a surprisingly long time for the freezer to get more energetically expensive. Between 8-10 months depending on the brand.

Obviously, there's a lot of wiggle in these numbers. My estimates on the freezer assume that the entire freezer is in use (if not for peaches, then for something) and if this isn't the case, then your energy cost per unit goes up. Let's look, for example, at a scenario where the freezers are operating at 80% capacity:

Now we're talking about a 6-8 month time-period where freezing is more effective. However, we've still got a lot of assumptions built in here. For one, each time you remove a can, but do not turn off the freezer, you've got to replace that can with something, or you'll be incrementally be increasing the cost per unit to keep the other ones cold. The decision to use a freezer is committing you to an unknown proportion of energy going towards keeping empty space very cold, and unless you're willing to turn off the machine and eat the remainder at some point, you could end up with some really bad efficiency. On the other hand canning uses only the resources necessary to preserve the food you've got.

The other set of assumptions revolve around manufacturing costs and cleaning costs being approximately equal.

So now that I've identified all these problems, I'm a little less sure about my result. I think that if you already own the jars and the freezer, this analysis gives you an idea of how best to utilize them, but I think in terms of the original question, I'm going to have to dig deeper.

Thursday, October 23, 2008

Scientific Misconduct (Part 1)

This is something I've previously published elsewhere. But I was thinking about it the other day, and I think it fits in with the overall content here. Oh, and last week didn't happen. This series will be continued, although I don't know when. :)


The use of the scientific method has, to put it succinctly, completely revolutionized the modern human experience. However, the underdiscussed backbone of this method is its dependence upon two critical components: A larger scientific community and a generally honest set of scientists. The larger community is necessary to provide critical review and to duplicate results. The honest individuals are necessary to prevent tremendous amounts of time and effort from being wasted running down dead ends.

These two critical components have, on occasion, broken down. The primary question is: What can we learn from these cases of scientific misconduct?

Scientific Misconduct by Individuals

In 2001, Jan Hendrik Schön (along with Hong Meng and Zhenan Bao) published a paper demonstrating that a thin layer of organic dye could be used as a transistor at the molecular scale. In this paper Schön claims “The fabrication of monolayer transistors and inverters might represent an important step towards molecular-scale electronics.” The paper is compelling, offering demonstrations of molecular structure and transistor characteristics of the materials he used.

Unfortunately, the results were a complete fabrication. In an editorial published along with the retraction of this paper, Nature questions what was going through Schön’s mind when he decided to fabricate his results.

“Was he trapped in a spiral of expectations that could only be fulfilled by deception?” (“Reflections on scientific fraud”, Nature, 2002, Vol. 319, p 417)

In the case of Schön’s work, the first hint that something was suspect came when someone noticed that the figures from several of his papers were identical. Following a lengthy investigation by Bell Labs (Schön’s employer), Schön’s was fired, his co-authors were exonerated, and journals were informed of the results. At the end of the 127 page report detailing these findings (which is no longer available through Bell Labs website), Schön responds to these findings:

“Although I have made mistakes, I never wanted to mislead anybody or misuse anybody’s trust. I realize that there is a lack of credibility in light of these mistakes, nevertheless, I truly believe that the reported scientific effects are real, exciting, and worth working for.”

The case of Jan Hendrik Schön is probably the most extreme form of scientific misconduct available to an individual, but it is certainly not the only form. Scientific misconduct generally falls into one of three larger categories: Fabrication, plagiarism, or ethical misconduct.

Fabrication such as that practiced by Schön has been rarely reported. Data on misconduct is scarce, but of 30 cases of scientific dishonesty reported by Denmark, just 2 were labeled ‘fabrication’ (Riis, 2001, J. of Clin. Pathology). A survey of just over 3,200 scientists being funded by the National Institutes of Health found that 0.3% had falsified data and 6.0% had failed to present data that contradicted one’s previous research. Even within the category of fabrication, often the kind of fabrication taking place is not as severe as that seen in the Schön case. Take, for example, the case of Dr. Robert Millikan.

Dr. Millikan was a physicist born in 1868 and prominent throughout the turn of the century. His greatest claim to fame is the oil drop experiment he did that established, once and for all, the charge on an electron. The experiment consists of balancing a small droplet of oil between a manually adjusted electrical field and the gravity of the earth. Since the gravitational field is known, and the electrical is known, the charge of the oil droplet can be calculated. What Millikan found was that the charge of the droplets was always a multiple of a single value: The charge of an electron.

When Dr. Millikan originally published his results, another scientist, Felix Ehrenhaft, published contradictory results suggesting a charge smaller than the electron charge existed. Millikan returned to the lab to obtain more precise results, and that is exactly what he got.

As it turns out, those precise results were partially the result of subtle data manipulation. Millikan measured close to 175 drops over the course of several months, but he reported the data of only 58 and claimed they were measured over 60 consecutive days. Some of the 175 could be legitimately removed due to obvious malfunctions in the machine used to conduct the experiments, others seemed to be removed solely to reduce the error in his final measurement. That these drops had gone unreported was not discovered until years after his death and upon closer examination of his lab notebooks. Millikan’s motivations were clear: He wanted to establish his reputation as a premier scientist. By selectively choosing the data he presented, he reduced his error by an order of magnitude and dismissed the objections of other scientists. In this case, his theories and results have proven accurate.

Another example of scientific misconduct demonstrates just how difficult it is to ascertain whether or not anything inappropriate has occurred. Gregor Mendel is commonly called the father of modern genetics. He lived in the latter half of the 19th century and raised pea pods in a garden in his monastery. Mendel’s primary contribution to science is the description of how traits are inherited. In 1865 Mendel published “Experiments on Plant Hybridization” in the Proceedings of the Natural History Society of Brunn, a minor journal in Moravia. For the next 35 years it was almost completely ignored, then in 1900 Carl Correns rediscovered the work and forced other scientists to acknowledge its significance. Gregor Mendel’s place in history was firmly establish over a decade after his death.

Almost immediately the scientific community noticed that the results Mendel got were too good to be true. W.R.F. Weldon, in a 1902 paper, noted using the newly developed χ2 test revealed Mendel’s results to be astonishingly close to the predicted values. In 1936 R.A. Fisher (in Annals of Science), showed rather convincingly that Mendel’s data must have been altered in some way. For the past 70+ years the debate has continued. Various explanations both plausible and apologetic have been put forth, from an eager-to-please assistant to selective acquisition of data to random chance. A review by Fairbanks and Rytting in the American Journal of Botany (2001) noted:

“There is substantial disagreement about his objectives, the accuracy of his presentation, the statistical validity of his data, and the relationship of his work to evolutionary theories of the day.” (p. 737)

Fairbanks and Rytting conclude that no real evidence that Mendel conducted misconduct exists, but this is far from a universally accepted interpretation. Other recent cases of fabrication can be similarly difficult to uncover. As authors Montgomerie and Birkhead lament in their 2005 article entitled “A Beginner’s Guide to Scientific Misconduct”:

“Indeed it should be possible for a clever scientist in our field [behavioral ecology] to fabricate all of their data without raising even the slightest suspicion...” (p. 21, Bulletin of the International Society for Behavioral Ecology)

Clearly, data fabrication is a problem of unknown extent upon which the scientific community can find little agreement. However, fabrication is hardly the only form of scientific misconduct that has been uncovered.

(Stay tuned for part II “Plagiarism” in the near future)

Thursday, October 9, 2008

Unionid Mussels

One of the most imperiled classes of animals in North America are the Unionid Mussels. There are 11 species of mussels on the Kansas Threatened or Endangered species list, and there are more that are definitely in need of conservation. Historically, these species were harvested for buttons (like on your shirt), and a massive industry existed within Kansas to harvest these species out of the Arkansas River, Verdigras River, and Neosho River (to name a few). Massive water quality issues compounded the mussel's decline through the early part of the 1900. Even into the 1970s, the mussel-rich portions of Kansas waters were experiencing massive fish kills due to runoff from feedlots and poor municipal water treatment facilities. Once the Clean Water Act came along and cleaned up the water (the importance of the CWA can never be understated), the surviving mussel populations were isolated by impoundments and low-head dams. Consequently they've been slow to make any kind of comeback. This is why KDWP is propagating mussels in an effort to circumvent barriers that are isolating them. The initial results of this are quite promising, but I should really save that for another post.

Regardless, last week I went out and did a mussel survey and relocation. A temporary stream crossing will be going across the Verdigris River, and we came to insure no mussels were harmed. In particular we were looking for the Ouachita Kidneyshell Mussel (Ptychobranchus occidentalis), and we were unsuccessful in finding it. We did find shells from 13 mussels, and live individuals from 5 (about 20 individuals overall), including a couple that are fairly rare. Hope you enjoy the pics:

The Verdigris River. If you look closely, you can actually see a lot of mussel shells on the stream-bottom and on the gravel bar even in this picture. There were literally thousands of mussel shells here.

A fairly common species, the Pistolgrip (Tritogonia verrucosa).

A smaller Pistolgrip and a White Heelsplitter (Lasmigona complanata complanata).

A Threeridge (Amblema plicata plicata). I got these confused with Washboard (Megalonaias nervosa), but I guess the key is the area where the ridges begin. In a Washboard there would be distinct 'patterning' there (the overall body shape is different as well). Incidentally, the three ridges are not characteristic (more ridges will form if the animal is given enough time to grow), but they were harvested for buttons only when they were large enough to have 3 ridges. These are thick, heavy shells that would probably make a lot of buttons.

We packed all the live mussels into a bucket and moved them upstream, so that erosion caused by the stream crossing wouldn't affect them. We also found some live Pimplebacks (Quadrula pustulosa pustulosa), Mapleleaf (Quadrula quadrula), and Bleufer (Potamilus purpuratus).

I didn't really dump them all in one location, but we forgot to take pictures of us putting the live ones back in the river. This is our 'creative recreation' of the event.

Thursday, October 2, 2008

No New Post Today

My plan is still to do these every Thursday, but over the last week the whole fam has been sick, including an ER visit for the baby. I'm exhausted, and I can't think straight, so no new post this week.

Wednesday, September 24, 2008

The Monster

There is no more obvious face of American environmental problems than the cow. In the name of cattle production the American farmer has damned up streams to create livestock watering opportunities, ripped out native grasses to plant brome and fescue, plowed under wetlands and riparian lands to plant alfalfa and hay, and concentrated them into a location so densely that rainwater becomes lethally toxic. Cattle production (or maybe just farming in general) is probably directly responsible for more species becoming extinct than any other human activity in North America.

But that doesn't mean the cow itself isn't a fascinating animal with a cool story. The scientific name of the cow is Bos primigenius (at least, that's my understanding...there's some taxonomy confusion here), and it was first domesticated back in the 6th millenia BC in Mesopotamia. The original animal is known now as the Aurochs and holy god is it a cool animal. Aurochs once roamed basically all of Europe and Asia, and were independently domesticated at least 3 times. This is particularly amazing if you read the following account by Caesar about the aurochs in Germany:

Gallic War Chapter 6.28, "...those animals which are called uri. These are a little below the elephant in size, and of the appearance, color, and shape of a bull. Their strength and speed are extraordinary; they spare neither man nor wild beast which they have espied. These the Germans take with much pains in pits and kill them. The young men harden themselves with this exercise, and practice themselves in this sort of hunting, and those who have slain the greatest number of them, having produced the horns in public, to serve as evidence, receive great praise. But not even when taken very young can they be rendered familiar to men and tamed. "

I've never seen much written about animals using domestication as a life-history strategy, but this is one species where it has obviously been an advantage. The domesticated aurochs (i.e., cattle) began wiping out the wild aurochs almost immediately. Humans found cattle to be incredibly useful animals: You can hitch your wagon to one to pull things, you can feed it grass and it will produce milk, and killing even a single adult will give you enough food for months. As a result, humans agressively aided the expansion of cattle at the expense of aurochs. The last known aurochs lived in Poland and were 'protected' by royal decree. Nevertheless, the last individual died in 1627 and its skull currently resides at the Livrustkammaren in Stockholm. Two brothers, Heinz and Lutz Heck, had the bright idea of recreating the aurochs back in the 1920s (oddly enough, as part of a Nazi propoganda campaign). Theoretically, this might be possible if all the original genes are still around, you would just need to combine them. The results of these efforts are the Heck cattle, and man, you need to look into this yourself, because there is no end to the awesome (see awesome picture below).

Modern cattle have been developed into distinctive breeds for different purposes. In the United States, a federal grading standard in 1927 somewhat stupidly lead to meat quality becoming associated with 'marbling', and so breeds like Angus and Hereford have been the ideal. Marbling was considered important primarily because it made farmers more money. Marbling happens because grass fed cattle are 'finished' on a grain-heavy diet. In particular, a guy named Alvin H. Sanders, editor of Breeder's Gazette, promoted this idea so strongly that it caught on with the Department of Agriculture. The stated purpose was to promote meat that was of high quality culinarily, but as it turns out, marbling contributes relatively little to the overall tenderness of cooked meat. The U.S. eventually altered the grading system to lessen the importance of marbling, but is still one of only three countries in the world that grade beef on fat content (Japan and Korea are the others).

Cattle are generally slaughtered between 15 and 24 months in the U.S. (usually closer to 2 years), while in Europe the slaughtering times vary with the culinary traditions (Italians: 16-18 months; 3-4 years in France and England prior to prion diseases). Generally these variations have to do with the toughness of the meat and the flavor, although a lot of both has been sacrificed on the alter of efficiency. For instance, most culinary applications value the flavor of grass-fed beef, yet in the U.S. the economies of scale and a traditional over-abundance of cheap corn have resulted in massive feedlots where cattle are raised for 4-8 months on grain instead of grass.

I've never eaten veal and I can't honestly say I see the appeal. Veal is essentially beef that tastes and feels nothing like beef. The longer an animal uses its muscles, the tougher and more colored the meat becomes. Veal are usually confined so they can't move and slaughtered before ever given a chance to eat solid foods. The result is meat that is pale, extremely tender, and delicate in flavor. My feeling is that if you want to eat pork, just eat pork!

Because cattle are so closely associated with humans, there is ton more information out there: Their relationship to other ungulates, the amazing amount of fish kills that they caused prior to the clean water act, and their impact on rangeland birds are all interesting topics. However, I just got back from vacation and this is all I'm going to write today.