@romainbrette
Looking at protists with the eyes of a theoretical neuroscientist. Looking at brains with the eyes of a protistologist. (I also like axon initial segments) Forthcoming book: The Brain, in Theory. http://romainbrette.fr/
Seriously I am stunned by how so many people seem to have abandoned the very idea of democracy. For example, AI-automatized peer review might be bad for science, but it's coming anyway so we have to adapt. What happened to the idea that people, not companies or robots, should be in control?
The alignment problem is not between anthropomorphized AI and humans. It is between powerful profit-seeking organizations and the common good. Let's start worrying about real threats before we care about hypothetical threats.
(some thoughts here:
romainbrette.fr/on-the-exist...)
Here's another deep dive on 'What Is Life? Revisited' for Friction Philosophy.
Surely there's nothing more to be said about Schrödinger's famous book?
Think again!
Join us as we travel from quantum mechanics to genetics & molecular biology via statistical mechanics, thermodynamics, & cybernetics
Excellent summary.
In Greek mythology, Theseus managed to find his way out of the Minotaur’s labyrinth thanks to Ariadne, who gave him a thread he attached to the door. To escape the labyrinth, he just had to follow the thread back to the entrance. Out of the labyrinth, one could solve the path integration problem by tightening the thread, so that the thread takes the shape of the shortest path to the starting point, a straight line. Solving this problem involves no computation. Whatever Theseus’ position, the action that solves the problem is always the same: pulling on the thread. The procedure is neither computation nor information processing. Instead, it relies on interacting with the environment. In neuroscience and cognitive science, this is related to the concept of situated or embedded cognition. The interesting point about this example is that everything we have said earlier about the computational structure of behavior remains valid. It is still the case that the homing vector is obtained by iterating the operation x(t+dt)=x(t)+v(t)dt, and yet neither the brain nor the organism computes the homing vector. This is not just a question of boundary, i.e., of whether cognition occurs within the boundaries of the skull or is extended (Clark and Chalmers, 1998), because the thread does not implement the vector update operation either.
Finding one's way home can be solved by dead reckoning or by tightening a thread.
It follows that computation is not the only kind of problem-solving activity, even when the problem looks computational.
press.princeton.edu/books/paperb...
To build an electronic computer, stable states are constructed out of dynamical systems (flip-flop circuits), such that the dynamical nature of the underlying hardware can be entirely ignored: computation occurs as transitions between computational states, entirely shielded from the dynamics of electrons. Such shielding does not exist in brains. Thus, biological cognition cannot be reduced to elementary computations, supposedly implemented by neurons. Rather, computation is an elaborate form of cognition.
Computation is a particular kind of cognitive activity. It does not follow that cognition is entirely made of tiny computations (as cognitivism would make us believe).
press.princeton.edu/books/paperb...
Excited to share our new preprint exploring how Paramecium achieves diverse flow functions, i.e. feeding and swimming, simultaneously. This work was spearheaded by our ExM expert, PhD student Daphne Laan @daphnelaan.bsky.social :
www.biorxiv.org/content/10.6...
Great to see our paper on light-intensity dependent swimming patterns in #Chlamydomonas out now in Phys Rev Lett. as an Editors' suggestion! With a nice commentary by @philipcball.bsky.social.
Chlamy actively modulate the beat planes of their #cilia!
journals.aps.org/prl/abstract... #protistsonsky
nice!
Efficient coding theory postulates that neurons encode stimuli such as images in such a way as to transmit the maximum amount of information (Barlow, 1961; Olshausen and Field, 2004). This works by reducing redundancy, as in data compression. For example, in the Lempel-Ziv-Welch (LZW) algorithm, repeated patterns are assigned to shortcut symbols. In the same way, spikes are postulated to encode common patterns. This might sound like a reasonable principle, but the LZW algorithm is useful only because the table of correspondence between shortcut symbols and data patterns is also communicated, in addition to the compressed data. Without the table, one cannot decode the compressed data. Unfortunately, neurons do not communicate tables together with the encoded messages.
On the limitations of "efficient coding".
press.princeton.edu/books/paperb...
Yes, it's a circular explanation, exactly.
Well but the cell of that organism is supposed to be the product of the code, so it cannot be taken as a premise. The genomic code supposedly explains species differences, but you need the different species to already exist to express those differences.
So what’s the genome then? The genome is a transmissible constraint on development, which channels the growth and division of a cell. The outcome always depends on what cell there was in the first place, as well as on other conditions of development. 6/7
How do you know what enzymes there are? Simple, look at their genes, and what they code for. How do you know what they code for? Well…
So it’s a code, but only to the extent that the entire system from nucleotides to functional protein is invariant. But it’s not invariant across species. 5/7
What about the genetic code for proteins? Surely that’s the prototypical case of a code in biology. Simple, each nucleotide triplet stands for a particular amino acid. How do you know which one? Simple, look at which enzymes do the transcription (the aminoacyl tRNA synthetases). 4/7
The genome cannot represent the typical form of the species, since you need to know the typical form of the species before you can answer. It is circular. 3/7
Because to know what the genome codes for, you need to express it in a cell of the species that the code was supposed to specify in the first place. For example, if you put the genome of one species into a cell of another species, it will not develop into the typical form of either species. 2/7
The genome is not a code, a model or a representation of the organism or species. These are all variations of preformationism: the little person in the embryo. However you call it, the genomic code/model/representation is self-referential and therefore incoherent. 1/7
Reproduction always involves a cell lineage (here oocyte rather than spermatozoa).
It is of course true that not all of the organism influences the descendant (such as fingernails). But since no organism grows from a naked genome, part of the parent must also have some influence.
It's an important point but germ cells are also cells, and all biological reproduction is based on cell division; eg consider the dynamical system formed by the lineage of germ cells. Also as you point out, in many species development occurs initially in the host or sth made by the host (egg).
Writing a book worth reading *should* take time. It should take effort. The crafting of it and the thinking in it go hand in hand. And the rewards, for both the author and the readers, come from that effort. That the AI bros don't understand this is disturbing and revealing.
Thanks!
Imagine! I mean, imagine how hard it is for a quadratic equation to understand itself! Imagine how hard it is for that statement to have any meaning whatsoever!
Next challenge: find a journal where this might fit!
(Yes, I already got a rejection from biorxiv)
11/11
Philosophically, this replaces the substance-based view of reproduction (invariance by default, we explain change) with a process-based view (change by default, we explain stability), a better fit to living organisms, which are far-from-equilibrium organizations of processes.
10/11
What is the genome’s role here? It is not a representation, code or instructions, but a transmissible constraint on development. In the same way as an enzyme is a constraint: it doesn’t change but acts by favoring certain reactions. Which reactions actually happen depend on the initial state.
9/11
5) The reproducing sequence could converge to a cycle rather than a fixed point. Example: Medusozoa alternate between larva, polyp and medusa (e.g. jellyfish).
6) Speciation is a process by which basins of attraction cease overlapping.
8/11
The dynamical landscape of reproduction. The ball rolls down to a valley, and returns there after a perturbation.
4) Robustness of development is a consequence of convergence (the fixed point must be stable). Like a rolling ball ends up in a stable “homeostatic” position.
7/11
A Paramecium with a spine reproduces. The spine eventually disappears.
3) Perturbations may resolve over several generations. Example: sometimes Paramecium has a little spine because of a division accident. The spine is inherited and (sometimes) progressively disappears over a few divisions.
6/11