Many students trying to pick classes/majors in college will end up consulting with their counselors/academic advisors who, in turn, will almost always reply with very generic advice along the lines of: “study what you love”.
But as my girlfriend once pointed out, the problem with asking academic advisors that question is that academic advisors tend to be academics – and in academia, you can make a career out of studying anything. Outside of academia, that is not so true. Look no further than the paradox of how we have record high unemployment for recent college graduates despite almost every startup I’ve spoken with expressing concerns about finding and retaining qualified employees?
Obviously, our education system is failing to meet the needs of our students and employers. But, other than hope that the system miraculously fixes itself, my advice to students is this: take classes that teach broadly employable skills. You don’t need to take a lot of them, and nobody’s asking you to major in a something that you don’t want to – college is, after all, about broadening your horizons and studying what interests you. But, in a competitive job market and a turbulent economy, the worker that is in the best position is the worker who can move between industries/jobs easily (getting out of bad jobs/industries and moving into better paid/more interesting ones) and who can quickly demonstrate value to their boss (so as to make them indispensable faster).
So what sort of skills am I referring to? Off the top of my head (I’m sure there are others), three come to mind:
The skeptic will point out that a lot of this can be outsourced. And, that’s certainly true – but in my experience, there is not only a limit on what companies are willing to outsource, there is also just huge value for any employee to tack those skills onto what they are already doing. A salesperson who is also good at crunching statistics on who to sell to next is far more valuable than a “regular” salesperson. A marketing guy with programming chops probably has a better understanding of a product or a technology than a “regular” marketing guy. And, a operations guy who also understands the nitty gritty financial details is going to be able to do a better job than an operations guy who doesn’t. Not to mention: the skills are broadly applicable; so if one company doesn’t have a good spot, there’s always another organization somewhere that will.
Its hard to believe that Google Reader has only been “dead” for a few weeks. I use the quotes because while the core RSS reader functionality is still going, the reason it was all-consuming for me (and, frankly, one of the biggest sources of my goodwill towards Google) – the social functionality – is dead and gone.
I tried using Google+ as a means of sharing for two weeks – I really did. But it didn’t stick. First, the sharing from within Google Reader was clunky at best – I had to hit the “+1” or the new “G+ share” button, then select the Reader circle I had made, and then do another click to share – awkward process. Secondly, Google+ just didn’t cut it with what I used Google Reader’s social functionality for. I use Google Reader to read. Google+ is great for sharing snippets and pictures and thoughts – but its not a reading platform, so treating it like a replacement for Google Reader’s sharing functionality was never going to make it. Lastly, the point I brought up from my previous post on different levels of interest on different types of content still rings true – the people who I shared with on Google Reader were opting in to my content shares – most of my friends on Google+ are opting in to my personal shares. The two aren’t always the same.
So, ultimately, I threw in the towel and decided to use Tumblr as an alternative. As you may know, Tumblr is a popular and fairly versatile mini-blogging tool – it lies somewhere between Twitter (where you are limited to 140 characters) and WordPress in terms of simplicity. But, it packs a ton of cool features to make it, from what I can tell, an okay substitute for Google Reader’s sharing functionality:
Its not perfect. Its not integrated into Google Reader anymore – so all sharing/interaction will need to be done using the bookmarklet or on the site directly. But, the full-length RSS feed means we can keep reading and the sharing/Disqus functionality means we still can like, re-share, and comment.
I’m hoping my friends who once used Google Reader will join me on Tumblr, and I’m hoping my friends who were using Tumblr all along will welcome me to their world
. I just started with the integration, but I am hoping to play around with the templating system to more tightly integrate the two sites in the near future.
One of my fondest memories from high school (which also happens to be one I worked the hardest on) is the one hour Hamlet film I made with several of my classmates. That was a massive undertaking for us as we cut the lines, memorized them, structured a complicated shooting schedule/strategy, spent 3-4 days non-stop in front of Adobe Premiere and Adobe After Effects trying to edit the sucker, and threw in a couple of “inspired” special effects
.
Flash forward a few years and one of my friends from college (who had to suffer through watching the thing
because I was so proud I showed it to anyone willing to watch!) sends me an email with the subject line: “Why Didn’t Ben Do a Musical?”
Having seen the video she included, I can only respond: good question.
I now know what to make for my next video project!
Oh, and of course, my girlfriend has to throw in her own answer to that question: “because Ben can’t sing.” Also very true
.
Another month, another paper (and unlike with last month, this time I’m on time!)
This month’s paper is about stem cells: those unique cells within the body which have the capacity to assume different roles. While people have talked at lengths about the potential for stem cells to function as therapies, one thing holding them back (with the main exception being bone marrow cells) is that its very difficult to get stem cells to exactly where they need to be.
With bone marrow transplants, hematopoietic stem cells naturally “home” (like a missile) to where they need to be (in the blood-making areas of the body). But with other types of stem cells, that is not so readily true, making it difficult or impossible to use the bloodstream as a means of administering stem cell therapies. Of course, you could try to inject, say, heart muscle stem cells directly into the heart, but that’s not only risky/difficult, its also artificial enough that you’re not necessarily providing the heart muscle stem cells with the right triggers/indicators to push them towards becoming normal, functioning heart tissue.
Researchers at Brigham & Women’s Hospital and Mass General Hospital published an interesting approach to this problem in the journal Blood (yes, that’s the real name). They used a unique feature of white blood cells that I blogged about very briefly before called leukocyte extravasation, which lets white blood cells leave the bloodstream towards areas of inflammation.
The process is described in the image above, but it basically involves the sugars on the white blood cell’s surface, called Sialyl Lewis X (SLeX), sticking to the walls of blood vessels near sites of tissue damage. This causes the white blood cell to start rolling (rather than flowing through the blood) which then triggers other chemical and physical changes which ultimately leads to the white blood cell sticking to the blood vessel walls and moving through.
The researchers “borrowed” this ability of white blood cells for their mesenchymal stem cells. The researchers took mesenchymal stem cells from a donor mouse and chemically coated them with SLeX – the hope being that the stem cells would start rolling anytime they were in the bloodstream and near a site of inflammation/tissue damage. After verifying that these coated cells still functioned (they could still become different types of cells, etc), they then injected them into mice (who received injections in their ears with a substance called LPS to simulate inflammation) and used video microscopes to measure the speed of different mesenchymal stem cells in the bloodstream. In Figures 2A and 2B to the left, the mesenchymal stem cell coated in SLeX is shown in green and a control mesenchymal stem cell is shown in red. What you’re seeing is the same spot in the ear of a mouse under inflammation with the camera rolling at 30 frames per second. As you can see, the red cell (the untreated) moves much faster than the green – in the same number of frames, its already left the vessel area! That, and a number of other measurements, made the researchers conclude that their SLeX coat actually got their mesenchymal stem cells to slow down near points of inflammation.
But, does this slowdown correspond with the mesenchymal stem cells exiting the bloodstream? Unfortunately, the researchers didn’t provide any good pictures, but they did count the number of different types of cells that they observed in the tissue. When it came to ears with inflammation (what Figure 4A below refers to as “LPS ear”), the researchers saw an average of 48 SLeX-coated mesenchymal stem cells versus 31 uncoated mesenchymal stem cells within their microscopic field of view (~50% higher). When it came to the control (the “saline ear”), the researchers saw 31 SLeX-coated mesenchymal stem cells versus 29 uncoated (~7% higher). Conclusion: yes, coating mesenchymal stem cells with SLeX and introducing them into the bloodstream lets them “home” to areas of tissue damage/inflammation.
As you can imagine, this is pretty cool – a simple chemical treatment could help us turn non-bone-marrow-stem cells into treatments you might receive via IV someday!
But, despite the cool finding, there were a number of improvements that this paper needs. Granted, I received it pre-print (so I’m sure there are some more edits that need to happen), but my main concerns are around the quality of the figures presented. Without any clear time indicators or pictures, its hard to know what exactly the researchers are seeing. Furthermore, its difficult to see for sure whether or not the treatment did anything to the underlying stem cell function. The supplemental figures of the paper are only the first step in, to me, what needs to be a long and deep investigation into whether or not those cells do what they’re supposed to – otherwise, this method of administering stem cell therapies is dead in the water.
(Figures from paper) (Image credit: Leukocyte Extravasation)
Paper: Sarkar et al., “Engineered Cell Homing.” Blood. 27 Oct 2011 (online print). doi:10.1182/blood-2010-10-311464
I was asked recently by a friend about my thoughts on the “Occupy Wall Street” movement. While people a heck of a lot smarter and more articulate than me have weighed in, most of it has been focused on finger-pointing (who’s to blame) and judgment (do they actually stand for anything, “its the Tea Party of the Left”).
As corny as it sounds, my first thought after hearing about “Occupy Wall Street” wasn’t about right or wrong or even really about politics: it was about John Steinbeck and his book The Grapes of Wrath . It’s a book I read long ago in high school, but it was one which left a very deep impression on me. While I can’t even remember the main plot (other than that it dealt with a family of Great Depression and Dust Bowl-afflicted farmers who were forced to flee Oklahoma towards California), what I do remember was a very tragic description of the utter confusion and helplessness that gripped the people of that era (from Chapter 5):
“It’s not us, it’s the bank. A bank isn’t like a man. Or an owner with fifty thousand acres, he isn’t like a man either. That’s the monster.”
“Sure,” cried the tenant men, “but it’s our land. We measured it and broke it up. We were born on it, and we got killed on it, died on it. Even if it’s no good, it’s still ours. That’s what makes it ours—being born on it, working it, dying on it. That makes ownership, not a paper with numbers on it.”
“We’re sorry. It’s not us. It’s the monster. The bank isn’t like a man.”
“Yes, but the bank is only made of men.”
“No, you’re wrong there—quite wrong there. The bank is something else than men. It happens that every man in a bank hates what the bank does, and yet the bank does it. The bank is something more than men, I tell you. It’s the monster. Men made it, but they can’t control it.
And therein lies the best description of the tragedy of the Great Depression, and of every economic crisis that I have ever read. The many un- and under-employed people in the US are clearly under a lot of stress. And, like with the farmers in Steinbeck’s novel, its completely understandable that they want to blame somebody. And, so they are going to point to the most obvious culprits: “the 1%”, the bankers and financiers who work on “Wall Street”.
But, I think Steinbeck understood this is not really about the individuals. Obviously, there was a lot of wrongdoing that happened on the part of the banks which led to our current economic “malaise.” But I think for the most part, the “1%” aren’t interested in seeing their fellow citizen unemployed and on the street. Even if you don’t believe in compassion, their greed alone guarantees that they’d prefer to see the whole economy growing with everyone employed and productive, and their desire to avoid harassment alone guarantees they’d love to find a solution which ends the protests and the finger-pointing. They may not be suffering as much as those in the “99%”, but I’m pretty sure they are just as confused and hopeful that a solution comes about.
The real problem – Steinbeck’s “monster” – is the political and economic system people have created but can’t control. Our lives are driven so much by economic forces and institutions which are intertwined with one another on a global level that people can’t understand why they or their friends and family are unemployed, why food and gas prices are so expensive, why the national debt is so high, etc.
Now, a complicated system that we don’t have control of is not always a bad thing. After all, what is a democracy supposed to be but a political system that nobody can control? What is the point of a strong judiciary but to be a legal authority that legislators/executives cannot overthrow? Furthermore, its important for anyone who wants to change the system for the better to remember that the same global economic system which is causing so much grief today is more responsible than any other force for creating many of the scientific and technological advancements which make our lives better and for lifting (and continuing to lift) millions out of poverty such as those who live in countries like China and India.
But, even keeping that in mind, I — a firm believer in freer markets and globalization — am hard-pressed not to sympathize with the idea that the system has failed on its promise of expanding prosperity for a broad swath of the population. What else am I (or anyone else) supposed to think in a world where corporate profits can go up while unemployment stays stubbornly near 10%, where bankers can get paid bonuses only a short while after their industry was bailed out with taxpayer money, and where the government seems completely unable to do more than bicker about an artificial debt ceiling?
But anyone with even a small understanding of economics knows this is not about a person or even a group of people. To use Steinbeck’s words, the problem is more than a man, it really is a monster. While we may not be able to kill it, letting it rampage is not a viable option either — the “Occupy Wall Street” protests are a testament to that. They may not be generating any policy recommendations which can stop the problem, but their frustration is real and legitimate, and until politicians across both sides of the aisle and individuals across both ends of the income spectrum come together to find a way to “tame the monster’s rampage”, we’re going to see a lot more finger-pointing and anger.
I’m pretty late for my September paper of the month, so here we go
“Omics” is the hot buzz-suffix in the life sciences for anything which uses the new sequencing/array technologies we now have available. You don’t study genes anymore, you study genomics. You don’t study proteins anymore – that’s so last century, you study proteomics now. And, who studies metabolism? Its all about metabolomics. There’s even a (pretty nifty) blog post covering this with the semi-irreverent name “Omics! Omics!”.
Its in the spirit of “Omics” that I chose a Science paper from researchers at the NIH because it was the first time I have ever encountered the term “antibodyome”. For those of you who don’t know, antibodies are the “smart missiles” of your immune system – they are built to recognize and attack only one specific target (i.e. a particular protein on a bacteria/virus). This ability is so remarkable that, rather than rely on human-generated constructs, researchers and biotech companies oftentimes choose to use antibodies to make research tools (i.e. using fluorescent antibodies to label specific things) and therapies (i.e. using antibodies to proteins associated with cancer as anti-cancer drugs).
How the immune system does this is a fascinating story in and of itself. In a process called V(D)J recombination – the basic idea is that your immune system’s B-cells mix, match, and scramble certain pieces of your genetic code to try to produce a wide range of antibodies to hit potentially every structure they could conceivably see. And, once they see something which “kind of sticks”, they undergo a process called affinity maturation to introduce all sorts of mutations in the hopes that you create an even better antibody.
Which brings us to the paper I picked – the researchers analyzed a couple of particularly effective antibodies targeted at HIV, the virus which causes AIDS. What they found was that these antibodies all bound the same part of the HIV virus, but when they took a closer look at the 3D structures/the B-cell genetic code which made them, they found that the antibodies were quite different from one another (see Figure 3C below)
What’s more, not only were they fairly distinct from one another, they each showed *significant* affinity maturation – while a typical antibody has 5-15% of their underlying genetic code modified, these antibodies had 20-50%! To get to the bottom of this, the researchers looked at all the antibodies they could pull from the patient – in effect, the “antibodyome”, in the same way that the patient’s genome would be all of his/her genes, — and along with data from other patients, they were able to construct a “family tree” of these antibodies (see Figure 6C below)
The analysis shows that many of the antibodies were derived from the same initial genetic VDJ “mix-and-match” but that afterwards, there were quite a number of changes made to that code to get the situation where a diverse set of structures/genetic codes could attack the same spot on the HIV virus.
While I wish the paper probed deeper into actual experimentation to take this analysis further (i.e. artificially using this method to create other antibodies with similar behavior), this paper goes a long way into establishing an early picture of what “antibodyomics” is. Rather than study the total impact of an immune response or just the immune capabilities of one particular B-cell/antibody, this sort of genetic approach lets researchers get a very detailed, albeit comprehensive look at where the body’s antibodies are coming from. Hopefully, longer term this also turns into a way for researchers to make better vaccines.
(Figure 2 and 6 from paper)
Paper: Wu et al., “Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing.” Science (333). 16 Sep 2011. doi: 10.1126/science.1207532
If it hasn’t been clear from posts on this blog or from my huge shared posts activity feed, I am a huge fan of Google Reader. My reliance/use of the RSS reader tool from Google is second only to my use of Gmail. Its my main primary source of information and analysis on the world and, because a group of my close friends are actively sharing and commenting on the service, it is my most important social network.
Yes, that’s right. I’d give up Facebook and Twitter before I’d give up Google Reader.
I’ve always been disappointed by Google’s lack of attention to the product, so you would think that after announcing that they would find a way to better integrate the product with Google+ (a product I recently came out as being fairly positive on) that I would be jumping for joy.
However, I am not. And, I am not the only one. E. D. Kain from Forbes says it best when he writes:
[A]fter reading Sarah Perez and Austin Frakt and after thinking about just how much I use Google Reader every day, I’m beginning to revise my initial forecast. Stay calm is quickly shifting toward full-bore Panic Mode.
(bolding and underlining from me)
Now, for the record, I can definitely see the value of integrating Google+ with Google Reader well. I think the key to doing that is finding a way to replace the not-really-used-at-all Sparks feature (which seems to have been replaced by a saved searches feature) in Google+ with Google Reader to make it easier to share high quality blog posts/content. So why am I so anxious? Well, looking at the existing products, there are two big things:
Now, of course, Google could address these concerns by implementing additional features – and if that were the case, that would be great. But, putting my realist hat on and looking at the tone of the Google Reader blog post and the way that Google+ has been developed, I am skeptical. Or, to sum it up, in the words of Austin Frakt at the Incidental Economist (again bolding/underlining is by me)
I will be entering next week with some trepidation. I’m a big fan of Google and its products, in general. (Love the Droid. Love the Gmail. Etc.) However, today, I’ve never been more frightened of the company. I sure hope they don’t blow this one!
A few weeks ago, I blogged about how the web was becoming the most important and prominent application distribution platform and about Google’s efforts to embrace that direction with initiatives like ChromeOS (Google’s operating system which is designed only to run a browser/use the internet), Native Client, and the Chrome Web Store.
Obviously, for the foreseeable future, “traditional” native applications will continue to have significant advantages over web applications. As much of a “fandroid”/fan of Google as I am, I find it hard to see how I could use a Chromebook (a laptop running Google’s ChromeOS) over a real PC today because of my heavy use of apps like Excel or whenever I code.
However, you can do some pretty cool things with web applications/HTML5 which give you a sense of what can one day be possible. Case in point: enter Chrome Remote Desktop (HT: Google Operating System), a beta extension for Google Chrome which basically allows you to take control of another computer running Chrome a la remote desktop/VNC. While this capability is nothing new (Windows had “remote desktop” built in since, at latest, Windows XP, and there are numerous VNC/remote desktop clients), what is pretty astonishing is that this app is built entirely using web technologies – whereas traditional remote desktops use non-web based communications and native graphics to create the interface to the other computer, Chrome Remote Desktop is doing all the graphics in the browser and all the communications using either the WebSocket standard from HTML5 or Google Talk’s chat protocol! (see below as I use my personal computer to remote-control my work laptop where I am reading a PDF on microblogging in China and am also showing my desktop background image where the Jedi Android slashes up a Apple Death Star)
How well does it work? The control is quite good – my mouse/keyboard movements registered immediately on the other computer – but the on-screen graphics/drawing speed was quite poor (par for the course for most sophisticated graphics drawing apps in the browser and for a beta extension). The means of controlling another desktop, while easy to use (especially if you are inviting someone to take a look at your machine) is very clumsy for some applications (i.e. a certain someone who wants to leave his computer in the office and use VNC/remote desktop to access it only when he needs to).
So, will this replace VNC/remote desktop anytime soon? No (nor, does it seem, were they the first to think up something like this), but that’s not the point. The point, at least to me, is that the browser is picking up more and more sophisticated capabilities and, while it may take a few more versions/years before we can actually use this as a replacement for VNC/remote desktop, the fact that we can even be contemplating that at all tells you how far browser technology has come and why the browser as a platform for applications will grow increasingly compelling.
One of the things I regret the most about my background is that I lack good knowledge/experience with programming. While I have dabbled (i.e. mathematical modeling exercises in college, Xhibitr, and projects with my younger brother), I am generally more “tell” than “show” when it comes to creating software (except when it comes to writing a random Excel macro/function).
So, when I found out that my girlfriend needed some help with her glaucoma research and that writing software was the ticket, I decided to go out on a limb and help her out (link to my portfolio page).
The basic challenge is that the ophthalmology research world uses an arcane but very difficult-to-do-by-hand scoring system for taking data on a glaucoma patient’s vision (see image below for the type of measurements that might be collected in a visual field test) and turning that into a score (the AGIS visual field score) on how bad a patient’s glaucoma is (as described in a paper from 1994 that is so old I couldn’t find a digital copy of it!).

So, I started by creating a program using the C programming language (developed by the late Dennis Ritchie, and explained in the seminal programming book to the right, who was also one of the two leading brains behind the UNIX operating system) which would take this data in the form of a CSV (comma-separated values) file and spit out scores.
While I was pleasantly surprised that I still retained enough programming know-how to do this after a few weekends, the programming was an awkward text-based monstrosity which required the awkward step of converting two-dimensional visual field data into a flat CSV file. The desire to improve on that and the hope that my software might help others doing similar research (and might get others to build on it/let me know if I’ve made any errors) pushed me to turn the tool into a web application which I’ve posted on my site. I hope you’ll take a look! Instructions are pretty basic:
Hope this is helpful to the ophthalmology researchers out there!
(Image credit – example visual field) (Image credit – C Programming Language)
A few weeks ago, I did a little farewell tribute to Apple CEO and tech visionary Steve Jobs after he left the CEO position at Apple. While most observers probably recognized that the cause for his departure was his poor health, few probably guessed that he would die so shortly after he left. The tech press has done a great job of covering his impressive legacy and the numerous anecdotes/lessons he imparted on the broader industry, but there are a few things which stand out to me which deserve a little additional coverage:
(And, yes, the title of this post is an homage to the Jobs’s trademark means of introducing new products at the end of each of his speeches)