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Tag: brain

Loading a second brain

Before ChatGPT, the hype among productivity boosters was a PKMs or Personal knowledge management system.

It gained popularity through Tiago Forte’s book ‘Building a second brain’, and (for academics perhaps a more useful read) ‘How to take smart notes’ by Sönke Ahrens.

These books promote new techniques for note-taking (and for storing these notes) such as the PARA-method, the CODE-system, and Zettelkasten.

Unmistakable Creative has some posts on the principles behing the ‘second brain’ approach.

Your brain isn’t like a hard drive or a dropbox, where information is stored in folders and subfolders. None of our thoughts or ideas exist in isolation. Information is organized in a series of non-linear associative networks in the brain.

Networked thinking is not just a more efficient way to organize information. It frees your brain to do what it does best: Imagine, invent, innovate, and create. The less you have to remember where information is, the more you can use it to summarize that information and turn knowledge into action.


A network has no “correct” orientation and thus no bottom and no top. Each individual, or “node,” in a network functions autonomously, negotiating its own relationships and coalescing into groups. Examples of networks include a flock of birds, the World Wide Web, and the social ties in a neighborhood. Networks are inherently “bottom-up” in that the structure emerges organically from small interactions without direction from a central authority.

-Tiago Forte, Tagging for Personal Knowledge Management

There are several apps you can use to start building your second brain, the more popular seem to be Roam Research, LogSeq, and Obsidian.

These systems allow you to store, link and manipulate a large collection of notes, query them as a database, modify them in various ways via plugins or scripts, and navigate the network created via graph-views.

Exactly the kind of things we need to modify the simple system from the shape of languages-post into a proper topos of the unconscious.

I’ve been playing around with Obsidian which I like because it has good LaTeX plugins, powerful database tools via the Dataview plugin, and one can execute codeblocks within notes in almost any programming language (python, haskell, lean, Mathematica, ruby, javascript, R, …).

Most of all it has a vibrant community of users, an excellent forum, and a well-documented Obsidian hub.

There’s just one problem, I’m a terrible note-taker, so how can I begin to load my ‘second brain’?

Obsidian has several plugins to import data, such as your Kindle highlights, your Twitter feed, your Readwise-data, and many others, but having been too lazy in the past, I cannot use any of them.

In fact, the only useful collection of notes I have are my blog-posts. So, I’ve uploaded NeverEndingBooks into Obsidian, one note per post (admittedly, not very Zettelkasten-like), half a million words in total.

Fortunately, I did tag most of these posts at the time. Together with other meta-data this results in the Graph view below (under ‘Files’ toggled tags, under ‘Groups’ three tag-colours, and under ‘Display’ toggled arrows). One can add colour-groups based on tags or other information (here, red dots are posts tagged ‘Grothendieck’, the blue ones are tagged ‘Conway’, the purple ones tagged ‘Connes’, just for the sake of illustration). In Obsidian you can zoom into this graph, place a pointer on a node to highlight the connecting dots, and much more.

Because I tend to forget such things, and as it may be useful to other people running a WordPress-blog making heavy use of MathJax, here’s the procedure I followed:

1. Follow the instructions from Convert wordpress articles to markdown.

In the wizard I’ve opted to go only for yearly folders, to prefix posts with the date, and to save all images.

2. This gives you a directory with one folder per year containing markdown versions of your posts, and in each year-folder a subfolder ‘img’ containing all images.

Turn this directory into an Obsidian-vault by opening Obsidian, click on the ‘open another vault’ icon (third from bottom-left), select ‘Open folder as vault’ and navigate to your directory.

3. You will notice that most of your LaTeX cannot be parsed because during the markdown-process backslashes are treaded as special character, resulting in two backslashes for every LaTeX-command…

A remark before trying to solve this: another option might be to use the wordpress-to-hugo-exporter, resulting in clean LaTeX, but lacking the possibility to opt for yearly-folders (it dumps all posts into one folder), and it makes a mess of the image-files.

4. So, we will need to do a lot of search&replaces in all files, and need a convenient tool for this.

First option was the Sublime Text app, which is free and does the search&replaces quickly. The problem is that you have to save each of the files, one at a time! This may take hours.

I’ve done it using the Search and Replace app (3$) which allows you to make several searches/replaces at the same time (I messed up LaTeX code in previous exports, so needed to do many more changes). It warns you that it is dangerous to replace strings in all files (which is the reason why Sublime Text makes it difficult), you can ignore it, but only after you put the ‘img’ folders away in a safe place. Otherwise it will also try to make the changes to these files, recognise that they are not text-files, and drop them altogether…

That’s it.

I now have a backup network-version of this blog.

As we mentioned in the previous post a first attempt to construct the ‘topos of the unconscious’ might be to start with a collection of notes (the ‘conscious’) and work on the semantics of text-snippets to unravel (a part of) the unconscious underpinning of these notes. We also mentioned that the poset-structure in that post should be replaced by a more involved network structure.

What interests me most is whether such an approach might be doable ‘in practice’, and Obsidian looks like the perfect tool to try this out.

What we need is a sufficiently large set of notes, of independent interest, to inject into Obsidian. The more meta it is, the better…


Previously in this series:


The enriched vault

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the future of this blog (2)

is decided : I’ll keep maintaining this URL until new-year’s eve. At that time I’ll be blogging here for 5 years…

The few encounters I’ve had with architects, taught me this basic lesson of life : the main function of several rooms in a house changes every 5 years (due to children and yourself getting older).

So, from january 1st 2009, I’ll be moving out of here. I will leave the neverendingbooks-site intact for some time to come, so there is no need for you to start archiving it en masse, yet.

Previously I promised to reconsider this blog’s future over a short vacation, but as vacation is looking to be as illusory as the 24-dimensional monster-manifold, I spend my time throwing up ideas into thin and, it seems, extremely virtual air.

Some of you will think this is a gimmick, aiming to attract more comments (there is no post getting more responses than an imminent-end-to-this-blog-post) but then I hope to have settled this already. Neverendingbooks will die on 31st of december 2008. The only remaining issue being : do I keep on blogging or do I look for another time-consumer such as growing tomatoes or, more probably, collecting single malts…

For reasons I’ve stated before, I can see little future in anything but a conceptual-, group- blog. The first part I can deal with, but for the second I’ll be relying on others. So, all I can do is offer formats hoping that some of you are willing to take the jump and try it out together.

Such as in the bloomsday-post where I sketched the BistroMath blog-concept. Perhaps you thought I was just kidding, hoping for people to commit themselves and them calling “Gotcha…”. Believe me, 30 years of doing mathematics have hardwired my brains such that I always genuinely believe in the things I write down at the moment I do (but equally, if someone offers me enough evidence to the contrary, I’ll drop any idea on the spot).

I still think the BistroMath-project has the potential of leading to a bestseller but Ive stated I was not going to pursue the idea if not at least 5 people were willing to join and at least 1 publisher showed an interest. Ironically, I got 2 publishers interested but NO contributors… End of that idea.

Today I offer another conceptual group-blog : the Noether-boys seminar (with tagline ; _the noncommutative experts’ view on 21st century mathematics_). And to make it a bit more concrete Ive even designed a potential home-page :

So, what’s the deal? In the 1930-ties Emmy Noether collected around her in Goettingen an exceptionally strong group of students and collaborators (among them : Deuring, Fitting, Levitski, Schilling, Tsen, Weber, Witt, VanderWaerden, Brauer, Artin, Hasse, MacLane, Bernays, Tausky, Alexandrov… to name a few).

Collectively, they were know as the “Noether-boys” (or “Noether-Knaben” or “Trabanten” in German) and combined seminar with a hike to the nearby hills or late-night-overs at Emmy’s apartment. (Btw. there’s nothing sexist about Noether-boys. When she had to leave Germany for Bryn Mawr College, she replaced her boys to form a group of Noether-girls, and even in Goettingen there were several women in the crowd).

They were the first generation of mathematicians going noncommutative and had to struggle a bit to get their ideas accepted.
I’d like to know what they might think about the current state of mathematics in which noncommutativity seems to be generally accepted, even demanded if you want to act fashionable.

I’m certain half of the time they would curse intensely, and utter something like ‘steht shon alles bei Frau Noether…’ (as Witt is witnessed to have done at least once), and about half the time they might get genuinely interested, and be willing to try and explain the events leading up to this to their fellow “Trabanten”. Either way, it would provide excellent blog-posts.

So I’m looking for people willing to borrow the identity of one of the Noether-boys or -girls. That is, you have to be somewhat related to their research and history to offer a plausible reaction to recent results in either noncommutative algebra, noncommutative geometry or physics. Assuming their identity you will then blog to express your (that is, ‘their’) opinion and interact with your fellow Trabanten as might have been the case in the old days…

I’d like to keep Emmy Noether for the admin-role of the blog but all other characters are free at this moment (except I’m hoping that no-one will choose my favourite role, which is probably the least expected of them anyway).

So please, if you think this concept might lead to interesting blogging, contact me! If I don’t get any positives in this case either, I might think about yet another concept (or instead may give up entirely).


Arnold’s trinities

Referring to the triple of exceptional Galois groups $L_2(5),L_2(7),L_2(11) $ and its connection to the Platonic solids I wrote : “It sure seems that surprises often come in triples…”. Briefly I considered replacing triples by trinities, but then, I didnt want to sound too mystic…

David Corfield of the n-category cafe and a dialogue on infinity (and perhaps other blogs I’m unaware of) pointed me to the paper Symplectization, complexification and mathematical trinities by Vladimir I. Arnold. (Update : here is a PDF-conversion of the paper)

The paper is a write-up of the second in a series of three lectures Arnold gave in june 1997 at the meeting in the Fields Institute dedicated to his 60th birthday. The goal of that lecture was to explain some mathematical dreams he had.

The next dream I want to present is an even more fantastic set of theorems and conjectures. Here I also have no theory and actually the ideas form a kind of religion rather than mathematics.
The key observation is that in mathematics one encounters many trinities. I shall present a list of examples. The main dream (or conjecture) is that all these trinities are united by some rectangular “commutative diagrams”.
I mean the existence of some “functorial” constructions connecting different trinities. The knowledge of the existence of these diagrams provides some new conjectures which might turn to be true theorems.

Follows a list of 12 trinities, many taken from Arnold’s field of expertise being differential geometry. I’ll restrict to the more algebraically inclined ones.

1 : “The first trinity everyone knows is”

where $\mathbb{H} $ are the Hamiltonian quaternions. The trinity on the left may be natural to differential geometers who see real and complex and hyper-Kaehler manifolds as distinct but related beasts, but I’m willing to bet that most algebraists would settle for the trinity on the right where $\mathbb{O} $ are the octonions.

2 : The next trinity is that of the exceptional Lie algebras E6, E7 and E8.

with corresponding Dynkin-Coxeter diagrams

Arnold has this to say about the apparent ubiquity of Dynkin diagrams in mathematics.

Manin told me once that the reason why we always encounter this list in many different mathematical classifications is its presence in the hardware of our brain (which is thus unable to discover a more complicated scheme).
I still hope there exists a better reason that once should be discovered.

Amen to that. I’m quite hopeful human evolution will overcome the limitations of Manin’s brain…

3 : Next comes the Platonic trinity of the tetrahedron, cube and dodecahedron

Clearly one can argue against this trinity as follows : a tetrahedron is a bunch of triangles such that there are exactly 3 of them meeting in each vertex, a cube is a bunch of squares, again 3 meeting in every vertex, a dodecahedron is a bunch of pentagons 3 meeting in every vertex… and we can continue the pattern. What should be a bunch a hexagons such that in each vertex exactly 3 of them meet? Well, only one possibility : it must be the hexagonal tiling (on the left below). And in normal Euclidian space we cannot have a bunch of septagons such that three of them meet in every vertex, but in hyperbolic geometry this is still possible and leads to the Klein quartic (on the right). Check out this wonderful post by John Baez for more on this.

4 : The trinity of the rotation symmetry groups of the three Platonics

where $A_n $ is the alternating group on n letters and $S_n $ is the symmetric group.

Clearly, any rotation of a Platonic solid takes vertices to vertices, edges to edges and faces to faces. For the tetrahedron we can easily see the 4 of the group $A_4 $, say the 4 vertices. But what is the 4 of $S_4 $ in the case of a cube? Well, a cube has 4 body-diagonals and they are permuted under the rotational symmetries. The most difficult case is to see the $5 $ of $A_5 $ in the dodecahedron. Well, here’s the solution to this riddle

there are exactly 5 inscribed cubes in a dodecahedron and they are permuted by the rotations in the same way as $A_5 $.

7 : The seventh trinity involves complex polynomials in one variable

the Laurant polynomials and the modular polynomials (that is, rational functions with three poles at 0,1 and $\infty $.

8 : The eight one is another beauty

Here ‘numbers’ are the ordinary complex numbers $\mathbb{C} $, the ‘trigonometric numbers’ are the quantum version of those (aka q-numbers) which is a one-parameter deformation and finally, the ‘elliptic numbers’ are a two-dimensional deformation. If you ever encountered a Sklyanin algebra this will sound familiar.

This trinity is based on a paper of Turaev and Frenkel and I must come back to it some time…

The paper has some other nice trinities (such as those among Whitney, Chern and Pontryagin classes) but as I cannot add anything sensible to it, let us include a few more algebraic trinities. The first one attributed by Arnold to John McKay

13 : A trinity parallel to the exceptional Lie algebra one is

between the 27 straight lines on a cubic surface, the 28 bitangents on a quartic plane curve and the 120 tritangent planes of a canonic sextic curve of genus 4.

14 : The exceptional Galois groups

explained last time.

15 : The associated curves with these groups as symmetry groups (as in the previous post)

where the ? refers to the mysterious genus 70 curve. I’ll check with one of the authors whether there is still an embargo on the content of this paper and if not come back to it in full detail.

16 : The three generations of sporadic groups

Do you have other trinities you’d like to worship?

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You may not have noticed, but I’m in a foul mood for weeks now because of comments and reactions to the last line of the post on Finding Moonshine. I wrote

Du Sautoy is a softy! I’d throw such students out of the window…

and got everyone against me for this (first floor) defenestration threat…

That’s OK! I sometimes post what’s on my mind and if you don’t like it you are free to leave a comment, and, usually I won’t even bother to reply to it. But occasionally, stuff is bottling up un-healthily.

So, I thought it was a good idea to have a prolonged easter-vacation, somewhere in the south of France. The weather, food, rest, drinks, company and all that were just gorgeous

but …

A quick recap. Here’s the relevant section in duSautoy’s book again :

One of my graduate students has just left my office. He’s done some great work over the past three years and is starting to write up his doctorate, but he’s just confessed that he’s not sure that he wants to be a mathematician. I’m feeling quite sobered by this news. My graduate students are like my children. They are the future of the subject. Who’s going to read all the details of my papers if not my mathematical offspring? The subject feels so tribal that anyone who says they want out is almost a threat to everything the tribe stands for.
Anton has been working on a project very close to my current problem. There’s no denying that one can feel quite disillusioned by not finding a way into a problem. Last year one of my post-docs left for the City after attempting to scale this mountain with me. I’d already rescued him from being dragged off to the City once before. But after battling with our problem and seeing it become more and more complex, he felt that he wasn’t really cut out for it.
What is unsettling for me is that they both questioned the importance of what we are doing. They’ve asked that ‘What’s it all for?’ question, and think they’ve seen the Emperor without any clothes.
Anton has questioned whether the problems we are working on are really important. I’ve explained why I think these are fundamental questions about basic objects in nature, but I can see that he isn’t convinced. I feel I am having to defend my whole existence. I’ve arranged for him to join me at a conference in Israel later this month, and I hope that seeing the rest of the tribe enthused and excited about these problems will re-inspire him. It will also show him that people are interested in what he is dedicating his time to.

For starters, I’m getting old so I’m from those long-forgotten days when you had to do a Ph.D. to prove that you could conduct research independently.

A fortiori this meant that the topic of your thesis was your own choice and interest. The role of your Ph.D. advisor was to get you going and, occasionally, to warn you when you were straying too far afield but that was it.

You, and only you, were responsible to get the thesis finished and defended.

Today, the Ph.D. is just another item on the market to be consumed.

Graduate students shop around looking for the advisor having the best sales-pitch, offers the best deal and, if possibly, the best after-phd service aka the promise of an academic career.

Topic and main outline of the proofs are provided by the advisor and an exceptionally good student today means that (s)he proved a few results along the way on her/his own.

University policy and the promotion-rat-race appear to make the Ph.D. more important to the advisor than to the defendent.

Independence of research today means that after your PhD is obtained, you ditch your advisor and try to get into the slipstream of another more powerful guru, having better after-phd service prospects…

For those who stick with their old advisor, the moment of truth comes when they fail to get a renewal of their grant or a permanent position.

At that time one can hear complaints such as : “That persons’ student got ranked ahead of me and I always thought you were better than that person?” or “The better ranked people for the position are all doing that topic instead of ‘ours’, so I guess your topic isn’t so important after all!”. duSautoy’s captures it all in this one key sentence :

They’ve asked that ‘What’s it all for?’ question, and think they’ve seen the Emperor without any clothes.

As if, failing to get a permanent position is the advisors fault, more than yours…

Just for once, try to be honest to yourself : count the number of hours a day your brain-power gets you over 120 IQ. Substract from this the number of hours a day lost surfing the web idly, trying to read unreadable hep-th papers, socializing, kissing asses, socializing, doing fun things with you fellow graduate students, socializing, working on a relation, chatting, texing, emailing insults but softening it all with a closing smily 🙂 , socializing, etc… (you know the daily-drill of a 20-30-something phd-student a lot better than I do)

I’ll be damned if you get a positive outcome. But if you do, I’ll be happy to take you on as a PhD student…

Well, it’s no threat, it’s a promise : the first ex-student who gets me into a ‘why was it all good for?’ discussion will experience first floor defenestration! (provided I’ll get my window open in time)

And, to soften it all, I’ll add the obligatory 🙂


yahoo pipes on iTouch

The next thing on my tech-to-do-list : learn all about Yahoo Pipes :

Pipes is a powerful composition tool to aggregate, manipulate, and mashup content from around the web. Like Unix pipes, simple commands can be combined together to create output that meets your needs. Here are a few popular ways the service can be used:
– create your ultimate custom feed by combining many feeds into one, then sorting, filtering and translating them.
– geocode your favorite feeds and browse the items on an interactive map.
– remix your favorite data sources and use the Pipe to power a new application.
– build custom vertical search pages that are impossible with ordinary search engines.
– power widgets/badges on your web site.
– consume the output of any Pipe in RSS, JSON, KML, and other formats.

I’ve posted before on setting up your own lifestream, or your own planet, or scraping feeds, or subscribing to my brain, or … whatever. The good news is : all these ideas are now superseded by Pipes!

Pipes is a free online service that lets you remix popular feed types and create data mashups using a visual editor. You can use Pipes to run your own web projects, or publish and share your own web services without ever having to write a line of code. You make a Pipe by dragging pre-configured modules onto a canvas and wiring them together in the Pipes Editor. Once you’ve built a Pipe, you’ll be able save it on our server and then call it like you would any other feed. Pipes offers output in RSS 2.0, RSS 1.0 (RDF), JSON and Atom formats for maximum flexibility. You can also choose to publish your Pipe and share it with the world, allowing other users to clone it, add their own improvements, or use it as a subcomponent in their own creations.

This is the essential message to get : yahoo-pipes allows you to remix the web, filtering out all noise! And the good news is

  1. There are plenty of public pipes around to get you going, and
  2. Pipes has an iTouch-friendly interface (see above left). All you have to do is to Safari to and use them.

Here are a few public-pipes you can use out of the box!

  • iPhone / iPod Touch: The Most Comprehensive Feed Ever!, doing what it promises : giving you the best iTouch-posts without having to roam for them.
  • JSON Geocoder, returning lat/lon/address info from the the given address.
  • Uber Blog Search, Search all the blogosphere with one query. Hits Google, Ask, Technorati, and icerocket then returns the unique results. Below the web-interface giving the results for ‘noncommutative’…

and finally, one of my favorites, implementing to some extend the Lifestream-idea (iTouch-interface above left)

  • lifefeed – virable, Easily Aggregate your social whereabouts great for blogs profiles and more! Aggregates Your Feeds From: -Digg -Twitter -Flickr and your very own blog Adopt and Improve, enjoy!

I’ll promise to spend some time soon to set up my very own pipes and make them available…


wednesday bookshelf

The Newtonian
is a free online book by Nick Evans. If you want a (somewhat
over-positively) review about it, head here. For me, it just didn’t work but then I’m
an avid consumer of thrillers and like to be surprised. I read though to
page 80 (of 138) which is pretty good as I usually lay down an
unreadable book much sooner (most are lend from the public library, so
I’d rather start a new one as soon as it becomes tiresome). But then I
wanted to ‘learn about the frontier of particle physics within a fast
paced crime adventure’. One exchange is pretty telling though (p.

“Rule is don”t get involved in popularising
science.” “That”s a bit harsh. We have to tell people what we”re doing
if we want them to fund us,” said Carl. “Yeah, but it”s all lies. The
theories are all mathematics, yet we say all words. That”s why we get
these nut cases writing to us sometimes with “new theoriesiÃÇ. They”ve
just read a popular science book and mistaken it for the core of
science. They change some words and think they have a new theory. They
don”t understand that you have to get the numbers right for every
experiment you can think of. It”s just misleading.” “Well, OK,”conceded
Carl, “but you can make the point that you”re just reporting a
simplification and that if people want the real thing, they”d need
maths.”Everyone sought inspiration in their pints again.

So, that’s why it is impossible to write about mathematics for a
general public! Anyway, a bit frustrated I went to my favorite bookshops
and read a blurb which sounded all too familiar.

Oxford, 2006: a young woman is found brutally
murdered, her throat cut. Her heart has been removed and in its place
lies an apparently ancient gold coin. Twenty-four hours later, another
woman is found. The MO is identical, except that this time her brain has
been removed, and a silver coin lies glittering in the bowl of her
skull. The police are baffled but when police photographer, Philip
Bainbridge and his estranged lover, Laura Niven become involved, they
discover that these horrific, ritualistic murders are not confined to
the here and now. And a shocking story begins to emerge which
intertwines Sir Isaac Newton, one of seventeenth-century England’s most
powerful figures, with a deadly conspiracy which echoes down the years
to the present day, as lethal now as it was then. Before long those
closest to Laura are in danger, and she finds herself the one person who
can rewrite history; the only person who can stop the killer from
striking again…

The first half of the
is rather promising (and at least its well written).
Mathematics even makes a short appearance as daugther Jo is studying
maths. Not that she contributes much of her talent to the story (apart
from contributing to solving one riddle) and in the end it seems to be
much more important to date the right boyfriend than to do math! The
book really becomes laughable when the couple is trapped in a maze 100
feat below the Bodleian library. Pure Indiana Jones-remake : expecting
pitfalls? here they come! what else do we remember of the movie?
arrow-traps! sure enough they appear. Oh, this must be that movie, so
whats next? well, sure enough (p. 343 “A massive block of stone crashed
down from the lintel of the archway, landing squarely with a thump on
the dusty floor. They were sealed in.” Presumably the authors
inspiration dried out!

Mind you, I do not want to be negative on
principle. Sometimes (too rare) I do read an enjoyable, interesting,
intelligent thriller. The last one Ive read was

Brother Grimm by Craig Russell is a must read if you are into
serial-killer stories. Heres the synopsis

A girl’s
body lies, posed, on the pale sand of a Hamburg beach, a message
concealed in her hand. ‘I have been underground, and now it is
time for me to return home…’ Jan Fabel, of the Hamburg murder
squad, struggles to interpret the twisted imagery of a dark and brutal
mind. Four days later, a man and a woman are found deep in woodland,
their throats slashed deep and wide, the names ‘Hansel’ and
‘Gretel’, in the same, tiny, obsessively neat writing, rolled
tight and pressed into their hands. As it becomes clear that each new
crime is a grisly reference to folk stories collected almost two hundred
years ago by the Brothers Grimm, the hunt is on for a serial killer who
is exploring our darkest, most fundamental fears – a predator who kills
and then disappears into the shadows. He is a monster we all learned to
fear in childhood.

An original point of view, an
unorthodox setting (Hamburg!), interesting and real life personages what
more do you want? Oh, you want to learn something from reading a
bestseller? To me, this book was an eye-opener. Ever wondered why all
these serial-killer-books become bestsellers? Here’s the answer (p.


p>”Weiss toke a novel from the bookshell before him!! ‘Today
we continuously reinvent these tales. The same stories, new characters.
This is a bestseller – a story about the hunt for a serial killer who
ritually dismembers his victims. These are our fairy tales
today. These are our fables, our Maerchen. Instead of elves and kobolts
and hungry wolves lurking in the dark corners of the woods, we have
cannibals and dissectors and abductors lurking in the dark corners of
our cities.
It is in our nature to guise our evil as something
extraordinary or something different: books and films about aliens,
sharks, vampires, ghosts, witches. The fact of the matter is that there
is one beast that is more dangerous, more predatory, tan any other in
the history of nature. Us.”

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bookmarks tuesday cleanup

Geeky Mom : Why am I blogging?
. Been there before. Sooner or later
all non-pseudonomenous bloggers are faced with the same dilemmas.
There’s really no answer or advice to give except : blog when you feel
like it, if not do something different, after all its just one of those
billion of blogs around.

Texmaker : another
LaTeX-frontend, possibly having a few extras such as : a structure-pane
including labels you gave to formulas, theorems etc. (click on them
brings you to them). Intend to use it now as I’m in another rewrite of
the never-ending-book..

Microformats : “Designed for
humans first and machines second, microformats are a set of simple, open
data formats built upon existing and widely adopted standards.” May
have another look.

Quicksilver : a recurring
link. At times when I feel learning key-strokes may save me a lot of
time I have (another) go at Quicksilver. Last week, Ive reinstalled this
blog more or less post by post and used keystrokes to send a line in the
SQL-file of the database dump of NEB as a clipping to Scrivener to
MultiMarkdown it further. I used the app Service Scrubber
to define my own key-strokes. Must have another go at Quicksilver soon.
Im sure it distinguishes ‚”power mac users” from the rest of

List of GTDTools
: a good list of GTD-software. I’m probably just
too chaotic for GTD to improve my workflow but somehow I cannot resist
trying some of these things out.

LifeDEV : One of those sites that tells
me I should take GTD more seriously

DoIt : One of
these GTD-tools. It is said to go well with Quicksilver, so maybe, one

: Here a little seemingly completely useless tool which works well (at
least for me). No, it does not make you think, but at least it helps you
while you are thinking (or doing anything a bit focussed). Install it
and enjoy! The principle is that it just blocks out all other open
windows (and there are keystrokes (yes, again) to get you quickly in
and out.) Besides, it looks great. It’s in my dock and this says it

Thinkature :
a brainstorming tool. Dont know why I did bookmark this. Perhaps one
day, a few years from now

Stafford Talk :
a talk by Toby Stafford I came across by accident. Maybe there are other
interesting talks on the site?

Science Scouts : a great
idea! Give yourself badges for how well you do science (or talk/write
about science). Have to collect my badges soon. I’m sure this only
works for people with a scouting-history, but who

MacResearch : Here’s a site
that may become useful. is an open and independent
community for scientists using Mac OS X and related hardware in their
research. It is the mission of this site to cultivate a knowledgeable
and vibrant community of researchers to exchange ideas and information,
and collectively escalate the prominence of Apple technologies in the
scientific research community. They have some interesting articles
and tutorials on e.g. DevonThink and BibDesk etc. Worth to

Jennifer in love : well‚ should I say something about this?
probably best not.

Breakthrough CLI
: another pamphlet in favor of the Command Line! A
must read for those who perfer GUIs to CLIs.


p>CLI – the
: Rod is working hard on CLI-20. Whenever he releases version
2.0, neverendingbooks will be among the first sites to run it. I still
love the idea.

Why do I bother? : an n-category post I got briefly interested in,
but was somehow flooded by professional

Newton Legacy Reviewed : just that, a first review
on the next bookmark.

the Newton
: a free online book, a murder mystery with a physics touch.
Perhaps this is the best investment of time/energy : write a popular
science book rather than another paper. Read half way through it (sorry
but not the best prose Ive read so far), may continue but was held up
reading a (real) murder mystery Equinox featuring also Newton and
alchemy (must be in the air somehow), also not the best mystery read
so far

Stalking with Googleearth
: no comment

(to be continued)

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my lifestream

The old
concept of getting your
brain subscribed to
has a reincarnation into the
lifestream idea : add a page to your blog listing all
your timed actions on the web. I stumbled upon it via the
Lifestream – ala wordpress
post containing a link to the original Streaming my life away
article by Jeremy Keith. After far
too much time I managed to install Chris Davis’
Lifestream wordpress plugin
. Here are some comments that may make it easier to install a
lifestream page yourself. To begin, don’t download the plugin at the
top of the page, but rather scroll down to comment 886-59 by Gunnar
Hafdal and download via the link given there (or use this direct link).
This version at least contains a readme file (even after reading through
all the php-code of the other version I didn’t have a clue as how to use
it, in the readme file I finally learned that you had to create a new
page and use Lifestream as a page-template…). Next, I could’t
get it working until line 78 of stream.php was
commented out (the Copenhagen-time line). Also don’t use the
Dashboard-Manage-Lifestream page in the hope to change your
RSS-subsriptions, but rather hard-code them in the
life.php file. Bear in mind that not all RSS-data will
work with Lifestream. I’ve tried out all of the social bookmark sites of
which the logo is given at the bottom of a post, and found that only six
of them work without doing extra work : co.mments, digg,
ma.gnolia, furl, netvouz and (the last one modulo the fact
that it doesnt give the accurate time). At the moment I’ve added just
co.mments, digg, magnolia and netvouz to my lifestream but I may add
other streams later. Of course one can solve problems with the other
RSS-feeds by scraping them and writing new feeds which Lifestream (or
rarther the underlying magpieRSS bundled with wordpress) can handle. I
assume this is the idea behind the other Lifestream plugin by Elliot Black (I havent
tried this one out). The last thing to do is then to change the
stream.php file so that it produces a page with more or
less the same look and feel of the rest of the blog. Apart from a few
things which I still have to remedy, I’m happy with my
Lifestream. Now it is time to have a serious go at some of these
social-bookmarking sites…

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get your brain subscribed to

In the
to my brain’ post
I promised to blog on how-to get your own

button up and running on your homepage. It seems rather unlikely
that I’ll ever keep that promise if I don’t do it right away. So, here
we go for a quick tour :

step 1 : set up a rudimentary
: read the FoaF post if
you dont know what it’s all about. The easiest way to get a simple
FoaF-file of your own is to go to the FoaF-a-matic
and fill in the details you feel like broadcasting over the
web, crucial is your name and email information (for later use) but
clearly the more details you fill out and the more Friends you add the
more useful your file becomes. Click on the ‘foaf-me’ button and
copy the content created. Observe that there is no sign of my email
adress, it is encrypted in the _mbox_sha1sum_ data. Give this
file a name like _foaf.rdf_ or _myname.rdf_ and put it on
your webserver to make it accessible. Also copy your
_mbox_sha1sum_ info for later smushing.

step 2 : subscribe to online services and modify your
online-life accordingly
: probably you have already a few of
these accounts, but if not, take a free subscription just for fun and
(hopefully) later usage to the following sites :

  • a social bookmarks manager
  • citeUlike a service to
    organise your academic papers
  • connotea a reference management
    service for scientists
  • bloglines a web-based personal news
  • 43things a
    ‘What do you want to do with your life?’ service
  • audioscrobbler a database that
    tracks listening habits and does wonderful things with statistics
  • backpackit a ‘be better organized’ service (Update october 2017 : Tom Howard emails: “I thought I’d reach out because we’ve just updated our guide which reviews the best alternatives to Backpack. Here’s the link
  • flickr an online photo management and
    sharing application
  • technorati a Google-for-weblogs
  • upcoming a social event
  • webjay a playlist

So far, I’m addicted to and use
citeUlike but hardly any of the others (but I may come back to this
later). The great thing about these services is that you get more
value-information back if you feed more into the system. For example, if
you use as your ‘public’ bookmarks-file you get to
know how many other people have bookmarked the same site and you can
access their full bookmarks which often is a far more sensible way to
get at the information you are after than mindless Googling. So, whereas
I was at first a bit opposed to the exhibisionist-character of these
services (after all, anyone with web-access can have a look at
‘your’ info), I’ve learned that the ‘social’ feature of
these services can be beneficial to get the right information I want.
Hence, the hardest part is not to get an account with these services but
to adopt your surfing behavior in such a way that you maximize this
added value. And, as I mentioned before, I’m doing badly myself but hope
that things will improve…

step 3 : turn these
accounts into an OPML file
: Knowing the URL of your foaf-file
and sha1-info (step 1) and your online accounts, go to the FOAF Online Account
Description Generator
and feed it with your data. You will then get
another foaf-file back (save the source in a file such as
_accounts.rdf_ and put it on your webserver). Read the Lost Boy’s
posts Subscribe to my
and foaf:
OnlineAccount Generator
for more background info. Then, use the SubscribeToMyBrain-
to get an OPML-file out of the account.rdf file and your sha1.
Save the source as _mybrain.opml_.

step 4 :
add/delete information you want
: The above method uses generic
schemes to deduce relevant RSS-data from an account name, which works
for some services, but doesn’t for all. So, if you happen to know the
URL of RSS-feeds for one of these services, you can always add it
manually to the OPML-file (or delete data you don’t want to
publish…). My own attitude is to make all public web-data
available and to leave it to the subscriber to unsubscribe those parts
of my brain (s)he is not interested in. I know there are people whoo are
mainly interested to find out whether I put another paper online, would
tolerate some weblog-posts but have no interest in my musical tast,
whereas there are others who would like me to post more on 43things,
flickr or upcoming and don’t give a damn about my mathematics…
Apart from these online subscriptions, it is also a good idea to include
additional RSS-feeds you produce, such as those of your weblog or use my
to have your own arXiv-feeds.

step 5 : make
your ‘subscribe to my brain’-button
: Now, put the
OPML-file on your webserver, put the button

on your
homepage and link it to the file. Also, add information on your site,
similar to the one I gave in my own
subscription post
so that your readers know what to do when do want
to subscribe to (parts of) your brain. Finally, (and optionally though
I’d wellcome it) send me an email with your URL so that I can subscribe
(next time you’re in Antwerp I’ll buy you a beer) and for the first few
who do so and are working in noncommutative geometry and/or
noncommutative algebra, I’ll send a copy of a neverending book. Mind
you, this doesn’t apply to local people, I’m already subscribed to their
brain on a daily basis…

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added to MyBrain : arXiv

Clearly, someone who
subscribed to your brain
shouldn’t have to check the arXiv every morning only to find out
that you still haven’t posted _the_ paper s(h)e is expecting of
you, based on your recent BrainActivity…

So why not
package this into your Brain subscription? It is easy enough to get all
posts by a specific author from the archive but, unfortunately, the
arXiv doesn’t provide RSS-feeds of this information (at least, not to my
knowledge). Still, it is possible to fix this with a tiny

So copy the code and adjust it replacing MyInfo
by Yours (or sligthly safer, get the
file as I had to add a few spaces to get it un-parsed) and safe it
somewhere on your system.

So how to put this to use? Btw. I know
that all of you know this by heart and that I may have given you the
(false, i swear) illusion to be fairly knowledgeable writing a
Perl-script in half an hour, but believe me, in two months (and sooner
when it’s up to me) I will have completely eradicated all this
techie-stuff from MyBrain. Then, it will take me infinitely longer to
remember/reconstruct things than it will take me now to blog this here,
so please either bear with me or go somewhere more interesting.

You’d better have Perl installed on your system, but then you have to
install extra modules from CPAN the
Comprehensive Perl Archive Network (this is to Perl what CTAN is to TeX for the mathematicians
among us). That’s pretty easy if you remember the correct commands. The
generic way to do this is by firing up your Terminal and typing things

 iBookLieven:~ lieven$ sudo perl -MCPAN -e shell
Password:  cpan shell -- CPAN exploration and modules installation
(v1.83) ReadLine support enabled  cpan> install Template::Extract

and similarly for the other modules you’ll need,
LWP::Simple and XML::RSS. You may be asked questions but just go for the
default. If something goes wrong and you get a message that the module
failed to install, you have to go for a manual override…

Go to CPAN and do a search on the module’s name. You’ll
be given a list op files to download, go for the one you need and
download the souce somewhere. Then, again in Terminal do the following

  • cd to the downloaded and extracted directory
  • perl Makefile.PL
  • make
  • make test
  • sudo make install

Even if the test fails with
certain errors, just go ahead (it will not matter for the trivial uses
we have for these modules) and the last command is Mac OSX only (I’m
pretty certain that Linux-fanatics know what to do instead and for
Windows-diehards, well….).

Having all modules installed
you can execute the file with


(assuming you created the Directory in which the program
is supposed to safe the arxivXXX.rdf file and assuming you made it
writable). That’s it. You now have your own RSS feeds of all your papers
on the arXiv which you should make for of YourBrain subscription).

Just one more thing you should do. Make this a cron
. Check at what local time the arXiv puts online the new papers
of the day (assume it is 3am) then do a sudo crontab -e
and then add a line to the file as

5 3 * * Mon-Fri perl

and your subscribers will
only have to wait 5 minutes to know whether you did it…(or not).
You can check it out either by subscribing to MyBrain or subscribing to

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