On the Naming of Sports Teams II: Non-Indian Warriors & Groups with Local Associations

October 8th, 2014

This is the second installment of my thoughts on the naming of sports teams, leading up to my proposal for dealing with the Washington Redskins name, which will appear a couple of posts later, to universal applause, I’m sure. In my previous blog post, I discussed the very popular use of animals and birds for names and suggested categories into which the names could be organized.

Here are my proposed categories for the next-most popular type of team names, those in which either the fierce animals are replaced by fierce human beings or the less fierce totem-like animals are replaced by people having a special association with the team’s home territory. Team names that are Beings of Good or Evil, though few in number, seem to warrant a category of their own. As before, I give only one example for each subcategory in the list, but mention more in the discussion that follows. I am saving the discussion of the use of names associated with Native Americans, which naturally belong in the categories 3 or 4 below, for a separate treatment in the last post of the series.

3. Fierce fighters from history or myth (non-local)

(A) brave warriors (Spartans)
(B) ruthless plunderers (Raiders)
(C) mythical (Titans)

Groups with local associations

(A) historical non-military (Sooners)
(B) historical military (Minutemen)
(C) occupational (Steelers)
(D) representative / emblematic (Texans)
(E) students at the school (Cadets)

5. Beings of Good or Evil

(A) Good (Angels)
(B) Evil (Blue Devils)

I’ve suggested that naming teams after animals is psychologically akin to the choosing of animals as emblems for totem groups. Names based on groups of historical people come closer to actual identification, being roughly equivalent to veneration of heroes or honoring of ancestors. Although most people probably don’t think about it more than they do for teams named after animals, I wonder if this doesn’t unnecessarily elevate some bloodthirsty qualities in the case of fierce fighter names, especially, of course, those of category 3B, with whom no one should want to identify.

Among historical brave warrior names (3A) are the Michigan St. Spartans, USC Trojans, and Holy Cross Crusaders.

There are numerous teams with Native American warrior names, but I’m putting that discussion off for later. It’s really striking how few of the non-Indian warrior names there are. Were the Spartans chosen over their formidable military rivals, the Athenians, because Sparta’s side ultimately won the Peloponnesian War? It’s probably because Athens is more renowned for its philosophers than its fighters, while the severe military culture of the Spartans automatically makes one think of warriors. Winning can’t be the only criterion for being deemed worthy of a team’s name, or how would the Trojans, who lost to the Achaeans, get the honor? Have the Achaeans been left out of naming because they had to use a ruse to conquer Troy? Or is it just because most people would call Troy’s besiegers Greeks, which wouldn’t work as a name due to modern associations that would override any Homeric allusion? Romans can be ruled out on similar grounds. Somehow the Trojans managed also to get a condom brand named after them, so clearly they are the ultimate winners in terms of lasting name recognition.

Some would no doubt object to my including the Crusaders in category 3A, since they are typically viewed these days as early European imperialists, conquering and oppressing the Arabs of the Holy Land, centuries before the next wave of British and French came to dominate the region. In fact, the European knights who waged the Crusades were at a technological disadvantage, but nevertheless managed through their zeal, courage, and battle skills to win and hold a good chunk of territory in the Holy Land for decades. And it should be remembered that the Crusades occurred in the context of centuries-old Arab rule of Portugal and Spain. The clash between the warriors of Islam and Christendom in the Crusades of the Middle Ages went on for almost two centuries, far surpassing in length the wars in which the Trojans and Spartans fought; not to mention the Punic wars between the Romans and Carthaginians (neglected also). Saracens, as the European crusaders called their Arab warrior opponents, might make a good name in the historical warrior category, but it will never be chosen, especially in the context of modern Jihadism. I have to wonder how long the College of the Holy Cross will hold on to the Crusader name.

To the ruthless plunderers category 3B I would assign the Minnesota Vikings, Oakland Raiders, Pittsburgh Pirates, Tampa Bay Buccaneers, and Idaho Vandals.

I’m sure that, beyond their image of ferocity, part of the attraction of these category 3B names is their association with anarchic freedom and adventure. But this is anarchic freedom with respect to those who are being raped, killed, enslaved, and plundered; and the adventure is in the hunt for new human prey. Someone looking for a name-changing moral crusade (oops, that word!) might want to consider eliminating names of category 3B before going after Native American names equivalent to those of category 3A.

The name Idaho Vandals, while evoking images of juvenile window breakers, makes reference to the “barbarians” that sacked Rome in 455 A.D., an allusion which few are likely to get without help. I wonder why the Vandals were chosen over the Visigoths, who also sacked Rome? Syllable count perhaps. Other invaders that terrorized Europe, such as the Mongols and Huns have also been shut out of the ruthless plunderer name category. As I will say more than once, I think the fewer of these kind of names the better, so I’m not proposing them for new teams.

Given the merciless way the inhabitants of conquered cities were usually treated in ancient times, the distinction between brave historical warriors and ruthless plunderers may seem to rest more on what characteristics the namers have sought to attach to their teams (martial virtues or sheer ferocity, roughly) than to degrees of savagery. But Trojans and Spartans did abide by some rules of war, such as truces for burial of the dead, recognizing places of sanctuary, and keeping (for a while anyway) of treaties, and there was an element of patriotism or a higher cause in their struggles. This sets them apart from marauders like pirates, who were thieving cutthroats out for bloody personal gain and nothing more.

I think the association of a team with fierce human fighters risks taking on their moral shortcomings in a way that identification with blameless wild animals doesn’t. Mythical warriors (3C) such as the New York and San Francisco Giants and the Tennessee Titans are more like animals in that regard. The Houston Oilers (4C), when they moved to Nashville, became the Tennessee Titans (obviously chosen for alliteration, 3C), that name being available because earlier the New York Titans (lame New York Giants imitation, given the location) chose a rhyming name (Jets) when the New York Mets got a MLB franchise.

In the case of local associations, the names are an assertion of local pride, whether in city or in State, at least in the beginning; but sometimes the association fades and the meaning of a name becomes obscure to everyone, eventually coming to mean little beyond the athletic team itself. The transformation of an obscure local group reference into an animal totem sometimes occurs, as I mentioned in the previous blog post on animal names for the case of the Oregon Webfoots (people, 4A) becoming Ducks. Similar examples are mentioned below.

To the category 4A (historical non-military) belong the Oklahoma Sooners; Dallas, Wyoming, and Oklahoma St. Cowboys; Virginia Cavaliers; Texas Rangers; North Carolina Tar Heels; San Francisco 49ers; Philadelphia 76ers; San Diego Padres; New England Patriots (see discussion); Seattle Mariners; Notre Dame Fighting Irish (see discussion); and New York Knickerbockers and Yankees.

The Cavaliers are borderline military. So are the 76ers and Patriots through their ties to the American Revolution. The Cowboys and Mariners could arguably be put in the occupational 4C category, but the historical association seems stronger to me. There are several other team names in category 4 for which the subcategory is not clearcut, but their existence is not sufficient reason to dissolve the boundaries between subcategories, in my mind.

The Sooners were, strictly speaking, cheaters, as they were the early bird homesteaders that went into Oklahoma to claim land well before they were authorized to in 1889, but I guess they get credit for their initiative, and they got to keep the land they claimed. Oklahoma was supposed to be Indian Territory, but there’s nothing unique about that kind of takeback. Given the Oklahoma football team’s success over the decades, Sooners has become a name that defines a team, rather like the Dodgers and Lakers names do, making the historical reference largely irrelevant.

North Carolina’s Tar Heels name seems to be the local equivalent of Hillbillies (and might go into either 4A or 4D depending on whether the historical aspect is emphasized). Similarly, since the Texas Rangers (State law enforcement officers) still exist, they could arguably be paired with Houston’s Texans as representatives of the State in 4D, but I think the historical association is stronger. The 49ers (4A) of San Francisco could evoke the frenzy of a gold rush, but they also are a case where the team has come to define the name rather than the reverse.

The New York Knickerbockers name (Google it) probably fits best into 4A, given its roots in stories of New Amsterdam. Now everyone just says Knicks, and few probably know how the name originated, but I think everyone feels Knicks are somehow New Yorkers. This is just another of the team names that might be placed in either 4A or 4D, depending on how current the usage of the name is deemed in denoting inhabitants of the team’s territory.

It’s hard to say where to put Notre Dame’s Fighting Irish, as it’s a name that brings to mind short-tempered brawlers (who may have had too much to drink) rather than warriors. I think historical association with tough Irish Catholic immigrants is the best way to look at it, making the name a sort of extension of category 4A.

Historical military names (4B) include the Massachusetts Minutemen, Mississippi Rebels, Tennessee Volunteers, and (originally) Kansas Jayhawks.

The U. of Massachusetts Minutemen name is a nice example of 4B. The name was originally the Redmen, but that was wisely abandoned for one having a local historical military connection. The New England Patriots name is in the same general line, though the name Patriots associated with Boston in particular evokes memories of Paul Revere, Sam Adams, and the Boston Tea Partiers, as well as those who fired the shots heard round the world, and I have placed Patriots in 4A. The original Patriots logo, which was sort of comical, showed a guy wearing a three-cornered hat (making it clear that the reference was to the time of the American Revolution) and down in center position with a football. The current logo shows instead the face of a nonexistent comic book superhero “Patriot,” known locally as the “Flying Elvis.” Imagine a whole team of those characters. Ugly vision.

The Rebels of the University of Mississippi are named for those who took up arms in support of secession from the United States in order to preserve the institution of slavery. That is the fact. Of course, many rebels fought bravely and most were not personally slaveholders, but this is a case where courage can’t be separated from the cause it supported. The Civil War does not belong to the forgotten past, and the riots that accompanied the enrollment of the first Black man, James Meredith, at the University in 1962 are a century closer. There is now a statue of Meredith at the University, and the Confederate officer sideline mascot has been transformed into a “Rebel Black Bear,” but the team name remains Rebels, and it should also be retired.

The Kansas Jayhawks name (4B, originally) is a quasi-military historical reference, made even more obscure by the metamorphosis of the Jayhawk into a cartoonish totem bird. The Jayhawks fought on the anti-slavery side in Kansas before the Civil War, and, in reality, may have been more like marauders than minutemen, but they have receded into the mists of history. A mythical bird is now used to depict the Jayhawk, since the totem animal (1A) impulse has once again triumphed, as it did with the Oregon Ducks. The “Jayhawk” does not look much like a hawk. It resembles Heckle and Jeckle, a pair of cartoon magpies, though with a somewhat curved bill, to suggest hawk. It is hard to imagine a large group of these cartoon birds, as the plural of a team name implies.

Names associated with local occupations (4C) include: Pittsburgh Steelers; Purdue Boilermakers; Green Bay Packers; Nebraska Cornhuskers; UTEP Miners; and Edmonton (also in the past, Houston) Oilers.

I would imagine most colleges with occupation-based names gain nothing from them for out-of-state recruiting of athletes. If you grow up in Nebraska, you may take pride in the name, but if you were from California would Cornhuskers be attractive? At least it’s a lot more attractive than the team’s original name of Bugeaters (a local bat, 2A). Still, with enough success, the team defines the name, and the name can become an asset.

In the 4D category I would put the New York Mets and Islanders, Houston Texans, West Virginia Mountaineers, and Ottawa (also in the past, Washington) Senators.

The Senators name sticks out in that group as one that applies only to a small number of the city’s inhabitants, but it doesn’t seem right to file it under occupational. The name is just a way of stating the town is a seat of government, and not just historically.

The name of the New York Mets (4D) is a short form of Metropolitans, which seems quite appropriate for a NYC team, since the shortened form is used when speaking of the Metropolitan Museum or the Metropolitan Opera. Through rhyming imitation, though, the Mets name inspired the unfortunate inanimate object Jets and Nets names.

The Los Angeles Dodgers (originally trolley dodgers) name was a kind of local reference in their early Brooklyn days, but now it’s just a name with a lot of baseball tradition and no particular meaning beyond baseball. Dodgers could be assigned to 4D with an asterisk. The same thing might be said of the Los Angeles Lakers name, which made sense when the team was in Minneapolis.

The Boston MLB team is lucky to have shed Beaneaters, an early 4D name. I assume the Iowa Hawkeyes would originally have gone into 4A or 4D, but following the totem-transformation principle, they are now indistinguishable from hawks (1A), though I can’t say much for the quality of their logo.

College teams named after the members of the student body (4E) include Army Cadets, Navy Midshipmen, and Texas A&M Aggies. The military academies’ students shed those names upon graduation, but an Aggie is an Aggie for life. At least it was so in the past when A&M was all-male and required ROTC, and I imagine it still is for most. I remember hearing an Aggie friend of my (non-Aggie) father say that he had decided there were only two kinds of people in the world: Aggies and non-Aggies.

Beings of Good (5A) include the Los Angeles Angels of Anaheim and the New Orleans Saints, though both need an asterisk.

While I’ve designated the Los Angeles Angels of Anaheim as the example of a team named for Beings of Good (5A), which is technically true, the name may be better suited to an extended view of 4A or 4D, since it comes from the Spanish name for the Ciudad de los Angeles, thus making Angels a historical association, though not with an actual human group, and also emblematic. The New Orleans Saints name is in rather a similar position, since it obviously comes from historical association of the city with the famous jazz hymn, rather than with an actual group of people. Within Catholic Church tradition, I think Saints would be classified as 5A, since no one becomes recognized as a Saint while alive on this Earth, and such recognition requires miracles of intercession to have been made through said Saint, verified to the satisfaction of the Church. The 5A classification probably makes as much sense as any, though I have no idea what is in the mind of New Orleans football fans. As with many teams, the team has come to define the name to the point where the word Saints makes many people think of football, just as Yankees makes them think of baseball.

In category 5B are the Duke Blue Devils, Wake Forest Demon Deacons, Arizona St. Sun Devils, and New Jersey Devils.

Except for one (sort of, supposedly), the teams named for beings of Evil (5B) have no excuse of history or geography to justify their choice. The namers just wanted to symbolically acquire the power of Evil and the ability to inflict the pains of Hell, judging from their team logos. I’m sure this is all meant tongue in cheek and not really thought of for the most part, as is the case of all team names. Still, I think this is a bad idea, even worse than identifying the team with ruthless felons.

The Jersey Devil is supposedly a legendary, chimeric creature said to inhabit the Pine Barrens of New Jersey, but the team logo clearly has horns and a pointed tail on the J of NJ, and the arena “mascot” is made to resemble the traditional depiction of Satan; so whatever the origin of the name, it’s associated with the Evil One or his cohorts now. The Arizona St. logo is a horned, tailed, pitch-forked Devil. Now, for those who don’t believe in supernatural evil powers, the choice of devils for the team name may seem something like the choice of Titans, a mythological sort of unrestrained afflictive force, carrying no more moral responsibility than the choice of blameless animals. I think, however, the strong identification of devils with Evil, whether or not one believes in them, makes them unworthy of providing names to a team. Interestingly, the Duke Blue Devils and Wake Forest Demon Deacons (what a combination!) were, when the names were chosen, at least, schools in close relations with Protestant churches, having loosely used Methodists and Baptists as team names earlier.

The NBA Sacramento Kings don’t fit into any of my categories, and don’t warrant having one of their own. They were the Cincinnati Royals (originally with alliteration in Rochester) before moving to Kansas City, which already had the Kansas City Royals MLB team. Keeping the connection to royalty, while regaining alliteration with the name Kansas City Kings, may have seemed like a no-brainer, but the idea of a whole team consisting of kings seems pretty ludicrous to me. Still, it’s only a little more problematic than one made up solely of chiefs, which Kansas City already had in its NFL team at the time the name was chosen. An opportunity was missed to change the name from Kings when the team moved to Sacramento. I just noticed the Old Dominion Monarchs, so there’s at least one other name like the Kings, but I am not adding a category for hereditary rulers anyway. Whoa, I forgot the Los Angeles Kings NHL team (Stanley Cup Champions!). If I ever revise this analysis (unlikely), I’ll have to think about adding monarchs.

I think that if I were naming a team, I would choose either an animal name, a color identifier, or a local non-military group association, avoiding even a hint of glorifying historical butchery or support for a bad cause. The next installment in this series will deal with team names that are abstractions, forces of nature, or inanimate objects.

On the Naming of Sports Teams I: Animals & Birds

September 29th, 2014

My foolhardy and woefully unfulfilled goal back when I started this blog was to have one post per week. But that was before the App Store called and before I got on Twitter (@onscrn). I think I may be able to meet that schedule at least for the next few weeks. So, stay tuned. It’s only fitting that I should turn to a Twitter-worthy subject, but one that requires far more than 140 characters to begin to do it justice: the naming of sports teams, which has been under discussion in the context of the recently controversial Washington DC National Football League team name, Redskins.

First, I mean to discuss and analyze this phenomenon and then to provide a solution to the problem of the Washington Redskins name. Rather than do all this in a single post, as I had originally intended, I’ve decided to spread it out over four posts to avoid having a post that’s longer than what almost anyone would read.

Why do sports teams need names anyway? There is a practical aspect. “The Cubs are in town today,” is a succinct way of saying “Chicago’s National League Baseball team is playing here today.” But, beyond that, the need for associating some name and image to a team seems part of our psychic makeup. Primitive societies subdivide tribes into totem groups, each group identified with and named for a specific animal or bird. Nor can we overlook the lions and dragons of heraldry or the eagles of the Roman legions. The emblem gives a sense of reality to an abstract concept of group membership. That is easiest, of course, when the name is concrete instead of abstract. I am very glad that no team I naturally support because of where I live or where I went to school has a name like Magic.

The types of names—I’ll say names rather than mascots to avoid confusion with actual animals sometimes seen on the sidelines (such as Bevo, the Texas longhorn) or with the unfortunate walking cartoon characters with disproportionately large heads, who seem a requirement at games now—fall into a few categories. Very few team names have more than three syllables, and I can’t think of any with more than four. So shortness is a criterion. The name needs to be easily shouted in cheers. Alliteration, as in Jacksonville Jaguars and Pittsburgh Pirates, is obviously a feature that team namers love.

In this blog post and the following three, I shall take a stab at defining the various categories into which team names fall. I’ll be giving a single example in category itemization, but will mention more in the discussions that follow. It will be obvious that some names could fit into more than one category and that my classification scheme is not the only one that might be devised. It should serve to organize the discussion though. My ideas on where the various Native American team names fit into this scheme will be presented in the final post of the series. Here are the first two of my categories, the ones I discuss in this post.

1. Fierce animals and birds

(A) wild predators (Lions, Hawks)
(B) belligerent male herbivores (Bulls)
(C) other combative “domesticated” animals (Bulldogs, Gamecocks)
(D) stinging insects & venomous reptiles (Hornets, Diamondbacks)

2. Totem animals and birds, not noted as fierce

(A) local (Horned Frogs, Orioles)
(B) non-local (Huskies, Owls)
(C) humorous/offbeat (Anteaters)

I haven’t made a survey, but animals and birds would seem to provide the most team names. Since team names are most often meant to present an image that’s intimidating to opponents and inspiring to the team it represents, wild carnivorous beasts and fowls predominate, but the totem-like aspect of the association of a group with an animal can’t be ignored. Some obvious names come to mind in the fierce animal predator category (1A), with some of the names attached to several teams: Detroit Lions; Chicago and Baylor Bears; UCLA and Boston Bruins; Memphis Grizzlies; LSU, Missouri, Auburn, and Detroit Tigers; Cincinnati Bengals; Houston, Brigham Young, and Washington St. Cougars; Carolina, Florida (NHL), and Pitt Panthers; Jacksonville Jaguars; Kentucky and Kansas St. Wildcats; Minnesota Timberwolves; Michigan Wolverines; Florida ‘Gators, to name a few of the current professional and college team names. The prevalence of feline predators is notable, probably due to the suddenness of their attacks. Fierce feathered predators (1A) include: Philadelphia and Boston College Eagles; Atlanta Hawks and Falcons; and Seattle Sea Hawks (Ospreys). These birds, like the wild cats, are also noted for their sudden attacks, and share with them long, sharp claws, which make for an imposing aspect.

Sometimes these animals also have a geographical association with the team, as the ‘Gators with Florida. Historically speaking anyway, most of the North American mammals and birds probably have some geographical connection with the teams whose names they supply. Non-mammalian animal names, such as Gators, for teams are pretty rare, presumably because it’s harder to identify with a Gator than, say, a fellow mammal like a Bear.

Herbivores, both wild and domesticated, if perceived as strong and dangerous, may also be chosen as a team’s fierce animal image (1B), e.g. Chicago Bulls, St. Louis and Fordham Rams, Milwaukee Bucks, and Colorado Buffaloes. Bulls, Rams, and Bucks make the association with aggressive males specific. The Dallas Mavericks, viewed as adult males, rather than calves or generic cattle, could fit into 1B also. Of course my Texas Longhorns, a name with obvious local associations as well, are in this category. I don’t know what their dispositions are like, but those intimidating horns could impale a person or other large mammal, which is why Bevo, the sideline animal, is actually a testosterone-limited steer instead of a bull.

I think other domesticated animals with a reputation for combativeness are worth a separate subcategory (1C). Bulldogs (Georgia) were bred for the cruel sport of bull-baiting and are feared watchdogs today. South Carolina’s Gamecocks are fighting non-predatory birds, though it’s illegal to actually set them on each other for sport these days. I’ll put the Arkansas Razorbacks (feral swine) into 1C, but a case could be made for expanding 1B to include these pigs, since these non-predators are reputedly just mean by nature and were not bred to fight. One could also make a case for putting hawks and falcons in category 1C, given their use in the sport of falconry.

Even more difficult to identify with than the Florida Gator is the Arizona Diamondback (rattlesnake, 1D), but there is again a geographical association, and there’s no denying the things are intimidating. Ditto for the San Jose Sharks (1A), who really don’t have much of a geographical argument in their favor. The Georgia Tech Yellowjackets and Charlotte Hornets (1D) sacrifice all pretense to intelligence to maximize the intimidation factor, in a way that suggests a swarming onslaught. I think I’d rather support a team with a more intelligent animal than a reptile or insect as its namesake, but I suppose one gets used to it. If I can support a team designated by the color of its “Sox,” why not?

A handsome bird such as a Baltimore Oriole (2A), Toronto Blue Jay, or St. Louis Cardinal is sometimes chosen with or without strong local association, instead of a raptor, but never an ugly or overly common bird such as a sparrow. And never a carrion eater, or one whose diet is primarily carrion, anyway. I had assumed Oregon’s Ducks would naturally fit into category 2A or 2B, but a Wikipedia article revealed that the original team name was Webfoots, which referred to some early human settlers, thus corresponding to category 4A (to be revealed in the next post). The image and name of the webfooted bird has taken over, though, and has assumed a totem-like role. I imagine the charming Delaware Blue Hen is a local totem bird (2A). The New Orleans Pelicans are surely local totem birds, as I can recall when Louisiana license plates had a pelican on them. The owl (1A or 2B) is carnivorous and brings death to small animals just as surely as other flying predators, while lacking the speed of the falcon or the grandeur of the eagle. The owl carries a certain mystique associated with silent, nocturnal flight and its supposed wisdom, and Rice and Temple Universities have chosen the owl as their symbol.

My favorite of all bird names belongs to the minor league baseball Toledo Mud Hens (2A). We called coots mud hens in Texas too. I’ve been wishing Toledo could get a major league team just for the name. The Mud Hens may be an exception to the rule I postulated above that no ugly birds would serve for a team name. I knew they had to be a local totem bird, (2A) because how else would they have come up with the name? Wikipedia confirmed that the original ball park was located next to a marsh inhabited by American Coots. The Atlanta Thrashers, formerly an NHL team, were obviously a local totem bird (Georgia’s State bird is the Brown Thrasher) with a tough-sounding name in the context. The U of Texas at San Antonio Roadrunners would seem to fit nicely into category 2A, as roadrunners are plentiful around San Antonio and are not perceived to be fierce. They are a bit like the owl and badger in having a case for technical inclusion in 1A, since they actually prey on lizards, rodents, and snakes, not just insects. But perception is paramount in a team symbol, and the cartoon Roadrunner has formed people’s impression of the bird, at least where it is not native, so some might perceive the name as belonging to category 2C. Anaheim Ducks began as a Disney film tie-in (Mighty Ducks), but have since moved into the totem category (dropping the “Mighty”), as is the natural tendency.

The Beaver of Oregon St. is obviously a geographically linked totem animal (2A) since the State flag of Oregon displays a beaver. Minnesota Gophers (2A or 2C?) is an odd name, since the small rodents are usually viewed as varmints. They gain some prestige (hinting at something magical?) by being called the Golden Gophers, and, I must assume, gophers are plentiful in Minnesota. An alternative breakdown of “non-fierce” totem animals might have been into spirited and placid ones. The Wisconsin Badgers (2B, 1A) don’t sound all that intimidating, though I wouldn’t try reaching into a badger burrow, and they certainly prey on gophers. I imagine they would go into the spirited subcategory, while the gophers and beavers probably wouldn’t. The TCU Horned Frogs (actually lizards) fit the local non-fierce totem category (2A), but their thorny skin and horns do give them an intimidating appearance. To me, as a kid, they were just the “horny toads” we used to pick up by the tail for fun. They puff themselves up to appear more formidable and are known for squirting blood from their eyes to thwart predators. Despite their appearance, they are really about as placid as could be and are less intelligent, even, than gophers.

Unbroken horses like SMU’s Mustangs and Denver’s Broncos can do a lot of damage with their hooves, even if they are less likely to charge than a bull or bison, and they are certainly swift (another prized descriptor for a sports team) and spirited. They might belong in 2A, given the western locations of the teams they symbolize. The committee that chose the name for the Washington Huskies made a rather strained case for its referring to a totem animal with a local connection, saying Seattle was recognized as the “Gateway to the Alaskan frontier,” but I’m calling it non-local (2B). The Husky name replaced the local group reference name Sundodgers, which might belong in the comical made-up name category (7D in later post).

Some relatively recent names are of aquatic animals not normally thought of as fierce, but associated with the area of Florida teams: Miami Marlins, Tampa Bay Rays, and Miami Dolphins. I’d call them all totem animals with a geographical tie (2A). Chicago’s Cubs are the only example that comes to mind of a team named for a baby animal. Since they have not matured yet into fierce predators, I’m putting them in 2B. Wait, what about the Indianapolis Colts? Since they started in Baltimore, I’m thinking they were envisioned as old enough to race, not wobbly foals. The Pittsburgh Penguins of NHL hockey were no doubt chosen for the alliteration, as well as for seeming at home on the ice, but technically they belong to 2B.

There aren’t very many names that belong in the comical or semicomical category 2C. I think they are basically mistakes, as they display a certain contempt for the idea of sports team allegiance. But even for these names, the totem principle asserts itself. Anteaters for example. I have no doubt that the 60‘s choice was meant as a kind of parody choice when selected by student vote, but now they actually have Anteater pride at UC Irvine. Bowdoin once went by the Fighting Pine Trees, but later became Polar Bears. Stanford’s sideline mascot dresses as a tree now, but how long will this last? I had assumed the Tufts Jumbos (circus elephant) must belong in this class, but the truth was a little different. P. T. Barnum was a Tufts alum, and he donated the stuffed actual Jumbo to the school. Supposedly, the coaches and athletes decided to become Jumbos. Unfortunately, the remains of Jumbo were consumed in a fire in 1975. Given the Barnum connection, I think category 2A is appropriate for the Jumbos. I have a problem with a whole team being named after an individual though. UConn Huskies (get it?), as distinguished from the serious totem (quasi local) animal, the Washington Huskies, must have been chosen for the chuckle value originally, but I’m sure it is now a serious totem animal. I can only think of one team using an extinct animal in its name: Toronto Raptors, which doesn’t seem worth making a separate category.

My next post will deal with teams named after fierce warriors or groups associated with regions, exclusive of Native Americans.

OnScreen DNA Complete: Save 25% With Our New DNA-Learning iPad App Bundle

September 18th, 2014

bundle

Apple has just introduced the ability for app developers to bundle multiple apps on the App Store into a single package priced below the cost of the individual apps purchased separately. And if you’ve already purchased one or more of the apps in the bundle, you can apply what you’ve already paid to the cost of completing the bundle. This Complete My Bundle works just the same as the iTunes Complete My Album feature for people that have bought one or more songs off an album and want to download the rest of it without paying what the sum of the individual tracks would amount to. This is a feature I had been wishing for and had even tried to figure out a convoluted ways of implementing myself via in-app-purchases. I’m very glad I didn’t, as it has all been taken care of beautifully now.

I’m delighted to announce OnScreen DNA Complete, which is a bundle of OnScreen DNA Model, OnScreen Gene Transcription, and OnScreen DNA Replication, our three iPad apps that show the structure of DNA and how it works in a cell, all using the same 3D interactive model with animations that are scientifically accurate, within the limits of the molecular model. The model has been chosen to show the essential molecular components and the double helix structure of DNA, unobscured by the atomic details of the molecules. See the following links for some reviews and descriptions of the apps.

Each of the three apps in the OnScreen DNA Complete bundle currently (9/18/14) sells for $4, and the bundle costs $9, which translates to a 25% discount. Purchasing the apps in the bundle is like getting two of them at full price and the third for only $1. Which is exactly what someone that already has bought two of the apps at full price will pay to get the third. Anyone that has bought one at full price, can get the other two for $5 total.

That means you can try one app, see how you like it, and then apply what you’ve already paid to the bundle price that gets you the other two. You don’t have to remember what you paid for an app, as Apple remembers for you. If you have already paid as much or more than the total bundle price, then you can download the rest of the bundle for free, which will be great for people that have bought apps before a big price drop. That won’t apply to the OnScreen DNA Complete bundle at this point, since the apps have not sold at a higher price, but it will for some other bundles. Apple does insure that the bundle price on any day must be less than the price of the component apps total price for that day, so there is no danger of a false bargain.

NOTE: As I write, there is an ugly bug in the iPad App Store app that makes full-screen views of the app screenshots associated with bundles look terrible. Believe me, our screen shots look great. If you want to see how the images look filling the iPad screen, go to the descriptions of the individual apps. Hopefully, Apple will catch this soon. I filed a bug report.

The apps have all been tested to work great under the new iOS 8 system without upgrade. Go get that OnScreen DNA Complete bundle!

We’re Celebrating DNA Day (April 25) Again with a One-Day Sale: All DNA Apps at Half-Price!

April 24th, 2014

Sixty-one years since the double helix structure of DNA was discovered! Eleven years since the human genome was mapped!

From the Centers for Disease Control and Prevention (CDC) website: “National DNA Day is a special day when teachers, students, and the public can learn more about genetics and genomics. The National Human Genome Research Institute (NHGRI) at the National Institutes of Health has sponsored DNA Day for the past ten years, to commemorate the completion of the Human Genome Project in April 2003 and of Watson and Crick’s discovery of the double helix structure of DNA.”

To celebrate DNA Day, we are reducing our price on all DNA-related apps by $2 for the day on the US App Stores (with comparable price reductions on app stores for every country).

The apps selling for only $1.99 (50% off) on April 25 are:

OnScreen DNA Model for iPad

OnScreen DNA Replication for iPad

OnScreen Gene Transcription for iPad


OnScreen Retrovirus for iPad

OnScreen DNA Model for Mac

And selling for only 99¢ (67% off) is
OnScreen DNA Model for iPhone

The OnScreen DNA Model apps (on iPad, iPhone, and Mac) focus on the details of DNA’s double helix structure, using a 3D, color-coded, virtual model that the user can rotate and zoom. Explanatory text deals with the molecules and chemical bonds of the double helix. Animations show two important lab and biotechnology phenomena of DNA: denaturation, in which the strands separate, and renaturation, in which they reunite.

OnScreen DNA Replication
makes use of the same DNA model to show how, through the action of specific enzymes, a DNA molecule is perfectly duplicated before cell division. The various steps in the process, including the action of telomerase to prevent strand shortening, are shown in 3D animations and described in some detail.

OnScreen Gene Transcription makes use of the same DNA model to show how a genetic recipe stored in the sequence of molecules of DNA is copied by construction of a messenger RNA molecule. The various steps in the process, shown in 3D animations that make it clear that messenger RNA is constructed as part of a hybrid RNA/DNA double helix, not a 2D ladder, are described in some detail, emphasizing the role of certain enzymes.

OnScreen Retrovirus models nucleic acids in the same way as the other apps in the suite. Its simulations show step by step how a retrovirus (such as HIV) copies its single stranded RNA genome into double stranded DNA ready to be inserted into the host cell’s DNA.

The apps show details of structure and processes that are sometimes depicted in erroneous ways in places that should know better. Animations make the processes memorable. Discussion of the chemistry involved is at an introductory level, so the apps are useful for learning about DNA to a wide range of students or anyone interested in the science of Life. There really is nothing comparable on the internet.

Educational purchasers enrolled in Apple’s Volume Purchase Program still get 50% off the sale price when buying twenty or more copies at a time.

Spread the word. This is a one-day-only sale.

Welcome to Boston, Science Teachers! Have a Free DNA App!

April 2nd, 2014

The National Science Teachers Association (NSTA) is having its national meeting in Boston, April 3-6. Around 10,000 science teachers and school administrators are expected to attend. Given that I live a subway ride away from the meeting site, it was a no-brainer for me to take advantage of this opportunity to see what is going on the world of science teaching, to which I feel I belong, but only as a virtual teacher, making apps to teach science. I expect to talk to some of the people that have direct contact with students every day. I’m hoping to get some useful critiques of my apps, as well as making more people aware of them.

As part of this effort to make more science teachers, especially biology teachers, aware of my suite of interactive DNA apps, I’m making OnScreen DNA Model for iPhone (usually $2.99) free for the duration of the NSTA meeting (through April 6). This app, except for the smaller screen size and consequent shorter DNA strands, is identical to the iPad app OnScreen DNA Model. The other OnScreen Science apps dealing with nucleic acids in the cell are iPad-only. I recently wrote about some good reviews they’ve received, including three for inclusion in the NSTA Recommends online database. Links (App Store buttons) to the other apps can be found in the right sidebar. Of course, OnScreen DNA Model for iPhone is now free to anyone.

Here is the link to the free appOnScreen DNA Model for iPhone.

Enjoy, spread the word, and, if you like the app, please go to the App Store to rate and review it.

dna model

And the Winner for Best DNA Simulation on an iOS Device Is…

March 18th, 2014

No, in this imperfect world no one is going to be excited when the envelope containing the name of the winner in that sadly neglected category is opened. Still, my cell biology apps for the iPad have gotten some good reviews in the past several months in places that command respect, and I thought I’d gather links to them here to have a page that I could in turn link to whenever I wanted to make people aware of the reviews. Reviews of iPad apps to teach DNA structure and function are not to be found in highly traveled spots on the internet. Coverage of education apps is pretty thin, and what little there is mainly concentrates on very young learners, as does the Education category on Apple’s App Store, where apps with cartoon animals (goofy expressions preferred) dominate.

I keep hoping Apple will add a Science category to its App Store, but for now I have to choose Education (no chance to be visible as one of the top 200 paid apps) or Medical (slight chance to make the top 200 occasionally). I have opted for Medical, but, fortunately, someone at Apple noticed OnScreen DNA Model and selected it to get a certain amount of visibility in the Education category for iPad apps. Currently it is featured under Apps For the Classroom->Biology and Apps for High School->Biology->Cell Biology & Genetics. Of course I’d put it in Middle School also, but I’ll take whatever I can get. I’m sure it’s the main way people actually hear about OnScreen DNA Model, which can then lead to the other apps.

Although they are less likely to be seen than a mention on the App Store, detailed positive reviews from respected sources are great to receive. Just to have them all in one place, here are links to the seven reviews I’ll briefly comment on below.

Genetics Engineering & Biotechnology News

May 1, 2013 OnScreen Gene Transcription

June 1, 2013 OnScreen DNA Model

July 1, 2013 OnScreen DNA Replication


December 1, 2013 OnScreen Retrovirus

NSTA Recommends

February 21, 2014 OnScreen DNA Model


February 21, 2014 OnScreen DNA Replication


February 21, 2014 OnScreen DNA Replication

I ran across the Genetics Engineering & Biotechnology News online magazine site early last year and saw that they had a monthly Best Science Apps feature (alternating every two weeks with Best of the Web). The reviews were concise, but meaty enough to show that the reviewer was obviously spending some time with the apps and making useful observations about them, and that the reviewer was actually knowledgeable about the science. Since the section was called Best Science Apps, they weren’t publishing reviews of apps they didn’t like, but the apps weren’t all getting the four stars highest (“Excellent”) rating either. Some were as low as the two-star “Good” category. I thought my apps, dealing as they do with the basic structure and function of nucleic acids would likely be of interest to them.

In January 2013 I emailed the reviewer to suggest OnScreen DNA Model and OnScreen Gene Transcription for review, offering to provide promo codes for free download. This is not a form of bribery (apps were $3-4), but rather a courtesy to the perspective reviewer, who couldn’t be expected to buy every app that might be worth reviewing. Apple provides a certain number of these promo codes free to developers just so they can get the apps onto the devices of potential reviewers and such. Anyway, the response was positive to taking a look at the apps, sometime in the next month or so. When, in March, the reviewer gave me the go-ahead to send the promo codes (they expire four weeks after being created—the codes, not the apps downloaded with them), I sent codes for the two apps I’d mentioned plus one for OnScreen DNA Replication, which I had finished and gotten onto the App Store in the meantime.

I hoped for the best, but as with most creators awaiting judgment of their work (think of the playwright, at least in movies, awaiting the morning editions after opening night), I was a little anxious. I was 99.9% sure I didn’t have any scientific errors, but would the reviewer appreciate the things I was proud of, like the background text I had spent so much effort on? At least, if the apps weren’t even deemed “Good,” I would just get no review at all.

That would be cold comfort, but it’s more than can be said about online reviews posted by app customers on the App Store. One-star reviews there mean “hated it,” and every app developer will sooner or later gather a few nasty (sometimes plainly inaccurate) and unfair reviews, while having no way of responding to the reviews on the App Store. I keep meaning to write about that subject, but that’s not what I have in mind for this piece.

When I saw OnScreen Gene Transcription had made it to the Best Science Apps section of the May 1, 2013, issue of Genetics Engineering & Biotechnology News and had been rated a four-star Excellent app in the review, I was both gratified and relieved. As might be expected, my opinion of the reviewer rose even higher, but not just because of the overall rating. It was rewarding to see that someone knowledgeable and conscientious had appreciated my work, including parts of it I wasn’t sure would be noticed, like the background text and commentary and just the way it was designed. The short summation of the praiseworthy elements of the app (beside a check mark) was “Background section, nice simulation graphics and commentary.” In the spot for the not-so-hot attributes (beside an X) was a simple “None.”

For all I knew, that one review would be it for Genetic Engineering & Biotechnology News. Maybe they wouldn’t want to have more apps from the same developer, at least for a while. But in the very next batch of Best Science Apps (June 1, 2013), there was a review of OnScreen DNA Model, once again with the highest rating. Among other things, the reviewer noted how the simulation of denaturing and renaturing of the two DNA strands made the interaction between them intuitively clear. By the check mark was “Great 3D DNA model, great text content.” By the X: “None.”

Now I really hoped OnScreen DNA Replication would also be reviewed. And it was, in the next issue containing Best Science Apps (July 1, 2013), once again with the highest rating. By the check mark was “Great text content.” For the first time something appeared by the X: “The simulation graphics are a bit convoluted.” Within the text of the review appears “Due to the complexity of the process, the simulation is a bit difficult to follow; however, credit must be given to the attention to detail.” The ending of the review was about as complimentary as it could have been. “Just like the other apps by this developer, the OnScreen DNA Replication app is incredibly educational and fun to use.

The fourth of the OnScreen Science apps using the same basic 3D model of nucleic acids is OnScreen Retrovirus. This app made it to the App Store in June of 2013. For some reason, I didn’t send a promo code to the reviewer for the new app right away. Maybe in the back of my mind was the feeling that I shouldn’t press my luck, though I certainly hadn’t decided not to ask for a review. I was busy getting all the apps ready to run on iOS 7, which was a pretty major job that took weeks. I hadn’t even checked out the Genetic Engineering & Biotechnology News site until mid January of this year, where to my surprise I saw that OnScreen Retrovirus had been reviewed without my having provided a promo code. The review had a great beginning: “The people at OnScreen Science are at it again, this time using their 3D nucleic acid model to simulate cDNA synthesis from a viral RNA template following infection by a retrovirus.” I love that “at in again.” And the rating made my apps four-for-four in gaining the Excellent designation. By the check mark: “Great interface, easy navigation.” By the X: “None.”

Just to put the Excellent ratings in perspective, the distribution of the ratings for other apps (excluding the OnScreen apps) in the issues in which the OnScreen apps were reviewed was 6 Good, 12 Very Good, and 5 Excellent. OK, it’s not quite as impressive as an Oscar or a Nobel Prize, but it’s pretty good. I have no way of knowing if it’s actually helped sales of the apps, since I can’t tell who is buying them, never mind where they learned of them. There was no noticeable spike in sales after the publication of the reviews. Still, if nothing else, those reviews are something I can refer people to for confirmation that the apps are of a high quality. Not to be overlooked, either, is the morale boost one gets from feeling one’s work validated. The income from those apps is hardly enough to justify the effort required just to maintain them every time Apple comes out with a new iOS version or device; so recognition really helps, even if it’s recognition in an out-of-the-way niche on the internet. The apps are, after all, pretty much in the niche category. I will resist the temptation to advertise that the apps have received “prestigious” four-star awards, as one hears so often about a supposed honor, the very existence of which is known only to a few.

In case it hasn’t come through already, I recommend the Genetic Engineering & Biotechnology News site’s Best Science Apps section as a great way to find intelligent and useful evaluations of apps for biology and chemistry in particular, both for educational and research aid purposes.

The other reviews I want to mention are those recently placed online in the National Teachers Association’s data base called NSTA Recommends. Again, only reviews for apps that the NSTA reviewer, typically a science teacher, heartily recommends are included in there.

To quote from the web site:

Our panel of reviewers—top-flight teachers and other outstanding science educators—has determined that the products recommended here are among the best available supplements for science teaching.

Why no negative reviews? They can be fun to read, even to write, but teachers are pressed for time—so only products that are reviewed favorably make their way into NSTA Recommends.

I emailed NSTA with a suggestion that the three apps devoted to DNA’s structure and functioning in the cell be considered for review and got a favorable response. It took quite a while after the NSTA contact said they’d be interested in looking at the apps before they actually got to them. One set of promo codes expired and the next was getting close to its expiration date before NSTA lined up a reviewer who downloaded the apps. I was just glad it was happening, since the NSTA is a large organization, with over 55,000 members engaged in science education, spanning the whole K-College range of students. I don’t know how many teachers use the data base, but getting a spot on NSTA Recommends list with favorable reviews couldn’t hurt.

The reviews, once they had been reported and published on NSTA Recommends, were all I could have hoped for. Again I was gratified to see that my work had been appreciated by someone that obviously had the experience to make his opinion valuable. And the grade level was listed as 6-College, exactly as I would have said myself! The NSTA reviews were not only thorough and insightful; they had a very practical, classroom-oriented angle, always focused on the question of what value would these apps be to a teacher. I thought it was a very good observation by the reviewer that the apps could serve to increase the teacher’s knowledge and understanding of the material covered in the apps, not just the students’. I was delighted that the reviewer made a point one seldom hears about apps that aren’t free, when he referred to the apps as “low-cost.” The reviewer had also noticed that there is a version of OnScreen DNA Model available for the iPhone (and iPod Touch) and mentioned that the students could download that app onto their personal devices, an observation that deserves extra points, I think.

The reviews made the observation that a teacher could project the iPad screen image onto a bigger screen for all the class to see, whether because only the teacher had an iPad or to make sure certain points were getting across. All of the features of the apps, including the organization and content of the background text, the ability to pause the simulations whenever desired for making a comment or reading commentary, the multiple views of the process, with the 3D model and the linear representation of the strands’ base sequences, and the attractiveness of the apps to students, were commented on in favorable terms.

Reviewing apps for NSTA Recommends must still be quite new. Although the reviews appropriately designated the format as “App,” the menu for restricting the NSTA Recommends online database search by format didn’t include “App” as an option. I’ve pointed this out, so it may be fixed by the time anyone reads this. The time to be considered “New” on NSTA Recommends is only two weeks, during which time a new review will show up when a searcher checks the New box. After that, only apps found by word in the title, author, or word in the text show up (with the option to restrict the search by format) in a search of the database. Unfortunately, due to some glitch, for all but the last three days of the OnScreen Science Apps’ time to show up as New, their reviews appeared without images, which was about as appealing as a Facebook or LinkedIn profile without a picture, especially for apps that are, above all, graphical in nature. That’s fixed now. Check them out.

RTFRB: The Obstruction Rule Should Not Have Ended Game 3

October 30th, 2013

I am posting this even as I hope it will be of little interest after tonight’s Game 6 of the World Series, since I’m pulling for the Red Sox to win and make the unfortunate end of Game 3 just an oddity with no lasting effect on the outcome of the Series.

Still, I want to counter the prevailing idea that, while it was a shame to have such an important game decided in such an unusual and unsatisfying way, the decision of third base umpire Jim Joyce to call obstruction on Red Sox third baseman Will Middlebrooks, and thus award the winning run to the Cardinals in the bottom of the ninth inning, was the correct call and really a clearcut enforcement of the rule on obstruction, which made no allowance for any consideration of the fielder’s intent.

The widespread feeling that something was nonetheless wrong about having the game end this way has led to talk that “Major League Baseball” might want to revisit the rule to make it more flexible, so, that in the future, the umpire would have more discretion in deciding whether true obstruction (with intent, as opposed to unavoidably) had taken place. Here’s a link about that. The writer of that article, Ken Rosenthal, argues against making such a change, for the simple fact that it will probably never come up again, and, moreover, that explicitly including “intent” in the rule would only make things worse. According to my argument below, a careful reading of the rule shows that likely (not provable) intent is already in the rule implicitly, so that what is needed is not a change to the rule but a more reasonable enforcement of it.

I did not know the rule on obstruction of a runner by a fielder by heart before this event. However, I was able to read it, as anyone else can, online. What I see in the rule is not at all a vindication of the umpire’s call.

The rule, without consideration of its accompanying Comment, might seem clearcut: “OBSTRUCTION is the act of a fielder who, while not in possession of the ball and not in the act of fielding the ball, impedes the progress of any runner.”

But the Comment cites as an example the case where a fielder has dived for a ball and remained lying on the field in the path of the runner. There is room for reasoned judgment in making the call in such a case. Here’s what the Comment on the rule says about a case very similar to what happened (ground ball instead of thrown ball the only difference): “For example: an infielder dives at a ground ball and the ball passes him and he continues to lie on the ground and delays the progress of the runner, he very likely has obstructed the runner.”

I want to call attention to a couple of phrases in that sentence. First, it says “and he continues to lie on the ground.” I think the reasonable reading of this is that the fielder does not promptly get up off the ground, with the strong implication that he is deliberately staying on the ground to be in the runner’s way. This implication of intent is strengthened by the ending “he very likely has obstructed the runner.” Very likely! Now he clearly has obstructed the runner in the strictest sense of the word if he has impeded the progress of the runner, so the “very likely” can only point to the fielder’s likely intent. Intent cannot be proven, of course, so the obstruction rule can be invoked when it seems likely that deliberate obstruction was involved, or that what has happened is essentially indistinguishable from deliberate obstruction.

Now if the fielder is trying to get up, but is prevented from that by the runner being on top of him, how can the fielder be blamed for not getting up? How long must the fielder stay on the ground to say he “continues to lie on the ground”? It is clearly a judgment call about whether the fielder has probably impeded the runner on purpose, without, of course, requiring the umpire to be a mind reader. There is no automatic call based on the mere fact of contact with a runner having been made by a fielder lying on the ground.

The common sense call would have been that the impeding of the runner’s progress was inadvertent, since the play happened so fast with both players in the same small area from the start. Contact occurred almost immediately after the ball got past the fielder. It was not the case of a shortstop continuing to lie in the base path to slow down a runner rounding second after the ball had gotten through the infield.

A judgment call based on the probable intent of the fielder, which should have been made, would have left the runner free to advance at his own risk (to be tagged out at home in the case in question). Instead, what should have been an extra-inning World Series game with uncertain outcome became another game made memorable by Jim Joyce, who seems to have a knack for spoiling games of great interest with bad calls.

Of course, I don’t know any more than anyone else whether Middlebrooks was trying to impede Craig. I also don’t know if Craig’s decision to go over Middlebrooks instead of around him was based on the hope of getting an obstruction call. But based on the wording of the rule, including its significant appended Comment, the play should have been allowed to continue without umpire interference. It may be that umpires are taught to enforce the rule the way Joyce did, despite its wording. If so, that needs to be changed, but it doesn’t take a rule change for that to happen, for the rule is reasonable as it stands.

OnScreen Retrovirus Shows How the AIDS Virus Copies Its Genome

September 12th, 2013

OnScreen Retrovirus, my latest iPad app has been on the App Store for a couple of months now, so it’s high time I said something about it. Since the new iPad & iPhone operating system iOS 7 will be available to the general public September 18 and Apple is now accepting submissions of new apps and app updates written for it, I can show what the app will look like with the new interface. Let that be a justification for the delay.

retro action

The AIDS virus is the most notorious of the retroviruses, which is why I put it in the headline, but there are many more, including some nasty ones that cause cancer. I didn’t know much about retroviruses, or any viruses for that matter, until a year or so ago, when I decided I really should learn more. The detailed knowledge of how DNA works, which I gained during the course of developing the other DNA apps (OnScreen DNA Model, OnScreen Gene Transcription, and OnScreen DNA Replication), had heightened my curiosity about viruses, while providing me with the background to make the road to understanding easier.

Viruses are very strange creatures—or should I say objects? To quote from the first paragraph of my entry on Viruses in the app (from Useful Stuff popover view in one of the images below):

Are viruses alive? Look up virus metabolism, and you’ll come to a blank page. So viruses aren’t alive in the usual sense that living cells and multicellular creatures are. Yet viruses consist of proteins and genetic material, which are crucial constituents of living creatures, and, when in the proper environment (in their “host” cell), viruses can reproduce in their own unique way. So it’s really a matter of taste whether to call them alive or not.

Just as “real” organisms do, viruses make use of nucleic acids to store instructions for making the proteins vital to their survival. These proteins are few in number since the virus doesn’t have to make a living, but only hole up safely until it can enter a cell to reproduce, making use of a cell’s protein-construction apparatus. The full set of nucleotide sequences of the virus’s nucleic acid (which may be DNA or RNA, single-stranded or double-stranded, depending on the type of virus it is) is its genome.

The genome of a retrovirus is contained in a single strand of RNA. The way in which a retrovirus uses a few enzymes (proteins) it contains to construct a double-helical-strand of DNA, which also contains its genome, the virus’s RNA serving as a template, is fascinating. Mind-blowing, I think, as it depends on there being certain sequences of nucleotides at just the right place and in just the right order to enable nucleic acid strands involved in DNA synthesis to separate and then join again at another place in order to continue the process. Anyway, the simulations of OnScreen Retrovirus show how this happens in a detailed way that I think makes it very clear. And clearly mind-blowing!

retro commentary

OnScreen Retrovirus doesn’t show either the full virus entering the cell or the completed DNA being inserted into the host cell’s DNA. There are some good animations you can find online to see, at least in a sketchy way, those events. What I have not found online is any detailed simulation of the genome replication, and that is what OnScreen Retrovirus takes care of, making use of the same three-dimensional ball-and-stick model of nucleic acids featured in the other OnScreen Science iPad simulations.

The app’s Useful Stuff items and the Commentary for each step of copying the retrovirus’s RNA genome to DNA explain what you see in the simulations, necessarily introducing several key concepts, of which the screen shots should give an idea.

retro contents

It’s a bit disconcerting to think of it (like the knowledge that our bodies contain more bacteria than human cells), but our DNA, for all its stability in the context of ordinary cell metabolism, contains many short segments called transposons that either move from place to place in their chromosome or make copies of themselves to be inserted at another location. Transposons accomplish their transpositions by utilizing the cell’s machinery to produce the enzymes needed to accomplish the task. In particular, those called retrotransposons have their DNA transcribed to strands of messenger RNA, some of which are used to synthesize enzymes, which act on other strands of the RNA to make double-stranded DNA to be inserted elsewhere in the cell’s DNA. Exactly the way a retrovirus does. So the simulation of OnScreen Retrovirus provides a simulation of a retrotransposon’s DNA synthesis as a bonus.

About iOS 7, I can say that for the OnScreen Science DNA apps, the changes are basically cosmetic and, I think, all for the good. The old tool bars and buttons of previous versions of iOS seem awfully dark and gloomy compared to the new ones. The new “buttons” are really more like links on a web site, just colored text on a light background, but people are used to links, and I think that change will go over well.

I hope to have all four of the OnScreen Science iPad apps that deal with DNA and RNA ready for sale on the App Store before the public release of iOS 7. The new updates will continue to support iOS 6, though not iOS 5, which means they are saying goodbye to the original iPad. Anyone wanting to run these apps on an original iPad had better hurry to get them before the updates go through. The updated apps will run on iOS 6 and just switch over automatically to their iOS 7 versions once they are running on a device with iOS 7 installed.

Update: before I could post this, I got word that version 2.5 of OnScreen DNA Model was going live on the App Store. So it is now too late to get it for the original iPad. I think Apple has app updates for iOS 7 on the fast track for approval, since I submitted only yesterday. So, you really must hurry if you have an original iPad and want to run these apps.

FLASH! (added 9/21/13) Although Apple has not announced it yet, it is now possible (and hopefully a permanent new feature) to download earlier versions of apps that have been left behind when updates raised the minimum iOS requirement. That means it is still possible, for instance, for people using the original iPad, which can’t run any iOS version greater than 5.1, to purchase OnScreen DNA Model even though the most recent version 2.5 requires iOS 6 or greater. Version 2.4 of the app, which is virtually identical, can still be downloaded. Just proceed as if you hadn’t noticed the iOS requirement. The App Store software will detect that your device can’t support the latest version of the app and will ask if you want to get a previous one your device can run instead. If you say yes, the older version will download and install. And all is as if you had purchased the app when that version was the latest. You are entitled to free updates on other devices in the future. I verified all this myself with actual downloads, but we can’t know whether it’s a permanent feature or just a test of a possible one until Apple says something about it. So far, they have only acknowledged it for updates on older systems.

We’re Celebrating DNA Day (April 25) with a One-Day Sale: All DNA Apps Only 99¢!

April 24th, 2013

Sixty years since the double helix structure of DNA was discovered! Ten years since the human genome was mapped!

From the Centers for Disease Control and Prevention (CDC) website: “National DNA Day is a special day when teachers, students, and the public can learn more about genetics and genomics. The National Human Genome Research Institute (NHGRI) at the National Institutes of Health has sponsored DNA Day for the past nine years, to commemorate the completion of the Human Genome Project in April 2003 and of Watson and Crick’s discovery of the double helix structure of DNA.”

To celebrate DNA Day, we are reducing our price on DNA-related apps to 99¢ for the day (with comparable price reductions on app stores for every country). The apps to be priced at 99¢ on April 25 are:

OnScreen DNA Model for iPad
 (regularly $3.99)

OnScreen DNA Replication for iPad (regularly $2.99) 

OnScreen Gene Transcription for iPad
(regularly $2.99) 

OnScreen DNA Model for iPhone (regularly $2.99) 

OnScreen DNA Model for Mac (regularly $2.99)

The OnScreen DNA Model apps (on iPad, iPhone, and Mac) focus on the details of DNA’s double helix structure, using a 3D, color-coded, virtual model that the user can rotate and zoom. Explanatory text deals with the molecules and chemical bonds of the double helix. Animations show two important lab and biotechnology phenomena of DNA: denaturation, in which the strands separate, and renaturation, in which they reunite.

OnScreen DNA Replication
makes use of the same DNA model to show how, through the action of specific enzymes, a DNA molecule is perfectly duplicated before cell division. The various steps in the process, including the action of telomerase to prevent strand shortening, are shown in 3D animations and described in some detail.

OnScreen Gene Transcription makes use of the same DNA model to show how a genetic recipe stored in the sequence of molecules of DNA is copied by construction of a messenger RNA molecule. The various steps in the process, shown in 3D animations that make it clear that messenger RNA is constructed as part of a hybrid RNA/DNA double helix, not a 2D ladder, are described in some detail, emphasizing the role of certain enzymes.

The apps show details of structure and processes that are sometimes depicted in erroneous ways in places that should know better. Animations make the processes memorable. Discussion of the chemistry involved is at an introductory level, so the apps are useful for learning about DNA to a wide range of students or anyone interested in the science of Life. There really is nothing comparable on the internet.

For iPad users, DNA Day is a chance to get all three OnScreen Science’s DNA apps for less than the regular price of OnScreen DNA Model alone. The apps work great and look great on an iPad Mini.

Educational purchasers enrolled in Apple’s Volume Purchase Program still get 50% off the sale price when buying twenty or more copies at a time.

Spread the word. This is a one-day-only sale.

OnScreen DNA Replication—The Name Says It All

February 25th, 2013

I am happy to report that OnScreen DNA Replication, my iPad app that simulates the process in its title is now available for purchase and download. In joining the previously released OnScreen DNA Model and OnScreen Gene Transcription on the App Store, it completes the suite of interactive apps designed to teach the details of DNA’s structure and function using the same three-dimensional model.

The guiding concept of these OnScreen DNA apps is that seeing the basic molecular components of nucleic acids in a sufficiently detailed three-dimensional ball-and-stick model, one that requires unwinding the strands of DNA before they can used as templates for daughter strand or messenger RNA construction by complementary base pairing (also shown, of course), will foster an intuitive grasp of Nature’s beautiful solution to the problems of critical biological information storage, retrieval, and inheritance. The necessity of enzymes for the processes is also emphasized in a conspicuous way.

second okazaki

There is a thirty-second video excerpt of the simulation online that shows the part of the simulation seen in the image above, which should give an idea of how the model is used to display the processes that occur in replication, but note that the video was made with an iPad simulator and runs more slowly than the actual app on an iPad does. Unfortunately, Firefox can’t show it.

Just to summarize the OnScreen DNA Replication iPad app’s key features and advantages, I note that it:

  1. Shows three-dimensional, color-coded double helix structures, not two-dimensional ladders.
  2. Uses animations that show hydrogen bonds being formed (as sticks connecting base pairs in the ball-and-stick representation) and broken.
  3. Models proper right-handed DNA (depressing how many images and even simulations depict left-handed DNA).

  4. Indicates the enzymes enabling the reactions shown and where they are acting.

  5. Includes background material in a popup view.
  6. Shows every major step in replication, with commentary available in a popup view.
  7. Provides the option to run the simulation without pause (except when the user intervenes) or to automatically pause after key steps in order to conveniently read commentary if desired.
  8. Provides a key to the color code etc. in a popup view.
  9. Provides a visual representation of strand polarity.
  10. Maps the nucleotide-base sequence of the 3D model to a GCAT base-by-letter linear representation.
  11. Deals with the end problem: telomerase reverse transcription shown.
  12. Calls attention to the crucial action of the enzyme pyrophosphatase.
  13. Allows the user to zoom in or out and rotate the model by touchscreen gestures to see it from different perspectives even as the simulation is running.
  14. Is suitable for just about anyone wanting to learn how DNA works, from middle school students to intellectually curious adults, since no advanced chemistry knowledge is assumed.

The replisome enzymes responsible for replication are identified, but their visual representation is confined to the linear (GCAT) sequence view. This has the advantage of making the point that the process requires the enzyme, while showing the location of its catalytic activity, but without obscuring the basic structural changes that are occurring in the model view. The RNA of the enzyme telomerase, however, is shown in the model view as well as in the sequence view, since there is base-pairing to be seen in the model view during the reverse transcription process.

Let me mention some features of DNA replication that can be difficult to grasp, which I think the app’s simulations convey clearly. Nature has not provided the cell with an enzyme for beginning the construction of a daughter DNA strand with a DNA nucleotide. A DNA nucleotide when it is paired to a nucleotide in the template strand must also be connected at its phosphate-bearing end to a nucleotide already present in the daughter strand. There is an enzyme to begin a daughter strand with RNA nucleotides, however, and this is utilized in DNA replication. The construction of “primer RNA” is of course shown in the simulations of OnScreen DNA Replication. RNA’s point of difference from DNA, the different sugar-phosphate backbone, stands out by virtue of its color in the model. The simulation shows three RNA nucleotides in each primer RNA chain, which is smaller than the number in Nature, but long enough to illustrate the principle. The app is a teaching model, not a perfect mapping of reality in every detail.

This requirement of primer RNA is why the so-called lagging daughter strand of DNA is constructed with a series of Okazaki fragments from which the RNA must be replaced by DNA and a final connection made between the fragments. If you don’t know what leading and lagging strand refers to or what Okazaki fragments are, OnScreen DNA Replication will teach you, while showing all the steps and enzymes required in their construction and modification.

The necessity for starting a new Okazaki fragment with primer RNA leads to the “end problem” in the replication of linear (not circular) DNA. I encountered this problem for the first time in a very practical way when I was programming simulations for OnScreen DNA for the Macintosh a few years ago. Okazaki fragments could be dealt with by having the primer RNA replaced by DNA–except at the very end of the lagging strand. What happened there? I had to do a good bit of digging to find out how to deal with the problem, since introductory treatments of DNA replication ignored it altogether. I learned then how the enzyme telomerase solved the problem, so I added telomerase’s action to the simulation. Since telomerase makes use of reverse transcription to extend the lagging DNA strand, the demonstration of that process, which is also utilized by retroviruses, is a bonus. Telomeres and how telomerase prevents strand-shortening are discussed both in the Useful Stuff and in the Commentary popup views.

OnScreen DNA Replication also shows a crucial step in nucleic acid polymerization that is usually ignored in introductory treatments: the reaction that breaks into two phosphate molecules the pyroposphate molecule which is a by-product of the polymerization. WIthout this splitting of the pyrophosphate molecule into the two phosphates, which is brought about by the action of the pyrophosphatase enzyme, the reaction to reverse the polymerization (that reverse reaction being thermodynamically favored to occur) would make life that utilizes chains of nucleic acids impossible. Since the two-phosphate state is even more highly favored over pyrophosphate, catalyzing the splitting of pyrophosphate makes the overall chain of reactions practically irreversible. Pyrophosphatase also performs this life-saving action for other reactions in the cell, but this is the one of immediate concern in DNA replication.

We highlight this crucial step by representing in the model view the pyrophoshate given off with every formation of a new phosphodiester bond as a newly appearing ball traveling away from the reaction site and then splitting into two smaller balls. This is meant both to arouse the curiosity of the observer to read about what is happening and to reinforce the necessity of this step. A water molecule is also shown leaving the site of polymerization just to plant the idea that a condensation reaction has occurred, as is the case in the synthesis of all the important biological macromolecules. You can see this in the video clip linked to above. The water molecule and pyrohphosphate breakup are also shown in the OnScreen Gene Transcription iPad app’s simulation of messenger RNA construction.

The description of OnScreen DNA Replication as it appears on the app store follows.

Looks great on an iPad Mini as well as “full-size” iPads. Go see the short video excerpt on the nondummies.com website. We know of no other simulation, app or internet, that shows what happens in DNA replication as thoroughly as this app does. OnScreen DNA Replication shows all of the several steps (indicating the corresponding enzymes responsible for those steps) necessary for one double helix to become two identical to the original. Through the use of engaging 3D animations with a virtual double helix model (not a 2D ladder) it makes clear and memorable how DNA daughter strands are constructed nucleotide by nucleotide in replication.

Students from middle school on up can learn from the app, as no advanced knowledge of chemistry is assumed. The model is exactly the same as the one found in OnScreen DNA Model, a companion app that teaches the structural details of DNA, and in OnScreen Gene transcription, another companion app that shows how protein recipes are copied into messenger RNA. Detailed commentary on what the animations demonstrate in each step is available in a popover view, and a wealth of background material is to be found in a “Useful Stuff” popover.

The sequence of events in DNA replication unfold in three-dimensional simulations that don’t skip over the need for unwinding the DNA after the strands have been separated. The formation of a hybrid DNA-RNA double helix during the first step of primer RNA construction is correctly shown. DNA and RNA nucleotides are seen to move into place and then form hydrogen bonds with their base-pair mates in the template DNA strand. Important details about replication that are often given short shrift or omitted altogether, such as the essential role the enzyme pyrophosphatase plays in the cell, are included.

The concepts of leading and lagging strands and what the Okazaki fragments are and how they are constructed and then joined together through the actions of various replisome enzymes are made clear and memorable through the three-dimensional simulations in the Model View and the representations of enzymes in the Sequence View.

The “end problem” of linear DNA strand replication is not swept under the rug as often happens. Instead, the basic principle of how the enzyme telomerase uses its own RNA to extend the lagging DNA strand by means of reverse transcription is illustrated using simple models with only the RNA and DNA showing.

Set the simulation to pause after each new significant step or pause it only when you want. Commentary on what is happening is literally at your fingertip in a popover. Rotate, translate, or zoom the model during the simulated replication for a better view just by finger slide gestures.

The ball-and-stick model has the advantage of clarity at the expense of atomic detail. The replisome enzyme complex, while not shown in the view with the DNA model, so as not to obscure what is happening with bonds and strands, is depicted in the Sequence View below the model, thus making the point that it moves along the DNA, as it initiates and controls the reactions in replication. Furthermore, the actions of the individual enzymes that make up the replisome are also indicated in the Sequence View.

For efficient and enjoyable learning about DNA’s structure and how it works both to pass on protein recipes in transcription (messenger RNA construction) and to replicate itself into two double helix structures identical to the original, I confidently recommend the three apps OnScreen DNA Model, OnScreen Gene Transcription, and now OnScreen DNA Replication.