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, 214 OnScreen DNA Model


February 21, 214 OnScreen DNA Replication


February 21, 214 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.

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.

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.

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.

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.