Category Archives: Comments

Personal Development for Smart People: review of Steve Pavlina book

Personal development wasn’t so far the subject of any post on this blog, and that’s not a surprise – it’s hard to hard to measure, hard to study and full of published trash. However, I’m interested in the topic and one of my favourite blog on the topic is “Personal Development for Smart People” written by Steve Pavlina. While Steve is quite controversial (as you’d expect from somebody who develops his physic abilities, is a raw foodists and experiments with polyphasic sleep) and I sometimes strongly disagree with him or have a hard time believing in some stories, often enough he writes very interesting and useful articles.

When he announced that his book will be released in October, I was planning to buy it but I got a pre-release as a part of promotion offer. The offer required to post a review, not to praise the book, so here’s my honest and biased opinion.

I will not go into detail on the contents of the book. You can get a pretty good feeling what it is about here. The book doesn’t overlap very much with excesive content of Steve’s blog – most of the practical issues of self-development are covered on the blog, the rest is pretty much original.

This is not an easy book and it will not leave you happy and motivated. It’s not easy not only because it requires some basic knowledge (for example, Law of Attraction mentioned few times is not defined anywhere), but it will ask you to question lots of your beliefs and assumption. For example, Steve asks to rate several aspects of your life, and then re-rate anything below 8 as 1, claiming that if you don’t have exactly what you really want, you simply don’t have it, period. You can call it a trick, but taking it seriously may be somehow difficult. Also, it doesn’t have any motivational stories, it doesn’t call you to act or to punch your chest – it has just down to earth description of the process of personal growth. My biggest complain was that it was too short – it felt like an introduction, not comprehensive guide. Also, from a scientist point of view (I know, this is not research paper) I missed some background and comparison to ideas other people have written over the years.

You can read this book and extract lots of practical hints on how to achieve something faster/more efficiently, or how to develop necessary habits, but it’s not definitely why this book was written – from my perspective it’s an invitation to think more seriously about personal growth and to challenge the status quo of what we think about ourselves. And I would like to accent the word “invitation”. Steve is not aggressive and does not try obsessively to prove he is right (as it happens too often in other books). It’s an invitation you don’t have to answer.

What’s in this book for scientists? That’s a hard question. This book wasn’t written for scientists, poker players, truck drivers or startup founders. It was written for people who want to grow and need some help on the way. Definitely, it can serve as a reminder that even science should be ethical and should provide a value, but on the other hand I don’t think majority of you need that reminder at all. As a side note, Steve explains in the book why scientists (and other professions) are paid so little (he calls it low social value), but we knew that anyway :).

What I got from the book was help in making my non-profit plans more clear. Although you don’t need to start a non-profit to find this book worth reading.

You can order the book at Amazon.

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Posted by on October 16, 2008 in Comments


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Future of Science on the (ZuiPrezi) map

I’ve just stumbled across map of predictions about global science and innovation created at a recent IFTF workshop in Singapore (the interface is a novel service for online presentation called ZuiPrezi – it looks very promising and I’m waiting for it to come out of private beta). The map contains a few points that resonate with my own scientific interests:

  • bioelectricity, microbial fuel cells and self-assembly for molecular electronics were for me areas where synthetic biology comes into play
  • scientific publications changing from journals to articles and proposal to make an institute for free exchange of ideas looked like indications that Science 2.0 memes are spreading very well
  • and finally, I’m happy to see more people believing that real-time, non-invasive and possibly 3D sensing of biological processes (aka “how is my cholesterol level building up?”) will be available sooner than in 50 years

As usuall with such predictions, I feel like many of them are quite conservative – or even schematic. Only very few were completely new to me, but that’s not necessarily a bad thing. It means that actually most of these predictions will turn out to be true in some time. I would like to see something that would immediately blow me away, but on the other hand it’s all relative :).

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Posted by on September 30, 2008 in Comments, Research


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How far one can push online collaboration in research?

History comparison reports highlight the chang...Image via Wikipedia

A week or so ago I’ve asked on the FriendFeed if there’s an interest in writing a cyclic publication on the status of Science 2.0. I thought that summarizing every year advancements in openness of science would be a good idea. During discussion it turned out that there’s a need to write a first major publication on Science 2.0 concepts because there isn’t one published in the life sciences field. The final conclusion of interested people was to meet face to face on the upcoming conference and discuss things in detail.

And this made me think.

I started to wonder why people who live, breathe and do research online still need to meet in person to plan and discuss some stuff. The very obvious explanation is that the conference was only two weeks ahead, so there was nothing more than that, but some patterns (brainstorm online, then meet in person, then finish online) repeat so often that I started to believe an online collaboration can only go to a certain point.

The excuse is not in the tools, especially given how fast the new ones appear.  As an examples may serve recently launched Adobe Acrobat site, which contains online editor and live collaboration suite (contains screen sharing, notes, chat, audio, video) or its analog for programmers: Assembla (svn, git, trac, wiki, milestones).

My feeling is that what makes a difference is not a quality of interaction while working on a certain project, but the possibility of discussing things not directly related to this project. Online collaboration is usually very focused. When editing a document online it’s usually hard to side-track it, so at the end it’s about something else than it was planned. Calls or videoconferences have usually a schedule. No place for non-related stuff. No place for a beer/coffee/glass of water and a chat about how life was good in old times. No place for discussions on random things and coming to the main project from a different angle and with completely new ideas.

I’ve been trying for quite a long to work online with other people on some projects from my home office (which is in the middle of nowhere). As you can guess, it works to a certain point and majority of them were improved upon meeting face to face. And this left me wondering how far can I push online collaborations. It isn’t usually an issue in IT field, but so far it doesn’t look very promising in research.

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Posted by on August 27, 2008 in Comments, Community, Research


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By any measure I’m average at most

Nature, Science and PNASImage via Wikipedia

As you have probably noticed, yesterday’s BioBarCamp was covered in depth over at FriendFeed and additionally Cameron was streaming video live from the event (it’s still available under the same address). One particular session drawed my attention, because it was about measuring impact of scientists. It’s something I have very strong opinion about since couple of weeks, so forgive me this rant.

Peter Binfield (PLoS) and Pedro Beltrao did a great job on presenting current status of the issue and presented potential way to measure impact of a publication (quoting after Shirley“your article received x citations, viewed x times, received x comments, bookmarked x times, rated x by experts, discussed on x respected blogs, appeared in x news media, etc etc” – instead of single “your article was published in journal with IF of X”). And while two months ago I was really interested in such discussions and willing to help, today I simply don’t care. The reason is simple and is presented in the post title: by any measure, I’m average at most.

That’s absolutely obvious that majority of scientists is at most average by any standard or measure. And that is not going to change, at least not much. Those who are at the top by Impact Factor today, will be at the top by other measure. Those who do some not-that-important stuff like me, will be still pretty average by other measure. One of the reasons may be all kinds of issues with normalization of the field size (there’s too much problems with biological ontologies to believe that dividing science space into fields is going to work much better). Another thing may be relative importance of the field (that’s something different from field size) – human research will always draw more attention than electrochemistry. And I could go on and on – all these issues aren’t novel and have been described and discussed in thousands of blog posts. The point is that even if such new ideal measure is going to be fair, it will not change life of majority of scientists. Not only because some of us do average things, but also because some of us have average money (BTW, I haven’t found much discussion on including in the measure research budget, which surprises me given the fact that amount of money spent on a project correlates pretty much with the IF of the journal it is published in afterwards).

So, I don’t really care if IF stays or not (although people working on improving measuring get my deep respect). Reputation-wise I’m going to be in the middle unless I will make something extraordinary. But honestly to make a scientific breakthrough the last thing I need is a number describing quality of my thinking.

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Posted by on August 8, 2008 in Career, Comments, Research


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FriendFeed: where the conversation happens

The start of this post (see the image above) may be a good reason for many people for not to join FriendFeed 🙂 . It shows what happened to number of visitors to this blog after I joined FF – it had dropped by half (actual numbers aren’t relevant, graph shows monthly statistics). The reason is pretty obvious for any long-time blogger – no posts, no visitors. I don’t post as often as before for a good reason – sharing news, interesting links and the whole conversation around these happens on the FriendFeed. While I didn’t set up a dream system I wanted to (see my comment on previous post on the FF), I don’t have any issues with so-called “information overload“. Actually, I don’t believe in any information overload – we are just pretty bad at managing incoming information – but that’s a story for another post.

Rooms are neat feature of FriendFeed – they act a filter and keep the conversation focused. Instead of looking at a stream of titles ranging from linux hacks, through hardcore programming stuff and other bioinformatics-related topics, up to cancer research and science philosophy, I can just go into one of the rooms and see only items related to a particular topic. Yesterday Deepak wrote on the new rooms at FF (for Python, Ruby and R for Bioinformatics) that were created by people from life-science community. There is also a room for Science 2.0 and Open Science, DIYBiology and even a room which collects links to a must-read material – BioGang classics (since I started this post, Ricardo had created OpenWetWare FriendFeed room).

Rooms help in keeping the flow of links under control, but the conversation is the key point of using FriendFeed. Almost every single item posted into The-Life-Scientists room generates comments, sometimes turning into pretty long discussion. Because FF aggregates Twitter updates, majority of “Dear Lazyweb” Twitter requests result in FriendFeed based conversations. And there’s more and more people participating (The Life Scientists room has over 200 members). As usual, there’s a catch – focus and depth are not good sides of FF comments (for example, compare reaction to the recently posted very nice essay by Michael Nielsen on The Future of Science: number of comments on his blog and on the FF are comparable, although discussion/arguing with the essay points happened mostly on the blog). But that’s not a problem – it’s just a result of a speed with which items appear and disappear on the FriendFeed (some of you have seen that tracking real-time stream from concurrent sessions on the recent ISMB conference).

Even such shallow and quick interactions with people on the FriendFeed generate some level of trust, and that I think will lead to couple of interesting things:

  • more people will try how does the online collaboration work (for example, in reflection after recent Cameron’s talk Brian Kelly from UKOLN wants to write his article online)
  • PI-level scientists will join FF to participate in the discussion (we see that already, although so far there’s only very few of them)
  • there will be serious articles why FriendFeed, Twitter and online collaboration are bad for scientists and how these can break their academic career, in similar way as there were for blogs (see recent Pedro’s post)
  • we will see (and read, since it’s going to be open-access) first peer-reviewed publication from an idea that originated at FF/Twitter

Is FriendFeed going to be a hub for science? I don’t really think so. At the time, when mainstream science will pick up FriendFeed I think we are going to be already somewhere else, because there will be more interesting and more useful platforms for scientific collaborations (like for example – looks promising, although it’s not yet optimized product). But the time spent at FF will give us an advantage: connections, collaborations, wide spectrum of information and advice from smart people.

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Posted by on July 28, 2008 in Comments, Community


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Growing in open source business model

cleanedImage by *w* via Flickr

Last couple of months I’ve been quite busy with writing PhD thesis and few other projects, but also I was trying to start an open project balancing between academia and industry. This balance sounds like an opportunity, but in fact it was an issue instead. The issue wasn’t in the money – I was lucky to find people willing to help me in getting funding. The issue was rather in what I need to give away in exchange for the money – openness, control over the project or all intellectual property rights. Being already established scientist or a business person would solve such issues immediately, but I am still PhD student, so I need to face it. And while I have still plenty of people to talk to (I think it will take another month or two), that left me thinking about career on the border between industry and academia.

On both sides, in academia and industry, career path (and I’m not talking here only about having a job, but also about starting a business by yourself) is somehow clear and one can get a significant help along the way, but I haven’t found such clear path on the border between these two. Open source business model seems to work well mostly for very established players (such as Apache or RedHat) – growing in such model looks much more difficult than on either of sides. Probably Antony Williams from ChemSpider (who was one of the people that inspired and encouraged me to follow this path) would say much more in here, especially how easy (is not) to get a financial support for working on a project like ChemSpider.

I don’t think about working in one or the other environment anymore. Being freelancing scientist has a lot of good sides and growing wouldn’t be an issue (for example I have enough collaborations and ideas to cover financially next 3-4 years from grants; publications would follow). But, as I wrote before,some of the projects I’d love to work on are unlikely to be funded in academic system. On the other hand, openness is too important for me to give it away, so only a merger of these two sounds interesting. There are few examples of successful merging industry and academia, but they all seem to operate on different principles, compared to my recent attempts. Craig Venter’s model was as far as I know most of the time double-sided – he had a non-profit search unit and a company that commercialized its discoveries. Pretty similar has also David E. Shaw. So I have started to wonder if sticking to borderline is actually the very best idea. Being involved on two fronts at the same time sounds pretty overwhelming, but so far these are the only examples when this whole idea seems to work. Are you aware of any others?

My other hope is that new ways of growing on the borderline will very soon emerge. There’s quite a lot happening right now on the front of supporting innovations (including open models), so maybe over there I will find my niche. We’ll see.

(The image above is not my desk. While I work in a home office, mine doesn’t look so clean.)

Further reading:

A microfunding system for research and innovation.

Pharma looks at new ways of innovate.

Discussion around business model around Open Data is building up.

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Posted by on July 21, 2008 in Career, Comments, Research


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PhD thesis in LaTeX

For the record: here you can see a single (still unfinished) page of my PhD thesis prepared in LaTeX. I used PhD thesis style prepared by Jamie Stevens and wrote the whole thing using Kile editor. An image on the margin can be inserted with command:

     Caption text

Posted by on June 19, 2008 in bioinformatics, Comments


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Blogging overtaken by life streaming

I don’t post new things as often as I used to couple of months ago, but it’s not all my fault. FriendFeed and Google Reader (especially the newest feature of adding notes to shared things) create so much better space for rapid thoughts exchange than a blog, that I comment, link and share most of the things over there, and that includes even making scientific collaborations. This blog is going to loose a little of its dynamics, but already after few weeks I see advantages (like saving time) of moving micro-posts to World Wide Talk Show, as Robert Scoble calls FF.

Amount of interesting conversations at FF and Twitter combined is so huge that I don’t do random web browsing anymore (and I’m not the only one who says that). And I don’t even subscribe to thousands of people – it’s less than a hundred in total on both services. This list includes scientists (here’s probably already outdated list at Nature’s blog Nascent of scientist at FF), technologists and other interesting chaps.

So join us at Twitter or FriendFeed – my login at both services is “freesci”. Life is about interesting conversations, isn’t it? 🙂

UPDATE: Pierre Lindenbaum has obviously similar thoughts.


Posted by on May 15, 2008 in Comments


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Bug tracking systems in science

I’m not going to describe painful process of correcting entries in biological databases or errors in publications when one is not the author – we all know how difficult and unrewarding it is. All major databases contain wrong entries – I see misannotated (or nonexistent) genes in Genbank, artificial domains in PFAM or poorly solved structures in PDB. It’s even worse in publications, where across the whole spectrum of journals I see errors which in theory shouldn’t slip through peer review (this includes such prominent publishers like NPG).

One of the best idea I heard that addressed this issue was to build a bug tracking system (I would like to give credit to the author, but I cannot find the source; wasn’t that one of biobloggers?). It’s simple and efficient. Something is wrong? Fill a bug report. It would be linking to the original entry, would be available for aggregation (for example to track report’s author activity), and possibly could be closed by somebody else than database maintainers or authors if it’s wrong. Because it would be external to all databases, maybe it could grow to provide “community corrected” versions of these databases?

What do you think? How useful such system could be?


Posted by on April 18, 2008 in Comments, Community, Software


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Changes and updates

Here’s a summary of changes that happened in the meantime on Freelancing Science blog:

  • Freelancing Science has its own domain ( in case you wonder), but for readers nothing changed: all links, feed urls seem to work as they did so far. The main change is in your browser’s address bar and my email (pawel at new domain name).
  • I have added another box with Google Reader starred items. Feel free to subscribe, although I star something in GR based on my loose impression (not necessarily valid) that particular piece is worth coming back to. Because my reading list is constantly enlarging (more on this below), expect large amount of items in this feed.
  • I’ve added a number of blogs to link list in the sidebar (this list is constantly expanding). Among others there are: blog of Daniel Lemire, computer science professor from Montreal, Reasonable Deviations – everything scientific and challenging, from math to finances, Molgraph3D – visualization (of course!) of molecules with various techniques by Ludovic Autin and Biosingularity – news blog about advances in bioengineering.
  • I keep updating Images of molecules page, although I put all new stuff also in my Flickr “Molecular renderings” set, which is easy to track as it provides RSS feeds (to track people’s lifestreams I recommend FriendFeed – couple of fellow biobloggers have their account there).
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Posted by on March 21, 2008 in Comments


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