Tuesday, December 28, 2010

The Light Side of the Road

Since I don’t own a scale, I can’t tell you exactly how much my bike weighs. But rest assured, it is heavy. It’s a secondhand steel-frame model purportedly manufactured by Sears department store, probably in the 1970’s. Friends complain of its unwieldy mass (particularly anyone hoisting it onto their car’s bike rack) and more than one person has suggested “upgrading” to something more modern. But I’ve bonded with the vehicle and strive to paint it in a positive light. Sure, it sucks carrying the behemoth up a flight of stairs to shelter when it rains. But overall, it’s a solid bike. Sturdy and hardworking. “And a comfortable ride too”, I tell the skeptics, “not like those flimsy featherweight carbon-frame bicycles that retail for ten times as much.” And so I eagerly put aside any ambitions of doing a year-end top ten science innovations/headlines/etc. list (you’re surely as sick of them by now as you are of holiday cookies) to report on this merry little piece from the British Medical Journal's Christmas edition, in which an anesthesiologist attempted to determine if the newer, lighter bikes had any advantage over their clunkier predecessors.

Being fortunate enough to have two bicycles available for his daily commute, the good doctor designed a simple experiment to examine which of the bikes was the more efficient way to get to work. Over a 6-month period, (winter to summer) he chose his bike for the day by flipping a coin. The riding time for each round-trip journey, as well as the top speed, was recorded by a bicycle computer. During the experimental period, Dr. Groves made 30 trips on the steel-frame (809 miles) and 26 trips on the carbon-frame (711 miles). * At the end of month 6, he totaled the data and, wouldn’t you know it, the older, heavier steel bike fared no worse than the shiny new one, which had been purchased for what is almost a month’s salary to an average person without an MD.

The author discusses several physical forces that can affect the cyclist; rolling resistance, drag and gravity. Rolling resistance (the friction encountered by round objects, such as bike tires, moving on a flat surface) is minimal on paved roads, so the additional work needed to overcome it is slight. The effect of drag (aka air resistance) on the cyclist is significant. However, drag is an odd force. It is independent of mass and instead varies relative to velocity. More velocity results in more air resistance. It’s a drag, but not any more so on a heavier bike. This leaves gravity as the most relevant consideration. As you may vaguely recall from your first semester of physics, more work is needed to push a bike with greater mass up a hill. But since a round-trip commute can’t actually be all uphill both ways, things should even out a bit as you coast downhill. Unless, of course, you were crazy enough to purchase a fixed-gear bicycle.

On average, Groves’ commute was about 7 minutes shorter in summer than in winter. He attributes this in part to the poorer weather and bulkier clothing that plague winter cycling, but he also mentions that greater caution taken to avoid falling on the ice and snow may be an additional slowing factor. This raises an interesting question. Was the upper speed limit in the summer months a result of the physical limitations of how fast the rider could propel his bike, or merely the highest speed at which the rider could safely control the bike. If it was the latter, then one of the bikes might be less efficient and the rider may just be working harder to achieve the maximum comfortable riding speed on that vehicle. The author made no mention of whether he felt a greater desire for a cold alcoholic beverage following commutes made on the steel bike.

It’s understandable then if you still feel that a lighter bike would be easier to peddle. But keep in mind that you’re also hauling your own weight up those hills. Groves’ steel-frame bike was about 9 lbs heaver than his carbon-frame (the bikes were about 30 lbs and 21 lbs, respectively). This looks like an impressive weight difference until you add to each bike the weight of its rider. Couple this the frequently-made observation that lighter bikes are less comfortable (rumor has it one feels the bumpy road more on the newer bikes), and it’s hard to justify paying more money for less mass.

To be fair, I should note that the author of the bicycle paper does not claim that his single-subject study is a conclusive and exhaustive exploration of the subject. My willingness to generalize his findings to all bicycles on both sides of the Atlantic is a result of the human tendency to gratefully accept any data that supports one’s existing conceptions. ‡ I like my bike and have no plans to get a newer, lighter one. And as far as I’m concerned, there is now medical literature to back me up.

* That’s 56 total trips, so either he doesn’t work a 5-day week or he used other means of transportation more than half the time.

† This makes sense when you think about it. On a reasonably calm day, the “wind” blowing at you as you ride the bike is created by the forward motion of the bike. The faster you go, the windier it feels.

‡ That’s confirmation bias, for those with a fondness for psychological terminology.

Friday, December 17, 2010

Natural’s Not In It

To be clear, I should start by telling you that I’ve never much cared for meat. I deleted it from the menu at age 19 and was completely unfazed by the change. Prior to that I’d favored meat products that were so chopped, burnt and salted that their original source could scarcely be detected. I don’t find steak delicious or barbeque irresistible. I have never wistfully looked at friends eating hamburgers and thought, “Sigh, that could be me.” These days I eat fish from time to time and enjoy it, but if society outlawed the consumption of sea creatures, I doubt I would spend much time mourning the loss. In short, the question of whether or not scientists will be able to produce in vitro meat is not really my problem. I won’t be eating it either way.

Many of my fellow humans don’t share my preferences. People around the world can’t seem to get enough meat, and the growing demand for it threatens not only the health of the consumers and the quality of life of the consumed, but also the planet we all occupy. (So I guess this subject may affect me after all, beyond just the level of scientific curiosity.) The inefficiency of meat production is no secret. 70% of agricultural land is allotted to livestock farming, mostly to supply food for these animals. More than double the amount of water and energy is required to support a meat-eating diet than a vegetarian one. How do we go about fixing this issue? Some think the answer lies in finding a way to grow meat without growing animals.

In vitro meat is real muscle tissue grown from stem cells of animals.* While being able to grow a steak in a Petri dish would theoretically eliminate many of the problems of traditional meat production, it is (as with many laboratory endeavors) more complicated than it might initially sound. Scientists in the Netherlands had been dutifully working toward assembling the world’s first in vitro sausage, but came up with only about a tenth of the material needed when their funding ran out last year. The logistics of lab-grown meat are complicated, especially with the ultimate goal being the ability to grow meat on a large enough scale to meet the demands of a carnivorous populace. For one thing, an animal-free growth medium must be found. Regular cell-culture medium is made from fetal calf serum and thus using it would require, well, cows. This hardly solves the problem of maintaining livestock. So far the best contender is a medium made from maitake mushrooms. Additionally, just letting stem cells proliferate yields a limp, texture-less product. The lab-grown tissue needs exercise to resemble that from live animals. This can be accomplished by regularly administering an electrical current to the growing cells. But of course this process requires electricity, not to mention that it would likely fuel the “Frankenfoods” name-calling that will inevitably greet in vitro meat at its grand debut.

Despite these hurdles, some victories have already been reported. In 2002, scientists successfully grew goldfish fillets in a laboratory using whole muscle biopsy pieces rather than isolated stem cells. The samples grew between 13% and 79% (depending on the type of culture medium used), which makes the experiment sound more like meat amplification than the creation of in vitro meat. It’s sort of like the Bible story about the loaves and fishes, except in this version Jesus dons a lab coat, cuts the fish into small slices, centrifuges the slices into pellets and lets them sit in growth medium for week. Amen. After growing the fillets, the team marinated them in lemon, pepper, garlic and olive oil and fried them (I am not making this up, it’s in the Methods and Material section of their article) and presented them to a panel to be viewed and smelled, though not tasted.† The observers concluded that the product appeared to be edible. Not bad, considering that people aren’t exactly queuing up to eat goldfish from any source.

Taste and public willingness to ingest such a new and novel form of meat are potentially bigger stumbling blocks than any of the technical problems that have thus far arisen. Lab-grown meat is doomed to be perceived as “unnatural”. At this stage, scientists are mostly working on making an in vitro version of processed meat. Because the muscle can only be grown to a limited thickness without creating some sort of artificial vascular structure, steaks are still very far from being realized. The current goal is to make enough thin strips to grind up, flavor and assemble into something like a sausage or a patty. It doesn’t sound especially appetizing. However, consider what consumers already tolerate (not always knowingly) in processed meat made from real animals. Let’s examine how natural the common hamburger is.

Once upon a time, ground beef was made by taking a piece of beef and putting it through a meat grinder. Simple enough. And while the best cuts of beef may not have been selected for this honor, it was at least a single piece of meat from a single cow. With the rise of factory farming and the push for more and cheaper meat, things have gotten a bit messier. A package of ground beef purchased from a modern supermarket is a grim potpourri of meat products from multiple cows, slaughter houses, cities and countries. Much of the meat used in ground beef is what is referred to as “fatty trimmings”. These are parts cut off from higher-grade meat. They come from sections of the animal that are the most susceptible to E. coli contamination. In order to offer the consumer a lower-fat ground beef (something more comparable to what could be made by grinding whole cuts of high-grade meat) these trimmings can be mixed with processed “texturized beef product”, a substance made by centrifuging fatty trimmings. (Look! A centrifuge, just like in the lab.) About a decade ago, an innovation made it possible to sell trimming that would previously have been usable only in pet food, due to their high bacterial content. This ingenious method involved simply adding ammonia to the product to kill bacteria. Ammonia, in case you’ve forgotten, is the chemical you use to clean your toilet. Miraculously, the FDA approved this as safe and, since ammonia is considered a “processing agent”, it needn’t even appear on the ingredients of processed beef.‡

The lab-grown meat is starting to sound pretty tasty, isn’t it? If nothing else, it’s at least free of E. coli. Real animals have digestive systems that house this bacteria. Muscle grown in a Petri dish doesn’t generate solid waste, thus eliminating the problem of elimination. But if bad PR doesn’t thwart in vitro meat, cost likely will. So far the research is expensive and there is no solid plan for making the product cheaper than the already rock-bottom (in price and quality) meat pastiches of our modern world. The obvious question is whether creating meat that is kinder to the environment and to animals is even the right approach. Given all the possible hindrances, it might actually be easier convince society to reduce its meat consumption. I wouldn’t expect meat enthusiasts to give up the product entirely, but the low quality of the meat being consumed says something about its erroneously-perceived necessity. Are people really so desperate to consume this substance that they’re willing to buy beef soaked in toilet cleaner? Maybe meat should be an occasional splurge rather than a daily dietary requirement. Much of the scary processed beef I described in this article is sold to cash-strapped public schools that need to cut back on the cost of their lunch programs. Why not just go the extra step and not buy meat at all?

As for which is more sick and wrong, in vitro meat or regular processed meat, it’s up for debate. One of the more creative objections to lab-grown meat I encountered while researching this article was the possibility of cannibalism. If one can grow muscle tissue from pig or cow explants without killing the animals, one could also grow human meat. In fact, there’s no reason a person couldn’t grow meat from tissue samples from their own body. Given the bizarre items that adventurous gourmands will go out of their way to eat, lab-grown human flesh doesn’t seem out of the question.§ But there is no need to address these ethical concerns yet. We’ve yet to even finish that lab sausage. It’s just food for thought. Bon appetite.

* Thus far this has been done using adult stems cells, which have already differentiated into a specific tissue type (in this case muscle). Unlike the pluripotent embryonic stem cells you hear about in the news, adult stem cells are not immortal. They have a finite number of cell divisions in them before they expire.

† Society is still somewhat unclear as to whether or not it is legal to eat what is still an experimental product. If anyone gave in to curiosity and took a bite of the fried goldfish before feeding it to the trash, they wouldn’t be encouraged to disclose their observations to us.

‡ The punch line to this story is that, following complaints about the nasty smell and taste of ammonia, the processors reduced the amount of the chemical being added to levels that may not be sufficient to kill bacteria. So there is now simultaneously too much and not enough ammonia in America’s hamburgers.

§ Cheese fermented by live maggots (Casu Frazigu), coffee made from beans ingested and excreted by exotic mammals (Kopi Luwak), deliberately rotten eggs (“century egg”). The list goes on.

Who told you this?

Jones, N. 2010. “A Taste of Things to Come?” Nature 468: 752-753.

Marloes, L.P. et al. 2010. “Meet the New Meat: Tissue Engineered Skeletal Muscle.” Trends in Food Science & Technology 21: 59-66.

Benjaminson, M.A. et al. 2002. “In Vitro Edible Muscle Protein Production System (MPPS): Stage 1, Fish.” Acta Astronautica 51: 879-889.

Hopkins, P.D. and Dacey, A. 2008. “Vegetarian Meat: Could Technology Save Animals and Satisfy Meat Eaters.” Journal of Agricultural and Environmental Ethics 21: 579-596.

Moss, M. “The Burger That Shattered Her Life.” The New York Times. October 3, 2009.

Moss, M. “Safety of Beef Processing Method is Questioned.” The New York Times. December 30, 2009.

Friday, December 10, 2010

Desperate Living

Amidst this week’s buzz surrounding Wikileaks, the arsenic-eating bacteria of California’s Mono Lake is almost forgotten. But last week, it was front-page news and people who normally cared little for microbiology were updating their Facebook pages with exuberant quotes about a newly-discovered organism that “redefined life” and somehow related to NASA and the existence of space aliens. In actuality, the discovery was not quite as earth-shattering as your friends would have had you believe. Ever the voice of reason, I’d like to offer a bit of perspective, along with some other organisms to get excited about.

In case you somehow missed the headlines, here’s happened in California. NASA-funded scientists scooped some bacteria out of Mono Lake, a salt-water lake with a high arsenic concentration, brought it back to the lab and then tried to grow it in an arsenic-rich, phosphorus-deprived environment. The idea was to see if the bacteria could be persuaded to replace phosphorus, an element essential to all previously-discovered life, with arsenic, which is conveniently located one row directly below phosphorus on the periodic table and shares certain chemical properties with it. Phosphorus is incorporated into proteins and lipids, fuels metabolic reactions in the form of ATP and, perhaps most notably, helps form the backbone of DNA. It’s an important element.*

Well, the big news was that the bacteria, christened strain GFAJ-1, lived. This bacteria was selected specifically because it was already tolerant of arsenic, an element that is toxic to many living things.† The hopeothesis‡ was that this tolerance would enable it make do with arsenic in its daily maintenance if phosphorus was unavailable. And make do it did. However, that is all it did. GFAJ-1 didn’t exactly thrive on its new diet. While the bacteria still managed to grow in arsenic, it fared much better when provided with phosphorus.

More disappointingly, in recent days criticism from numerous biologists has threatened to turn an unexceptional experiment into an embarrassing one. The NASA team has been accused of science that is literally sloppy – poor washing of DNA and that sort of thing. Critics suggest that arsenic found in GFAJ-1 may be from contamination rather than actual incorporation into its DNA, and that the bacteria simply survived by grabbing every shred of phosphorus it could find (phosphorus couldn’t be completely removed from the growth medium, just significantly reduced). Luckily for the authors of the original paper, which appeared online in Science last week, these concerns have thus far appeared mostly on blogs, and everyone know you can’t trust those things. Nonetheless, doubts have been planted that GFAJ-1 is merely an arsenic-tolerant bacteria that builds its DNA using phosphorus just like the rest of us.

And why should you be impressed by an arsenic-tolerant bacteria? GFAJ-1 is just one of many extremophiles living in equally improbable environments on our planet. Extremophiles are organisms that live at temperatures, pH and salinity well outside the norm.§ They not only live in these environments, they grow best in them, having adapted to their unique challenges. You don’t read about these life forms very often because they are incompatible to your own external, and often even internal, environment. Their names don’t turn up food recalls. Such microorganisms would wither and die if exposed to a world as ordinary as an undercooked hamburger or a sun-soaked potato salad.

Take, for instance, psychrophiles, who have optimum growth temperatures below -20°C. They won’t even start growing until the thermometer gets down to 0°C (the freezing point of water). They live in climates where the snow never melts; permanent ice fields. If normal bacteria could do this, the freezer would be as bad a choice as a cupboard for storing your perishables. Thermophiles and hyperthermophiles live on the opposite end of the temperature spectrum, with optimum growth temps of above 45°C (113°F) and above 80°C (176°F) respectively.** These organisms can grow in places like hot springs, which are often at boiling point for their altitude, and have been known to find their way into artificial hot spots, such as water heaters. Changes in enzymes and cell membrane structure enable these organisms to flourish in environments that would quickly kill mesophiles like ourselves.

Thermophiles add brilliant colors to a hot spring at Yellowstone National Park, while psychrophiles can turn ice red. How cool is that?

Other organisms have adaptations that allow them to live in extremely salty environments (these are called halophiles) or strongly acidic or alkaline environments (acidophiles and alkaliphiles respectively). The acidophilic (and thermophilic) archaeon Thermoplasma acidiphilum was originally discovered in a self-heating coal refuse pile (pH of about 2), which sounds easily as uninviting as an arsenic-filled lake. And if there is no oxygen available, that’s not a problem. Thermoplasma acidiphilum can also use sulfur for respiration, which is unequivocally awesome. You are amazed.

So where does this leave poor GFAJ-1? Well, to survive in Mono Lake it already had to be a halophile and an alkaliphile, not to mention its striking ability to handle arsenic. It was an impressive bacteria in its own right before it got swept up in all this arsenic-eating hype and inevitable backlash. And there is no reason to think any less of it. It’s still a fine extremophile, it’s just not the organism that revolutionized biology.

But let’s pretend for a moment that the lab techniques of the NASA experiment were flawless and that the entire scientific community agreed on the results. How important is the creation of an organism that can build DNA from arsenic? How does this “redefine life”? The definition of life is already a complicated and changing one, which can’t be summarized in a single sentence. While living things tend to be made up of the same batch of elements (carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus), being assembled from these ingredients is not the criteria for being considered alive. Living things grow and reproduce. They have some sort of metabolism. They hold their cellular components together and resist entropy, at least while they are alive. In theory, anything that succeeds in these activities could be categorized as “life”, regardless of which elements it uses. The reason the word “life” is often paired with qualifiers like “as we know it” or “carbon-based” is that we acknowledge that the organisms we have found thus far may not represent the only possibly system of life. Had scientists made or discovered an organism that actually used arsenic in its DNA, this would not overturn previously held scientific beliefs, it just would confirm ideas that have yet to be matched to empirical evidence. We can’t say that arsenic-based or silicon-based organisms do not or cannot exist. But we might have to admit that nobody, including the folks at Mono Lake, has yet encountered such an organism.

* Phosphorus in living things exists mostly as phosphate (PO43-). The arsenic analog is arsenate (AsO43-). These molecules, rather than elemental P and As, were used in the NASA experiment.

† Arsenate can be harmful specifically because it is so similar to phosphate. It bonds to receptors intended for phosphate and gums up all sorts metabolic pathways.

‡ This is my attempt to create a new word. It means a hypothesis that is based more on wishful thinking than on likelihood of outcome. You can help me get it to catch on by using it in daily conversation.

§ Most known extremophiles are microorganisms in the domains Archaea and Bacteria. However they don’t have to be. Who knows, perhaps in the future some lucky explorer will find a species of squirrel or cat that lives in active volcanoes. It could happen.

** The recommended setting for a hot tub is no higher than 104°F, and even then you might pass out and drown if you stay in it for over 20 minutes. And you shouldn’t be in the thing at all if you’re pregnant or on blood thinners or have a heart condition….The list goes on. Humans are sissies.

Who told you this?

Wolfe-Simon, F. et al. “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.” Science. Published Online December 2, 2010.

Feller, G. and Gerday, C. 2003. “Psychrophilic Enzymes: Hot Topics in Cold Adaption.” Nature Reviews Microbiology 1: 200-208.

Stetter, K.O. 2006. “Hyperthermophiles in the History of Life.” Philosophical Transactions of the Royal Society of Biological Sciences 361: 1837-1843.

Baker-Austin, C. and Dopson, M. 2007. “Life in acid: pH homeostasis in acidophiles.” Trends in Microbiology 15: 165-171.

Grossman, L. “Doubts Brew About NASA’s New Arsenic Life.” Wired.com December 7, 2010.

Zimmer, C. “‘This Paper Should Not Have Been Published’.” Slate.com December 7, 2010.

Wednesday, December 1, 2010

Species of the Month: DECEMBER

The quaint holiday decoration you invited into your home and hung over your doorways is a vicious parasite that leeches nutrients from innocent host trees. It is riddled with cytotoxins, and its seeds are dispersed via bird crap. Merry Christmas.

Parasitism: It’s Not Just For Bacteria and Worms
Pretty things can be parasites too. Viscum album is one species of mistletoe*, a group of parasitic flowering plants in the order Santalales. It is an obligate hemiparasite. This means that while it does not derive all of its sustenance from a host plant, it does need some interaction with the host to reach its mature state. † As a hemiparasite, Viscum album need only steal from to its host tree’s xylem, the transport tissue that handles water and water-soluble nutrients. It is gracious enough to eschew the host’s phloem, which transports sugars. This makes it less of a pathogen, as the host loses water but not food to the parasite.

Host Infection
Viscum album bears a fruit that some birds find rather tasty. The seeds of its white berries are covered in a gluey substance called viscin. Birds eat the berries and then fly off to another tree where they eventually expel the digested remains of the fruit, its viscin coating still adhering to the seeds. The sticky seeds cling to the new branch and begin to grow. As it enlarges, the plant forms a peg that drills through the host branch and eventually reaches the xylem. Now the parasite develops its haustorium, a root-like appendage that allows it to siphon nutrients from the host.

Life in the Old Country
Viscum album is native to Europe and parts of Asia. It is the original Christmas mistletoe, a leafy green shrub adorned with white berries. It has a wide host range, infecting over 450 tree species, including both hardwood and coniferous varieties. So, yes, hypothetically your Christmas mistletoe could attack your Christmas tree. It’s a rather unsavory mental image.

Coming to America
Viscum album made its way from Europe to the new world in 1900, when horticulturist Luther Burbank deliberately allowed the plant to infect trees in Northern California so that the parasitic shrub could be harvested for Christmas decorations. Over the past century it has expanded its territory by about 4 miles, which isn’t exactly cause for alarm. Despite Burbank’s efforts, most U.S. holiday make-out mistletoe is more likely to be Phoradendron flavescens, which is native to North America.

Can it Hurt You?
Mistletoe contains strong cytotoxins (harmful to cells). Those festive white berries are fine for the birds, but you should definitely not add them to Christmas fruit cake. Nor should you feed them to your dogs or cats or children. Ingesting mistletoe can cause gastrointestinal problems and slow heartbeat, among other things. If anyone at your holiday party eats more than a couple of them, you might want to call poison control.

Can it Help You?
Mistletoe may offer humans something beyond just a flimsy excuse to steal a kiss. In Europe, Viscum album extract (VAE) is widely used in the treatment of cancer, often under the name Iscador. Mistletoe as cancer therapy was first introduced in 1920 by Rodolf Steiner, founder of anthroposophy.‡ Clinical trials of VAE have not always demonstrated consistent results and many doctors, particularly in the U.S., are skeptical of its efficacy. In Europe it is generally used as a complementary, rather than primary, cancer treatment and it credited more with improving quality of life than increasing survival rates. Still, given the unpleasantness of cancer therapies, such an improvement is an impressive contribution. Especially for a parasitic lowlife like mistletoe.

What Does This Have To Do With Jesus and/or Kissing?
As far as I can tell, very little. Like many peculiar holiday customs, mistletoe usage likely predates Christianity. It crops up in discussions of Norse Mythology and Druid rituals, but nobody seems able to form a cohesive narrative of how it came to be that a person could demand a kiss if they managed to lure somebody under the hanging holiday decoration. Most references to mistletoe as a Christmas ornament appear in the 18th century or later, by which time its role was already established. I asked a few scholars of things European and didn’t get anything more concrete. I did, however, learn about a popular 19th century song called The Mistletoe Bough which tells the charming tale of a young bride who suffocates in a chest while playing a game of hide and seek. How’s that for holiday cheer?

* I will refer to Viscum album throughout this article as mistletoe. However multiple plants go by that moniker. To properly distinguish it from its fellows, it should be addressed as European Mistletoe, or Common Mistletoe.

† As opposed to an obligate parasite, a facultative parasite can, in a pinch, grow without the aide of a host. A holoparasite, in contrast to a hemiparasite, lacks chlorophyll and thus cannot photosynthesize . It is completely dependent on its host for both water and carbon (aka food).

‡ Anthroposophy is described as a spiritual philosophy. During my New York City days, I once lived down the street from the Center for Anthroposophy. It always seemed closed when we walked by it. Mostly I just made fun of its ambiguous, hybridized name and joked that one day I would start my own spiritual philosophy, which would be called Knowlogy and would be devoted to the accumulation of random trivia…. I am perhaps on my way to doing that here.