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.

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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.

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A Valentine Memory Revised

February 14th, 2013

In a Valentine’s Day post I made here in 2010 (A Valentine Memory: Art, Love, and Pain in the First Grade) I recalled an incident from back when I was in the first grade. At least I thought it was the first grade. I went back and forth trying to decide whether it was the first or the second, finally deciding to go with my longstanding conviction that it had been the first grade. My mind has evidently continued to work on the problem in the unconscious background, and I am now almost completely sure that I combined two strongly remembered events, separated by a year, into one, which was the source of my uncertainty. I recommend to anyone that wants to understand fully the rest of this post that they go back to the original post, linked to above.

The emotional truth remains. The terrible dread I felt as I had to make and then present the “I love you” cards to all the girls in the class was real. The pain of disappointment I felt as Carol tossed my card aside disdainfully was true, and I can still feel it. My mind knitted together the two events into a narrative that enhanced the story in a way.

I did have to make the cards for the girls in the first grade, but Carol was not the girl I “claimed” in the first grade. Linda Jane was. Linda Jane had moved across town before the second grade and attended a different school that year.

Carol was the girl whose esteem I most valued in the second grade, which seemed right as I was trying to decide before, since I knew Linda Jane had been every boy’s dream girl in the first grade. But in order to sensibly make the two events become one, I had pretty well convinced myself that by the second semester my affection had been transferred to Carol. The thing that really made me realize I’d been wrong is that I clearly had the feeling that I was in my second grade classroom, as I watched Carol look through her stack of Valentine cards. I am totally sure of that now, in a way I could never explain. Somehow that vague feeling of the room I was in kept getting stronger to the point of certainty. Yes, I was seven years old, and not six.

I was tempted not to make this confession of my having joined together into one the two episodes from my early life, but the very fact that my mind came up with a plausible way to do it is interesting, and full adherence to the truth demands disclosure to the few that have actually read the original reminiscence. I imagine—not saying I remember now—that I did give special care to the card I made for Linda Jane, wanting to please her and gain her attention.

I also imagine that there was something special about the card I gave to Carol, something that would distinguish it from the silly “Bee mine” cards, even though it was not handmade, as all the first grade cards had been. Yes, I’m feeling that. It must have been a more expensive and expressive card of the type a boy would give to his girl friend. I would not have been watching so expectantly for her reaction otherwise. That makes it even worse, as the intent would have been more obvious. Yes, I feel pretty sure that was the case now. There’s really no reason for me to have been so interested in her response otherwise.

So, all I got wrong was my hope that my artistic talent would win favor with Carol, but that is only wrong for the imagined card. I certainly did hope to impress with my drawing ability. Naturally, the only boy in the class that could draw as well as or better than I was Philip, the boy Carol really liked. I might as well illustrate that with another memory involving Carol and Philip. We learned cursive handwriting in the second grade, and our ability to form the letters beautifully was a great point of pride. Cursive writing, as we saw it, fit into the category of artistic achievement. I know we also viewed it as a step into maturity to master handwriting.

Philip, Carol, and I must have had seats in the classroom very close to each other. I recall a time we were working on our cursive writing. I was evidently very impressed with my results as compared with Phillip’s and saw an opportunity to gain an advantage over him in Carol’s eyes by drawing her attention to our writing and asking her to judge which was better. This was entirely my doing. Though only seven years old, Carol was diplomatic. They were both really good, and she really couldn’t choose one over the other. I knew she was just trying to spare Phillip’s feelings, but I was not letting this opportunity slip by. I insisted that she choose which got the prize. Seeing that I would not relent, she reluctantly admitted that Phillip’s was just a little better. I was dumbfounded.

That is the merciful end of the memory. I have no memory of any expression on Phillip’s face. Or Carol’s. If I argued the point further, the memory of it has been mercifully obliterated. Nor can I begin to make out what our writing samples were like. Probably they were similar. At the time I was sure Carol’s decision just showed how much she preferred Philip to me, since I could see, as anyone could, that my handwriting was clearly superior to his. Thus gross injustice was added to the disappointed hope of winning favor, which made it even more crushing, because it meant there was no hope for me with her.

But did I really abandon hope? Which came first—the handwriting contest or Valentine’s Day? In any case, I know I really fell for Carol Ann, Snow White to my Prince Charming (walk on role), in our class’s stage production of Books Are Our Friends before the year was over. Sadly, she moved out of town in the summer. But the memory of regret is weaker than the memory of rejection.

So strange to enter again into my seven-year-old mind and feel once more the staggering smackdown of the handwriting judgment. I can never know how my life would have been different, if in any significant way, but for that hard lesson, but I know that it taught me not to be so sure of myself, perhaps at the everlasting expense of my self-confidence. In any case, those memories of painful disappointment (along with those of great joy) are among the few that persist.

ADDENDUM (February 15, 2013): My mind has not stopped trying to complete my memory of those long ago Valentine’s Days and has come up with yet another version that brings the two events closer to the single one I described three years ago. I have come to believe that I did make a Valentine card for Carol in the second grade. I’m sure it wouldn’t have said “I love you,” but it might have said “Be my Valentine.” It would have been the only one I made by hand that year. It’s a little hard for me to imagine myself having the courage to do that, but when I think about how I watched to see Carol’s reaction and how crushed I was when she tossed it aside with hardly a glance, I feel that it had to have been a rejection of more than a card I had bought. As I mentioned above, I did rate my artistic ability highly, never mind how accurately. It would also explain how I so easily conflated the two events when I first wrote about them. As of now I’d say I’m 95% sure that the making of cards for all the girls at the insistence of my mother was in the first grade and 95% sure that the watching for Carol’s reaction when she looked at my card was in the second grade. I’m at a somewhat shakier 90% certainty that it was an artistic creation of mine that Carol disdained. And that is the last I will have to say about it.

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Conned in Cannes

July 7th, 2012

A Facebook friend’s posting of a picture of Les Beaux-de-Provence has reminded me of a trip I took to the South of France by rental car from Torino back when I was working there for a year (see The Perfect Italian Woman for a little about that) and how I have had in mind that someday I’d write here about a couple of incidents in that short trip for this totally neglected blog. I know no one is actually coming to this blog expecting to find anything new by now, but I will apologize to such an imaginary person for having dropped out of the blogosphere for so long. The reasons are twofold: my tweeting away (i.e., on Twitter as @onscrn) all the pent up desire to communicate something about my thoughts to others and my spending time developing apps for the iPhone and iPad. Enough about that.

Anyway, it was late March and a time when I was feeling alienated from Italy and desperate for a change of scenery and culture. I rented a car and took off after work on a Friday without a very clear destination, but knowing the South of France was a place I’d been wanting to visit, so it didn’t matter exactly where I went when. I had some regional Michelin guides to refer to. The drive did nothing to make me regret my decision to take a break from Italy. Almost all the roads were toll roads, which raised the cost of the trip considerably above what I had estimated. There were carabinieri stroking their machine guns at one of the toll entrances. Those kids with the lethal weapons always made me nervous. Fortunately, they were only stopping traffic and searching cars going the other direction.

My first interaction with people in France wasn’t encouraging. I pulled over at a truck stop outside of Nice for supper and got steak, fries, and a beer. I swear the piece of meat had gone bad before cooking. The people there weren’t friendly, and I couldn’t help wondering if they’d knowingly pulled out the spoiled meat for the American traveler. I ate only a bite or two of the meat and left without saying anything about it, feeling dissatisfied with myself for having accepted the inedible meal without protest, but not having it in me to demand a new steak or my money back, especially in French. If the proprietor had been interested in having a satisfied customer or had any pride in what he served, I think he would have said something to me on seeing how little I’d eaten. I imagined the laughter that had followed my exit. By the time I got to Cannes I was really tired after five or so hours on the road and was glad to find a cheap hotel there for the night.

For what follows I should explain that I have a tendency to hypoglycemia or low blood sugar. This trait is most strongly manifested in the morning, where I operate at a low level before I’ve had a good breakfast, by which I mean protein: ham and eggs, for example. I’m able to prepare my own breakfast easily on auto pilot in my own kitchen, but if I’m traveling I need to find a place that serves a real (not “continental”) breakfast before I can do anything that requires much in the way of brain use. Finding such an “English breakfast” as it seemed to be called on the tourist trail in Italy had sometimes been difficult on my travels there, but I had usually been able at least to find a coffee bar that sold panini with ham and maybe hard-boiled eggs. I sometimes carried a few small tins of tuna fish for an emergency protein breakfast. I had no such backup for this whim of a trip, but when I’d been in Paris I had been able to get a couple of eggs nature (sunny side up) in the morning, so I wasn’t too worried about finding breakfast in France.

The Cannes hotel I stayed in had no restaurant, so I set out the next morning in the car to find something to eat before heading on to Arles, where I planned to spend the next night. It was a beautiful day as I recall, though cool. This was too early in the year for there to be a beach scene, not that I would have been a part of it anyway. The beach was deserted, which suited me fine, and the sea was smooth, the sky clear. Driving along the beach, I came to a good-sized café that I figured must have something to eat. The pickings turned out to be very slim. I bought a café au lait and a couple of croissants, which to my dismay were quite sweet. A sweet croissant was worse than a regular one, which, being heavy on the carbohydrates, was bad enough. Sugar, for one that’s hypoglycemic, stimulates overproduction of insulin, which in turn leads to the sugar level dropping to a level even lower than before the eating of the sugar.

I was in a familiar slightly dizzy and definitely dumber than usual state as I got back into my rental car and proceeded on to the Cannes Bureau de Change to convert some more of my Italian lire into spendable French francs. This was of course before the Euro came into use, or my adventure would never have occurred.

It was late enough for the Bureau de Change to have opened, but there was no one about on the street as I walked to the Bureau after parking the car. Then an irritatingly friendly guy suddenly appeared, intercepted me in the street with a greeting, and started up a conversation with me. He began in French, then switched to English when I didn’t respond immediately. Was I English? From London? Oh, American. He had a sister in Washington DC. It was so expensive to live there. How did I find prices in France compared to those in the US? I told him I hadn’t had a chance to find out yet. I believe I would have probably said I was in a hurry and gone about my business if I had had a decent breakfast, but there’s no way to know.

Not surprisingly, given his flood of attention on me, the guy turned out to be a kind of salesman. He imagined I was on my way to exchange my money for French francs, and was in the business of exchanging money himself, but on the “black market,” which was the way he described it. He could give me a great exchange rate on my dollars.

I told him I had no dollars, but any disappointment he had at this news was fleeting, as he assured me that Italian lire were also in great demand by the French. He said that Mitterand limited the amount of French currency that could be taken out of the country, presumably thus limiting how much French travelers could purchase in other countries. He mentioned things such as Italian leather goods French tourists liked to buy in Italy. I didn’t quite understand this, but I assumed if a black market for lire existed there must be a reason for it, even though I knew the lira was supposed to be “weak.” He was ready to give me an exchange rate for my lire that was well above the official rate.

He showed me his French money and offered to let me go purchase something small with one of the banknotes to demonstrate its genuineness. I seriously doubt the possibility of counterfeit bills would have occurred to me, but I suppose his offer made the whole scheme seem more credible, though it could have had the opposite effect of raising suspicion of trickery. The guy was probably in his mid twenties, and his general appearance was a bit sleazy, but that was probably to be expected in his line of work.

I would never have thought to go looking for a way to get a few extra francs for my lire. But here the guy was, so maybe I should take advantage of his offer. Maybe I’d be foolish not to. Was the official rate just for chumps? He was just doing his job, so why shouldn’t I help him out? Maybe everybody in the know did it. My political orientation in those days was such that I had no scruples about violating a bourgeois rule governing the exchange of money.

Still, since the guy was working outside the law and I had no great interest in a marginal gain, why should I perhaps put myself at risk? And why should I trust someone that was in the technical sense a criminal after all? I didn’t focus on those practical aspects of the situation that much though. I think the black market for lire idea still sounded a little fishy to me, so I wanted to make sure there wasn’t trickery involved in his offer. With my brain practically running on empty, I struggled to quickly do the exchange rate computations in my head to be sure he wasn’t making me an offer that was actually lower than the official rate. What was the catch? Was he really planning to cheat me? This should have been an easy comparison of one rate to the other, but what does the rate mean anyway? Which way does the rate need to change for me to be coming out ahead? Was it francs per lira or lire per franc? I kept doing the calculation wondering if I wasn’t after all making a mistake. Was he actually quoting a price that was a factor of ten off? Maybe the guy just relied on people not knowing how to calculate the difference.

So there I was, somehow stuck talking to the guy and repeating the calculation in my head, as though that was what really mattered. Looking back at it, the episode had a certain dreamlike quality to it, the kind of dream I sometime get stuck in right before I’m completely awake in the morning, condemned to repeat a calculation or computer task over and over in an endless loop.

The illegality of the proposed transaction and its inherent risk was suddenly emphasized when he said to me “She’s watching us!” I didn’t turn to look to see who “she” was since he told me not to look. He led me around the corner, presumably out of her sight. I thought maybe he was a little paranoid. He continued to be concerned about this woman he assumed to be with the police the rest of the time we were together, mentioning that she was watching us a couple of times more.

I agreed to sell him 100,000 lire. He dismissed this as “nothing.” Inexplicably in his spell, I agreed to double the amount to 200,000, which was worth about $125 at the time. So now it was time for money to change hands. And indeed “she” was still watching.

He had a standard way of proceeding, of course, and told me not to hand him the Italian money yet, but to keep it in my pocket. Perhaps, I assumed, due to some experience of his with disputes with “customers” after a transaction or just having the wisdom to eliminate the possibility of such disputes, he insisted that I count, bill by bill, the wad of French money he was about to give me, just to verify it was the correct amount. And it seemed a good thing I had counted, for the sum did turn out to be short by 100 francs. But he took the money back and pointedly added a 100 franc bill to make up the difference before handing me the French money. Having the francs safely in my pocket, I handed him my Italian money, which he didn’t bother to count. This was done very quickly to be sure no one would see us. I did wonder about the money counting exercise. Had he deliberately left one bill off? And if so, why? Perhaps he just wanted to demonstrate how right he had been that the counting was necessary?

He was in a great mood at the end of our business, really on top of the world it seemed. He walked with me back around the corner in sight of the Bureau. He asked me what I was going to be spending all those francs on, mentioning I think, some of the food and wine it might procure. He asked me how long I was going to be in Cannes, and I answered truthfully that I was leaving right away. He shook my hand with great pleasure, once again telling me to enjoy spending my French money. I was glad to be rid of him, and went on to my original destination, the Bureau de Change to get yet more French money in exchange for my Italian.

Once inside the office, I pulled out the dozen or so bills he had handed me and glanced down at them. Perhaps I shouldn’t have been quite as shocked as I was to see that my big wad was, except for the the outer bills, composed of cut up newspaper! I was, however, dumbfounded.

What a laugh! Here I had only been worrying about whether the rate made sense as a win for me, never suspecting that I would be so completely cheated. Conned! Everything he had done and said had been directed to getting me to swap the money quickly (she’s watching us!) without looking at it. Except he had given me the illusion of having checked it carefully, bill by bill. He had obviously made a quick switch of the wad of fake bills for the wad of real ones when he added one real bill after I had had my hands and eyes on the real ones. Fortunately, something had kept me from giving him all my money. He had never convinced me that there was no way he could be cheating me. I had never considered the possibility of a switcheroo though.

As I sat down to write about this incident, the most important detail seemed to be my state of lowered mental capacity due to having low blood sugar. That’s why I explained how eating sweet croissants had made it worse than if I’d skipped breakfast altogether. Now I’m not so sure. Perhaps I would have just passed on by the annoying salesman if I’d had my usual breakfast, but would I really have been less susceptible to his techniques of manipulation? Yes, my diminished capacity made me struggle to calculate whether the rate he was offering was really the great deal he claimed it was, but my willingness to make that effort meant that I had already agreed that having it be true was desirable and that I was inclined to complete the deal as soon as I confirmed it. I would probably have been no more capable of catching on to what was happening once I had landed in his web than any other naive person.

The man was a pro. Let’s review his technique a bit more. First he sought to engage me in friendly conversation, but every question had a purpose. Of course I was on my guard, knowing he was almost certainly wanting to sell me something, but I, like most people, find it difficult to be rude even to someone with an unwanted proposition for me. Once the guy knew where I was from he would likely know what kind of money I had. He missed that one, but quickly switched to saying Italian lire were also in demand by the French. I imagine the question about how I found prices in France compared to those in the US was to give him an idea of how much money I was planning to change based on what kind of items I compared prices on, or perhaps to see how long I had been in the country.

He quickly moved on to the subject of money changing, using the term “black market,” which is something Americans have heard of but are likely to have little or no experience with. It has the ring of something that is outside normal channels, but probably so widespread that it’s basically condoned. It’s something the average tourist may not get to participate in, so it has a certain allure from that standpoint. At this point all of his emphasis was on the big advantages and the commonplace nature of dealing with him.

As an aside, I just found through google an article online advocating that travelers (and I mean currently) take advantage of black market rates of exchange in countries with overpriced currencies. Evidently there are illegal banks set up for these transactions.

The offer to have me make a test purchase with one of his banknotes was probably designed more to draw my interest in the potential transaction than to reassure me of the authenticity of the money. Anything that could engage me on the path to a final deal was to his advantage. Once he had me well on the road to a black market transaction, which was really not that big a deal to the authorities, he could inject the reality that what we were doing was not without jeopardy, since illegal, and thus speed the transaction along. By giving me the idea our actions might be being watched, he made the quick, hidden exchange of money seem prudent.

His raising possible ways an unscrupulous black market dealer might cheat someone (using counterfeit money, short-changing me) and then satisfying me that those were not an issue with him were also no doubt designed to give me confidence and keep me from considering the one true way he was about to rip me off. In my case the raising of the cheating possibility worked to his advantage since it diverted so much of my attention to checking the reality of the advantage from the exchange rate he was quoting. Of course the ruse of first giving me the banknotes to count and then showing me the one he was supposedly adding to the ones I had just counted was crucial. It’s the classic misdirection of attention every magician uses when making a quick switch.

Beyond his techniques, the psychology of the con man is something I find interesting. I think there must be kinship between the con artist and the compulsive gambler. The gambler may lose all his money, the con man may go to jail. For each, success brings the elation of having gotten something for nothing by having taken a risk that the contemptible ordinary lot of humanity is too cowardly for. But the successful con artist has a bonus in knowing he has succeeded not by being the darling of fortune but by manipulating a person into doing his will, thus demonstrating his superiority to that dupable one.

I can’t help thinking that it was the success of his trick that elated him more than the monetary gain that verified it. He had outsmarted the gullible, hence contemptible, foreigner. He definitely took joy in knowing that I was there with scraps of newspaper in my pocket which I would soon discover. Why else would he talk about the wonderful things I’d soon be buying with it? Perhaps he would regale his partners in crime with the story. But beyond that he knew that I would recall his words as a derisive twist of the knife. I think this reveals some additional malevolence in the con artist’s feeling of superiority over the one he has duped.

But let’s not forget the con artist’s kinship with the actor! No wonder he prolongs the parting from his latest sucker with handshakes and congratulations. They have to take the place of the applause from the audience and his bows of acknowledgment.

I don’t think I could be taken in by a scheme like that again no matter how low my blood sugar was, and not just from having learned my lesson, for the truth is that had I not been willing to break the law the guy wouldn’t have gotten me that time, and my general principle is to obey the law now, even if I don’t think it’s a good or important law. Well, I drive a little faster than the speed limit, but that’s not a crime. Really. Is it? Just a few miles per hour?

I was mad when I discovered the expensive trick that I’d fallen for, but mainly at myself for having been so stupid. I took perhaps an overly charitable view of the swindler’s behavior, since it was, after all, his way of making a living. I hardly considered the possibility of hanging around in Cannes hoping to catch the guy and demand my money back. He probably had a contingency plan for that and could pretty well count on my not going to the police with a complaint. It was sort of like my response to the bad meat I’d been served the day before. Put it behind me and hope for a better time to come.

Ah, another realization just came: how neatly my possibly having been served inedible meat on purpose and possibly having been the object of derision after my departure from the truck stop foreshadowed the undeniable cheating and derision that followed the next morning. My congratulations to the comic novelist that was authoring my life at that time! Things did start to look up in Arles, though there was disillusionment in store there also. That story may yet be told.

It has occurred to me that the other actor in this story, though by now far from young, might still be running through his act outside the Cannes Bureau de Change. Or perhaps someone else has taken over the business, as I’m having trouble picturing my old friend being able to pull off his trick as old as he must now be. The techniques have surely been developed over many years, so there must be a sort of school for con artists to get all the details down. If anyone reading this happens to go to Cannes, I’d love to hear if the game goes on.

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We’re Celebrating DNA Day (April 20) with a One-Day Sale: All DNA Apps Only 99¢!

April 20th, 2012

From the National Humane Genome Research Institute website: “DNA Day is a unique day when students, teachers and the public can learn more about genetics and genomics! The day commemorates the completion of the Human Genome Project in April 2003, and the discovery of DNA’s double helix. This year, NHGRI will celebrate National DNA Day on April 20, 2012.”

We are reducing our price on DNA-related apps to 99¢ for the day. The apps to be priced at 99¢ on April 20 are:

OnScreen DNA Model for iPad (regularly $3.99)

OnScreen Gene Transcription for iPad (regularly $3.99)


OnScreen DNA Model for iPhone (regularly $2.99) 

OnScreen DNA Model on the Mac App Store (regularly $3.99)

The OnScreen DNA Model apps 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 phenomena of DNA: denaturation, in which the strands separate, and renaturation, in which they reunite.

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 animations, are described in some detail, emphasizing the role of certain enzymes.

The apps show details of structure and process that are sometimes depicted in erroneous ways in places that should know better. 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.

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OnScreen Gene Transcription Shows How DNA Works

February 10th, 2012

It took longer than I thought it would (no surprise there), but the second installment  of a projected three-app suite to teach the structure and function of DNA has been approved by Apple for placement on the iTunes App Store. The title of the app is OnScreen Gene Transcription, and it’s for iPad only.

mrna construction

Here’s the app description:

What good is DNA, anyway? OnScreen Gene Transcription uses engaging animations with a virtual double helix model to make clear and memorable how a recipe for a protein stored in a DNA gene sequence is made available for use by being copied nucleotide by nucleotide in the construction of a messenger RNA molecule. 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.

The sequence of events in gene transcription 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 RNA construction is correctly shown instead of the two-dimensional ladder structure sometimes depicted. Important details about transcription that are often given short shrift or omitted altogether, such as the essential role the enzyme pyrophosphatase plays in the cell, are included.

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 transcription for a better view just by finger slide gestures. Background material on DNA and RNA are found in the Useful Stuff popover.

The ball-and-stick model has the advantage of clarity at the expense of atomic detail. The RNA Polymerase 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 transcription. We know of no other simulation of gene transcription on the internet or anywhere else that shows what happens as thoroughly as OnScreen Gene Transcription does.

Following the lead of its companion app, OnScreen DNA Model, the new app includes a Useful Stuff popover (hidden unless summoned) with several items, some of which are extensions of those found in the earlier app with mention of how a feature of DNA also is found somewhat modified in RNA and others that are specifically on topics of gene transcription. An example of a Useful Stuff item can be seen in the screen shot below.

useful stuff popover

The Mac and Windows software (OnScreen DNA) which inspired the iPad apps makes use of a tutorial format, with comments for before and after steps in the simulations displayed in a small window that is always visible to explain what is happening. There’s not room for this on the iPad, but the commentary on the gene transcription steps is available in a popover, hidden from view until the Commentary button is tapped and then hidden again by a tap anywhere else on the screen.

transcription commentary

OnScreen Gene Transcription joins OnScreen DNA Model in the Medical category on the app store, since Apple hasn’t yet realized the need to have a Science category. The Nobel Prize for Medicine usually goes to biologists, so it’s not terribly miscategorized, I guess. Since it is an educational app, why don’t I put it in the Education category? It’s mainly because that category is swamped by toddler and early learning apps, and the chance for visibility is very small unless an app is somehow featured. Anyone deliberately searching for a DNA app through the App Store keyword search will find the app not matter what category it’s in.

I was pleasantly surprised and gratified to see that someone at Apple had recognized OnScreen DNA Model was a biology education app and had seen fit to put it in the featured Life Sciences: General Biology section of the iPad Education category that turns up on the iTunes App Store, desktop version. It has definitely helped sales. OnScreen DNA Model is my top selling app, and the Mac version is doing relatively well too. I’m hoping to see OnScreen Gene Transcription appear in the same featured section as OnScreen DNA Model. Unfortunately that would seem to mean another app would have to be bumped, if the limit is twelve per section. I could give Apple a hint that any app that shows DNA as a left-handed double helix in one of its screen shots shouldn’t be featured, which would take care of that problem. It is not OnScreen DNA Model that makes that basic error.

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Coming Soon to the Big Screen—OnScreen Pitch Count for iPad!

July 2nd, 2011

I am happy to announce that OnScreen Pitch Count, my app for recording, calculating, and reviewing pitch results and stats of baseball and softball games will be available in a new version for the iPad on the iTunes App Store very soon. Barring the last minute discovery of a bug, which I don’t expect at this point, I’ll be submitting it for review in the next couple of days. For news and more information about OnScreen Pitch Count and other apps from OnScreen Science, Inc., see the web site nondummies.com or follow me (@onscrn) on Twitter.

I think I’ll just show one screen shot from the new app now, since I’ll probably want to make another short blog post when it’s really on sale, and I can show more then. The one below was taken from a game I was recording to test the app. Cliff Lee of the Philadelphia Phillies had just had his no hitter broken up by the leadoff batter in the sixth inning, as you’ll be able to see if you look closely at the stats. Well, they may be too small to see there, but you’ll have no problem reading them full-size on the iPad. The hit is about to be registered. The general layout of the screen is described in some detail below.

ipad pitch count

As a further preview, here is the description of the app as it will appear on the App Store (subject to modification):

OnScreen Pitch Count, the most highly regarded pitch stat app for the iPhone, has come to the big screen! Designed by a baseball/softball coach who knows what coaches and fans need to know about pitch results, OnScreen Pitch Count stands out among pitch count apps.

Increase your enjoyment of ball games by giving more attention to the details in a way that’s not burdensome. OnScreen Pitch Count is just the right medium between barebones pitch counters and extremely detailed apps.

With the big screen of the iPad you can see lots of stats at the same time, even as you record pitch results. And you can transfer the results you’ve already recorded on the iPhone to the iPad just by emailing the app file as an attachment, as the files are compatible between the two versions.

OnScreen Pitch Count allows you to keep the running totals of

• kinds of strikes: foul, swinging, called, ball put in play
• third strikes: swinging, called
• balls
• total pitches
• first pitch strikes and balls
• strikes and balls in the last ten pitches
• batters faced
• outs recorded
• strikeouts
• base runners
• how many runners reached base by: walks, hits, errors, hit by pitch, other
• runs allowed
• wild pitches

just by tapping easily learned buttons on the screen.

If your interest is in one particular pitcher, you can just follow that one. If you want a complete record of pitch results for every pitcher in the game on both teams, you can track them. There is no limit to the number of pitchers you can record in a game, and OnScreen Pitch Count properly charges runs to pitchers who allow base runners but leave the game before the runners score.

As you record pitch results, you see the cumulative stats of the pitcher updated immediately on the screen. Display total numbers as well as percentages at the same time. Compare the current pitcher’s numbers with the opposing pitcher’s. The stats are on the screen to see. While recording a game you can see the stats for up to three pitchers at a time. When reviewing previously recorded games, you can see four at once. Or compare totals and percentages side by side.

As you record pitches you also see the count on the batter and the number of outs and baserunners, so you never lose track of what the situation is.

Did you tap the Ball button, only to hear the umpire call the pitch a strike? No problem. Tap the Undo button to take the ball away. Tap the Strike button to correct the count. The results of up to two consecutive pitches can be undone. In case you’ve somehow lost track through a distraction, you can edit the count on the batter, outs in the inning, or number of base runners, though the undo feature should be used when possible.

What if you record a strikeout for the third out, only to see the catcher drop the ball and the runner reach base safely? No need for the Undo button. Tap the button for batters reaching base by ways other than putting the ball in play; select the case for reaching base after a strikeout; and the out is then removed, while the strikeout remains tallied, and the number of base runners increases by one.

After you’ve finished with a game, which can be as soon as the pitcher you’re interested in has finished, the results are automatically stored on your iPad for later review, and you can email the results of a single pitcher or all those on the team. Email just a text summary of the results or attach a csv file that you can import to a spreadsheet. AND, if you know someone else with this app—either the iPad or the iPhone version—email them the actual file you’ve recorded for them to view with the app on their device. Or email the file to yourself as a backup.

OnScreen Pitch Count has been available for the iPhone and iPod Touch since August of 2009, and of course that version can be used on an iPad, but only in a sort of little iPhone window on the iPad screen or blown up with pixel doubling, which simply magnifies the iPhone image, while making it look worse. Running the iPhone version of OnScreen Pitch Count on an iPad does not free the app from the iPhone’s limitations, most notably its small screen. The iPhone’s small screen is just the price one pays for its great portability and convenience.

I was gratified and relieved to see that as spring and a new season for baseball and softball in the USA arrived earlier this year, sales of OnScreen Pitch Count ramped up nicely and were running well above the previous year’s level. This indicated that there was an ongoing need for the app and that a fair number of people were taking the trouble to actively search for pitch count apps and then to splurge on a $3.99 app based on the app description, screen shots, and high customer ratings they could see on the app store. It would be interesting to know how many of those who download OnScreen Pitch Count do so after disappointment with a cheaper competing app. My guess is quite a few, so that in a way the higher price of OnScreen Pitch Count compared to its competitors may actually be giving them more sales, as people decide to “risk” 99¢ first.

OnScreen Pitch Count, while not making enough money to brag about, has been a hit, in terms of user enthusiasm. This is evident in the user reviews, which abound in exclamation marks and high praise, and in the emails I’ve received. Some of the reviews are so glowing (“The best app I have ever bought!!!!”) that I worry that they’ll be seen as bogus, but they are 100% real reviews. Well, there was one negative review that I’m 99.99% certain was actually meant for a competing app, since the specifics of the comments clearly applied to the other app and not at all to OnScreen Pitch Count. That one hurt sales for a while and probably cost me a couple of hundred bucks. I plan to write about app developers’ susceptibility to harmful, uninformed reviews sometime. Anyway, despite having sold something less than 1,000 copies of the app, I feel very satisfied to know I’ve conceived and created an app that a good number of people have found very useful, even delightful. Would that there were a way to get the word out to the many other parents, coaches, and fans who might also love it if they only knew about it!

Sometime back in March I decided that my next app development project should be bringing OnScreeen Pitch Count to the iPad. I hoped that I could have the iPad version finished sometime in May so that it wouldn’t entirely miss the peak time for baseball and softball, which means Little League and high school seasons. That time constraint for peak sales potential was really the determining factor in my decision to work on this app next. I hadn’t thought through exactly how I would take advantage of the greater screen area of the iPad, but I knew it would be possible to eliminate a lot of switching from one view to another as compared with the iPhone version.

As is usually the case, the job took longer than I’d hoped. Back when I first started app development I had also originally meant to get OnScreen Pitch Count for the iPhone ready for a spring debut, and had barely gotten it on the App Store while it was still August, so there has been improvement!

I had already developed an iPad app (OnScreen DNA Model) but in that effort I had been able to avoid one complication that I’d have to deal with for OnScreen Pitch Count—the need to make the app completely usable whichever way the user wanted to orient the device. Apple reviewers are pretty insistent on this unless you have a good reason not to, which I was able to argue for in the case of the DNA model. For an app with numerous user interface elements and data displays in various views on the screen, this is not a trivial task. I guess it probably added a month to the development time. Knowing what I now know, of course, I could do the same thing again (and with better code design) in a much shorter time. Every app developed makes it that much easier to develop the next.

The main question to address was how was I going to use all that extra screen space to enhance the app? I wanted to use as much of the iPhone app’s code as I could and also make the iPad app seem immediately familiar to anyone that already had the iPhone version. One of the difficulties in adding a new type of pitch data to the iPhone version is the lack of space on the screen to present it. I’ve had users request the ability to record and see first pitch strikes and balls and the number of strikes in the last ten pitches, for example. There was room for these and more on the iPad screen, so I couldn’t use the lack of space excuse on the iPad and have indeed coded the iPad app to keep track of these numbers. The users of OnScreen Pitch Count for iPhone can expect to see these features incorporated in an update before long. I’ll come up with a way to show the new data, even if it’s not a pretty way.

I played around with a number of ideas on how to use the extra screen area of the iPad but eventually decided that the default (and currently, only) use should be to display pitch result data for the different pitchers in the game. All those results are available for viewing with the iPhone version, but the user has to swap out the pitch recording screen in order to see the complete pitch results, and still the results can be seen for only one pitcher at a time, even for completed games being reviewed.

The bottom right panel of the iPad contains the buttons for recording pitch results and a display of the current situation: count on batter, runners on base, and outs. The lower left panel shows the cumulative pitch totals in various categories for the pitcher currently on the mound. These are updated after every pitch. The default layout is then to have the same data displayed in the upper left panel (also kept current), only in the relevant percentages that go with the numerical totals show below it The upper right panel displays the totals for the pitcher on the opposing team, if that team’s pitches are being recorded. If there are more pitchers, or if the user wants to display percentages for a pitcher other than the default, he or she can make that choice. So there are three panels available for showing pitch totals while a game is being recorded with the lower left panel always showing the current pitcher. For reviewing completed games, all four panels are available for displaying pitch results at the user’s choice, both in terms of which pitcher and whether totals or percentages.

The last major upgrade feature added to OnScreen Pitch Count for iPhone was the ability to send as email attachments files containing the recorded pitch data in a format that anyone with the app could read and display on their own device. In addition to file sharing this feature provided a way to back up files on any computer. Of course, I wanted to make it possible for users of both the iPad and iPhone versions to share each other’s app files as well, and this turned out not to be that difficult. So anyone with games recorded on the iPhone version can email them to the iPad for viewing the data of up to four pitchers at once.

I’m really glad to have the basic coding of this app behind me and can’t wait to see how people with iPads like it. As always, I invite anyone with a problem, question, or suggestion to email apinfo@onscreen-sci.com.

Maybe I’ll take a break from coding long enough to write something for this blog, or should I say blog archive, since that’s all it’s amounted to for the past several months?

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A Memorable, Otherwise Worthless, Evening

February 12th, 2011

I have a list of possible blog subjects, mainly memories of events in my life that made a sufficient impression on my mind to endure at least in outline, while most of my life has faded from memory. There is no plan or ordering of when, if ever, I’ll choose one to write about. Some are of events in my life that are hard to take up because I know I can’t really do them justice.

The memory I turn to today is not one of those. It comes from an aimless time in my life in which one day was much like another, in the actual living as well as the memory. Why this atypical, yet far from momentous, evening with a barroom setting has come to the top of the list today I cannot say. Yet there it is, and it will get its few words now and be checked off the list for good.

Although I can’t be certain of the time, I believe it was during the winter after I returned to Cambridge, Massachusetts from Italy, some twenty-six years ago. Now that I think about it, the heaps of snow everywhere outside now as I write may have helped turn my mind back to an earlier similar setting. In truth I can’t be sure whether it was before or after my year in Italy. I’m only sure it was a time when I was without girlfriend or wife and thus totally adrift.

I started the evening out in a certain restaurant and bar in Harvard Square. It was a weekend night, probably Saturday, and the place was already crowded when I got there, with no stools free at the bar. I drank my beer standing. I really wasn’t there with any purpose; I wasn’t planning to meet a woman or engage in conversation or get drunk. It was just a place to be amidst people that to me were neither intolerable nor very interesting. Nor likely to turn violent, which is a consideration when choosing a bar. Being there was more appealing than being home alone, though I can’t even say where that was at the time.

Standing near me was a rather small fellow who evidently felt our proximity called for conversation, as though we were guests brought together for the first time at a party. I didn’t really care to talk, and I can’t remember how the conversation started, but I do remember that the man’s name was Seamus, which was a name I’d never encountered before. Seamus was not a man to put one at ease, because he didn’t look to be at ease himself. I don’t know how long we’d been talking before the subject turned to baseball. That made a big difference. Seamus told me how relieved he was to hear I was interested in baseball, because he had been anxiously searching for a subject of mutual interest, and now, having found one somewhat unexpectedly, he could relax. I would have preferred to silently drink my beer in the semidarkness, thinking about nothing, interacting with no one, but I give Seamus credit for not accepting such a sorry situation. I don’t remember anything else about my time there that night, but I must have been there for hours.

This bar had an earlier closing time than some. It’s not much fun to be at a bar when it closes. I can’t remember if I ducked out before that happened or not, but I do know that instead of going home I headed on foot for a nearby bar that had a later closing time.

The other bar, which doesn’t exist anymore, was called the Ha’penny. It was a small bar I seldom went to, and I seem to recall that it was somewhat below the street level. There weren’t many people in the bar this night, but the atmosphere was convivial. The young bartender (whom I doubt I had ever seen before) greeted me and straightaway introduced me to the man next to me at the bar, or rather announced to me who he was: Seamus, the poet. Two Seamuses in one night! How strange to have gone through my whole life without hearing a name, and then to meet two with it on the same night. I think the bartender may have said Seamus taught at Harvard. This Seamus seemed calm and self-assured, in contrast with the first Seamus I’d met.

There were only a few people in the bar, among them two young women with a male friend, and another guy sitting silently alone. There were probably others, but those are all I remember. It was a much more intimate and friendly scene in the Ha’penny than the one I’d just left. Soon I was engaged in a conversation with the women and the poet. I can’t remember talking to the man who was with the women, but I don’t have the feeling he was attached to either of them. The women were both nurses.

One of the nurses lived in a town across the Charles River. She was not unappealing, but her looks couldn’t compare with those of her blonde friend, who was visiting from Colorado. She was gorgeous. The women were seated around the corner of the bar from where Seamus and I were standing.

As we all talked, the woman from Colorado leaned back, knees above the bar level, revealing lovely thighs. “Look at that,” I said to Seamus sotto voce, which wasn’t exactly poetry, but spontaneously expressed what I felt must be a shared sense of awe for the feminine beauty before us. It was not something I would normally have said to a stranger, or anyone for that matter, so I must have felt a quick rapport with this poet, though the effect of the beers I’d drunk can’t be discounted.

I don’t remember anything of our conversation beyond the facts already related, but I know we must have talked with the nurses for some time after that. The next thing I do remember was an eruption of ugliness that broke the evening’s spell. The previously silent, sullen young man at the bar, whom we had all ignored, was on this feet shouting “You’re all a bunch of assholes!”

He stood there looking around hatefully through his drunkenness as though waiting for someone to challenge his assertion. The suddenness of the outburst and its striking contrast with the prevailing spirit it so quickly chased away was stunning really. I think he may have continued to repeat his proclamation. A response seemed necessary, yet none of us responded. Seamus obliquely excused our inaction by saying to me “The man might be a poet,” and I nodded my concurrence, but without really pardoning myself. What should one’s response be to the equivalent of a mad man’s raging? Perhaps if I myself had been totally sober it would have been easier for me to shrug it off as merely something to get away from.

I don’t remember the bartender intervening in any way with the aggressively unhappy drunk. Maybe it wasn’t unusual. Maybe it was nearly closing time anyway. The next thing I can recall is being outside in the cold shortly after the nurses and their male companion had left the bar, driven out basically. We were parting with no plans to meet again.

The two women and the man crossed the street to where their car was parked, while I headed up the street toward home, wherever that was. There was snow piled up beside the streets. Then one of the nurses is shouting. “Bob! I love you, Bob!” I look back, see it’s the local one, wave to her, and walk on. It was one last thing I’d remember from that night, something that could boost my ego a little (and counter the shame I was feeling for my passivity in the face of loutishness), even if the way my apparent conquest had been announced pointed to the local nurse’s having been more than tipsy.

So far as I know I never saw either of the nurses again. I may never have returned to that bar. I think I must have seen the first Seamus again, but never the second, though I did meet someone later who had taken a writing seminar with him. I wonder if his memory of that night is better than mine, if he remembers details I don’t? A poet might.

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Taking OnScreen DNA Model to the Mac App Store

February 10th, 2011

I’m happy to say that OnScreen DNA Model for Mac, barring an unexpected delay by Apple’s gatekeepers (it’s been waiting for review for a week), will soon be available on the Mac App Store. Check out nondummies.com for news. I’ll intersperse a few screen shots from the app below as a preview of things to come. While I’ve read of some independent Mac developers worrying about what the advent of the Mac App Store might mean for their sales and profits, I am almost certain it will be beneficial for the OnScreen Science, Inc. apps.

macapp

The Mac App Store (limited to Macs running at least OS 10.6.6) provides a virtual shopping center for Mac users wanting to purchase software to run on their Macs or just to browse through the selections—conveniently categorized—for future reference, much as the iTunes App Store has been doing for iPhone and iPad users for quite some time.

Of course Apple keeps 30% of each sale for itself, but in addition to the great drawing power of an Apple-run app store, it’s providing a lot more for that. Start with buyer confidence. If an app is for sale on an Apple-run app store, Apple has at least verified that it is not obviously buggy nor, in the reviewer’s judgment, totally worthless. Furthermore, buying the app is very simple, as the buyer’s credit card info is already in Apple’s (presumably secure) possession, and installation of the app on the user’s computer is automatic and immediate. And the procedure will already be familiar to many users from earlier experience with iTunes and its App Store.

Each app approved for sale on the app store is given a chance to present its best face through the developer’s own description and up to five screen shots (chosen by the developer), showing the app’s features. I should add that the feature page for the app can also serve to give users clues as to which apps are likely “crap apps.” Personally, I’m always a little suspicious of apps with only one or two screen shots.

Apps not only appear (with name and icon) in the array of apps displayed by category but can be found via keyword search. This search feature is crucial for niche apps such as those sold by OnScreen Science, Inc. because after a few days an app that’s not a big seller tends to become practically invisible to all but the most dedicated browsers, as the app moves farther down the list ordered by release date. The big sellers remain visible by virtue of their sales in a separate list devoted to the most popular apps.

Now, for games, the importance of being on the list of popular apps is obvious, and this is what has driven the “race to the bottom” for app prices, as the presence of high quality games selling for 99¢ can make an app, even a “serious” one in a very different category, seem outrageously expensive at $4.99 in some minds. I think there’s also something about the ratio of the price of the app to that of the device it runs on (and screen size) that makes app prices so low for apps on the iTunes App Store. But in the final analysis it’s really the ability of some developers to make a lot of money selling apps at a low price, thanks to the enormous number of potential customers, all funneled to a single buying point, that keeps prices low. That and the “free” apps, which I may write something about at a later time.

Let me say a little about the “desktop” OnScreen DNA apps from which the OnScreen DNA Model apps spring. OnScreen DNA, sold in three flavors—Lite, Standard, and Pro—has been available for Mac and Windows computers for several years. All these apps, especially aimed at biology teachers for use with students or for classroom demonstrations, are presented in a tutorial format that guides users through activities, complete with animations, designed to teach the structure and function of DNA.

Anyone that already has OnScreen DNA Lite will not be getting anything essentially new by buying OnScreen DNA Model on the Mac App Store. Rotating the model with the mouse is easier in the new app, as it is done with mouse drags requiring no key to be depressed. Some might prefer the new presentation of DNA facts to the old tutorial method. But as far as the basic model and the two simulations go, nothing much has changed.

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The Lite version deals mainly with the structure of DNA, though it includes simulations of denaturation and renaturation. OnScreen DNA (without the “Lite” qualifier) adds simulations of gene transcription and DNA replication with a good deal of detail about the enzymes involved and an accurate depiction of the basic steps (hydrogen bond breaking, strand unwinding, nucleotide chain forming, etc.), including proper direction of chain-building, primer RNA and Okazaki fragment construction, and even the role of telomerase in solving the “end problem” of DNA replication.The Pro version adds simulations in which the user, not limited to observing processes unfold, tests his or her knowledge by actively selecting the proper enzymes at the proper time and choosing the next nucleoside to add to a growing polymer chain. I should add that these apps, being designed mainly for teachers, include interactive tests, the results of which can be stored on the computer (under password protection if desired). More details about these apps, which are still unique and still for sale, can be found at onscreen-dna.com.

The aforementioned web site has been (and is still at the time I write) the only place to buy these apps. Thus sales have largely been limited to the hardy Googler that seeks DNA teaching software, or is at least searching for detailed information about DNA. No one with just a vague interest in science and biology is likely to stumble upon the web site. The price for advertising in even a relatively small circulation magazine for science teachers is really too high to justify from the sales it would likely produce, based on past experience. Though a ninety-day, no-questions-asked, satisfaction guaranteed policy for complete refund is in effect for our apps, I’m sure many people are hesitant to buy from an unknown online source. Thus the Apple seal of approval could be extremely valuable.

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After the iPad was announced, I came to see it as a opportunity to bring some of the OnScreen DNA software to a larger audience (using the existing code for displaying the three-dimensional DNA images on the iPad). I knew from experience with “DNA Day” sales for which I announced large discounts for a short period via a few Mac news sites that there were people who were not teachers that might be interested in a way to learn more about DNA for a price that wasn’t too high.

By far the easiest path seemed to be to start with a port of OnScreen DNA Lite to the iPad. Partly from screen space considerations I decided to scrap the tutorial format. I refer the interested reader to an earlier blog post The Thinking Behind the OnScreen DNA Lite™ iPad App for more about the iPad app. In some ways I felt the iPad app to be better than the Mac/Win versions just because of the direct response to the fingers, unmediated by a mouse. But, due to limitations of the somewhat stripped down version of Open GL (graphics programming API) available on the iPad, some features were lost, such as the ability to ctrl-click on any component of the DNA model to see it labeled. Of course ctrl-click has no meaning for the iPad anyway. In place of the labeling feature I added a popover image with a key showing how all the different parts were represented in the model.

The iPad app was launched with the old name OnScreen DNA Lite, which didn’t make all that much sense in the iPad context. This was rectified by the new and current name OnScreen DNA Model, which is more descriptive and avoids the implication that there is a more advanced version of the app available for the iPad. At the same time as the name change, the app gained a significant enhancement with an on-screen (popover on iPad) guide to facts about DNA’s geometry, molecular components, and chemical bonds and how they are displayed in the model. The blog post OnScreen DNA Model for iPad and iPhone: New Name, More DNA Background illustrates the changes. Oh yes, as the title of that post indicates, a version for the iPhone and iPod Touch is also available.

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When the Mac App Store was announced, I had no doubt that I would want to bring the OnScreen Science, Inc. science education apps (OnScreen DNA and OnScreen Particle Physics) to it. It took a bit of thought to decide what to do first, but based on the relative success on OnScreen DNA Model on the iPad (sales have continued to rise, contrary to the usual fate of apps on the iTunes App Store), I decided to get a version of OnScreen DNA Model ready for the Mac App Store.

This was a decision to make the Mac version very similar to the iPad version, rather than a small modification of the existing OnScreen DNA Lite. Thus the tutorial and the division into activities are not found in the Mac App Store version of OnScreen DNA Model. I think this is a net improvement due to the greater freedom it gives the user, even at the risk of some important points possibly being missed and without the potential benefit of a guided discovery that aims to get the user thinking.

To a certain extent, how successful the new app is on the Mac App Store will determine how quickly I move to bring the simulations of OnScreen DNA to the store. There are a number of decisions, really, about what to attempt in the way of simulated DNA processes for the iPad version and whether to work on the iPad or the Mac version first. It may make more sense to get OnScreen Particle Physics (onscreen-sci.com), our classic particle detection chamber simulation, onto either or both App Stores first.

Time will tell whether I’m being too optimistic, but I’m really encouraged by the opportunity the Mac App Store is giving me and other independent developers to get our apps before a lot of new eyes and minds.

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Coming Back for More Or Just Stumbling In?

November 1st, 2010

I doubt if I have any regular readers by now, so I won’t waste a lot of time apologizing for not having written about anything but my iPhone and iPad apps for a long time—or anything at all, for over a month. Not wanting to overdo it on my first blog post not devoted to apps in so long, I will keep this post short. And easy to write, I might add.

This will be another in my series on what brings people to this blog, based on search strings they have used in Google, which I can see in the log for this web site. Previous posts in this vein were “What Brings You Here?”, “More Searchers Arriving at a Place They Never Imagined”, “Some Google Search Examples to Start Off July”, and “More Google Follies.”

It’s gratifying to see indications in a search string that someone has returned to the blog to read something a second time, or perhaps to finish reading a post. I’m going to mention a few of those, which, though they are not as amusing as the ones that show the searcher had something totally different in mind, may be of some interest as indications of the kind of details and words that can stick in a person’s mind sufficiently to serve as keys to finding a blog post. Perhaps the examples will interest a new reader or two in the old posts. As always, I’m keeping the original spelling of the search strings.

Of course, most of the time it’s not possible to know for sure what the Google searcher’s real target was, or if there even was a specific target. I’ll start with one that is far from certain to have been aimed at finding anything on this blog. “Animal fight cat and night creature” isn’t a perfect fit for my blog post “Cries in the Night,” but if you read that post you’ll see why I suspect it might have been meant for it, especially since the searcher did actually come here, or I wouldn’t know about it. It doesn’t seem the sort of phrase one would throw out without something specific in mind.

Just to follow with one I feel more confident about: “mac book pro boil water” fits so well the posts “Vista on My MacBook Pro is Hot—Boiling Hot!”, “Boiling Temperature—Not Just for Vista Anymore”, and “Can’t Boil Water With Vista on My MacBook Pro Anymore” that I’m claiming it as a definite.

I’m inclined to rank as almost definite the search strings “athiest breaking habits” and “Search for dawkins smoking” as having been motivated by a desire to come to my post “On the Breaking of Bad Habits Acquired in One’s Youth: Smoking and Atheism.” For all I know Richard Dawkins, the prominent atheist, has been trying to quit smoking, or perhaps there is another Dawkins associated with smoking in some way. But the referenced post, which talked quite a bit about Dawkins and his stated reasons for rejecting God, has been one of the most read of mine, so my guess is that those strings point to a purposeful search for it.

Also coming to that post was someone who entered the long direct quotation from Dawkins: “the universe we observe has precisely the properties we should expect if there is at bottom no design, no purpose, no evil, no good, nothing but pointless indifference.” Since it was a direct quotation, it could have come from anywhere, but it’s at least a possibility that someone copied it from the blog post mentioned in the preceding paragraph, having been impressed by it there and then wanting to return.

It’s a little disconcerting to see one’s own name in a search string, or it is to me anyway, but my name followed by “on screenscientist isaiah” was used to come to that same blog post on atheism, in which I quoted the Biblical verses Isaiah 55:8-9, so I assume that that text made an impression somehow, just as the Dawkins quote may have. I wonder if it was someone I know?

“Rest in piece roonie” probably was looking for “Ronnie Knox, Rest in Peace,” since the searcher did come here, but I can never know for sure. Kudos to Google’s spell guessing algorithms again.

The Googlers behind either or both of the search strings “drag racing going too fast” and “dragracing providence” could have had in mind “Times I Might Have Died” (the post they arrived at), though it didn’t recount an actual drag race.

“Last Days of Chestnut, Guinea Pig” brings people to this blog every day. They are usually looking for advice about what to do with a sick, dying, or dead guinea pig. “Prayer for a dead guinie pig” might fit into the looking-for-advice category, but it could also have been entered by someone wanting to read the piece again, as you will understand if you read it.

It seems interest in my post “Large Hadron Collider: What’s the Risk?” has waned now that the LHC has been running for months without even the whisper of universal annihilation, but I’d like to think that the search string “otto roessler wacky” was inspired by my personal contribution to the defense of the LHC, in which seeing a video of Rössler led me to write “as I viewed his smiling face, this thought came into my mind: I wonder what the German word is for wacky tabacky.”

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