Installing TPP 4.6.2 on Mountain Lion Mac OSX
This is for the open-source proteomics folks out there who run Macs. I finally figured out how to install the latest Transatlantic-Proteomics-Pipeline package (TPP 4.6.2) on my Mountain Lion Macbook Air. It was not fun, and involved debugging make and configure files.
Basically the workflow of the TPP build process is that src/Makefile contains the commands to build the TPP, but it will call several children Makefiles dotted all over the package. For instance, src/Makefile.incl contains the commands to build all the external dependencies (found in extern/) that are included in the TPP package.
To make TPP 4.6.2 work with Mac OSX Mountain Lion also known as BSD/Darwin, you will have to change
- src/Makefile
- src/Makefile.incl
- CGI/Makefile
- CGI/tpp_gui/tpp_gui.pl
and install the libraries
- libgd
- libpng1.2
1. Install libgd and libpng.
In the instructions, they suggest fink and macports, but I’ve had problems with these two packages, and now I prefer brew (based on Ruby goodness). So go install brew now.
Installing libgd is easy with brew (haha try installing libgd with macports):
brew install gd
First the TPP does not work with the latest libpng (version 1.5), so you must use libpng 1.2. To install that, use brew:
brew tap homebrew/versions
brew install libpng12
Now the links to these two need to be hard-coded into src/Makefile.incl. The relevant section is identified by the comment:
# use the next two lines if you use fink rather than macports
and you should replace the line:
GD_LIB= /opt/local/lib/libgd.a /opt/local/lib/libpng.a
with:
GD_LIB = /usr/local/lib/libgd.a /usr/local/Cellar/libpng2/lib/libpng12.a
2.The make cycle.
The biggest glitch I’ve found in the TPP make cycle is that the top src/Makefile passes the LDFLAGS into all the children makefiles. This causes all the extern packages to crash at the ./configure stage, where the ./configure test fails because it can’t find the libraries stated in the LDFLAGS of the top-level src/Makefiles.
So, to do this, we need to be sneaky and run make twice, once with the LDFLAGS turned off so that the extern packages compile, and a second turn to put back the LDFLAGS so that the TPP programs can find the libraries they actually need. So find the line:
LDFLAGS= ${SYSLIBS} ${DEBUG} ${EXPAT_LIB} ${HDF5_LIB}
Comment the shit out of it (add a ‘#’ at the front).
Then run make. It should compile all the extern dependencies and then crash somewhere in the compilation of the TPP.
Then uncomment that very line in src/Makefile, and run make again.
Everything should compile now. At this point, all the binaries should have been built, but not deployed.
3. deprecated copy options.
In the deployment, one of the Makefiles uses an option for the copy command cp that has been deprecated in BSD/Darwin. It is in CGI/Makefile. It is in the line:
cp -rfu tpp_gui/users/* ${CGI_USERS_DIR}
Specifically, -u option is not available in Darwin, so we simply delete it (it’s not very important anyway) and remove the -u option:
cp -rf tpp_gui/users/* ${CGI_USERS_DIR}
4. md5 is md5sum is not md5.
The last bit is due to an annoying difference between the md5 hash programs between BSD/Darwin and GNU/Linux. The numbers are the same but the text output is slightly different, enough to confuse the TPP. If md5 is not installed correctly, you can’t interpret passwords for user accounts.
So in the file CGI/tpp_gui/tpp_guil.pl, find the line:
'md5' => '/usr/bin/md5sum', # full path to md5sum
and replace ‘/usr/bin/md5sum’ with:
'md5' => '/sbin/md5', # full path to md5sum
5. Deploy.
Now you are ready to deploy. So go ahead:
sudo make install
And of course, you must then configure your local apache server, which is as described in the previous Mac OSX installation guides.
Vector Representation in Structural Biology
One of the questions that vexes computational structural biologists when writing analysis software, is whether to represent spatial vectors as an object with x, y, z components, or as a numeric array of floats with 3 members.
After turning over this problem in my head for the last decade, and writing vector classes in several languages, I can tell you now: go with the array of floats.
It might seem that you cam write cleaner code with named components: x, y, z. After all, you’re probably going to be translating algorithms from math or physics books, where x, y, z are used.
However the x, y, z designations are arbitrary. All of the laws of physics work just as well when you permute the x, y, z indices. Although some algorithms construct special matrices and vectors with specific formulae of the x, y, z components, such as populating rotational matrices from axis vectors, other algorithms can be written much more cleanly by looping through a spatial dimension index i through [0, 1, 2].
Unfortunately, once you’ve gone for x, y, z components, then you’ll have to tediously expand out such looping algorithms, or write an adaptor function to fetch the components using an index input parameter. It’s less painful going the other way.
More importantly, if you were ever to expand out your vector class to handle more complicated operations (such as principal component analysis), you will probably find that you want to leverage any one of the many excellent linear algebra libraries out there. This is where you will find that the choice of using numberic arrays really pays off. Because in that case, arrays of floats can often be put straight into such libraries.
I look at my code where I made the unfortunate decision to use x,y,z components, and I see many places where I’ve had to translate to arrays of floats to interface with different algorithms.
So don’t make the same mistakes I did and future proof your code: go with numeric array of floats for vectors.
Urinal-based Science Supervision
In a recent email conversation with Baker lab postdoc Jeremy Mills, I stumbled onto an important issue regarding supervision in science and ceramic bowls.
It started with me recounting an incident in the early naugties. I was then in a lab that ran out of money and unfortunately, I was the first to be asked to leave. I spent the next few months chasing around like a headless chicken for interviews on the west and east coast of the United States. On an off-chance, I even shot off an email to a professor down the corridor.
I managed to get some interviews, but nothing much came out of it. Then, one day, in my building on my floor, as I was in the toilet at the urinal, urinating, the professor down the hall comes in.
He takes up the bowl next to mine, and proceeds to urinate.
“Oh Bosco. I’ve been meaning to talk to you. I didn’t forget your email.”
“Uh .. uh, a-ha”. I am still pissing.
“I’m very interested in it. Let’s organize something”.
“Uh .. could I ..er shoot you um an email about it… later?”
“Sure,” he says, zips up his pants and leaves. “I’ll hear from you later!”
I eventually got that postdoc position but by recounting this formative experience, I had hoped to elicit a lol response from my colleague Jeremy. Instead, I got a rather nonplussed reaction. Jeremy informed me that in his experience, this pathology among professors was surprisingly ubiquitous.
“When I was at Scripps, there were notorious professors who had no compunction talking to their students about science while they were at the urinals.” Well color me yellow – it turns out my experience was not even unique.
Jeremy went on, “One chemistry professor there actually went so far as to make some sort of contact with one of his students. My mind is foggy on the details, but it was either a pat on the back, or a full on shoulder grab. Fortunately, my graduate advisor spent most of his time across the street from our actual building. I never had the “pleasure” of an awkward encounter with him in the restroom, but my heart goes out to those that have!”
Which then begs the question, how common is this really? I want to know. I’d also like to know if this is a purely man-on-man activity, or if there is a lady-scientist equivalent. Should supervisors supervise in the john? Is it effective? More importantly, did someone ever cross swords with their boss?
If you can contribute to this important topic, please please please leave a comment.
Non-fiction Reading Highlights 2012
I jumped on the bandwagon that is John Jeremiah Sullivan’s “Pulphead”. These are rightly considered to be some fucking great essays. I reread some of them recently and was struck by how clean the prose was. Nothing particularly fancy, but it is the authorial stance that is breath-taking. His approaches to his subjects come askance, exposing some unexpected facet of his own life, which oftentimes succeeds in illiminating a shared humanity. In one brilliant biographical essay, Sullivan was able to turn Axl Rose into a tragic figure. In another, he gazes straight into the maelstorm that is Michael Jackson, and manages to hold onto the music as the heroic center of genius. Indeed, the music essays in this book comes as closes to anything in modern journalism to explicate why music is so utterly essential to this modern life.
Like most Australians, I passed through the Australian school system and failed to learn any passable history of our nation of any consequence. I feel some shame in knowing more about the US presedential elections than our own political system. And so, it is with some relief that I read journalist George Megalogenis’ rather compact history “The Australian Moment”. The Moment which the book refers to was the economic jujitsu move that Australian prime minister Kevin Rudd did on the GFC, which smacked it so hard, that the Australian was able bounce from recession, and off onto the billowing safety of the onrushing Chinese mining boom. But really, the gimmick of the Moment is really just a hook into nothing less than a readable and authoritative history of 20th century Australian politics. It’s clearly a labor of love as the source material includes in-depth interviews with all the surviving prime ministers of Australia conducted over many years.
This year I read yet another translation of “Mumon’s Gateless Gate” by Koun Yamada, the central book of koans in the Zen canon. My favorite before this was Robert Aitken’s folksy American translation, which dissolved a lot of the weird mystical interprations in other translations. What is great about Yamada’s version is that it puts in a lot more context of each of the koans so much so that I could figure out some of the more obscure koans that had stumped me on previous translations. Yamada is also much more patient in laying out the logic of each koan. I also got a chance this year of reading different collections of essays by Dogen, the great medieval Japanese Zen master. Dogen is a minefield for the aspiring translator as he is one of the hardest writers to translate in what is an already difficult to translate genre. He invents terms out of whole cloth and is linguistically playful with his explanation of the dharma. With Dogen you can get a precise but pedantic and clumsy translation like Cleary’s translation. But you can also get a fluid translation such as Bob Myers’ “First Dogen Book”. In Myers’ translation, he makes many surprising and pleasing word choices that ripple through the whole texts. Getting these just right requires years of study and practice. Without this level of translation, it’s very hard to appreciate the true beauty of Dogen’s Zen.
Cities are the greatest creation of humanity. Well at least according to some, which include myself, and also P. D. Smith, who has written one of the best books on the city yet “Cities: A Guide for the Urban Age”. What is it exactly? It’s like a little encyclopedia, a collection of short essays, each devoted to one aspect of the city, or city life. This book has no particular agenda, it just wants to celebrate this most human of inventions and so, the topics range far and wide, from city gates to marathons. Of course, this book would not be noteworthy if not for the quality of the writing. And Smith is incredibly well-read and erudite. His tone is somewhat elegiac and I think this book will stand the test of time, providing as much intellectual sustenance for future lovers of the city.
Peter Watson’s “The German Genius” is one very long book. It’s dense, and it has nazis in it. Or rather Watson’s main contention is that the recent history of nazi Germany has unfortunately obscured the vast intellectual contribution that German culture has made on the modern world. This book aims to demonstrate, and I believe it does so in ample measure, that the culture of the modern world is Germanic in origin. How did a bunch of illiterate barbarians on the edge of the Roman Empire reinvent themselves into the most sophisticated society Europe had ever seen? Watson traces the influence of the Pietist branch of the protestant revolution in the development of German culture, from philology to philosophy, music, science, engineering and the arts. I’ve studied my fair share of physics and philosophy and I was constantly surprised by just how much Watson had absorbed. His thumbnail sketches of seemingly every significant German intellectual are astonishing. But more importantly I got to see how the development of German ideas went hand-in-hand with the political development of the German political state. What is disturbing though, as highlighted by Watson, is that the heights of German culture developed specifically at the expense of the development of their political system. There was a perverse parasitic relationship between the two, a relationship that would uncoil in the twentieth century in the worst possible book. This is an exhausting book, but the chance to see so many ideas tied together by a sure hand is rare to see indeed, and if you are a lover of the history of ideas, this is an absolute must.
Notable Books I Read of a Scientific Nature in 2012
After a barren few years for popular science books, I stumbled onto several good ones this year.
I first encountered evolutionary psychology about a decade ago in its former incarnation as social biology but was rather put off by it then, when it was rather short on data and long on theorizing, inevitably becoming a mirror for the writer’s political ideology. The field of evolutionary psychology has since progressed in leaps and bounds, and one of the glittering lights of the field is Jonathan Haidt, who also happens to be a gifted writer. His “The Righteous Mind” outlines a persuasive case that there are several underlying psychological modules that define human moral thinking, which to rattle them off carelessly are: care/harm, fairness/cheating, loyalty/betrayal, authority/subversion, liberty/oppression and the most interesting to me, sanctity/degradation. This theory is backed by oodles of cross-cultural research and steeped in careful evolutionary thinking. I think combining these insights with the work in evolutionary religion (David Sloan Wilson) will provide a doorway into 21st century religion.
As a scientist working in biology, looking for a connection to medicine is an important skill to improving one’s grant-baiting ability. Sadly, this does not mean I actually know anything about medicine; my knowledge of the history of medicine is rather meagre. I fortunately got a chance to fix this when I stumbled onto James Le Fanu’s “The Rise and Fall of Modern Medicine”, filling a rather surprising gap in the literature. It does this through a rather provocative hypothesis – that there was a golden age of medicine, and it has already passed. The first half of the book provides an extremely readable history of modern medicine, mainly over the course of the 20th century, structured in terms of 11 pivotal breakthoughs. This half of the book is wonderful and has definitely enriched my understanding of modern biology. The second half, where Le Fanu rails against modern day medical research, is rather uneven, and can be safely skipped.
In biology, two of hottest areas are neuroscience and developmental biology. In Rob DeSalle and Ian Tattersall’s “The Brain” we have a exposition that beautifully syntheses the two. This book explores,not just the brain, but the whole notion of a nervous system in terms of developmental biology. To do this the book reaches right back into the tree of life to trace the evolution of organic life, and at each stage of development, feeling out the functional requirements of a working nervous system, culminating into the nervous system of the human brain. Unlike other lesser books on the brain, the brain doesn’t even make an entry until 2/3 of the way into the book. More that the generally breezy quality of the writing, what impressed me most was how clued these guys were into the cutting edge of biology – they write about the fascinating world of non-coding RNA, transposonic elements, and the even more mysterious process of RNA editing. These are findings I’ve found to be still outside the mainstream (see for example many bioinformatician’s resistance to the idea that transposonic elements have any biological function at all).
I have had a hole in my technical education, ever since I skipped second-year Linear Algebra for what I thought would be the sexier subeject of Introductory Philosophy. It’s been a problem ever since as standard linear algebra theorems are often invoked to explain higher level physics. I’ve tried to rectify this over the years, but each time I’d try a new linear algebra text book, I died a little. The difficulty with teaching Linear Algebra is that there are no really overarching equations that binds it all together, instead there is a forest of numerical techniques to master, as well as a bunch of disconnected abstract algebraic theorems. As a consequence, half the linear algebra textbooks soar into abstractions which obscures the messiness of practical techniques, whilst the other textbooks dive into the nitty-gritty algorithms, but get lost in the ability to make sense of all the different techniques. Gilbert Strang’s “Linear Algebra” is that rare Linear Algebra textbook which perfectly straddles the two. It got me interested to learn all the theorems, which were presented in a way that handily motivates all the key techniques. You will learn how to reduce matrices into various canonical forms, but also how to use the abstract theorems to grasp the meaning of the solutions. As a result, I can now plow through some machine-learning papers in bioinformatics that has had me stumped for a while.
This was also the year that after many aborted attempts, I finally got my head around information theory. I settled on David MacKay’s “Information Theory, Inference and Learning Algorithms” because it was the only one that was willing to motivate all the theorems of information theory for a rank beginner. Before every theorem, MacKay patiently describes in elaborate and necessary detail the kind of problems each theorem would solve. Information Theory can be a beautifully abstract theory, but its power is in its ability to illuminate very specific computation problems. I loved the focus on practical consequences such as the explanation of how the gzip algorithm works as an elaboration of the use of entropy in encoding files. But more importantly, MacKay has taken the idiosyncratic (but ultimately correct) approach of teaching information theory as a branch of bayesian inference. The information theory then becomes a launching pad into machine learning. Thanks to this, I also got to learn the basics of machine learning for free. Booyah.
My Fiction Picks of 2012
2012 restored my faith in fiction. I read so many brilliant novels, phatagasmorphic books that dissolves reality and makes one ache for the pain of living. There was Kate Grenville’s “A Secret River”, a book that digs into the collective consciousness of the Australian psyche. It’s a richly imagined period piece of a man straddling the squalor of Victorian England and the prison colony of early white Australia. It’s an unbelievably tense collision of worlds, English, colonial Australia, and the indigenous world, with a ferocious climax that shook me up something wicked.
A page-turning juggernaut, “Hunger Games” is the first book in years that made me stay up till 3 in the morning to finish. Merely young adult fiction? Of course not, it is simply one of the greatest adventures ever written, right up there with Dumas’ “Man in the Iron Mask”. Suzanne Collins has given us one of the vivid heroines in literature. The arrow-slinging, steely-minded Kadniss Evergreen can prick the prissiness of every treacly Jane Austen archetype ever written.
Then there was Hilary Mantel’s “Bring Up The Bodies”, the continuation of one of my all-time favorite novels “Wolf Hall”. “Bring Up the Bodies” is every bit as bloody and visceral as its predecessor. But it is the voice of Thomas Cromwell that I crave, he is more real to me than friends I have known for years. This is a man as cultured as he is brutal, but pragmatic, and even generous when he can afford to be. I love the way Mantel captures the mind of a man who has deftly moved into the world of the Enlightenment and trying to drag the rest of England with him.
I didn’t get to read too much french this year, but I did get my hands on the latest from Justine Levy in “Mauvaise Fille”. It’s a short read but packs a double-handed whopper of plot: her mother dies of cancer as she gives birth to her first. It would be pure melodrama were it not for that hypnotic voice, wry and cerebral, but always on the verge of a meltdown. Sure it’s semi-autobiographic, but that makes it all the more entertaining.
Capping off a superb year, I was fortunate to read Junot Diaz’ “This is How You Lose Her”. The prose crackles off the page and the stories run the gamut of human of experience. I did not want this book to end; I wanted the stories to spin forever and forever. Diaz has managed the godly feat of creating a character that walks the poignant line between deplorable and incandescent. Oh Yunior, I hardly knew you. Diaz’ ability to conjure up the world of the Dominican Republican through a supple play of patois, over-sized characters and fatalistic myths remind me very much of the ferocity of Rushdie’s Booker-of-Booker “Midnight Children”. Yes, “This is How You Lose Her” is that good.
On the need for a canon of Australian literature
I never used to, but I now believe firmly in a canon – a bonafide list of Australian novels that everyone ought to read. My moment of conversion happened at, of all places, a literary event. It was an event organized by the literary magazine Meanjin to celebrate great women writers of Australia. A panel of writers and publishers was put together to discuss a list of novels written by Australian women, and to launch a literary American-Idol of said novels. Despite the overt nature of the event, I was originally skeptical of the idea of a canon. But during the event I was surprising converted to the necessity of embracing a canon, due entirely to some of the (deplorable) quality of discourse I witnessed on the stage.
The irony was that at an event celebrating a canon of women writers, half the invited panel were openly hostile to the idea. It seemed the more the individual panelist did not believe in a canon, the more moronic was the discourse. The makeup of the panel was five, three women and two men. Of the men, one was an established author who was openly contemptuous of women’s writing, proclaiming that he does not read novels written by women, whilst making bitter quips about women writers who had beaten him to several literary prizes. The other guy was a comedian who proudly admitted that he wasn’t much of a reader and when asked to read aloud a description of several novels, decided the best way to do this was by mocking the book. It felt not a little gross.
The ultimate irony was that one of the women panelists, a young children’s author, explicitly proclaimed she didn’t believe in a canon, and in the next breath, admitted she had read not one of the novels. As the list of books was rather large, her comment was revealing of the breadth of her reading, and as such, she was unable to make a single enlightening comment about any of the books that she had been invited to discuss. Sadly, the reason she had been invited to the panel was that she herself had won a prize for her own book, an active piece of canonization that she felt somewhat embarassed about, although she did admit that the prize did help her sell books.
As you can imagine, there were no books on the list that all the panel had read. But there were three members of the panel that had not read any of the books. The discussion degenerated into the most facile discussion of literature, not much better than a half-hearted social book club, where you have a bunch of people talking and critiquing books that they had not yet read. The very low point was when the comedian started making jokes about the books based on the blurbs he had been given. But really what was he supposed to do? And this was meant to be a high-point of the literature of Australian women writers. Sigh.
I am going to go out on a limb and say that if you want to discuss books, to really discuss them and get at the meat of them, you have to, you know, actually read them. At least you should be able to name the protagonist, be aware of the plot points, and then maybe dive into the poetry of the prose and the philosophical and social ramifications.
Now there is a world of books out there, and although the book industry may be dying, the number of books being published have not. From sheer numbers alone, it would be pure coincidence that any two random people will have read the same books. Obviously, a discussion requires at a minimum, two people. So to have a fruitful discussion, both conversationalists will need to have read the same book. Given the miniscule chance of any two random people reading the same book, there is really little chance that a meaningful discussion of literature can really take place. Contrariwise, this means that as a community, if we want to have a discussion of literature, we will need to define a small list of books that educated readers ought to have have read. We will need to define a canon.
It seems to me that as a reading public we have a choice. Either you disavow a canon and preclude any meaningful discussion of literature, or, if you want to actually discuss literature, you will have to accept the necessity of defining a canon of Australian novels. However, advocating such a list of books does not necesarily mean these books are the “best”, or the most “literary” or even the most “australian”. It’s simply that we need to build a platform to support a serious literary conversation, instead of the half-baked simulacra of a conversation that often passes for one. If we do manage to put together such a list, and almost any half decent list will do, it should be understood these books are simply meant to mark out points on our shared literary landscape. It would be just as effective for someone to despise the books on the canon as to love them. But having actually read the book, our happy hater should be able to articulate why they hate them, and then we can begin a real conversation, about the >ahem< books themselves. And this Meanjin list of Australian novels is a very good place to start.
Books 2012
[* highly recommended if you’re into it, but YMMV]
1. Judith Lasater, Ike Lasater, “What We Say Matters”
2. Cal Newport, “How to Become a Straight A Student”
3.* Kate Grenville, “A Secret River”
4.* Suzanne Collins, “The Hunger Games”
5. Roger Lowenstein, “Buffet”
6. Suzanne Collins, “Catching Fire”
7. Suzanne Collins, “Mockingjay”
8. Helen Garner, “Monkey Grip”
9. Raven, “Biology”
10. Haruki Murakami,“What I Talk About When I Talk About Running”
11. Don Riso & Russ Hudson, “Wisdom of the Enneagram”
12.* John Jeremiah Sullivan, “Pulphead”
13.* Gilbert Strang, “Linear Algebra”
14.* James Le Fanu, “The Rise and Fall of Modern Medicine”
15.* George Megalogenis, “The Australian Moment”
16. James Joyce, “Dubliners”
17. Ken Wilber, “Integral Spirituality”
18. Karen Salzberg, “Lovingkindness”
19. Stephen Batchelor, “Confessions of a Buddhist Atheist”
20. Fiona Maddocks, “Hildegard of Bingen”
21. Ken Wilber, “Integral Life Practice”
22. John Stillwell, “Naive Lie Algebra”
23.* Jonathan Haidt, “Righteous Minds”
24. Rumi, “Quatrains”
25. Hui Neng, “Platform Sutra”
26. Stephen Batchelor, “Buddhism without Beliefs”
27.* Hilary Mantel, “Bring up the bodies”
28. Alice Pung, “Growing up asian in Australia”
29. Robin Waterfield, “Diving the Spoils”
30. David Smith, “Dharma mind, worldly mind”
31. Montaigne, “Essais I”
32. Jeremy Duns, “Song of Treason”
33.* Koun Yamada, “Mumon’s Gateless Gate”
34. Duns, “The Moscow Option”
35.* David McKay, “Information Theory and Bayesian Analysis
36. Alberts et al., “Essential Biology of the cell”
37. Edward O. Wilson, “The Social Conquest of Earth”
38.* Desalle and Tattersall, “The Brain”
39. Gibbon, “History of Decline and Fall of the Roman Empire Vol I “.
40. Helen Garner, “The Spare Room”
41. Letters of Abelard and Heloise
42. Thomas Cleary, “Dogen’s Shobogenzo”
43. Dogen, Shobogenzo 13 essays
44.* Bob Myers, “First Dogen Book”
45. Muriel Barbery, “L’Elegance du Hérisson”
46. Jarret Walker, “Human Transit”
47. Cal Newport, “So Good They Can’t Ignore You”
48.* P.D. Smith, “A Guide for the Urban Age”
49.* Justine Levy, “Mauvaise Fille”
50.* Peter Watson, “The German Genius”
51. John Medina, “Brain Rules”
52.* Junot Diaz, “This is how you lose her”
53. Tim Ferris, “4-hour chef”
Thoughts on Cal Newport's "Too Good to be Ignored"
Cal Newport’s book "Too Good to be Ignored" is a timely book that lays out a carefully thought-out guide to construct an extraordinary career. It is not a book for the faint of heart: the book offers no shortcuts at all. Indeed, what is left unspoken is that, ultimately, few people will end up benefiting from the advice in this book, but those who do will find new clarity and purpose in the way they approach one of the hard questions in life: what is the work I am meant to do in this life?
There is a roughness to the book that I found engaging. This roughness comes from the fact that Newport is figuring this all this out as he’s going along. He would be the first to admit that he hasn’t as yet reached the dizzying heights in his career that many of the interviewees in the book has reached. He’s trying to figure out a useable blue-print for himself, and hopefully the rest of us as well. But this makes the book even better as the author has skin in the game, which results in a beguiling mix of uncertainty and bravado in his writing. On a side note, I love reading his blog where he discusses all the ways he has tweaked his own approach to research, collaboration and career management.
I see this book as a practical companion to books on talent like Malcolm Gladwell’s "Outliers" or Geoff Colvin’s "Talent is overrated". The reason is that Newport is not interested in the what, but in the how. In order to study the how, Newport makes a crucial distinction between two different types of talent. Perhaps the best way to illustrate this is to paraphrase physicist Marc Kac speaking about Richard Feynman. Kac states that there are two kinds of geniuses. There are the ones you can imagine that if you were much much smarter than you were, and worked a lot harder, then you could do what they do. Then there are the magicians. Newport is actually not talking about magicians, he is talking about the other bunch. And after having spent several years interviewing people with extraordiary careers, Newport has come to the conclusion that most people who achieved really interesting careers were not so much magicians but hard hard workers who stumbled into their ultimate career. That is great news, because while we can’t emulate the magicians, we can emulate the hard workers.
This is particularly pertinent as one of the themes of the book is to shoot down the prevailing wisdom in many career books of something that Newport calls the Passion Hypothesis. This is the hypothesis that the only thing between you and your dream job is your lack of convinction. The idea is that courage is your only obstacle – if you only had the courage to pursue your "true" passion, then you would finally live the fantasy life you’ve always dreamed about. Newport argues that not only is the Passion Hypothesis ineffective but it is downright malignant. He gives various examples of people who have naively followed their Passion and switched careers into their fantasy and watched their lives fall apart.
A particularly amusing part of the book is where Newport shows that many great careers trotted out as examples of Great Passion, such as Steve Jobs and Derek Silvers, were instead the result of some kind of lucky accident. Life is more random and disorganized than we’d like to think and it’s easy to understand though why a great career is often described as the end-result of some kind of Great Passion. Such an origin story lends a heroic aura to a life, making a career seem like the result of destiny. It’s a post-facto narrative that make us feel like we are in the presence of modern day gods.
By working backwards from his case studies of interesting careers, Newport figured out that there was often a method to the stumbling. Such careers seem to progress in stages and each stage is marked by the accumulation of something that Newport calls Career Capital. Namely, Career Capital is a rare or valuable skill that you have mastered and that someone out there is willing to pay you money for. You know that you have career capital when employers don’t want to let you go, or when people throw money at you for that skill. It is Career Capital that allows you to go forth and try out new career trajectories.
This concept may seem to be brutally economic but I think it is a profound insight that touches on the Heideggerean notion of authenticity as being-in-the-world. Heidegger argued that much of the philosophy of self, or authenticity, focused too much on interiority, whilst ignoring the context of the self in the rest of the world. The world constrains what the self is, and a sense of self that is sensitive to this is often translated as being-in-the-world. This problem with authenticity definitely infects the Passion Hypothesis where the secret to wordly success and self-fulfilment is supposedly locked up in your self as a frustrated passion. In contrast, Newport’s much more prosaic concept of Career Capital argues that you have to figure out what you can do that matches what the world can provide. This is being-in-the-world.
So how does one obtain Career Capital? Newport argues there’s no real alternative but to knuckle down and master a skill like a traditional craftsmen. This section echoes many of the books written on the topic (Gladwell’s "Outliers"; Colvins "Talent is Overrated"). The additional insight that Newport provides is that brute mastery of skills is not nearly enough. Career Capital augments the classic notion of mastery in two principal ways. First, that is not just mastering one set of skills, but it is the steady accumulation of a conjoined set of skills that opens up the opportunity for building an interesting career. Second, this requires a kind of meta-analysis to decide what skills are worth learning, and which ones are worth perserving in.
To justify this, Newport invokes Stuart Kauffman’s idea of the adjacent possible, which is a more prosaic way to think about Heidegger’s Being-in-the-world. As the world progresses and new technologies are brought into being, opportunities open up which require only a short sideways hop for someone with the requisite skills to fill up. Interesting careers are made by filling up the space in the adjacent possible. Those who dream much further out than the adjacent possible will have no easy way to engage the world. This explanation echoes Richard Hamming’s famous essay on "You and Your Research", where Hamming argues that one of the secrets to doing World-Class Research is the ability to appropriate new techniques and ideas from related research fields and use them to crack the fundamental problems in your own field. An interesting corollary to the adjacent possible argument is that if you do insist on working far from the adjacent possible in a well-established field, your skill level must be extraordinarily high to have traction in the world.
So, to summarize: if one has not reached the nirvana of self-fulfilling work, this means one must first search out new skills worth mastering, subject oneself to master these new skills, and then test the new skills out in the world to see if they stick. You keep going until your skill set reaches a critical mass. And only once you reach the crticial mass, will you be able to look back to see how the story unfolded. This is not the kumbiya advice of the Passion hypothesis where courage and self-discovery is all you need. It is pushing the self against the world and feeling the interconnect between the two.
Still, the book leaves many questions open. Namely, how does one go about mastering new skills? I mean if it takes supposedly 10,000 hours of deliberate practice to master any skill, there are only so many skills one can learn in a lifetime. As well, it seems to me that not anyone can learn any kind of skills. Different people are primed to learn different kind of skills. I think this is definitely an area that can be expanded on, which can draw insights from the growing field of positive psychology and concrete models of personality types. In terms of skill acquisition goes, one consequence is that you don’t want to stray too far from your current skill set to choose a new one. Perhaps this might cut down the 10000 hours required to master the new skill. An example is learning languages. It’s been said that once you start learning your 5th language, it gets a whole lot easier learning the next one. I’ve found this to be the case.
If we are to take Newport’s argument seriously, then there are certain personality qualities required to construct an interesting career. You must have the doggedness required to sustain the effort to master a skill. You must have the openness to constantly explore new ones. You need the pragmaticism to figure out which skill actually fits the world as it is. Doggedness, openness, and pragmaticism. These are three rather peculiar traits required to become someone who is so good that they can’t ignore you.
