Category Archives: Debate paper SMU

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.

The conserved genome

Something has to make a start, and a paper we recently discussed at SMU shall be it.

Along the lines of “it’s not about what (genes) you have but how you use them”, I came across this recent article: Systematic discovery of nonobvious human disease models through orthologous phenotypes .

The article itself seems, well, nonobvious at first. The subject is in the area of cross species genome comparisons. In essence, the more becomes known about genomes, the more people find similar genes in very dissimilar organisms. More, many genes appear in functional clusters, and these clusters are also to a large extent preserved in their unity across species and even phyla. Their genes do produce proteins with similar biochemical functions, but those same chemical functions in similar functional clusters produce very different outcomes (phenotypes) depending on the organism in which they occur – they perform totally unrelated organismal functions. So, structure is preserved, function is not, and the more is known about genes the more it appears that true novelty is rare and that most innovation in terms of species, depends on recycling and differently regulating existing genes.

There are many ways of looking at this – the surprising flexibility of genes and gene products themselves for instance to be reused for different functions, so that say, cilia related genes of unicellular organism have functions in producing neuronal networks in higher organisms. There is the aspect of finding new disease models by going from known disease related genes in humans, to finding new genes in the homologous genetic module of some different organism just by virtue of finding them together with unknown genes there.

To me this is yet another piece of evidence for one of my pet theories, that genes seems to be widely conserved, and that patterns of use and gene regulation are much more important for expressed features of organisms, than the nominally encoded genetic information. More and more, genes seem to be a rather generic thing, and that the differences in organisms seems to come about in how these genes are being used. On a higher level, this ties in with other puzzling facts of life, such as, why are plant drugs effective in humans at all? Why are very different looking and acting species so widely genetically similar?

The mix and match way of construction and innovation that life uses over and over – to simply re-use “old” genes that have been “invented” for an entirely different purpose – also offers a nice parallel to the way technology produces innovation by recombination of existing parts. One could have called this article “Life as ‘bricolage’: Innovation by recycling parts.”.

Here is some lighter reading on this paper, with background information.