Category Archives: Science ramblings and pet ideas

Avatar and biology

I finally saw the movie now. The one interesting idea of the movie that really stands out, is the idea of a real “wetware” avatar, to be inhabited by a human soul, to live in a wetware kind of Second Life. If you leave aside this basic idea, and the impressive CGI recreation of this world, I found the rest of the movie disappointing. The biology of it is once again unoriginal,  a lot of the plants and animals there are either direct copies of terrestrial organisms (trees), or easily recognizable transplants (some jungle plants looking and functioning as some well known brown algae). And never mind the plotline, which apparently marries the Captain Smith and Pocahontas love story with the leave-us-alone theme of Apocalypto (which I suppose also delivered the idea of blue colored humanoids). Coming back to the movie’s imagination of another world – in analogy to the last post on “natural” vs “artificial” architecture design it makes me wonder, can we at all imagine organic worlds that do not look like our known world? Must any organic-biological world have the same “design features” that we know from ours? That means, segmentation, axial and bilateral symmetry, tree-like growth, separation of neuronal and somatic networks, etc. Of course this movie actually copies known morphologies wholesale, as do most sci fi movies. But if it didn’t, would truly “other” morphologies still include features that we’d recognize as “organic” in origin?


Architecture, processes and materials

Can a thing develop organically and yet not look organic?

This is an attempt at thinking while writing. I have no idea where it is going. The main questions came to me when I was thinking about what I like and don’t like in architecture, so architecture is what was mostly on my mind.

It occurred to me recently that I sometimes like modern architecture. This surprised me because I have so often disliked it that I thought I could really only feel comfortable in places that are old, and which were built in traditional architectural styles. Good examples for this are what Bernard Rudofsky called “Architecture without architects”. That phrase itself may be a good metaphor for what I call here “organic development”. In any case I do like those architectural elements that you find in “traditional” buildings:  arcades, tiled traditional roofs, front porches, wood and brick and not metal and glass, and the like. These are also all design elements that Christopher Alexander has so well described as emerging naturally, organically if you will, from the traditional,the timeless way of building.

Alexander’s main claim is that traditional building processes create naturally well adapted solutions to architectural design problems primarily because they are slow and do leave detail decisions to the builder rather than attempting to resolve all decisions at the planning stage. Local authority trumps global authority. And this he claims, leads to fewer mistakes and better functional adaptation, and better esthetics too. He point out that the design space of architecture, the sum total of all possible design combinations, is so huge that mistakes are vastly easier to come by than good design, and that all design elements are so interconnected and interactive, that planning everything ahead of time is practically guaranteed to yield a sub-optimal solution. By way of contrast he makes a compelling case for traditional processes and their time-honored solutions. In his “A pattern language” he catalogues an enormous amount of architectural patterns that have been honed through practice and evolutionary, incremental adaptation, until all the bugs are worked out and the pattern “works” as a standalone, and also as part of the larger architecture it is embedded in. These patterns also feel – to me – almost instantly comfortable and intuitively “at home”. They were successful because they work.

Alexander also shows many examples where modern architecture fails to achieve well adapted form, never mind esthetics. He goes to great length to describe modern buildings as largely lifeless in “The nature of order”. But if this is so – and my feelings go in this direction – then why? On the technology side builders now have many more options for achieving certain solutions than the traditional builders did, and so it is easy to conclude that it is the materials that make a building “modern”. So when modern buildings don’t feel comfortable or well adapted to the needs of the inhabitants it is easy to blame the technologies and materials first. But the root of modernity lies rather in the industrial production process, the formalization of design, the extensive planning, than in the actual materials used.

In the modern, real world, Alexander’s ideas of designs as pattern languages have caught on, most intriguingly in computer programming, and his examples of patterns in architecture are also well received. But very few builders follow Alexander’s prescriptions for the design process because the modern bureaucratic requirements for licensing and permitting and planning require precise, detailed planning ahead of time. Alexandrian processes interfere with the permitting process in modern regulatory frameworks. So when modern architecture feels uncomfortable, modern processes may have more to do with this than modern technologies.

Consistent with the above, nothing in the Alexandrian building process framework forbids uses of “modern” technologies or materials. All that Alexander claims is necessary for well adapted architectural solutions to emerge, is a process of incremental adaptation – development on the fly during construction – in a well-defined order of steps he calls a generating sequence. This process coincides with the traditional process of building, and is also very close to the sequential development steps in pre-ordained order yet with much “local” authority, that are observed in biological (ontogenetic) development, i.e., growth and differentiation of an organism.

Now if the processes are more important for the functionality of the outcome than the materials used, then any form achieved through a process that is similar in nature to “organic” process, should be called organic, regardless of technology used. Conflating swiftly organic processes with Alexandrian generating sequences, this now relates to the architectural manifestation of the problem, resulting in the question of the beginning: Can a form be produced organically, for instance an architectural form produced through an Alexandrian generating sequence, and yet not look naïvely “organic”? After all we are all used to recognize what’s “organic” though the lenses of the only organic things we think we’ve seen, life as we know it. So is everything that doesn’t look organic, of a non-organic origin? Obviously things can be made to look fake organic, but can something of genuinely organic origin look “artificial”? Or will it always have recognizably organic features? Or maybe are these recognizably organic features so subtle, that say a modern building can look naïvely “modern” because of the materials used, whilst actually being the result of an organic process? Is it maybe for this reason that some modern buildings actually look and feel good to me?

I would like to think so, not just for theoretical reasons but because it would make for more genuinely interesting architecture to have more than just two polar opposites of choices – replicas of traditional styles that feel comfortable but that are stale in their development and don’t make use of modern technologies, or modern styles that never really feel comfortable. Of course there is always the possibility as well that modern buildings may just genuinely be well planned and built, with no organic process involved whatsoever, regardless of the low odds for this to happen, according to Alexander. My personal feeling though is that there aren’t enough modern successes of that kind.  There has to be a way to use modern materials and technologies in architecture, to produce striking, novel, interesting, modern shapes, and yet shapes that are well adapted to their function, and have a subtle, organic feel to them. I would like to think that using organic process with modern and non traditional materials is the way to achieve this.

Levels of meaning

There is one ubiquitous feature of biological systems which I believe is underrated in its implication. Worse, it is seen as the proverbial bug instead of a feature – the observation that many biological structures, including fundamental ones, seem to have several functions at once. They are part of several biological subsystems at the same time. I believe that this kind of organization results from a process of organic development, from the way complex systems generically grow. Human made but organically developing and evolving systems such as cities, economies, polities, also share this feature. Human made but constructed (engineered) systems by contrast, usually keep functions well separate from each other, for reasons ranging from the logics of production, assembly, and distribution processes, to ease in troubleshooting etc.

It is ironic when organization of and functions within complex biological systems such as genomes, are studied with the expectation to find a “neat” system – as if they had been engineered. I don’t think these systems can be understood when the questions are framed through an engineering metaphor. Of course in the larger scheme of things biologists assume evolution and not construction. But ground level research is usually framed with a “one purpose per component” assumption, and this suggests drawing a fundamental analogy to man made engineering. The whole idea of phylogeny and ontogeny though means all these biological systems originated in an entirely different way: they grew and evolved. In my mind this evolutionary logic has an even more important corollary: the process of growth comes first and the functions associated with components come later. The means justify the ends.

If function comes after structure, then meaning does so too, and it becomes easier to understand how several meanings can be overlaid onto the same structure. This can either happen synoptically in the same organism – say one DNA string, many functions – or over time: one conserved structure assuming different functions in phylogenetically related species. It would of course be impossible to infer the evolutionary model of descent with modification if this was not the case – how would we guess that one organisms descended from another if we couldn’t structurally relate their body parts, or their DNA? By contrast, some kind of change in function is also required if there is to be any kind of evolution to begin with. So, evolution means change in function, and proof of descent of one evolved structure and function from an earlier one needs a somehow conserved structure.

In the social sciences the same contrasting engineering vs. growth worldviews also exist, rough examples would be J-J Rousseau’s ‘social contract’ model compared to FA Hayek’s stance that many social and economic structures result from human action but not from (explicit) human design. Hayek quite explicitly believed that social structures usually result from growth – organic development – rather than from some kind of engineering of the social kind (see for example tome I of Law, Legislation and Liberty). And from yet another angle, Christopher Alexander’s life work can be read as one long and meandering affirmation that good architecture results from emulating the process of goal oriented, piecemeal, function oriented, organic growth, and not from design ex ante (see for example tome II of “The nature of order: ‘The process of creating life’ “).

For some reason, structures that grow seem to acquire meaning and purpose (function) at many levels during their evolution, while structures designed ex ante tend to be limited in the number of functions per component part. I have at least a partial answer as to why this should be so generically.

Take for instance the levels of meaning, in other words the complexity, of DNA. To quote from “What is a gene?”, a 2006 feature in Nature:

Instead of discrete genes dutifully mass-producing identical RNA transcripts, a teeming mass of transcription converts many segments of the genome into multiple RNA ribbons of differing lengths. These ribbons can be generated from both strands of DNA, rather than from just one as was conventionally thought. Some of these transcripts come from regions of DNA previously identified as holding protein-coding genes. But many do not. “It’s somewhat revolutionary,” says […] Phillip Kapranov. “We’ve come to the realization that the genome is full of overlapping transcripts.”

Simpler examples of this kind of complexity were known long ago, for instance a string of DNA can become part of several “genes” and can end up building different proteins through the process of alternative splicing. And of course the resulting different gene products may interfere with the function of a host of other genes. In other words, in a string of DNA there can have many levels of meaning.

So in the genome many elements have function, or meaning, at different levels. These levels of meaning don’t have to be hierarchically nested, quite the contrary, often there simply are various degrees of overlap in function. Thus some DNA string will not just have one function in one gene, but it will have a role in building several genes. A complete gene may not just participate in building one feature of an organism, but take part in several areas. And so on – the same gene may serve to regulate a whole set of genes on a yet again different level of function, or meaning.

This multi level overlap makes for a crucial difference to the common image many people have of complex systems, that of nested hierarchies with modular subsystems with a top-down “chain of command” and increasing numbers of half-autonomous subsystems below it, containing ever more subsystems. Human engineered systems of course are often built with this exact kind of modularity, and for good reason – it lends itself to economies of scale on the production side, and to simple command and control on the user side. Conceptually this would be close to Arthur Koestler’s “holons”, modules in nested hierarchies.

But systems that developed organically, biological or otherwise in origin, usually aren’t made of this kind of holons. Their “modules” if one should even call them so, are often interwoven with several functions at different levels, and controlled by several inputs, not just one coming from the top. Even more to the point, biological components are notoriously controlled not by purely exogenous inputs but by their own outputs, in positive/negative feedback loops. None of this is captured by strictly modular models or the “holon” model sensu Koestler.

At face value this multifunctionality makes it hard to reduce biological features to the level of single functions – they typically have many – and it makes it even harder to imagine how such an interwoven network of structures and functions could have been built, never mind how they are controlled. But, I believe the puzzle comes mainly from the framing of the problem as a presumed optimal engineering solution to a problem rather than a piecemeal growth process with “good enough” rather than optimal outcomes. And in this way the genome’s multifunctionality can maybe also stand as one giant metaphor for the entire ill-defined set of systems called “complex”.

A prototype description of a simpler, human system that grows and develops many levels of meaning in various degrees of overlap, is told in Christopher Alexander’s “A city is not a tree” (alternate link here). Here, Alexander contrasts the mathematical notion of a tree with the structure of a semi-lattice. In Alexander’s words a (mathematical, not biological) “tree” is a hierarchical structure where to go from one branch to another one of the same scale means one has to backtrack to a larger branch they both belong to. In a semi-lattice, by contrast, elements of the same level of scale overlap in such a way that they can connect directly. The real life example he gives for a (grown) semi-lattice structure is a street crossing, which may serve as a simple crossing, as a location for a newspaper or ice cream stand, as a meeting point, etc – all different functions not organized as end points in different locations of a tree-like structure, but overlapping in one and the same location. One can easily find reasons for how this organization came into being – the crossing served as a focal point and attraction that had several functions grafted on top os its “primal” or original “function”, and as a result now it has many. And this is precisely my point: structure comes first and “grows” meaning. Therefore, grown cities have overlapping functions in any particular location. Each structure has been given, or rather, has “found”, many meanings. “Constructed” cities by contrast tend to follow the tree like arrangement. For reasons of planning neatness, functions are deliberately kept separate. Koestler’s holism model incidentally is also a “tree”. In cities a lack of overlap – too much “tree-ness” – leads then to the anecdotal lack of connection and sheer inefficiency of planned cities. Maybe overlaps of meaning of this kind are common in organically grown systems simply because they are more efficient than the deliberately disjointed organization of many engineered systems.

Another case for levels of meaning as a proxy for complexity can be made for yet another human product: art. Depth of meaning in poetry, painting, the movies, etc. , arguably all arise when the piece of art in question has overlapping meanings at different levels, using one and the same structure – not simply when a particular principal storyline is made more ponderous. In writing a single sentence can have literal meaning, syntactic wordplay or semantic ambiguity, symbolic meaning at different levels, meaning within the paragraph, hyperbolic meaning within the chapter, foreboding meaning within the entire storyline, etc. – the levels of meaning are potentially endless. This not to forget that even the so called literal meaning of a word or phrase following Wittgenstein is already a result from its embedding in the mundane context in which it appears. One could spin this even further in that a richer context should therefore make for automatic increases in potential meaning of a component.

In the end, the richness in levels of meaning per component could practically serve to discriminate between the modes of organic growth vs. deliberate construction. “Irreducible complexity” may just be be the defining feature of organic, evolving growth, as opposed to the simpler, one-meaning-per-component kind of human design. Or, to use a different vocabulary, richness in levels of meaning is another measure of complexity.

Origins of life

In relation to the question, how and why are genes so very much conserved in apparently all of life on Earth, in our last debate I, Jason Woodard and Eric Clemons took off a tangent on the probability of other possible origins of life. Just now an article in the New York Times was published – HT Jason – that echoes many aspects of this discussion, which goes to show that the questions are out there and well understood, but the answers are not forthcoming – yet.

On Earth, the unity of life, or rather, its sole origin, are corroborated by a handful of strong, fundamental, shared features, and a host of less fundamental, but also ubiquitous features. Had life as we know it (LAWKI) several origins, we would have an escalating implausibility: first, that life emerged at all, second, that it emerged several times, third, that all resulting organisms would share many essential features, while coming from different sources.

LAWKI’s fundamental features start with the observation that it is individual-based – at its most basic it forms cells with cell membranes. How fundamental this is, is easily overlooked, and I can think of two examples of thinking of life otherwise right away – one, Stanislaw Lem’s “Solaris”, where life is an unstructured planetary ocean with an equally incomprehensible kind of intelligence, and two, of course, the Gaia hypothesis though really here life would have to be considered more of a society still of individuals. Next, and we are not eve at chemistry yet, LAWKI encodes a recipe about how to repair itself and how to make new LAWKI similar to itself. The only thing that is really replicated when LAWKI grows new individuals is this information, and with that, LAWKI takes what it needs form the chemical environment to make more of itself. Incidentally LAWKI conserves information, it prefers to vary little from individual to individual, and individuals are stable over time. None of these should be self-evident or a necessary condition for some, any, life. Again, if you go by Solaris or Gaia, one can think of forms of life that do not do this kind of thing.

There is a nagging suspicion by some people, that the infamous prion proteins could be thought of as a form of life – they are just molecules, but they have defined  information content – they always have a specific kind of configuration – and make more of themselves. They do not actually “replicate”, rather, they incite other similar proteins to take up their own unusual kind of protein folding. It’s not LAWKI, but then again, maybe we don’t see life if it doesn’t look like LAWKI. Current thinking of life is completely taken in by the computer code metaphor of life encoding its own processes in a kind of data string. Not by coincidence, cybernetics and AI/AL were all “invented” in the same era as the naming of biological information as the “genetic code”, ca. 1940-1960. The possibility of a fundamentally deeper embodiment of some other life’s information into a physical structure is hard to imagine in the age of digital code strings (incidentally computer code of course also implies a form of embodiment – “hardware”: computer code may not be encoded in a structurally embodied way, but it strictly speaking only turns into “code” or heavens forbid, “information”, once it meet suitable hardware, otherwise it is just garbled digits).

The rest of the argument for LAWKI’s unity is essentially all about specific chemistry. All of LAWKI uses the same genetic code encoded into very similar molecules, DNA and RNA, using very close cell chemistry. In building its physical units, LAWKI does not just use carbon and water. LAWKI uses a tiny set of all possible organic molecules: mostly a few sugars and their polymers, cellulose and chitin and starch, plus just 20 odd amino acids and their polymers, proteins, in a very small set of all possible protein foldings. More, both sugars and amino acids have the property of chirality, that means, chemically identical molecules can be symmetric, non superposable isomers (distinguished by whether they deflect polarized light either to one side or the other). LAWKI always only uses one of two possible isomers, and all of LAWKI uses the same, rather than having each phylum, or each species, picking their own preference at random. This is significant because for purely chemical reactions, it does not matter which isomer you use – they both have identical reaction or activation energies etc. But LAWKI cares because LAWKI controls chemical reactions via enzymes, and enzymes are highly sensitive to chirality (because they are 3D structures that physically bring molecules together in a lock and key fashion to make them react: a non superposable mirror-image yet chemically “identical” isomer is strictly useless to them). Note (1) LAWKI would not be usable as food for Martians or other non-LAWKI, and vice versa; (2) this ipso facto also means that likely, all enzymes that make and process the fundamental building blocks shared by LAWKI, also arose only once. Of course here it is possible that some enzymes may have been re-invented after the building block had already become a staple of LAWKI.

So LAWKI really looks like it had only one origin on Earth. Now the question becomes, is it easy to make life (many origins of life in the Universe likely), or is it hard? Current thinking seems to go in the direction that it is not too implausible – SETI and various conferences on the probabilities of alien life forms seem to believe it is very likely. In addition to this, LAWKI seems to have arisen fairly quickly after the planet had cooled down enough. And very sophisticated models such as Stuart Kauffman’s autocatalytic sets, also aim to convince the readership that proto-life is plausible as a form of organization, hence the title of Kauffman’s book , “At home in the universe“. The idea is, life is highly probable, and not a lucky accident.

One of the older ideas about possible origins of life is that life would have to be carbon and water based and that therefore only a tiny set of cosmic conditions would allow life. While this does sound quite anthropocentric already, the larger issue is that even if we accept this, it would be very hard to argue that the specific molecules of any and all should all be made from the same handful of components, coded in the same genetic code, and and use the same chirality organic monomers. So yes LAWKI has one origin. Now if it really were easy to make life at least under Earthly conditions, and if it does not have to look exactly like LAWKI, then where is it? On Earth, namely, since we assume that Earth had pristine conditions?

A number of possibilities come to mind: (1) other life exists in parallel but we don’t call it life (prions? Gaia? the economy as a system? the internet?) (2) other life sprang up repeatedly but was eaten by LAWKI (3) other life sprang up repeatedly but was out-competed by the far more efficient (first mover advantage!) LAWKI. Both (2) and (3) would be a form of pre-emption (Eric Clemon’s words). (4) other life sprang up on Earth but we don’t see it because it lives under the most extreme circumstances on Earth.

Ad (2) is unlikely – to me – because LAWKI is so idiosyncratic in its use of organic molecules. Only LAWKI can feed on LAWKI. The enzymes just won’t work on anything else, unless they adapt, but then, no more first mover advantage.

Ad (3) is unlikely as well in my eyes because of ecological niche theory. The entire theory of evolution is based on the idea of competition over scarce resources leading to natural selection among variants of “the same” organism (note cognitive dissonance if you wish so). Competition is highest among the most similar organisms (highest niche overlap). Recent case in point, “Individuals and the variation needed for high species diversity in forest trees” (Clark et al 2010). This paper concluded that homogeneous environments can produce large numbers of different species precisely because intra-specific competition is even fiercer than inter-specific competition: the individuals are more similar to each other. As a result it is “easier” to “break out” into a new species, than to compete against your true peers (in a sloppy way of putting it).

For some radically different life form this means, its “otherness” would actually have protected it both from predation and from competition, and made it easy for it to co-exist with LAWKI, had it occurred at all.

Ad (4) is of course possible, but it invalidates a little the idea that Earth would have been a favorable environment for LAWKI and by extension, for all life, to begin with. If extreme environments are the last chance we can imagine to find other life, then we might as well postulate that the more extreme the environment the more likely we’ll find it, but this just doesn’t sound right.

And finally, ad (1). This is a real possibility. But here one would have to go beyond chemistry into what theoretical biologists of the same affinities as a Robert Rosen would say, namely that one should not define “life” as a set of molecules and their corresponding metabolism or encoding, but as a form of organization (Robert Rosen, “Life itself“). In this way of thinking, diffused networked intelligence, or old-fashioned structures such as “the economy”, like it or not, may well have features of “life”.

Edit: Mysteries of consciousness – I misspelled my anagram, LAWKI, multiple times. I did not see it when I proofread the post. The next day I woke up and knew that I misspelled it. So when I wrote my post I saw, perceived, and memorized my mistake, but it took me 8 h and some sleep before I knew it. Corrected now, among some other spelling issues.