Monthly Archives: June 2013

Judy Blume – A look back to 1972 in NYC

ImageTales of a Fourth Grade Nothing, published in 1972, follows the life of a child growing up in New York City across the street from Central Park and his trials from growing up with a little brother (Fudge), parents who don’t always understand and the pressures of elementary school projects.

Reading this book now opened up a couple windows into the past for me. First, my own memory of reading this myself in Mrs. Nichol’s fourth grade reading class at Warner Elementary school in Wilmington, DE.

Second, my memory of being a kid in the 70s and 80s. It was a time where people must have felt more safe in the world than they do now. Children were allowed to go out and play by themselves, my parents never had any idea where I was and didn’t really care so long as I came home by dinner.

One chapter of ‘Fourth Grade Nothing’ really brought this home for me. The story centers around Peter and his brother, Fudge. Peter is in the fourth grade (10-11yo) and Fudge is 3. Yet, in one scene, the mother leaves Fudge in the care of Peter and his two friends in Central Park while she runs home to turn the oven on. Peter also mentions how he is allowed to come to the park himself, but it is unusual for his mother to leave Fudge in his care – not because of crime, but because Fudge is a disaster, dangerous to himself and all those around him.


Violent Crime in NYC – *indicates 1972

I think parents today would panic at even the idea of leaving their kids by themselves for almost any length of time, let alone if it was in the center of New York. What’s the reality? Is New York (as an example) more dangerous now that it has been? The answer is: no. Take a look at this graph of violent crimes committed per year in NYC. When crack was an epidemic in the 90s crime skyrocketed, but it’s come down, way down – below what it was before the rise in crime.

Today we live in a world of fear and think it’s normal. We hawk over our children all the time and worry about everything. I didn’t grow up like this, why would I default to it now?

“One possible reason fear of crime remains high is that powerful people have an incentive to ring the alarms anyway. Politicians score points by promising to get “tough on crime,” even after those efforts pay off and crime levels hit historic lows. Media play up only the most horrifying deeds. The result is a skewed perception of how dangerous the world is.”

Slate Magazine 

What do you think? Is the world safer or more dangerous? Do we over-react to reports of violence?

Leave a comment

Posted by on June 16, 2013 in Uncategorized


Tags: , , , , , , , ,

Release of ‘The Curse of Sisyphus’


The Curse of Sisyphus

The Curse of Sisyphus has been released and is available on the iTunes iBookstore. To celebrate the release, this, and its companion volume, The Thirteenth Labor of Heracles are both free until Sunday.

Zeus is not one to be trifled with. And Sisyphus has been a thorn in his side, defying him at every turn, yet escaping every punishment with uncanny cunning. But this time, the mortal has gone too far and Zeus has a special punishment befitting Sisyphus’ persistence.

The Curse of Sisyphus is the tale unlike others you may have heard about him before. Here you can find out exactly how Sisyphus defied Zeus yet again – and learn about the physics of motion, gravitation and orbit at the same time.

Leave a comment

Posted by on June 13, 2013 in Uncategorized


Tags: , , , , , , , , , , , ,

Unaltered genes are a product of nature and not patentable


See this Jim? It’s not patentable.

The Supreme Court of the United States released its ruling on the ‘Association for Medical Pathology v. Myriad Genetics, Inc.’ case today. Briefly, they ruled that Myriad’s patent is invalid as they merely discovered a natural entity. Because they did not alter the material in any way vital to their industry or possess a methods claim associated with this material, their patent fails because  “laws of nature [or] natural phenomena …lie beyond the domain of patent protection” according to precedent set under United States Code. 

Wait – you mean the USC clearly states that they couldn’t patent this stuff?  Well, no.

USC Title 35 Part II Chapter 10 Section 101

“Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor…”

The applicable precedent case is Mayo v. Prometheus___566 U.S. In that case, Prometheus had a patented clinical diagnostic kit that Mayo Collaborative Services (a nonprofit affiliated with the Mayo Clinic) used for some time until they developed their own version of the kit. (A pretty close precedent). In this case, the court ruled that, “Because methods for making such determinations were well known in the art, this step simply tells doctors to engage in well-understood, routine, conventional activity previously engaged in by scientists in the field. Such activity is normally not sufficient to transform an unpatentable law of nature into a patent-eligible application of such a law.”

My Interpretation

From these rulings it appears that in order to become a patentable entity a gene must be novelly transformed in some manner that makes it functionally distinct from the naturally occurring entity, or that the method for interrogating the gene involves some novel method beyond what is previously known art. 

Leave a comment

Posted by on June 13, 2013 in Uncategorized


Tags: , , , , , , , , , ,

Codecademy Problem

ImageI’ve mentioned many time on this blog how I am a big fan of codecademy. I think this is an excellent way to develop some coding skills in a simple hand-held way. I’ve been following the javascript track for some time and really enjoy it. Recently, Ruby and Python tracks have been introduced, although I have only given each one minimal attention so far. In the future, I am hoping to concentrate on the web programming elements in order to provide some context for the javascript work.

Presently, I have been stuck on a problem that should be easy, but the walkthrough does not seem to guide you in the right direction. The problem is intended to take a string of text and search for your name within this text. I think the difficulty arises from the fact that the walkthrough sounds like you should be solving the whole problem, but may actually be asking for less. 

Below, with a few extra details, I present a solution that effectively gets the job done. I’ve included some documentation so you can see what I was thinking as well as some debugging aids to visualize what the program is doing at each step.
ImageThis solution will get a ‘pass’ for the problem, but I am wondering how this might be simplified.
If you can simplify this solution, please leave a comment and I will update the code if significant advances are made.

/*jshint multistr:true */

var text = “hdajkslhgjalhjghjklhjackfghjdskghjkdfajlk”;  //the text we search through
var myName = “jack”;                                                  //what we are looking for
var hits = [];                                                                  //array storing match
var j=0;                                                                         //a counter for myName array

/////////first loop for match with myName[0]////////////
for (i=0;i< text.length;i++){
console.log(i); // enumerates position in text array
if (text[i] === myName[j]){

//////advances position in myName array, second loop continues search/////
for(var j=i;j<i +myName.length;j++){
console.log(“testing if”,text[j],” = “,myName[j-i]); //shows match test
if(text[j] != myName[j-i]){
hits.length = 0; //if no match, hits array is cleared
j=0; //array position in myName is reset
break; //exits inner loop
} //end ‘if no match’

if (text[j] === myName[j-i]){ //for each match, letter is pushed
hits.push(text[j]); //onto hits array
} //end ‘if match’
} //end inner loop

/////if reach size of myName array ////////
if (hits.length === myName.length){
console.log(“we found your name: “, hits); //output match
} //end ‘size of array
}//end outer loop
}//end program

/* output
testing if j = j
testing if k = a
testing if j = j
testing if a = a
testing if l = c
testing if j = j
testing if g = a
testing if j = j
testing if k = a
testing if j = j
testing if a = a
testing if c = c
testing if k = k
we found your name: [ ‘j’, ‘a’, ‘c’, ‘k’ ]


Leave a comment

Posted by on June 12, 2013 in Uncategorized


Tags: , , , ,

There’s a new Coronavirus in town, and it’s kickin’ ass and taking names

ImageThe most frequent coronaviruses we encounter are those that cause common colds, although other, more severe viruses occur within this family including the virus that causes SARS.

The current newsmaker, MERS-CoV, is a newly described coronavirus noteworthy for its high mortality (approximately 50% of patients diagnosed with the virus have died). Aside from high mortality, the name of the virus (MERS-CoV stands for Middle East Respiratory System Coronavirus) has drawn controversy because of its identity with the ‘Middle East’. Beyond that, this provides an opportune time to describe and discuss the coronavirus family in terms of structure and other characteristics, which might be a good place to begin.

The Coronavirus Family

Coronaviruses are a group of viruses with a plasma membrane envelope surrounding a helical nucleocapsid, which, in turn, surrounds the genetic material – in this case a positive strand RNA.

ImageCoronavirus genomes an extraordinarily large positive strand RNAs encoding a spike protein (S), and Envelope protein (E), a membrane protein (M) and a nucleocapsid protein (N). Additionally, the virus also encodes an RNA polymerase required for the copying of its RNA genome (a function unlike any naturally occurring in the host cell and therefore requiring a specialized viral protein).

The Envelope is derived from the intracellular membrane of previously infected cells that is taken during the process of viral ‘budding’. Coronaviruses are named for the corona-like appearance (by electron microscopy) of these envelopes and the distinctive viral proteins (E and S) radiating out from the surface. These proteins are essential for the virus’ ability to bind to, and enter, uninfected cells through specific protein:protein interactions.

Within the envelope is the nucleocapsid, a helical structure that self-assembles from capsid proteins in the host cell’s cytoplasm. As this structure assembles, it binds and takes up a viral genome that contains all the genetic information to infect and reproduce in subsequent host cells.

MERS-CoV by the numbers


I had a little bird,
Its name was Enza.
I opened the window,
And in-flu-enza.

So far, of the 55 cases the CDC recognizes as testing positively for the virus, 31 have died. That’s 56% of infected persons dying of the disease. The majority of these cases remain in the middle east, however a small number have also appeared in western Europe, but with identifiable ties to the middle east. Compare this to the 2.5% mortality rate from the devastating 1918 swine flue epidemic.

Naming Convention

Although the name has accepted been adopted (as well as ‘Saudi SARS’), it goes against a tradition opposing the use of locations in the name of the virus. There are two reasons for this convention – first, it may easily become inaccurate as the virus spreads and second, it can lead to stereotyping and persecution of a group of people. A previous example of this sort of mistake occurred when a new autoimmune disease was becoming prevalent amongst homosexual men in the US. Instead of using a more generically descriptive name, this virus was initially referred to as GRID (gay-related immunodeficiency virus). The virus, itself, had no idea it was supposed to stick to the gay population and before long it was discovered that everyone was potentially vulnerable. The name was then switched (or, more accurately, it finally got an official name, ‘HIV’, for human immunodeficiency virus). However, the damage was already done and many people adopted the belief that the virus only affected gay men, so straight people were not as likely to practice ‘safe sex’, and practitioners of hate speech added another arrow to their quiver: ‘Gay plague was sent by God, who was upset at homosexuals.’

Going Forward

Last week Novavax, Inc. announced the production of a nanoparticle vaccine candidate using the spike protein of MERS-CoV, a strategy that the company previously used in making a SARS vaccine.

Regardless of the method (vaccination, quarantine, etc.) it remains a vital priority to establish a protocol for maintaining public health prior to the Hajj, which is expected to fall between October 13-18, 2013. In 2011 the hajj saw An estimated 2.5 million pilgrims gathered in Mecca, most traveling from (and then returning to) countries outside the Arabian peninsula.


Leave a comment

Posted by on June 11, 2013 in Uncategorized


Tags: , , , , , , , ,

Starting with Unity

ImageI started a game design class last week that uses C# and Unity. So far the class has not moved much (it’s online and I am constantly checking for updates, but there haven’t been any – have I mentioned how much I dislike online classes?). So, to get moving, I have been following along with a great tutorial on youtube by quill18 for making a clone of the Atari game, Breakout.

This is a terrific place to start, because this game was Steve Jobs’ assignment at Atari, which he famously subcontracted to Steve Wozniak. Both Woz, in his book iWoz, and Jobs, through his biography by Isaacson, describe this anecdote as one of the first major collaborations between the two.

Additionally, it can be completely cloned with only minimal coding.

I’ve followed along fairly well, but suddenly, my objects don’t interact with one another (meaning the ball doesn’t bounce off the bricks) and I’ll be damned if I can figure out why.


Since I’m not teaching any biology this summer, I thought I would blog a little more on my coding ventures. If anyone else is out there working on similar material, I’d love to hear from you.

Leave a comment

Posted by on June 10, 2013 in Uncategorized


Tags: , , , , , ,

The Bohr atom at 100


Bohr and Einstein having a smoke

One hundred years ago, in 1913, Niels Bohr published a trilogy of papers describing the atom in ways that we are still referring to today. These papers synthesized several previous ideas into one and presented the atom as a positive nucleus encircled by a cloud of electrons that stayed in very distinct orbits that were proportional to their energy (i.e.  electrons in low orbitals were lower energy than those that inhabited higher orbitals). 

This sounds like a simple concept, but it has some very important ideas nested in it. Probably most importantly is the idea that the orbitals are distinct. That is, there is no ‘between’ orbitals. Electrons are in one orbital or another, but never in between. Also, it takes energy input to raise an electron into a higher orbital and energy is released (as light) when an electron drops into a lower orbital. As a biologist, I find this most interesting and useful to think of when contemplating photosynthesis and considering how photons are absorbed by atoms in the reaction centers of chloroplasts. This is done by raising an electron to a higher … let’s say ‘energy level’. Once this happens, we have energy stored (at least for a while) in this electron. That energy can be used to do work, passed on to another atom or it can release the energy into the environment as light.


Bohr Model

Here’s a good representation of Bohr’s model with the different energy levels / orbitals indicated by the dotted lines labeled n=1, n=2 and n=3 .

Until now, this model has been a good, workable theory that seemed to fit  mathematically with what was observed indirectly. However, two really cool papers came out recently that have provided the first direct observations of atoms / molecules. In the first, Hydrogen atoms were observed using photoionization microscopy. This was done with a hydrogen at resting state (it’s lone electron in the lowest orbital), and in several higher energy states attained by providing energy to the atom using a laser. Below is a figure from the paper presented in Physical Review Letters 110, 213001 (2013). In each subsequent panel the electron can be seen in increasingly higher (distinct) orbitals.



Ok, I’m just going to come out and say it, ‘This is totally f’n cool.’ This means that Bohr’s totally theoretical model of a century ago has just been directly shown to be completely accurate.

But wait, there’s more. 

We’ve been using Bohr’s model and others’ ideas to model how multiple atoms come together to form molecules. Again, these structures have always been imagined from indirect observation. But, in the May 30 Science, this too has been directly observed using non-contact atomic force microscopy. Here we can see atoms in a molecule as well as the covalent bonds between them. 



Here’s to you Niels. Bang up work!! ImageNot to mention Dimas G. de Oteyza1,2,*,Patrick Gorman3,*Yen-Chia Chen1,4,*Sebastian Wickenburg1,4,Alexander Riss1Duncan J. Mowbray5,6Grisha Etkin3Zahra Pedramrazi1Hsin-Zon Tsai1,Angel Rubio2,5,6Michael F. Crommie1,4,,  and Felix R. Fischer3,4, for imaging the covalent bonds.

And A. S. Stodolna1,*A. Rouzée1,2F. Lépine3S. Cohen4F. Robicheaux5A. Gijsbertsen1J. H. Jungmann1C. Bordas3, and M. J. J. Vrakking for visualizing the orbitals of Hydrogen atoms.


Posted by on June 6, 2013 in Uncategorized


Tags: , , , , , , , , , , ,

My knee-jerk reaction is to keep this a secret

But who am I fooling? 

I can’t keep a secret … and this isn’t one that should be kept anyway.

The secret is Iceland. A place I have always wanted to go, but never made a destination. But, recently, on the return from celebrating my tenth anniversary with my wife in Paris, we stopped for a long layover in Iceland and took the opportunity to spend the day at a hot-spring spa.

ImageThe one we chose was a tourist trap positioned perfectly for people with lay-overs just like ours, but we didn’t mind that. Instead, we embraced it and had a wonderful time discovering the rejuvenating, geothermally heated waters of ‘The Blue Lagoon‘.

Basically, Icelandair is a low-cast carrier for transatlantic flights. But consider: The worst part of transatlantic travel is the jetlag that makes you want to spend your vacation catching up on sleep and the makes the return home a nightmare of trying to get back on schedule just as you are supposed to be getting back to work. 

The solution is an 8 hr – 36 hr layover in iceland with a day at the spa. I know there are lots of other attractions in iceland, but this is the one I know, and it is the one that makes travel so much better. The rest are actual extensions of a vacation.

How to get there? The Flybus has regular trips between the Blue Lagoon and the airport throughout the day.

What about my luggage?No problem. The bus has space and so does the resort.

What about a bathing suit? Also no problem, you can rent one there. And if you get a premium package, you also get a robe, towel and flip-flops.

What about food? There is a restaurant (buffet included in the premium package) with excellent food, including a great sushi spread  – no changing required, just throw on a robe and flips and you’re set to go.

You can also enjoy a drink at the bar located in the bath and get a good shower before heading back to the airport refreshed.


1 Comment

Posted by on June 3, 2013 in Uncategorized


Tags: , , , , , , , ,