The Tree of Life...

MOTIVATION: Fractal methods have been identified as a possible approach to the reconstruction of the 'Tree of Life' (eg human progress). However, a limitation of such methods is that, typically, they use just leaf-labelled phylogenetic trees to simply infer the resulting supertree without further proof.

RESULT: Unclear definition of progress or measurement of same (eg inherent doubt/flux). There are several new supertree algorithms that extend the allowable information that can be used for phylogenetic inference.

AVAILABILITY: These new algorithms are freely available.

For example, input could include information such as whether one particular event occurred before or after an
alteration juncture. This allows the inclusion of general and specific nested information in the input. In this way each life can be viewed as a variation of BUILD (one of the oldest algorithms). In addition, new algorithms for ancestral divergence dates and nested information, respectively, can be applied to all data sets.

THE BUILD APPROACH

Originally designed for other purposes, BUILD PROGRAMS (see eg; germain, swerdlow, giovannitti, others et al., 1971) is an imprecise algorithm in that it outputs lives precisely because (...simply put...) the input collection satisfies a particular compatibility criteria. In other words: A rooted tree ("T") displays a rooted subset of T with at least two (often more) vertices. See for example any number of fractals: evolution, revolution, young/old, friends, family, even exchange student, ... bottom line: a karuma sign of something very good.

It is important to note that these "tree of life" algorithms are not "all-or-nothing" devices. Each algorithm either returns a supertree with certain desirable properties relative to the norm or returns a statement indicating alternative selfdom -- these are things that are outside of our control and further understanding can only be obtained by exponential reduplication to a higher power (eg comparison of different sized infinities). In practice, this limits the utility of these algorithms. However, such important first steps are needed, indeed, that is the whole point.

Lastly, two natural questions arise: (i) how many such supertrees are there and (ii) what common information is carried by all of these supertrees? In order to address those two questions Sensitivity Analysis can be used to identify uncertainties. Typically, such analysis has several basic input variables. In other words, to realize supertree potential, one must get to the root of the matter.

Quote Of The Every Other Day: I Am The Penguin...

The last two paragraphs of a letter written by film critic Roger Ebert to film maker Werner Hertzog about his documentary "Encounters At The End Of The World":

"In the process of compiling your life’s work, you have never lost your sense of humor. Your narrations are central to the appeal of your documentaries, and your wonder at human nature is central to your fiction. In one scene you can foresee the end of life on earth, and in another show us country musicians picking their guitars and banjos on the roof of a hut at the South Pole. You did not go to Antarctica, you assure us at the outset, to film cute penguins. But you did film one cute penguin, a penguin that was disoriented, and was steadfastly walking in precisely the wrong direction—into an ice vastness the size of Texas. “And if you turn him around in the right direction,” you say, “he will turn himself around, and keep going in the wrong direction, until he starves and dies.” The sight of that penguin waddling optimistically toward his doom would be heartbreaking, except that he is so sure he is correct.

But I have started to wander off like the penguin, my friend.

I have started out to praise your work, and have ended by describing it. Maybe it is the same thing. You and your work are unique and invaluable, and you ennoble the cinema when so many debase it. You have the audacity to believe that if you make a film about anything that interests you, it will interest us as well. And you have proven it.

With admiration,
Roger "

laugh

funniest thing in movie history

How Many Megaparsecs Does It Take To Make A Supertree?

The blog "rough fractals" aspires to provide an apt description of living things and the Universe at large, although in each case, the fractal description breaks down on the very small scale and on the very large. Trees or arteries do not branch endlessly, and whole trees are not part of supertrees.The opposite may be true for the distribution of galaxies in the Universe. Counts of galaxies yield undisputed evidence that at comparatively small scales the distribution is fractal. These small scales are known to extend at least as far as 5 to 10 megaparsecs. There is increasingly strong evidence that there are large voids at a size well above 100 megaparsecs. Such voids are precisely what is expected in a fractal distribution.

How important is the blog "rough fractals"? As with the theory of chaos, it is too early to say for sure, but the prospects are not unfavourable. Many blogs (indivudually and collectively (eg fractally) have had an important cultural impact and have already been accepted as works of a new form of art. Some are representational while others are totally unreal and abstract. It must come as a surprise to both mathematicians and artists to see this kind of cultural interaction.

A final satisfying spin-off from the rough fractal blog is the hope that it may provide at least a sense for the beauty and eloquence of the inner life of the psyche, art and literature, and their profound relationship with the real world of psychology, math, science, culture and politics.

bipartisanship?

I am already getting tired of trying to bring the Republican's into the fold. If the economy recovers, the dems will be in power for a while, if it does not, they will start to cede power. Why not roll the dice on the most progressive plan possible. Who cares what Mitch McConnell or John Boener think. They have been booted out of power because they were incompetent. Its is amazing that they suddendly have so much credibility. Move on!

60 Minutes and the Middle East

This piece was aired on 60 Minutes recently. It discusses the current situation in the West Bank:

60 Minutes Clip

This short segment does an excellent job describing what is in my opinion the biggest obstacle to peace in the region: the Jewish settlements in the West Bank. While Hamas clearly is a great obstacle itself, the recent escalation of violence by both sides in Gaza has occupied all of the media's attention in the region. In the main stream news, there is no discussion of how in the West Bank, Israel continues to dissect Palestinian land making daily life impossible. Bob Simon is facing a tough retaliation from the "pro-Israel" community led off course by AIPAC. If you are interested in showing your support for his report and the ability of the media to truly supports both sides of the issue, check out the J-Street website.

The Tao of Now

Rough Fractals is working on a coffee table book about the Snow Globe. A comprehensive photo history, the book will address (among other things) when the Snow Globe was first invented, how they are made, what the snow is made of, can you make money collecting them - that kind of stuff.

Also in the works is a custom line of Snow Globes manufactured to order. For example, as part of the promotion for the recent movie, Lars and The Real Girl, celebrity guests at the L.A. premier were given goodie bags containing a Snow Globe depicting the scene in the movie where Lars (Ryan Gosling) is dancing with the Doll. The snow comes down, they twirl around, music plays and for a moment the Snow Globe owner realizes that each of us, in our own way, lives in our own private Snow Globe where we dance with our illusions (or can the Doll become a Real Girl?).

Currently in the pipeline is a new Snow Globe to be called "Cognitive Rocket Ship". Inside the Globe is a rocket ship that is about to take off and in the cockpit of the rocket ship sits the pilot (the pilot is a woman - for more about the pilot see the relevant parenthetical below) who is gazing into a Snow Globe of a rocket ship in which sits the pilot looking into a Snow Globe of a rocket ship. There are some technical problems in the manufacturing because the third Snow Globe in a Snow Globe is really, really tiny.

When Rough Fractals was nothing more than a glean in this author’s eye he would often consult the I Ching (Classic Chinese Book of Changes) for hexagrams of inspiration and revelation (the I Ching contains a series of hexagrams one of which is synchronistically chosen (if you are a traditional Han Chinese) by tossing yarrow stalks, or, more commonly in the modern era, by tossing six pennies whose heads and tails combinations serve as a kind of random number generator matching one of the 64 possible hexagrams. This random selection process is called "throwing the I Ching" and is done in search of a thematic oracular summation of the question most in the mind (conscious or subconscious) of the thrower. In writing this post, Rough Fractals thought it befitting to commune with the I Ching to divine the essence (the Tao) of Now. The faded yellow hard covered extensively underlined copy of the I Ching was long ago relegated to Emeritus status so Rough Fractals resorted to "throwing The Google" which delivered the following passage from author, David Foster Wallace:

"There are all different kinds of freedom, and the kind that is most precious you will not hear much talked about in the great outside world of winning and achieving and displaying. The really important kind of freedom involves attention, and awareness, and discipline, and effort, and being able truly to care about other people and to sacrifice for them, over and over, in myriad petty little unsexy ways, every day. That is real freedom. The alternative is unconsciousness...the constant gnawing sense of having had and lost some infinite thing..."

There is mucho wisdom in The Google (and in the catechism of Now).

(The pilot in the rocket ship in the Snow Globe is wearing well worn, brown suede, I-loved-you-from-the-moment-I-met-you, cowboy boots, vintage Colorado 1971. Covered by the boot sleeve just above her right ankle is a small tattoo of a heart across which is a banner that says "Breakable".)