New cartoons, Nov. 22

Today’s themes:
Another visit to the Technology Transfer Office, sports for bacteria, and ALIEN ABDUCTIONS

  1. In fond memory of Fotis C. Kafatos, my former boss – an extraordinary human being, a scientist who dreamed of being a poet, a great mentor and friend, who died on Nov. 17. Fotis was a pioneer in studies of the mosquito immune system and efforts to combat malaria through resistant strains of Anopheles. And he had a beautiful laugh.

2.  “The score was tied between the GRAM-NEGATIVES and GRAM-POSITIVES in the finals of the BEACH VIRALBALL TOURNAMENT… when DISASTER STRUCK!”

3.

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New cartoons for November 21!

Today’s themes: A chromosomal Christmas calendar,
neurons sing James Brown,
and fine dining for macrophages!

1. Coming for December: the Chromosomal Christmas calendar!
For each day of the holiday season,
discover a strange new fact about the human genome
– presented by human and molecular celebrities.

German versions will be available on the MDC website
at www.mdc-berlin.de

2.  Introducing: Mr. James Brown! 3.  Fine dining for macrophages…

Celebrating blog post #201 with new cartoons…

Today’s topics: the synaptic dialogues continue, transcriptional humor, and a nuclear pore or two…

If you see any biology nerds lurking around,
or know one, or accidentally hit one with a pie,
please tell them about the site!

Feel free to use any images you like,
just cite copyright 2017 by Russ Hodge,
http://www.goodsciencewriting.wordpress.com

  1. The Synaptic dialogues continue…!

  2. And a little transcriptional humor…

3.  Nuclear pores & such

Time for another new entry in the Devil’s dictionary!

Today’s words:  Richter scale, olfactory, olafantory, osmosis, and imbibe

See the complete Devil’s Dictionary of Scientific Words and Phrases here.

3707_001

all entries in the Devil’s Dictionary copyright 2017 by Russ Hodge.

 

Richter scale  (named after Russia pianist Stanislav Richter)  a sequence of eight specific tones somewhere near the bass end of a concert grand piano. When played in the proper order at a precise rhythm, the scale produces long, overlapping sound waves which propegate through the Earth and intersect at a point 1240.8 km from the piano. There they intersect to cause a harmonic dissonance whose frequency is complementary to a structure commonly found in fault lines, leading to seismic disturbances. The first use of the term dates from a 1958 performance by Richter in Sofia. The titles of the works he played have been lost, but at one point he ventured into the bass and applied a bit more sostenuto to a passage than was his habit. A few minutes later a series of tremors completely wiped out a distant village. Conspiracy theorists hold that Richter was a part of a Soviet experiment to weaponize the concert grand piano, but there is little evidence to support this. In 1998 mathematicians at MIT submitted a paper to the journal Nature claiming that they had solved the scale, but their results were immediately classified.

olfactory  originally derived from “Olaf’s factory,” operated by a Medieval cheesemaker from Norway, whose cheese stank so badly that Olaf and the members of his family progressively lost their sense of smell, in response to which they made the cheese even stronger. Ultimately the stench rising from the factory reached an intensity that had the effect of a physical force, creatig high-pressure atmospheric conditions that altered the weather and affected many aspects of regional ecosystems. Local species, including lots of humans and the entire native elephant population of Norway, had to adapt or flee the area to avoid symptoms such as nausea, temporary insanity, and blackouts while operating heavy machinery. There were also beneficial effects: sinus conditions be cleared up even through a very brief exposure to the smell, and people who had been pronounced dead were sometimes revived for a few days.

Whenever a westerly wind became strong enough, the smell drifted over the border into Sweden, prompting a number of retaliatory military incursions, all of which were repelled by the smell long before coming close enough to the factory to destroy it. Today the cheese is classified as a weapon of mass destruction, in a category shared by biological agents, nerve gases, and nuclear weapons, and has been banned under various international treaties.

In biology the term has paradoxically been coined to encompass all the mechanisms of smell: beginning when external molecules called olafactors force their way into the bodily cavities of an olafactee, usually after bypassing the gasket-like structures that protect the nose and mouth. Really smelly molecules such as garlic, which have a pointy prow on one side, can also enter by piercing the eyes, ears, pores and that other bodily opening I am too polite to name here. From that point they progress along tube-like passages until they reach a gas chromatograph installed in the brain. The brain, which has just as much difficulty interpreting gas chromatography data as anyone else, enters a state of disarray that it interprets as smell. Olafactors are ranked on a five-point scale: 1) pleasant, 2) tolerable, 3) bad 4) indescribably bad, and 5) fatal.

olafantory  pertaining to olafants: a hybrid made by fusing the genome of an elephant with that of an ant. After the creation of the first olafant, which was the result of a mix-up in the laboratory, scientists discovered that the structure of their chromosomes makes this fairly easy to do. So far, olafants have not been found in nature, for reasons that are not completely clear, which means they can only be produced artificially through genetic engineering techniques. This was exciting the first few times, because it was hard to predict what would grow out of your cell culture. But olafants turned out to be quite pesky creatures, and enthusiasm quickly waned to the point that it has become hard to find them, except on-line.

osmosis  does not derive from the ancient term osmo (which means “smell” or “thrust”, or both in the case of very strong smells), as has been commonly assumed. Recent philatological studies indicate that the term is actually coined from the name Mosis, a mythological figure from the time of the ancient Hebrews, an illegitimate child who, immediately after birth, for reasons that are not totally clear, was sent on a voyage downriver in a very small vessel of some sort, perhaps to serve in the capacity of a spy, but after being kidnaped along the way by a sect he succombed to one of the worst cases of Stockholm syndrome on record. Over time Mosis became brainwashed to the point that he he was elected President of the cult, winning the electoral but not the popular vote, at which point he became genuinely unhinged and unleashed seven different weapons of mass destruction on the city of his origins, including a flood that most modern historians attribute to the bombing of the Aswan dam. Where the Hebrews got the bombs is unclear – perhaps from the Chinese, or from Atlantis. There is no evidence that they were nuclear in nature.

Amosis means the opposite of osmosis and is named for Mosis’ brother Amos, whose function in the stories was as a sort of control group for his sibling, an Abbott to Mosis’ Costello. Whenever Mosis claimed that God was speaking directly to him, for example, Amos would say things like, “Are you sure it’s not just a malfunction of your parietal lobe? Have you been taking your meds?”

For centuries the term wandered around Europe on a sort of extended backpacking trip, trying to find itself, until it finally acquired its modern meaning for biology or physics. The French were the first to tame it, as part of a great influx of vocabulary that was necessary upon the arrival of the Baroque period. The original term was au mosé and was restricted to perfume, which was rediscovered in the Baroque period. Scholars knew that something like it had existed in ancient Egypt and believed, for some reason, it had been one of the seven weapons of mass destruction unleashed by Mosis, a type of chemical warfare. This interpretation might have arisen because women were using lots and lots of perfume which is understandable given the fact that no one bathed during the period between 1130 and 1730.

At the time the cloud that accompanied someone wearing perfume was wall-like and would thrust you backwards, unless you were trapped and couldn’t escape. At that point the perfume molecules would penetrate the outer layer of skin and begin an assault on individual cells. Cell membranes offered a first line of defense, but eventually a point known as the perfume pressure limit (ppl) was reached. This triggered an opening of membrane channels called schnozzoporins, which allow perfume molecules to pass through the membrane in exchange for water. At some point all the water is replaced and the system is saturated. Astoundingly, most of the body’s metabolic processes function nearly as well when supplied by perfume as with water, depending on what brand is used.

In its current meaning in physics and biology, the term osmosis refers to just the downriver portion of the Mosis story. So osmosis in a cell, for example, is any process in which an object embarks on a journey downstream, is hindered by some obstacle such as a kidnaping by bandits along the route, who are subsequently subdued in some heroic way, permitting the protagonist to reach the other side. In the case of the mythical Mosis the barrier was a social and political one, but in biology the term usually refers to a physical barrier that something needs to pass through. For example, as it is expelled from the body, urine must overcome the obstacle of air to reach its destination, through a special form of osmosis known as pissing.

liquid chronotography  any system that uses water or another liquid, such as root beer or blood, as a basis for measuring time. Methods of torture that involve a regular dripping sound, for example, are examples of liquid chronotography. Not to be confused with liquid chromatography, which means painting with water colors.

imbibe  to drink, but in a polite and refined way, without slurps, burps, or other forms of musical accompaniment. Exbibe is to move fluid in the opposite direction: to eject it from the mouth as spit, or projectile vomiting, but only if the act is hidden by a handkerchief, or cleverly concealed in some other way, and only when it is not intended as a political statement. The analogous terms for solids are ingest and exgest. There the root gest originally derives from the word gesture, whose meaning dates back to a time when cannibalism was still common and considered a sport like geocaching. At that time offering a person your hand – a gesture – was a form of greeting taken to mean, “Please take a bite.” At some point a bright cannibal realized this could be prevented by wearing a metal ring, which would break teeth before any flesh was penetrated. This is the origin of the practice of kissing the rings of popes and other royalty.

 

THE EVOLUTION OF PIZZA: Novel insights into the fourth domain of life

Russ Hodge1*, Pablo Mier Munoz2, and Miguel Andrade2

 

  1. Max Delbrück Center for Molecular Medicine of the Helmholtz Association, 13125 Berlin, Germany
  2. Faculty of Biology and Center for Computational Sciences in Mainz (CSM), Johannes Gutenberg University Mainz, 55128 Mainz, Germany

* Corresponding author: Russ Hodge, hodge@mdc-berlin.de

Conflict of interests: This project has received no funding from the pizza industry or its competitors, and there are no other conflicts of interest.


INTRODUCTION

Pizza has long held a stigma in biological research that dates back to Linneaus, who was intimately familiar with its properties as an aphrodisiac but failed to recognize it as a living organism. As a result, species of pizza found no place within his elaborate system of classification, and have consequently been entirely omitted in the clade systems developed by evolutionary biologists. Add to this the nigh impossibility of maintaining pizza in laboratories, from which it tends to spontaneously disappear through mechanisms that are poorly understood, and the result is that pizza has been forgotten in the deep freeze as the life sciences have moved forward in great strides. The issue is complicated by the fact that from one point of view, a pizza resembles a single cell, with a crusty membrane and a diversity of clearly defined organelles, while from another perspective it shares properties of highly developed multicellular organisms, and from a third it seems to resemble an ecosphere containing a diverse range of symbiotic subspecies. Finally, the fact that pizzas never evolved a skeletal or exoskeletal system has led to a paucity of fossil remains which otherwise would surely have generated interest among the paleobiology community and provided insights into the descent of modern species.

The synthesis of Darwin’s theory of evolution with findings from genetics has led to modern, computational approaches based on comparisons of modern organisms, whose features permit a reconstruction of the characteristics of ancestral species. Here we apply the basic principle of “common descent” in a first attempt to construct an evolutionary tree of pizza.  Modern varieties have clearly undergone human domestication and selection, and a small number of mutant strains have spontaneously appeared in recent years. While these factors confound the picture to some degree, the method does, in fact, permit a means of resolving questions about pizza biology that have long resisted analysis.

The resulting diagram introduces considerable clarity into the path by which current species of pizza arose from a single common ancestor, through stages that became the founders of major branches, and finally to modern forms. It permits us to hypothesize the existence of ancestral forms that have homologs in the varieties that exist today. Finally, it provides insights into fundamental biological processes that are unique to pizza, supporting a claim that these species represent a fourth domain of life which is distinct from archaea, bacteria, and eukarya, but which has clearly interacted with them in ways that have shaped its evolution.

We find evidence that pizza has managed to co-opt fundamental biological processes from the other domains of life and mix them in a way that hints at hitherto unexplored evolutionary mechanisms. Pizza appears to have snatched genes from various sources on its way to becoming an independent organism, then undergone a phase in which it became wholly dependent on human domestication, leading to a simplification of its biology. Our study suggests that the appearance of pizza in complex ecospheres containing other life forms influences them on several levels – from the neurological to the behavioral to the social, altering patterns of predation and other types of interspecies interactions.


METHODS AND RESULTS

We visited approximately 100 different Italian restaurants in a sample of no less than five European countries over a period of 4 years (extrapolated from social media statistics of the authors: FourSquareTM, GoogleTM Location History, etc.) to gather the names and ingredients present in a total of 58 different pizzas (Supp.File1). While we did not taste them all, we can attest that none are venomous and their organoleptic qualities can therefore be successfully transmitted mouth-to-mouth to the next generation of diners.

The ingredients were clustered in 9 groups according to their origin and use in cuisine (Table 1). Tomato sauce and mozzarella form their own groups, as they are not considered ingredients but inherent components of the pizza (Combet et al., 2014). The pineapple was set apart in a group by itself as an obvious aberration, due to the fact that it is universally recognized as a dysfunctional mutation that arises from a hybridization event (somewhat like the mule) and cannot produce viable offspring.

Table 1. Ingredients considered per group.

Class Ingredients
Tomato sauce Tomato sauce
Mozzarella Mozzarella
Extra sauce Cream, truffle cream
Extra cheese Gorgonzola, parmesan, ricotta cheese, fontina cheese, scamorza, stracchino, asiago
Meat / eggs Beef, salami, raw ham, ham, bacon, sausage, bresaola, egg
Fish / seafood Tuna, anchovies, seafood
Pineapple Pineapple
Condiments / herbs Pepper/green peppers, oregano, rosemary, parsley, genoese pesto, garlic, olive oil
Vegetables Artichoke, zucchini, asparagus, spinach, peas, eggplant, assorted vegetables, sliced tomato, courgette flower, onions, olives, mushrooms, rucola/rocket, potato, french fries, corn, polenta, radicchio

It is notable that not a single pizza contains more than three ingredients from the same group, which hints that this might lead to some sort of synthetic lethality, or a genetic event along the lines of the acquisition of excess chromosomes.

The pizzas were scored by counting the number of ingredients they contained per group. Exceptions are the tomato sauce and the mozzarella, which were counted as three ingredients each due to their importance in the general composition of the pizza. The data was analyzed using the R programming language and Rstudio, to cluster the pizzas based on their ingredients. The result was plotted in a clustered heatmap using the pheatmap R package (Kolde, 2015).

Tomato sauce and mozzarella are the key components in the pizza and serve as classifiers (Figure 1). Ingredients from the meat/eggs and/or vegetables groups are often used as the toppings to go together with the main components of the pizzas.

 

DISCUSSION

Here we present the first rigorous attempt to sort out major questions regarding the origins and evolution of pizza, a domain of life that has been shamefully neglected by science even as it has been shamelessly ingested by scientists. It is difficult to determine the reasons for this neglect. One cannot definitively rule out some sort of large-scale conspiracy on the part of lobbyists for the international grocery industry, possibly in cahoots with the Mafia. Recognizing pizza as a life form would require the development of an entire apparatus of regulatory measures with regard to society’s wholly utilitarian approach to its handling and use – not to mention a plethora of ethical issues it might raise. Pizza is treated as an inanimate object with no consideration at all for the fact that it might have some sort of limited awareness and experience feelings of distress or pain.

It is important to note that in modern times, pizza species have become entirely dependent on human cultivation, like many plants, domesticated animals, and model organisms in laboratories and are no longer competent for survival in the wild. The biology of pizzas has become simplified through this dependency; modern forms have lost genes that were originally crucial to its survival. Thus their evolutionary path resembles that of pathogens and viruses. Under normal processes of natural selection, organisms that are tastiest to their predators are eaten more and are subject to intense negative selection. This would also be the case for pizza, particularly since it has no means of escape from its human predators. But domestication has reversed this trend, positively selecting for the forms that are most likely to be eaten.

Our observations of pizza in situ suggest that its basic biology draws on unique features which are hard to reconcile with those of tired old traditional models that people have studied to death and are now thoroughly bored with. Pizza is a fixture of worldwide ecosystems and global food chains, nourishing species as diverse as college students, cops, bowling teams, other categories of humans, dogs, cats, hamsters, pigs, rats, cockroaches, crocodiles, fish, etc. Old crusts that have fallen down cracks in sofas provide a rich environment for microbial life, including bacteria such as legionella, Yersinia pestis and Mycobacterium leprae which might otherwise become extinct. This gives it a central role in global biodiversity; one might even regard it as the glue that holds everything together. But this is somewhat speculative.

Technical obstacles have made it difficult to maintain pizza in laboratory cultures, resulting in a dearth of knowledge – practically a black hole of knowledge – surrounding it. This is alarming in light of the numerous epidemiological studies tying pizza to serious health problems including obesity, addiction, attention deficit disorders, frostbite, burnt tongues, and deaths related to placing aluminum foil in microwave ovens. Excessive consumption retards human cognitive development, pushing adolescence far into the college years, which can only be reversed by adding vegetables to the diet. Pizza has led to a major reduction of human motility, allowing people to sit on the couch as it is delivered to their homes. Soon they may not even need to get up to answer the door, now that Amazon has begun to deliver food by drone: a step in the company’s plan to achieve world domination.

We applied well-established methods of phylogenetic analysis to the features of pizza (namely, the ingredients found in 58 extant species) to derive the first systematic evolutionary account of its descent from an ancestral form. The results point firmly to a last common ancestor, providing insights into fundamental aspects of its biochemistry, development, and the selective forces that have shaped its evolution into diverse types. A key observation is that the ancestral pizza exhibited very little elaboration of specialized structures. It consisted of only three tissues: dough, tomato sauce, and mozzarella. Each exhibits a high degree of molecular complexity, but very stable biophysical properties that are crucial to maintaining the integrity of the organism over time.

  1. The pizza lifecycle

The pizza lifecycle is marked by the three phases of embryogenesis, maturation, and decline. Entry into a phase is determined by environmental factors: embryogenesis takes place at room temperature; maturation begins when the temperature dramatically rises to about 220 degrees Celsius and usually lasts 10-12 minutes. Returning to normal room temperature introduces a brief period of homeostasis after which pizza enters the phase of decline.

Laboratory experiments have shown that pizzas which have completed embryogenesis can be preserved through cryopreservation, which induces a state of dormancy or hibernation. They can be maintained this way for a year or two without any apparent damage. The decline phase can be prolonged by a day or two through cooling, after which a brief exposure to heat is used to revive the pizza. This may cause it to repeat the last stages of maturation and then enters the decline phase, which is now accelerated.

  1. Tissue structure through the lifecycle

Dough begins as an elastic substance under room temperature, which is characteristic of the environment of embryogenesis; in the heating phase it becomes crisp and remains that way as it cools, matures, and approaches death. The sauce begins as a thick fluid which crystallizes somewhat at the pinnacle of the heating phase, remaining somewhat gummy through the first phases of cooling, then hardens until it is nearly all crystallized at the end of cooling. Mozzarella begins as a rubbery substance, melts into a liquid under heat, and only hardens after an extended period of cooling over time. These transformations of the three tissues do not alter the basic structural integrity of the whole, unless the pizza is subjected to unusual forces such as those it would encounter when flung through the air. An embryonic pizza would stretch and fly apart; the hardness of a mature pizza gives it the properties of a Frisbee.

  1. Development

The earliest stage of pizza’s embryonic development bears some similarities to Dictyostelium, an organism that lies at the borderline between unicellular and multicellular life. Dough assembles in an environment containing sufficient concentrations of the necessary chemical and biological ingredients: particles of wheat, water, sugar, and some form of oil. Such environments usually contain abundant populations of yeast cells, which get dragged along as the components are attracted to a central location, probably by sensing chemokine-like molecules that have been secreted by a cook’s hands.

Upon arrival the components merge in a sort of symbiotic collective that draws on the genes of the wheat and yeast to trigger a series of metabolic reactions that derive energy from the sugar and oil. The result is to fuse everything into a pliant, undifferentiated mass of dough. Originally this is a ball-shaped mass with stem-cell like properties that may yield a single pizza or be pinched off to form genetically identical twins.

The ball spreads across a surface to form a flat, circular basal membrane on which new layers will arise. The dough induces the formation of tomato sauce, rapidly followed by a layer of mozzarella. This three-layered structure is highly reminiscent of the tissues that arise in animal gastrulation, except that their cells retain the ball-like shape. This single difference, combined with the fact that embryonic pizza does not have a womb to protect it from dramatic changes in temperature, probably severely restricted the amount that ancient pizzas could vary from the original design. While eventually they developed specialized organelles such as salami and funghi, there was never much variation to serve as the basis for selection. So the type of evolutionary tinkering that occurred in animals and shaped the formation of highly sophisticated organs, such as the brain, never occurred in pizza. The Cambrian explosion went by virtually unnoticed.


CONCLUSIONS

 Our investigation provides the first account of the evolutionary route by which modern species of pizza diverged from an ancient, ancestral form. We characterize the last common ancestor as sharing the three-layer structure of modern pizzas, which resembles the first stage of animal gastrulation; in contrast to animals, however, pizza got stuck there and never added additional developmental stages. It is interesting to speculate what might have happened if instead of flattening, dough had retained its original, ball-shaped form and built layers of sauce and cheese inside. (Pizza calzone, a modern species, has this structure, but its dough occurs as the final step in embryonic development.) Perhaps this branch of life would have followed an evolutionary path much more like our own, and pizza, rather than humans, would have become the preeminent form of intelligent life in the known universe.

From the point of view of thinkers such as Dawkins, the key value of intelligence is to promote the reproduction of a species’ genes. Pizza found an alternative by entering into a symbiotic or parasitic dependency on humans as a means of promoting its reproduction. That dependency increased over time, ultimately restricting the evolution of pizza to the path that produced the species we know to day.

Preliminary data suggest that it may be possible to push the ancestry of pizza back even farther, to a point at which the ancestral form diverged from other organisms such as crêpes, pancakes and burritos. We are currently pursuing this question in a large international consortium and will publish the results at a later date.


References

  • Combet E., Jarlot A., Aidoo KE., Lean ME. Development of a nutritionally balanced pizza as a functional meal designed to meet published dietary guidelines. Public Health Nutr. 2014 Nov;17(11):2577-86. doi: 10.1017/S1368980013002814.
  • Kolde R. (2015). pheatmap: Pretty Heatmaps. R package version 1.0.8. https://CRAN.R-project.org/package=pheatmap.

Supplementary files will be provided by the author upon request

The Devil’s dictionary rolls on…

Today’s words: optometry, locus, teleology, microbiome, gravid, gill bars, micromolar, and derivatives of the word -scope, all explained with mathematical models and all sorts of other complicated stuff.

See the complete Devil’s Dictionary of Scientific Words and Phrases here.

3707_001

all entries in the Devil’s Dictionary copyright 2017 by Russ Hodge.

optometry  a science that applies quantitative methods to the characterization of a delusional mental state called optimism.

teleology  the scientific study of 1) television sets and 2) the content they broadcast; i.e., the powerful hallucinations that occur when viewers are exposed to a television’s electromagnetic field. To avoid fatal accidents, the first type of study should only be carried out after disconnecting a television set from its source of electricity. The second should only be attempted after disconnecting the rational parts of the brain.

locus  a site in the genome occupied by a pestilential insect that prefers a diet of corn but in a pinch will eat other things, such as old shoes, slow pets, and rusty cars sitting on cement blocks in the backyard. When satiated, it retires to a tree where it sheds its outer layer, leaving a perfect but hollow replica of itself that you can place on your grandmother’s pillow, if you’re in the mood for some excitement. The plural form is loci, a word which no one knows how to pronounce, but is required when referring to a congregation of at least two locuses, until you discover that one is merely a hollow shell. (In everyday speech the plural of locus is “plague”.) Loci make frequent appearances in the Bible, usually at the moment someone thinks, “It surely can’t get any worse than this.” In one famous scene, for example, the Israelis use trained locuses to carry out a drone strike on Egypt; finding no corn, they eat a pyramid.

The Bible reports that locuses have only four legs, although any fool can see that they have six, like every other insect. Seeing six legs may be the work of Satan, however, who takes pleasure in making people believe they are seeing more legs than loci actually have. The conundrum presented by this Biblical passage remains unsolved despite the best efforts of scientists using million-dollar technology platforms, people in bars, golfers, motorcycle gangs, shoppers in WalMart, NASA, the Locus Genome Project, and the Federal Reserve of the United States of America, which is responsible for determining how much a dollar is worth. (Their reasoning is that the confusion between four and six may also arise in other situations, so no one really knows how much money is actually out there.)

Quite predictably, the nastiest, foulest discussions about locipedia take place within the theological community. At least ten Popes have been assassinated because of their stance on the issue – in fact, the true number may be higher because it is unclear whether whoever counted them used a methodology that took into account the possibility of a four-six switcheroo. Thus the true number of Papal deaths that should be attributed to locimortis may be as low as six or as high as 64. This demonstrates the need to provide a full record of protocols and computational environments in any experiment which produces more than 3 or fewer than -3 pieces of data.

microbiome  one millionth of a biome. This might be somewhat helpful if someone ever bothered to define the size of a biome, but there’s no consensus in the scientific literature. Some use the term “biome” to encompass ecosystems as vast as Antarctica, while others claim you have a whole biome living in your belly button. These two scales are so different that it is hard to see how they can be classified under a single term, but scientists learn mental contortions during their studies that permit them to do this and even stranger things.

Biomes differ not only in size, but also in composition: one of them contains penguins, for example, while the other normally does not. This breaks biomes into the two classical categories of penguin-positive and penguin-negative. Another difference is that Antarctica has almost no plants, whereas flora sometimes sprout from a belly button, through a phenomenon whose underlying mechanisms have not yet been fully characterized but have been negatively correlated to the taking of showers. Despite the lack of a rational, personalized approach to treatment, two methods are usually effective: dabbing a little weed-killer on the thing, or attacking it with a very small pair of garden shears. While the latter is a relatively minor procedure, it should only be undertaken by specialists or trained professionals, due to a risk of perforating the intestines when performing any surgical procedure on the belly button with a pair of shears. (Note that the effects of the two therapies are additive, which suggests that applying both generally leads to shorter sprouts, except in the case of a perforation, which is usually fatal to the plant after killing its host.)

gravid  an adjective used to describe someone whose body is full of eggs, either in anticipation of a pregnancy or in the aftermath of an egg-eating competition, or both. In medical practice it is important to tell the difference, usually by inserting some type of invasive probe. Another method which has performed almost as well in double-blind studies is to squeeze the person really hard. If eggs emerge from the mouth, they most likely entered during a competition. If they emerge from somewhere else, they’re probably the other type of egg, now out on the town and looking to get hooked up.

gill bars  the only regions in an aquarium where a gar can get a real drink.

micromolar  a millionth of a molar, which is a type of tooth. A micromolar happens to be the average distance that a bacterium can bore through tooth enamel in one second, as derived from the following formula:

mm1 = 1/bx (he / f * (t?)[(C – mm2) + mm3]) – DG

where mm1 represents the distance (in micromolars); b is the bacterium; x is the number of bacterium involved in drilling the same hole; h represents the hardness of the enamel, which can only be determined by solving the equation and then inverting and converting and doing whatever else is necessary to it so that he jumps over to the left of the equal sign and everything else is piled up on the right, often upside down; f is the force the bacterium is capable of applying; t is the amount of time spent actually drilling, which has to be corrected by ?, the so-called mystery variable, if t is not being measured in seconds; C is Colgate toothpaste; mm2 stands for the number of M&Ms a person has eaten in the recent past, and mm3  refers to “mom’s madness”, a quantitative measurement of the degree of physical force your mother is prepared to inflict on the anyone who fails to apply C after mm2 (note that as C – mm2 approaches zero, mm3 approaches infinity); and DG stands either for the degree of grinding that a particular molar undergoes when a person has to share the mm2 with someone of the opposite political persuasion, or Director General – I can’t remember which. Replacing the variables with true values produces mm1, which may need to be adjusted to account for the degree of freedom (otherwise known as the “fudge factor”) which means the number of times you are permitted to lie when filling in the values to solve the formula. Note that by definition, mm1 must always end up being 1; if this doesn’t happen, just change the answers for the other variables until it does. There’s a way to do this with Excel tables, but I couldn’t tell you what it was if my life depended on it. I’m having a hard enough time explaining this as it is.

The formula yields the result mm1 in terms of bacterial boring distance per second, but the result can be easily converted to minutes by multiplying mm1 by 60, into years by multiplying mm1 by 1315440, and in relation to the age of the universe up to the present date by multiplying mm1 by 1817938080000000000000000 + sn (where sn is the number of seconds that elapse between the time you read this and the moment you get around to making the calculation).

-scope  an instrument used to “check something out,” usually to determine whether it could serve as an appropriate sexual partner. The first scopes, in fact, were developed to search for genitals before scientists discovered their locations on the body. Later the suffix was attached to other types of instruments, including:

telescope  an instrument developed to look at things so far away they lie in another dimension, called teleology.

colonoscope  an instrument first developed to probe the depths of a person’s ear. Prior to its invention, no one knew the true depth of the auditory canal, so colonoscopes were made very long. With enough force the instrument could be pushed in so far that it emerged from the other end of a person. At some point scientists discovered that more information could be collected about the auditory canal by examining it from the other side, so they began inserting the colonoscope at the former exit point.

endoscope  this term was originally derived from the expression, “end o’ th’ scope,” and referred to the end that was farthest from the person in charge of the instrument, and closest to the victim. If it changed hands in the middle of a procedure, for example when the patient snatched it to end the abuse, endoscope now referred to the end held by the former patient, and the person who initiated the incident was called the endoscopee. This caused confusion in cases where two people both got their hands on the thing. If each tried to tell the other in no uncertain terms what he could do with his end of the endoscope, this produced garbled communication and often fatal results. A national committee was formed to find a solution. Eventually a consensus was reached through the creation of the new terms proximal endoscope and distal endoscope, also sometimes seen in the forms myendoscope and urendoscope, as defined by the end that was cleanest at any given time.

microscope  a type of scope that moves the eye one million times closer to whatever it is you are trying to look at. At the time of invention another theory was proposed to account for the functions of the instrument: it actually made objects one million times larger for a very brief period of time. Fortunately this is not the case, because a lot of the things you see with a microscope are disgusting enough without being made a million times larger. This early “expansion theory” of microscopy was not fully discarded until Einstein published the theory of relativity. Einstein proved that if two people with microscopes were standing on trains that were pulling away from each other at the speed of light, they would never see each other because rays emanating from the microscope’s light source would never reach the slide, unless they turned around and faced the other direction. At that point each would either see what the other person had looked like a million years in the past, or be crushed as the two trains underwent a sudden, million-fold expansion. Since neither outcome was particularly desirable, scientists discarded the theory for the one they liked better.

The microscope revolutionized science because it was so powerful it could detect things so small that they didn’t actually exist, which explained why they had been invisible to the naked eye in the first place. It also played a key role in the deanthropomorphization of science by disproving the concept of the Big Picture. Through a microscope one realizes that the Big Picture is nothing more than a lot of Smaller Pictures containing things so small they defy human cognition, unless they somehow manage to reach it by entering through an ear. Thus the Big Picture can be discarded altogether.

Understanding why this is the case can be demonstrated through a metaphor: Imagine cutting any normal puzzle into a million pieces. Now try to assemble it again. You’ll discover that this is impossible because the maximum amount of information in 1/1,000,000th of an image is an R, G, or B dot, and not even a whole one, and good luck matching that to the picture on the box. But you’ll never get that far because you’ll never find the corners. Theoretically you could, but it would take an amount of time that can be represented by the formula UP * (n)1,000,000/4!, where n = the time it takes you to locate a single corner piece that it has become so small that you have to apply the Uncertainty Principle (UP), which means that whenever you go looking for it, it probably isn’t where you think it is, and even if it were, it would be gone before you could grab it.

More technology transfer cartoons…

More from the OTTers (officers of technology transfer) today… This series is dedicated to my friends in the field, in honor of their patience as they encounter pitches that are… well, a generous way to put it would be “creative”. Often the first step in a project is to reach up and snag a basic researcher and tie him or her firmly to the ground, so they don’t end up sailing toward the stratosphere like a helium balloon. Because we know what happens to those.

For more cartoons, scroll down or select the category “Molecular biology cartoons” from the menu in the banner above. Enjoy! Pass along to your friends!