All my Life, is Changing Every Day, In Every Possible Way

This is actually a follow-up on a previous post, Information is Life In Formation.

I recently read on Slashdot about an article of Freeman Dyson, a well-known physicist and mathematician, supposedly about "Open Source Biology". His article, entitled Our Biotech Future, in turn, references the work of Carl Woese, famous American microbiologist - the discoverer of Archaea among other things.

Specifically, it references two of Woese's articles, "A New Biology for a New Century"(abstract|full text) and Biology's Next Revolution. Making a nice and interesting story abruptly short, in those articles Woese lends support to the idea that in the beginning, Life wasn't about Species. Instead, Life was Open Source, in the sense that in the primordial soup, primitive life-forms were exchanging genetic material in a kind of free, horizontal manner, like a sort of massively parallel rewriting system of sorts.

And all was wonderful in the Garden of Eden, till this organism (likened to Bill Gates) appeared, that didn't allow exchange of genetic material with the others. And so, Bacteria, Archaea and Eukarya or Eukaryotes developed in species, only transferring genetic material in a vertical manner - to their descendents, instead of the previously ubiquitous horizontal transfer. The species-based Life prevailed, probably being more resilient to destructive change, and the primordial soup organisms disappeared, but this also meant a significant slow down of evolution.One should note that HGT is still common in Bacteria, and even between Bacteria and fungi, for example, and it is thought to be one of the important causes of the development of bacterial drug resistance.

Nowadays, Dyson argues, the wheel has turned full circle and humans, through the use of advanced breeding and genetic engineering are able to transfer genetic material from some organisms to others, essentially being able to break the interspecies barrier, creating chimeras, transgenic organisms, like in the golden age of horizontal genetic material exchange.
Well, that sounded to me a lot like that previous post, that stated that all Life needed is Media for Information pattern storage and interaction, an initial Seeding of the media, and Time. Oh, and about the Tree of Life, there seems to be none. In the presence of HGT, the Tree of Life has no real root, but an initial Seeding.

How does this relate to cellular automata like Conway's Game of Life, where stable, resilient-to-change patterns also appear? Would a similar computational device be able to create a "full-blown" (whatever that means) species structure? Food for further thought.

Anyway, I (just may) have told you so [tm] :-). Actually, the most striking idea seems the fact that, although at the publishing of the former post about Information being Life in Formation I had almost no idea about HGT and the details about the development of primitive Life, and was composing a picture based on the Computational, Information-theoretic approach and intuitions, its main conclusions are largely confirmed by biological "facts". So, even if the Universe isn't, after all, a gigantic cellular automaton as some would say, it still seems that Information processing and Life are so intimately, essentially linked that there is no conceivable way one could exist without the other: the essence of Life lies at least as much in its Software, as in its Hard(Wet)ware (see also another post).

The fine print:

• The title of the post is actually made up of the first two verses of The Cranberries song Dreams;
• "The Young Family" is a work by Australian artist Patricia Piccinini.

Designer genes

Slashdot fortune: Do molecular biologists wear designer genes?

123133721

The Illusionist

The Illusionist (No Strings Attached)

The spirit drinks are finished,
Rusted are the wheels and chains,
No smoky trails in mirror relished,
Dismantled by our weary brains.

The magic flowers have withered,
The old hat is ripped and torn,
No phantom rabbits lingered,
In former white gloves never worn.

No dazzling tricks upon us
From your coffers to bestow,
But for the ghostly chorus
"As above, so below".

-- O. Cean - 1337 Magickal Spells

More numbers

Find numbers N and M such that:

1. N!*M! + N*(N+M)*(M+M)^N = (N+M)!
   
2. N!*M!*(N+M)! = N*(N*M)!
   

Trial and error

Science is about trial and error: you make an error, then you go to trial.

Metamath problem

Find numbers N and M so you can construct a valid mathematical formula with:

• N factorial signs (!);
  
• M multiplication signs (*), numbers N, numbers M;
  
• one equal sign (=);
  
• in addition, a plus (+).
  

and as many parantheses as you want.

Information is Life In Formation

What is Life?

I propose that Life is a phenomenon that needs these conditions:

• A medium that supports the encoding of information and allows the interaction of the encoded patterns
  
• Seeding of the medium (initial or continuous)
  
• Time to evolve

That's ALL. Or, as mathematicians would put it, these and only these are the required conditions. And that's the main idea of this post - the fact that any such system has the intrinsic potential to support arbitrary complex (and beautiful) Life-forms.

A system that fulfills these conditions will, sooner or later, exhibit emergence, the emergence of Life. Autopoietic systems, structures which are able to fabricate themselves, possibly with variations, will appear. Then Earth-like life is only a more or less huge number of millions of years away.

Yeah, that's right, YOU are not significantly more alive, or living than some information patterns, say, some moderatly complicated bit-strings, this is the message.

What are the implications of this bull^H^H^H^Htheory you ask? Well, there are two main implications:

• For any living systems, we can find the encoding medium and the ways it allows for their interaction.
  
• For any structure, physical or theoretical, that qualifies as a Life-supporting medium by having the above properties, we can think about the nature of Life it is able to support.

Can a Systems Biologist Fix an Electrical Engineer?

or,

Do Systems Biologists Dream of Electrical Engineers?

We're writing a seamless distributed computing library in, surprise-surprise, Ruby.
It's about distributing objects, using, and finally discarding them as if they were plain local objects. Yes, distributed computation is a harsh mistress... It's about "the network IS the computer", so popular a quote that there is (even? ha!) a Slashdot joke about it:

"Okay, the network is the network, and the computer is the computer. Sorry about the confusion."
--Sun Microsystems

Actually, that is not what this post is about. Not at all, really. As the fine folks of Monty Python would put it, it's about "Something Completely Different". But I had to start with that to get you on the wagon--literally--, well, not on an actual physical wagon, but rather on this train of thought, or is it stream of (serializable) consciousness? There is a connection though, but you'll have to read the whole thing to get to it. Good things come to those who wait (and read and think while doing so). So, if you're still here, why not just give it a try? My promise is that, by the spacetime you're done, you shall be able separate the earth from the fire, the subtle from the gross, suavely, and with great ingenuity and skill. Your skillful work will ascend from earth to heaven and descend to earth again, and will receive the power of the superiors and of the inferiors. So thou will have the glory of the whole world--therefore let all obscurity flee from thee.
Bottom line is: You Might Even Like It™.

---

Spoiler warning: if you haven't read "Stranger in a strange land" and "Solaris", beware of (plenty of) them below, and maybe choose not to read this pile now. Yes, this is a valid, author-endorsed reason not to read this, so, if you're who I think you are, this is your cue to exit.

A few days ago I read an article by Luca Cardelli entitled Can a Systems Biologist Fix a Tamagotchi?. Thanks again for sending it to me--you, the guilty part, know who you are :-) The title is a play on that of another article, Can a Biologist Fix a Radio? by Yuri Lazebnik.

Lazebnik's article emphasized on the need to develop a formal approach for studying biology, together with an adequate language, an approach that would focus on understanding the system as a whole, as opposed to cataloging myriads of more or less loosely connected pieces, since this way, "the paradox that the more facts we learn the less we understand the process we study" comes into play.

Cardelli takes this further, and proposes that the challenge of understand biological systems is more akin to the challenge of a systems biologist to fix a Tamagotchi. An electrical engineer could easily fix a radio, but fixing a software bug in an MP3 player would require expertise in the rather different field of software engineering, he argues. Cardelli rings again the bell (wake-up call?) of formal approaches for (systems) biology. The need of a language and the need to find the level on which the essence of a system is manifest are some other things he mentions, while pointing at Computer Science for some hints about how to discover and work with them. At one point, he half-jokingly refers to this language as the "Language of the Creator". The essence of life is in its software, at least as much as in its hardware.

Stranger in a Strange Ecosystem

If you've read Robert Heinlein's Stranger in a Strange Land, or just "Stranger" as its fans affectionately call it, you know about the grokking language, the one that Michael Valentine Smith is teaching to the people of Earth so they are able to grok--understand deeply and intuitively. Mike, after learning more about humans, decides that the only way to teach them how to grok is to first teach the grokking language to them, which he himself learned from the Martians. It seems that this grokking language has quite a few things in common with the "Language" that Cardelli writes about. Teaching this language is done, for pragmatic reasons :-), in the religious context of the "Church of All Worlds", that is created by Mike for this purpose--sort of like the Church of the Invisible Pink Unicorn has been created to... well, fool people into thinking more.

Know Thyself

Both Lazebnik and Cardelli try to analyze the state of the art or, rather, the status quo in the field of biology, and try to present the limitations of the current approaches, and make predictions about the way the field will evolve. In both papers, there are some striking similarities to Stanislaw Lem's metascience-fiction, as some have called it, or, for our purposes, pseudo-science-fiction novel, Solaris--also, the name of a computer operating system developed by, yet-again, you've guessed it, Sun Microsystems. If you haven't read it, please, for the love of a possible godlike being, at least read its above linked Wikipedia entry, this fragment and also Lem's essay.

One similiarity is in the way Lem describes the (evolution of the) field of science that humans develop to understand Solaris, the extremly powerful and seemingly intelligent alien entity that best resembles a planetary ocean, which, by the end of the book, seems like Nature's failed attempt at creating a God. Incidentally, I found an interesting note about Lem's religious affiliation.

The other similarity is in the fact that the godlike ocean can reproduce humans (or rather their recollections of others), it can copy them in great detail, and actually does this in what seems like an attempt to "understand" them. This attempt is doomed to fail, since the ocean seemingly "misunderstands" the essence of humans for their darkest thoughts and fears, and is ultimately unable to find an adequate language for communication. It is lacking, like biology today, the level at which the essence is manifest and the language to explore it. Solaris has plenty of excuses, being a live alien planetary ocean--albeit a godlike one--and, seeing how alien things begin to look in biology, maybe it has some down to Earth excuses too.

As Above, so Below

Okay, back to the distributed computing library. We're trying to make it seamless, more precisely, there should be exactly one added line to make a program written for a single computer work on many computers. Not quite there yet, but getting close.

"The network is the computer", or, in the spirit of the famous Tabula Smaragdina, "As on the computer, so onto the network". The Network and the Computer should be One, in Software. Software, which is the Essence of Life, its, if you will, Spirit, which is "As above, so below", as in Hardware, so in Software.
On a side-note, there is a lot of Magick in Heinlein's "Stranger". See this nice essay--free thelemic candy included. (You will not be charged extra for reading all those caps).

The Truth of the Matter
... lies in the Spirit.

This is why the non-aptly named "Computer Science" has perhaps the most to say about the essence of Life, the Universe, and Everything. It's as much about computers, as biology is about fixing radios. And no, it's not about keeping the clients and the shareholders happy.
It is about Spirit transforming into Process, and, thereby, creating Reality. It is about Spirit ascending from Concrete to Abstract and descending to concrete again and about the funny mark it leaves behind.

Many Worlds, One Ending

I wish You a day when all are Free.
As in Spirit, so in Software.