Granularity and no emergence in biology

This time a post that bears some distant relation to my thesis topic: granularity. About 1.5 years ago I got concerned that emergence, emergent properties, and emergent behaviour would complicate developing a formal theory of granularity, so I read up on the topic. While writing along the overview and analyzing both the philosophical aspects and proposed examples of emergence in biology, I came to the realization that it doesn’t complicate granularity, but on the contrary: that granularity actually serves as a useful methodology to investigate (hypothesized) emergence, in particular because of the modeling advantages and prospects for structured in silico simulations.

This is very nice for my granularity, but 20 odd pages to support a useful application area of granularity even though it is not the focus-area of applications (wandering off too far from the narrative), and thus taking up too much space in the thesis. So, I’m phasing it out. Problem is, that I don’t know of any outlet where a cocktail of bio, IT, and philosophy would be publishable, because specialists of each discipline wouldn’t be too happy reading too much about the other two fields and can smack it because it is not necessarily detailed enough for their own field, despite that the idea of combining granularity & (hypothesized) emergence may have some novelty to it. Interdisciplinarity has its drawbacks.

Things being as they are, I’m putting the pdf online after the printed paragraph was getting dust for some 1.5 years – for there might just be an interested reader out there. Comments are welcome of course!

Topics that pass the revue in the manuscript are:
1 Introduction
2 Renewed claims of emergence in biology
3 Emergence from a philosophical perspective
3.1 Epistemological emergence
3.2 Ontological emergence
3.3 Strong emergence
3.4 Weak emergence
3.4.1 Simulations
3.5 Examples
3.5.1 Example 1: pseudoplasmodium formation by cellular slime moulds
3.5.2 Example 2: horizontal gene transfer with metagenomics
4 Emergence and levels of granularity
4.1 Preliminaries of granularity
4.2 The irreducibility argument
4.3 Non-predictability and non-derivability
4.4 Characterisation of granular level from the viewpoint of emergence
5 Concluding remarks

The abstract of “Granularity as a modelling approach to investigate hypothesized emergence in biology” is as follows.

Abstract. Informal usage of emergence in biological discourse tends towards being of the epistemic type, but not ontological emergence, primarily due to our lack of knowledge about nature and limitations to how to model it. Philosophy adds clarification to better characterise the fuzzy notion of emergence in biology, but paradoxically it is the methodology of conducting scientific experiments that can give decisive answers. A renewed interest in whole-ism in (molecular) biology and simulations of complex systems does not imply emergent properties exist, but illustrates the realisation that things a more difficult and complex than initially anticipated. Usage of (weak- and epistemological) emergence in bioscience is a shorthand for `we have a gap in our knowledge about the precise relation(s) between the whole and its parts and possibly missing something about the parts themselves as well’, which amounts to absence of emergence in the philosophical sense. Given that the existence of emergent properties is not undisputed, we need better methodologies to investigate such claims. Granularity serves as one of these approaches to investigate postulated emergent properties. Specification of levels of granularity and their contents can provide a methodological modelling framework to enable structured examination of emergence from both a formal ontological modelling approach and the computational angle, and helps elucidating the required level of granularity to explain away emergence. I discuss some modelling considerations for a granularity framework and its relevance for the testability of emergence in computational implementations such as simulations.

10 responses to “Granularity and no emergence in biology

  1. Might I suggest either Biology and Philosophy or History and Philosophy of the Life Sciences? Both first rank journals. I very much like (and agree with) the view presented here.

  2. thank you for the kind words and suggestion; I might try.
    I doubt, however, that emergentists won’t find some weak spot in the argumentation, given that some of the articles I’ve read about emergence seemed almost desparate attempts to conjure up some way to keep existence of emergence in biology.

  3. The TOG accounts well I believe for physical and biological entities. And I see how it is theoretically possible to represent mental processes as wholes composed of process-parts from a biological granular level, and how it would therefore be possible to connect an ontology of psychological entities to an ontology of biological entities, without involving a notion of emergence. I also see how granularity can replace emergence in explaining the relation between organisms and the social entities they part of like nations, teams, and companies. But how does the TOG explains the connection of the realm of artifactual entities to the rest? If I pick the example of this text, the paragraph has sentences as parts, the sentences have words as parts, and the words letters. This is a legitimate granular partition. However, no matter how far I zoom, inward or outward, I can never arrive at a cognitive or biological or physical entity. There seems to be an impassable chasm between the realm of literary granularity and the others. And it may not be the only one. How do we connect discrete realms of granularity? Are the tools of the TOG sufficient? Emergence offers a solution to that problem: although the realm of artifacts is not a whole out of physical, biological, or cognitive parts, it emerges from and depends on the cognitive realm or level. What’s the TOG’s explanation? I couldn’t find an answer to that question in the paper.

  4. Frederic, thanks for your thoughts on this.
    You ask about “realm of literary granularity”, which I take in the context of this blogpost on no-emergence-in-bio. I explicitly focussed on bio as there’s my interest, and, given your question, I add that I do not know enough about the whole mind-thing at a scientific level to give a well-reasoned reply (well, as for pieces of text, there is obviously a physical level: that what it is written on). For instance, I do not agree with your “although the realm of artifacts is not a whole out of physical, biological, or cognitive parts, it emerges from and depends on the cognitive realm or level.”; but let me first ask you the questions how, in your view, you are convinced that artifacts emerge from the cognitive realm, and, w.r.t. the kinds of emergence mentioned in the paper, as which kind would you classify it?

    Note that the purpose of the TOG is not to explain away emergence, and was never intended as such. What it can do for the analysis of the subject-with-hypothesized-emergence under investigation, is –at least — providing a methodological approach and modeling/representation framework so as to be more precise on what we have at different levels and how those things relate, as opposed to the comparatively easy hand-waiving in the emergence literature. If the TOG is sufficient for that I clearly cannot tell; moreover: no one can. If I say it is sufficient but at some point there’s some claimed “emergence” that cannot be represented well with the TOG, then either the TOG is insufficient and needs some revising or extending (but cannot be the case as I, or someone else, would have claimed sifficiency), or we have emergence. But the TOG is not some sort of a litmus test!
    The TOG at present (as described here) is intended primarily for disambiguating granularity, defining some of its core notions, and providing a formal framework for representing levels of granularity in different granulation hierarchies (granualr perspectives).

    So yes, on your last comment, “What’s the TOG’s explanation? I couldn’t find an answer to that question in the paper.”: there is no answer to that — neither in the paper nor in the thesis. It is, however, open to further research….

  5. Maria,

    Thank you for your answer. First about your comment that “as for pieces of text, there is obviously a physical level: that what it is written on,” I would like to say that it is true that pieces of text are always on a sheet of paper, or a computer screen, or whatever they are inscribed on. But that’s just what they are supported by. The physical granularity of a text would rather be that the words are made of letters, letters of ink, the ink of molecules, etc, or the letters made of pixels, etc. But there is a difference between the marks on the paper or the screen and the words with meaning. The marks still exist when nobody perceives them, but it is not so clear that the meaning associated with the marks exists when the marks are not perceived by someone who can decode their meaning. So there seems to be two granular series: the marks composed of ink, molecules, etc., and the meaningful text composed of chapters, paragraphs, sentences, words, etc., the existence of which depends on somebody perceiving it.

    Second, to answer your question about my conviction that artifacts emerge from the cognitive realm, and what kind of emergence this is, my answer is that this kind of emergence is ontological and as far as I understand the distinction between strong and weak, I would say that it is strong. But I am not talking about the emergence of a whole from its parts, so I am not sure it fits the categories of your paper. Artifacts emerge from the cognitive realm insofar as they result from a process initiated by a thinking agent. I think that the granular system of artifacts emerges from the cognitive one, and that its existence depends on it (because artifacts have functions only for the conscious beings using them), but that the artifactual and the cognitive granular systems are discrete, i.e., they don’t enter in a part-whole relation. Emergence does not occur only from part to whole, and in such cases granularity is useless in explaining away emergence, I think.

    The reason I got interested in your work (and for my participation to this blog) is that I’m having concerns with the issue of interoperability between what I came to call granular systems. I define the notion of granular system as follow: a grain is a granular system iff it is constituted by finer grained parts and is not itself the finer grained part of a coarser grain. An example would be, I believe, the organic realm, i.e., the realm of entities that are alive. It seems to me that the cognitive granular system is in a sense part_of the organic granular system, because the cognitive processes part_of the life-process of the organism. If so, the cognitive realm would not be a granular system in its own right. But the same cannot be said of the artifactual granular system, which is located outside of our minds and organisms, and I don’t know how one would represent that using granular partition. I fear granular partition cannot account for the relation between discrete granular systems.

  6. As for your first comment: there are indeed different ways to divide things up, i.e., how to granulate a subject domain. I have developed a first categorisation for that in chapter 2 of my thesis, which has eight “leaf” types of granularity that each have their own criteria and constraints. You identify two “granular series” (in other literature that term goes under terminology such as ‘granulation hierarchy’, ‘granular perspective’, and, depending on the context, ‘granular partition’ ) that have a different granulation criterion (informally: material/physical piece of text and structure [organization] of a piece of text). The types of granularity help in (1) recognizing a type of how to granulate, (2) granulating in a consistent way, and (3) providing a foundation for dealing with the different hierarchies in a granulated information system (database, knowledge base etc.). Those fundaments can then be linked to a granular perspective that also have the requirement to record the criterion (well, in the TOG there is–elaborated on in chapter 3).

    When you are saying “a grain is a granular system iff it is constituted by finer grained parts and is not itself the finer grained part of a coarser grain”, then you limit all “granular series” to be of exactly 2 levels of granularity only, which is too restrictive–even you give an example of a series with more than two levels. However, having said the latter, you then go off with an example on organic & cognitive realm as two levels in one granulation hierarchy/partition/… (well, three if you are willing to admit to physics-organic-cognitive, which would be a counterexample to your definition): neither I with the TOG nor Bittner and Smith with their TGP–which you are probably more familiar with–aim or claim to deal with that. The TOG (and to a lesser extent the TGP) focus on the things that you mention in the first section of your comment instead.

    At the moment, I do not want to burn my hands on the whole philosophical discourse and fights about the relation between the physical (or biological) realm and/versus the cognitive. One of the reasons for that can be found in your second paragraph: given that you assume a strong ontological emergence, there is no option for scientific inquiry, but merely belief that one can decide to swallow or not.

    As for “Emergence does not occur only from part to whole, and in such cases granularity is useless in explaining away emergence”: this is cutting the corner too quickly, I think. You seem to conflate, or assume to be equal, granularity and partonomies based on mereology, whereas the latter is only one option (albeit an important one) for granularity. For instance, the Second Messenger System is not only constituted of some proteins, but also the relations between them (or: processes they are involved in), and where they are located, something that a ‘simple’ partonomy does not deal with. With the nfG type of granularity one can ‘fold’ the parts with their interactions (sometimes also called ‘inter-part relations’ or the ‘structure of the parts in a whole’ ) into the whole and be more comprehensive. Obviously, when one models a partonomy only and subsequently cannot explain the (behaviour of the) whole, that is cheating toward emergence, for we knowingly have omitted crucial aspects of the parts. In that respect, granularity is not necessarily useless, because it forces one to be more precise on what one puts in a level, why, and how the entities in the finer-grained level relate to each other as well as to those in the adjacent coarser-grained level. It’s not the holy grail, but just one of the methodologies to bring structure to investigating a claimed case of emergence.

  7. Maybe the formulation of my definition was not explicit enough then, because I didn’t mean to restrict a granular-system to two levels of granularity. I didn’t mean any specific number of levels. I just meant that there is always an upper boundary to a granular series, and that this boundary marks the outer limit of the granular-system. For instance, if you start with cells and follows the series of what is alive upwards, you go through, organs, organisms, populations, and perhaps species (that’s debatable), and the upper limit would be (perhaps, I’m not sure), the whole realm of organic beings. In contrast, the example of the piece of text I have been using would be a grain instance in a different granular-system, discrete from the organic one, and the upper boundary of which would be the whole realm of artifactual entities. I was aware that Bittner & Smith neither aim nor claim to deal with the issue of the relation between granular-systems, but I was not sure about you. I dare to think however that this is one of the next issues because ontologies of the various granular-systems are going to need to be interoperable.

    About emergence, I find strange your conception of ontological emergence as a mystical/magical process. You refer to Cunningham, so I went to read his paper, and I was astonished at the way he speaks about emergence. Although I am not a specialist of the literature on emergence, I think I read enough to say that his point of view is not representative. I agree that there is a lot of shamanism out there, but some philosophers of science like Mario Bunge, who represent the antagonism of any kind of mysticism, work I believe with a very justifiable concept of emergence (see Bunge, Emergence and Convergence: Qualitative Novelty and the Unity of Knowledge, 2003). His concept of emergence includes mereological and granular cases of emergence, but also cases of temporal emergence: a plant emerges out of a seed, without having the seed as its part; an offspring emerges from its parents, without having the parents as its parts, etc. Is that so irrational?

    Another comment about emergence: on page 4 you say that the removal of emergence from scientific inquiry should follow the removal of beliefs in god and the soul. I don’t see the entailment. I even think it should be the opposite, for evolution is a particular instance of emergence, the temporal emergence of new species from anterior ones. The concept of emergence came into use for the very reason that the static creationist world-view was destabilized. And it seems to me that getting rid of the concept of emergence would be favorable to anti-evolutionist modes of thought.

    Question: I have the vague impression that you hold the view that every entity is part of or is the finer-grained part of something else. Is that your view, or am I misinterpreting?

  8. Your original definition does restrict it to two, because the “grain” has only one layer of finer-grained grains, but cannot itself be part of a coarser-grain, but which, of course it could be. Moreover, it is a philosophical point if one decides to have boundaries, i.e., a most coarse- and a most fine-grained level, or allow levels ad infinitum either in one direction (i.e., no Atom or Urelement) or in both.

    Again, on the mechanism of granulation: please, please, do have a look at the taxonomy of types of granularity (ch 2 of the thesis) instead of putting words in my mouth that I have not said. Granulating by parthood –to which the TGP is restricted–is only one of the mechanisms of granulation, be it for the TOG or another theory of granularity. It may very well be the case that the taxonomy is incomplete, but the eight leaf types that are now linked to the TOG can keep you busy modeling and categorising the different kinds of hierarchies and helps you untangle the two fundamentally different things of
    (1) sticking with, say, a simple partonomic granulation within the structural aspects of organisms (like cell-tissue-organ-organism) or for multi-resolution databases point-2Dpolygon-3D shape (different representation of same entity at different levels of granularity), where within each sequence, each uses the same principle of granulation throughout the hierarchy, and
    (2) jumping from the structural aspects to the, in your opinion, other realm of cognitive stuff that emerges on the structural components, which uses another principle of creating, or identifying levels.

    As for the “temporal emergence” from seed to plant (a.o.): that is one of one’s own making due to the granularity of the time interval chosen, so does not count as real emergence. If one takes smaller time intervals, one observes a sequence of processes, which, by now, have been quite well explained scientifically.
    Regarding “on page 4 you say that the removal of emergence from scientific inquiry should follow the removal of beliefs in god and the soul. I don’t see the entailment.”: As mentioned in the previous response, (strong) emergence requires a lot of, inquiry resistant, belief. Emmeche et al (ref 12) gives a good explanation why one leads to the other.

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