For much of human history, Science and Religion have had a very tumultuous relationship.  Both are systems of beliefs that attempt to answer important questions like: “Where did we come from?” and “How did we get here?”  But because they use different methods to arrive at those answers, it is to be expected that they will not always agree.  Nor is there a guarantee that both sides will remain civil.

Yet, even though Religion and Science don’t always get along, this does not mean that their relationship is one of simple antagonism.  Unlike what modern commentators such as Sam Harris or Christopher Hitchens would have you believe, Science and Religion are not enemies.  Far from it, in fact.

If anything, Science and Religion are siblings.  After all, they share a common ancestry and purpose, and it’s only very recently (within the past 150 years or so) that any society – Western, Islamic or Eastern – has attempted to separate them.

Which is perhaps why it is so disturbing to see attempts by philosophers and believers to set them at each other’s throats.  Within the past few years, there has been a virtual renaissance of pro-Science (read, pro-atheist) books that have come out on the market.  These titles have advocated for a fact based morality, declared war on God, and argued that rational/scientific thought is incompatible with religious belief.  In one Slate.com piece, the author actually seemed to believe that Dr. Francis Collins shouldn’t hold a scientific leadership position because he happens to be an evangelical Christian.  (Never mind his hundreds of peer-reviewed publications and significant contributions to the field of genetics.  After all, it’s not like he sequenced the human genome or anything … )

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Tags: Göbekli Tepe,History,Religion,Science
Categories: Featured, Rants, Science/Medicine, Writing/Literature
2 Comments »

A little more than a year ago, I wrote an essay about writing.  I talked about how creative pursuits (at least for me) aren’t linear processes.  I explained how they often involve wandering about, getting lost in ideas, and general confusion.  Then, I ranted about how popular writing tools don’t allow for creative freedom.  They force you to work in a particular way rather than adapt to your needs.

But though most shackle you to a single workflow, not all are like that.  I highlighted a program on Mac OS X known as Scrivener and how it was an exemplar of software that I wanted to use.  And then, in the same breath, I railed against its limitations and bitterly complained that, while excellent for simple or creative writing, it didn’t handle complexity.

By the end of the essay, I decided to turn my frustration toward something productive.  Having looked at many available writing programs and not finding something that met my needs, I proposed something new: Why not take the creative features of Scrivener and integrate them into a program that excels at managing complexity?

People seemed to like this idea.  When I asked the developers of one such program (LyX) about it, they expressed support.  I got emails from potential users saying that such a tool would be of great benefit to them.  I even received a few donations to help “pay for my time.”

So, about two weeks after proposing the idea, I got to work.

In the beginning, the project progressed quickly. I was excited and motivated, and had the time necessary to make headway.  Within two months, I released a prototype and worked out most of the major design issues.  I even ported much of the prototype code from Python to C++ in preparation for the final phase of the project.

Then, I got stalled.

First, I got busy.  I decided to take on a new project at work and write a book.  I got frustrated with the lack of a decent backup program on Linux and decided to write my own.  My grandmother got sick and a lot of my free time filled with family commitments.

Second, I ran into “complications”.  While much of the user facing work – an improved outline pane, a navigational sidebar, and a corkboard – had been finished, there was still a lot to do behind the scenes.  I needed to write code that could integrate the Outliner with LyX itself and I needed to find a way for editing the document from specialized views.  (And it turned out that these two tasks were hard!)

Finally, my interests wandered.  Because of items one and two, I found that working on LyX-Outline wasn’t very much fun.  I’ve never care for C++, and I had no idea of how to proceed.  There were other things I needed to work on and I knew that re-starting LyX-Outline would require an enormous investment of time and energy. 

The end result was that I allowed my project to languish for the better part of ten months.  Until now, that is.

In the past few weeks, I’ve been hard at work and LyX-Outline has made some major progress.

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Tags: LyX,LyX-Outline
Categories: Computer, Cool Stuff, Featured, Programming
15 Comments »

When I first started my blog, I thought it would be an experiment.  I was exploring WordPress as a platform and wanted to know how customizable it was.  I wanted to know if it could grow and expand with my interests.  I wanted it to be a place where I could post pictures and maybe experiment with podcasts and other internet stuff.

What I did not intend, however, was for it to become a full-fledged website.  It was supposed to be a side project, and I figured that I would eventually tire of it and move on.  That’s why it was set up at Oak-Tree.us/blog rather than Oak-Tree.us.  Oak-Tree.us was always meant to be something special and I figured that a “blog” wasn’t quite “it”.

Over the past two years, however, Oak-Tree.us/blog has become quite a bit more than an experiment.  For a little hobby website, it gets a respectable amount of traffic (sometimes as many as 1,000 hits in a single day) and I think it’s time that it have it’s own respectable domain.  For that reason, I decided to move the website here, to blog.oak-tree.us.  (Now all you need to remember is a sub-domain, rather than a folder.)

For the most part, everything is the same.  All of the blog posts have been moved as are the comments.  If you go digging, you will find information about Time Drive and LyX-Outline.  You can even find most of the pictures in my photo library and the galleries devoted to Leonardo Da Vinci’s notebooks.

Allow me, then, to welcome to the new site; which, ironically, is just like the old one.

Tags: Moving Day
Categories: Featured
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Newsweek has a fascinating article about an archaeological site at Göbekli Tepe in Turkey that is well worth a look.

The site is the oldest religious temple ever discovered.  Preliminary carbon dating has determined that some of the artifacts date from 9,400 BC, which makes the place about 11,500 years old. (Which, just to be clear, is 7000 years before the Great Pyramid and 6500 years before Stonehenge.)  The article further explains:

The ruins are so early that they predate villages, pottery, domesticated animals and even agriculture – the first embers of civilization.  … [It] may be the very first thing that human beings ever built.

And yet, the site is amazing.  The pillars show beautiful stone carvings and there are examples of sophisticated engineering techniques.  The stone circles are nearly 30 yards across with pillars that stand more than 17 feet tall.  Many of the stones (some weighing up to 50 tons) were first quarried and then transported half a kilometer to the site, where they were erected.  What staggers me, though, is that the stone circles were roofed.

This quote from Ian Hodder, head of archaeology at Stanford University, summarizes my response pretty well:

[Göbekli Tepe] is unbelievably big and amazing, at a ridiculously early date.  The huge stones and fantastic, highly refined art [changes everything].  It overturns the whole apple cart.  All our theories were wrong.

This doesn’t happen often.  Scientists don’t admit mistakes and call for established theories to be overturned.  But when faced with such a revolutionary piece of evidence, you have little choice.

Göbekli  is literally an outlier in every way.  It shows engineering, organization, and artistic sophistication that seems to materialize out of nowhere.  The only other comparable examples won’t appear for five thousand years.

To really put this in perspective, consider the timeline below.  Arrayed across the bottom axis are the reigns of several ancient civilizations: the Chinese, Romans, Egyptians and Mesopotamians.  In addition to this information, I’ve also placed the approximate dates of the the ice age, stone age and examples of religious and cultural monuments (the oldest of which dates to about 3500 BC).

When compared with Göbekli, the great civilizations and monuments of the ancient world seem to to huddle in an upstart mob at the right of the chart.  Even the very oldest of the examples, a Mesopotamian palace, is separated from Göbekli by the same span of time that divides the ancient age from the modern day.

Such an amazing and sophisticated example at such an early date, literally, boggles my mind.  It’s absolutely amazing.  And, paradoxically, the amazement and wonder helps to explain why Göbekli has remained essentially unknown.  A discovery of this magnitude demands enormous attention and dedication.  It takes almost as much as it gives, particularly from those that discovered it; and not every scientist is willing to give that kind of commitment.  Thus, I completely understand the response of the man who discovered the site.

[Unable to interpret what he saw], the [American] archeologist who stumbled on [on the site] in the 1960s simply walked away.

But, even so, the evidence at Göbekli has the potential to completely transform the history of civilization.  And I, for one, look forward to seeing what emerges.

Note: You can view a high resolution PDF of the timeline by clicking on the image, or here.

Tags: Ancient Civilizations,Archaeology,Göbekli Tepe
Categories: Art, Cool Stuff, Featured
3 Comments »

When I graduated from college and had to choose between a career in industry or academics, I found it to be an easy decision: I stayed in academics.  I like to have my head in the clouds and enjoy the intellectual lifestyle.  (I actually consider the label of “absentminded” to be a compliment.)

It should come as no surprise, then, that one of the most enjoyable aspects of writing a book has been the opportunity to research my subject.  My reading list has included books on analytic design, illustration, anatomy, typesetting, scientific communication, web technologies, LaTeX, the history of science, statistics and informational graphics. And as I worked my way through it, I took some extremely interesting side trips.  One of the most intriguing, however, was an extended tangent through the notebooks of Leonardo Da Vinci.

Da Vinci died in the year 1519, nearly five hundred years ago.  Yet, the modern world remains fascinated by him.  His name adorns the side of best selling books and conspiracy fiction; and his drawings have become cultural icons.  As an example of his popularity:

In October of 2009, Martin Kemp, a professor of art and history at the University of Oxford, found a portrait of an Italian girl.  Up until Kemp took an interest, it was widely accepted that portrait had been painted sometime in the nineteenth century by an unknown artist.   After a great deal of investigation and the use of a multispectral camera, however, Kemp discovered something startling.  The painting had actually been done by Leonardo and nearly overnight, it went from a value of 19,000  British pounds to over 100 million.

I’m no different than the masses.  Leonardo fascinates me.  He had a very distinctive way of seeing the world and an engaging style.  Maybe that’s why it’s so easy to lose yourself in the details of his work.  Given my interest, a thorough study of Leonardo’s notebooks seemed only natural.

What I didn’t foresee, however, is that I would start to digitally collect his sketches; and in the past several months, I’ve put together a rather eclectic mix from across the internets.  Earlier today, I realized that the images might be of interest to others as well; thus, I’ve created a special online gallery for them.  It can be found under “Art and Photography” –> “The DaVinci Notebooks”  To get there more quickly, you could also just click here.

Enjoy!

Update (2011-09-08): Due to problems with the Gallery 2 Plugin for WordPress, I have removed the Da Vinci Gallery. I will replace it with something else in the near future. For now, thought, the link is dead.

Tags: Art,Leonardo Da Vinci,Sketches
Categories: Cool Stuff, Featured, rapidBOOKS
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In the past few weeks, I’ve had several observant readers ask about one of my “secret” projects.  They’ve wondered what I’m up to and why it’s detracting from other endeavors.  After answering another query this morning, I decided that it’s probably time to speak openly about it.  So, here’s my public confession: I’m writing a book.

It’s about scientific and professional writing and open source.  Moreover, it will be interesting, intriguing and revolutionary.  (Yes, I have an inflated sense of ego.)

Before really diving into the details, I’d like to give a bit of personal background.  This might help you understand why I’m passionate about the subject.

Background

Ten years ago, had someone told me that I would end up a scientist and engineer, I would have laughed at them.  At the time, I had just started at University and I was fully set on a career in either illustration, design or architecture.  I was much too “visual” and “right-brained” to surround myself by geeks, freaks and nerds.  It didn’t help that I spent a huge amount of time grooming myself to be an “artist”.

During high school, I had been cursed with moderate talent and highly indulgent instructors.  They praised my artwork.  They called it interesting and innovative.  They encouraged me to refine my technique and to major in visual arts.  So, I did.

But as time went on, I realized that I wasn’t very happy.  I realized that I had other interests.  I enjoyed art, I did well in it; but art classes weren’t my favorites.  That honor, as it turned out, was reserved for mathematics and science.

There was also another problem, I found that I lacked the discipline required to systematically create an individual style and build a portfolio.  I wanted create art for myself, not for other people; and that is a fatal flaw in an illustrator (the type of work that most interested me). Illustration, by definition, is work that has been requested for a particular use.  I was more interested in my own whims than those of potential clients.  Thus, not long after recognizing my problem, I decided to go a different direction and changed my major to engineering.

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Tags: Analytic Design,OpenSource Writing
Categories: Cool Stuff, Featured, rapidBOOKS
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Imagine how awesome it would be if this announcement read: “Time Drive has been completely rewritten from scratch (yet again) to take better advantage of the paradigms of modern computing!  Version 0.3 has hundreds of updates and new features which will make your life easier and more fulfilled!”

There’s just one little problem … such an announcement wouldn’t necessarily be true.  (Marketing hyperbole, I never knew thee!)

The truth is this: Time Drive is a simple backup program that does a good job of backing up your data.  It offers a nice list of potential backup options ranging from an attached hard drive to a computer over the network or across the internet.  It makes it easy to search for and restore a lost file.

In short, Time Drive seeks to change the world by making an act of computer maintenance more convenient.  I’d like to think that it Just Works.

But the real test of a program isn’t how well it works, but how easy it is to fix when broken.  A good program does what you want, but a better program helps you get back on track when things go wrong.  Back when I was looking at other backup programs available for Linux, this was my number one frustration.  Most of the applications would work (for the most part), but I could never troubleshoot or repair problems when they happened.  There just wasn’t enough information available.

For an example, let’s take SBackup.  It’s a lovely little program,  with one horrible flaw.  You have absolutely no way of knowing if it is working.  It doesn’t keep log files, it doesn’t notify you if a backup job failed.  It doesn’t let you know if it is running.  Its simplicity is actually symptomatic of a flaw: it’s incomplete.

These were problems that I desperately wanted to avoid with Time Drive.  And now that I’m announcing version 0.3 of the program, I’d like to think that I have.  So, instead of marketing hyperbole and false promises, here’s the real announcement:

Time Drive 0.3 includes a number of refinements that make it easy to both backup your data and to figure out why a backup might have failed.  It’s better, easier and more refined.  In the rest of this post, I’ll explain why.

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Tags: Backup,Linux,Mac OS X,Time Drive
Categories: Computer, Featured, Programming
7 Comments »

In part 1 of this article, I shared a few of the frustrations and reasons why I decided to write my own backup utility rather than submit to the tyranny of currently available solutions.  While some might find those ruminations interesting, the vast majority are probably far more interested in the end result.  There is a reason why “Get to the point” is one of the most important sentences in the English language.

Here’s the short version: After becoming tremendously frustrated by the state of backup on Linux, I decided to take matters into my own hands and create my own tool.

And though I only want a few things, I want that tool to do each very well.  First, I’m looking for a solution that can incrementally backup over the network and let me restore a file from an existing snapshot.  Second, those snapshots should be compressed, encrypted and secure.  Third, it should be easy to browse old backups for existing files and restoration should be a one-click affair.  Fourth, I want a backup system that can protect me from disaster, carelessness and pathological stupidity.

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Tags: Backup,Linux Backup,Time Drive,Time Machine
Categories: Computer, Cool Stuff, Featured, Programming
7 Comments »

It is a terrible thing to realize that you are stuck in a rut.  Being in a rut effectively means that you’ve stopped advancing and life has evolved to monotony.  No one likes to be around people in ruts, but it’s even worse to discover that you are personally trapped in one.  And, most unfortunately, I am in a rut.

Don’t believe me?  Take a look at the home page of this blog.  You will likely notice that a full six of the ten most recent posts have dealt with one subject: backing up your computer.  That’s pretty conclusive evidence of a rut.

Now, backing up your computer is a very important thing to do; you should do it regularly and have a plan.  But … well … it’s boring.  Talking, thinking and writing about nothing but backup is dull.  As one of the doctors I work with likes to say, “That isn’t sexy.  If I’m going to spend any time with it – women, food, wine; it doesn’t matter – it should be sexy.”

He’s got a valid point, backup is not “sexy” and I’d like to write about things that are, at least for a while.  This, therefore, will be my last post on backups, archives, or servers for the relatively foreseeable future (technology is just too cool to lay it aside for too long).  But before doing that, I want summarize where I ended up in my quest for the ultimate backup system.

Backup on Mac is taken care of, I use Time Machine to a Samba share.  More adventurous persons than I might even say that this arrangement approaches sexy.  It’s convenient, fast, and robust.  It even covers disaster recovery.

Backup on Windows is also covered.  The built-in file backup is easy to use and works well.  Moreover, setting up a disaster recovery system is relatively painless.

But the third major operating system, Linux, is a bit of the odd-man out.  Certainly, you can find some excellent backup systems, Back In Time is one such example.  With a bit of work, you can even tweak it so that it is almost perfect.  But it’s the “almost perfect” and closely related cousins (“mostly useful” and “good enough”) that are the problem.  They have those stupid qualifiers – almost, mostly, enough – bolted on.

Any time you hear a qualifier, you can rest assured that you aren’t going to like what follows.  Consider the rather innocuous phrase, “that may be a problem.”   Here, the term “may,” makes an already bad situation much worse.  Instead of specifying some probability of problemhood, it all but guarantees it.  Positive qualifiers are just as bad.

As a result, it angers me that nearly every backup program available for Linux requires some kind of qualifier.  It shouldn’t be like this.  Linux is a brilliant operating system in practically every way.  It is highly integrated, wonderfully modular and tremendously easy to extend.  So … after finding that nearly every backup utility in existence has failed to meet my needs, I found the situation intolerable and decided to do something about it.

I wrote my own.

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Tags: Backup,Linux Backup,Time Drive,Time Machine
Categories: Computer, Cool Stuff, Featured, Programming
6 Comments »

Writing anything – whether it be a book, or a short story or an angry letter to your boss – is substantially more than starting from the first idea moment of inspiration and continuing to the final draft. Rather, writing involves a fair number of idea fragments, fleeting moments of inspiration, and a tremendous number of dead ends.

It is incredibly unfortunate that most writing software, however, is geared to organizing and structuring the document after most of the hard work has already happened.  It simply assumed that most of the planning and layout has already happened and the author is ready to string words together.  Unfortunately, this assumption overlooks one important truth: ideas are best defined as they are expressed.  Thus, it’s usually about the time that the a writer sits down to compose the draft, that the document’s true structure becomes apparent.  In my own case, this often leads to a flurry of reorganization.  And it’s during the restructuring that the real battle begins.

When in full creative passion,  I am typically working with three or four different programs all at the same time: OneNote is open so that I can access my ideas, Word is there to start collecting the somewhat finished text, and I’ll also probably be using a MindMapper so that I can see a visual representation of the document structure.  The tools are separate and don’t communicate with one another.  Thus, a change made in one place needs to be made everywhere.  And all too often, that I end up fighting the word-processor and the notetaker, and the mind mapper.  It is tremendously frustrating to battle the tools of your adopted trade.  Luckily, I am not alone in my frustration.

In the past everal years, a number of programs have become available that leave the linear model of writing behind.  On the Mac platform, one such tool looms above the others: Scrivener.  Central to Scrivener’s function are two important metaphors: that of the outline and that of the corkboard.  And it works really, really well.  There are just a few minor problems.  First: Scrivener is only available for Mac and Scrivener’s lead developer has made it clear that there won’t be versions for other platforms.  Second: Scrivener was really designed with creative writing in mind.  Thus, while it can be used for long and complicated documents, this is a slightly less than straightforward process.  Last, to create said fancy documents, Scrivener requires the raw use of a markup language (and all of the associated headaches that come with it).

The document processor, LyX, however, excels in many areas where Scrivener falls short.  It is built upon the mature and robust underpinnings of LaTeX, the typesetting language of choice in the science and engineering.  And more importantly, it is easy to use (where LaTeX most decidedly is not).  But it fails in the same way as Microsoft Word and other word processors, it is a linear writing tool and doesn’t offer a great deal of work-flow flexibility.  That is where LyX-Outline comes in.

LyX-Outline is a marriage between Scrivener’s organizational tools and LyX’s typesetting tools.

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Categories: Computer, Cool Stuff, Featured, Programming, Raves
24 Comments »