This thread aims to catch all 'paradigms of biological complexity' we may be missing. In the beginning of the twentieth century Lord Kelvin famously declared: "There is nothing new to be discovered in physics now, All that remains is more and more precise measurement." That was before relativity and quantum mechanics. We thought the human genome project would unlock the workings of our bodies save a few details. Lets not make the same mistake twice. Lets explore with maniacal curiosity until, truly, all that's left is refined measurement and engineering.
"Mantis shrimp, the psychedelic reef-dwellers that can wallop their prey with an astounding 200 pounds of force, have a large collection of unique qualities. One is an unusually large number of photoreceptors, the light-sensing proteins that contribute to color vision. Humans have three types of color receptors, birds and reptiles have four, and mantis shrimp have an astounding 12 different kinds."
Robustness, the maintenance of a character in the presence of genetic change, can help preserve adaptive traits but also may hinder evolvability, the ability to bring forth novel adaptations. We used genotype networks to analyze the binding site repertoires of 193 transcription factors from mice and yeast, providing empirical evidence that robustness and evolvability need not be conflicting properties. Network vertices represent binding sites where two sites are connected if they differ in a single nucleotide. We show that the binding sites of larger genotype networks are not only more robust, but the sequences adjacent to such networks can also bind more transcription factors, thus demonstrating that robustness can facilitate evolvability.
"It has been suggested that some biological processes are equivalent to computation, but quantitative evidence for that view is weak. Plants must solve the problem of adjusting stomatal apertures to allow sufficient CO2 uptake for photosynthesis while preventing excessive water loss. Under some conditions, stomatal apertures become synchronized into patches that exhibit richly complicated dynamics, similar to behaviors found in cellular automata that perform computational tasks. Using sequences of chlorophyll fluorescence images from leaves of Xanthium strumarium L. (cocklebur), we quantified spatial and temporal correlations in stomatal dynamics. Our values are statistically indistinguishable from those of the same correlations found in the dynamics of automata that compute. These results are consistent with the proposition that a plant solves its optimal gas exchange problem through an emergent, distributed computation performed by its leaves."
"The concentration/meditation technique used by this particular individual seems to evoke a controlled stress response. This response is characterized by sympathetic nervous system activation and subsequent catecholamine/cortisol release, which seems to attenuate the innate immune response."
Colbert Sesanker's insight:
Wim Hof demonstrates volitional control over his endocrine, nervous and immune system. To date, he is the only person to have demonstrated volitional control over his endocrine and immune system.
"Recent studies show that dendritic spines are dynamic structures. Their rapid creation, destruction and shape-changing are essential for short- and long-term plasticity at excitatory synapses on pyramidal neurons in the cerebral cortex. The onset of long-term potentiation, spine-volume growth and an increase in receptor trafficking are coincident, enabling a 'functional readout' of spine structure that links the age, size, strength and lifetime of a synapse. Spine dynamics are also implicated in long-term memory and cognition: intrinsic fluctuations in volume can explain synapse maintenance over long periods, and rapid, activity-triggered plasticity can relate directly to cognitive processes. Thus, spine dynamics are cellular phenomena with important implications for cognition and memory. Furthermore, impaired spine dynamics can cause psychiatric and neurodevelopmental disorders."
Max Tegmark: "We examine the hypothesis that consciousness can be understood as a state of matter, "perceptronium", with distinctive information processing abilities. We explore five basic principles that may distinguish conscious matter from other physical systems such as solids, liquids and gases: the information, integration, independence, dynamics and utility principles. If such principles can identify conscious entities, then they can help solve the quantum factorization problem: why do conscious observers like us perceive the particular Hilbert space factorization corresponding to classical space (rather than Fourier space, say), and more generally, why do we perceive the world around us as a dynamic hierarchy of objects that are strongly integrated and relatively independent? Tensor factorization of matrices is found to play a central role, and our technical results include a theorem about Hamiltonian separability (defined using Hilbert-Schmidt superoperators) being maximized in the energy eigenbasis. Our approach generalizes Giulio Tononi's integrated information framework for neural-network-based consciousness to arbitrary quantum systems, and we find interesting links to error-correcting codes, condensed matter criticality, and the Quantum Darwinism program, as well as an interesting connection between the emergence of consciousness and the emergence of time."
Colbert Sesanker's insight:
If you like philosophy of mind and equations then you must read this paper
While studies of aging are widely framed in terms of their demarcation of degenerative processes, the brain provides a unique opportunity to uncover the adaptive effects of getting older. Though intuitively reasonable, that life-experience and wisdom should reside somewhere in human cortex, these features have eluded neuroscientific explanation. The present study utilizes a “Bayesian Brain” framework to motivate an analysis of cortical circuit processing. From a Bayesian perspective, the brain represents a model of its environment and offers predictions about the world, while responding, through changing synaptic strengths to novel interactions and experiences. We hypothesized that these predictive and updating processes are modified as we age, representing an optimization of neuronal architecture. Using novel sensory stimuli we demonstrate that synaptic connections of older brains resist trial by trial learning to provide a robust model of their sensory environment. These older brains are capable of processing a wider range of sensory inputs – representing experienced generalists. We thus explain how, contrary to a singularly degenerative point-of-view, aging neurobiological effects may be understood, in sanguine terms, as adaptive and useful.
Moran RJ, Symmonds M, Dolan RJ, Friston KJ (2014) The Brain Ages Optimally to Model Its Environment: Evidence from Sensory Learning over the Adult Lifespan. PLoS Comput Biol 10(1): e1003422. http://dx.doi.org/10.1371/journal.pcbi.1003422
Congenital insensitivity to pain (CIP), also known as congenital analgesia, is one or more rare conditions in which a person cannot feel (and has never felt) physical pain. The conditions described here are separate from the HSAN group of disorders, which have more specific signs and etiology.
complete insensitivity of physical pain can be achieved by a knocking out the ion channel coded by the SCN9A gene. Excellent example of a single gene acquiring a very precise meaning, aka evolutionary semantics.
"Bruce Carlson and his colleagues from Washington University in St Louis, USA, explain that electric fish not only convey information about themselves in the structure of each electric pulse but also vary the duration of the interval between pulses to communicate their behavioural state, such as whether they are subordinate or dominant and how aggressive they are (p. 2365). All sensory information is encoded by neurons into patterns of electrical spikes. In the case of electric signal perception by mormyrids, information is encoded by specialised receptors known as knollenorgans into both spike timing differences between receptors and interspike intervals within receptors. Carlson and his colleagues also describe how two subfamilies of pulse-type African mormyrids differ in their ability to distinguish differences in the waveform of emitted electric signals and they explain that these perceptual differences are due to differences in midbrain structures, as well as differences in the distribution of the knollenorgan receptors on the fish's bodies. The authors conclude by saying, ‘The mormyrid electric communication pathway is a powerful model for integrating mechanistic studies of temporal coding with evolutionary studies of correlated differences in brain and behaviour to investigate neural mechanisms for processing temporal codes.’"
"More Formally. Let O(t) denote the state of some subjective observer O at time t. Let H(t) denote its history of previous actions & sensations & rewards until time t. O has some adaptive method for compressing H(t) or parts of it. We identify the subjective momentary simplicity or compressibility or regularity or beauty B(D,O(t)) of any data D (but not its interestingness or aesthetic / artistic value - see below) as the negative number of bits required to encode D, given the observer's current limited prior knowledge and limited compression method. We define the time-dependent subjective interestingness or novelty or surprise or aesthetic reward or aesthetic value or internal joy or fun I(D,O(t)) of data D for observer O at discrete time step t>0 by I(D,O(t))= B(D,O(t))-B(D,O(t-1)), the change or the first derivative of subjective simplicity or beauty: as the learning agent improves its compression algorithm, formerly apparently random data parts become subjectively more regular and beautiful, requiring fewer and fewer bits for their encoding. As long as this process is not over the data remains interesting, but eventually it becomes boring even if it is beautiful. At time t, let ri(t)=I(H(t),O(t)) denote the momentary fun or intrinsic reward for compression progress through discovery of a novel pattern somewhere in H(t), the history of actions and sensations until t. Let re(t)denote the current external reward if there is any, and r(t)=g(ri(t),re(t)) the total current reward, where g is a function weighing external vs intrinsic rewards, e.g.,g(a,b)=a+b. The agent's goal at time t0 is to maximize E[∑Tt=t0r(t)], where E is the expectation operator, and T is death."
Colbert Sesanker's insight:
This seems like the right direction to formalizing intrinsic motivation and fun. Maybe this formalism could be used to create artificial worlds that maximize fun and intrinsic drive.
"The latest example of the scientific hype machine is a paper that comes from Alexander Wissner-Gross, a research scientist and entrepreneur affiliated with Harvard and M.I.T. who, according to the bio on his Web site, has “authored 15 publications, been granted 19 issued, pending, and provisional patents, and founded, managed, and advised 5 technology companies, 1 of which has been acquired.”According to one report (by a well-respected science journalist), Wissner-Gross and his co-author, Cameron Freer, “have figured out a ‘law’ that enables inanimate objects to behave [in a way that] in effect allow[s] them to glimpse their own future. If they follow this law, they can show behavior reminiscent of some of the things humans do: for example, cooperating or using ‘tools’ to conduct a task.” A start-up called Entropicaaims to capitalize on the discovery; the futurist Web site io9 and the BBC have both gushed about it."
Colbert Sesanker's insight:
critical review of Alexander Wissner-Gross's Theory below
"In a recent edition of PLoS ONE, Lore Thalerfrom the University of Western Ontario, with Stephen Arnott and Melvyn Goodale, report on brain imaging research that tries to sort out how individuals who can echolocate – who have what one blind activist calls ‘flash sonar’ – accomplish this perception neurologically."
A review and update of a controversial 20-year-old theory of consciousness claims that consciousness derives from deeper level, finer scale activities inside brain neurons. The recent discovery of quantum vibrations in "microtubules" inside brain neurons corroborates this theory, according to review authors. They suggest that EEG rhythms (brain waves) also derive from deeper level microtubule vibrations, and that from a practical standpoint, treating brain microtubule vibrations could benefit a host of mental, neurological, and cognitive conditions.
Colbert Sesanker's insight:
I've been following ORCH-OR, by Penrose and Hameroff, since 2007. I personally find Tegmark's paper (Consciousness as a state of Matter) significantly more interesting as it lays out a conceptual framework rather than focusing on a single mechanism.
In its early days Orch-OR was destroyed by almost every scientist that reviewed it. To make matters worse there was a conflict of interest. They seemed to force the science to fit the role and interpretation they wanted consciousness to have. --But Roger Penrose is pretty clever and in "Shadows of the Mind (1994)" he was quick to point out a number of reasons why mircotubules could have unique properties. Recently, some of these properties have been explored, and possibly demonstrated (note that these results have not been widely reproduced):
It's a fun story to follow. Whether it leads to anything, I don't care. I like the battle, the respect for empiricism, self-correction, and even Hamerof's dangerous emotional attachment to the ideas. Microtubules have been demonstrated to be interesting. That alone is worth it.
This authored monograph introduces a genuinely theoretical approach to biology. Starting point is the investigation of empirical biological scaling including their variability, which is found in the literature, e.g. allometric relationships, fractals, etc. The book then analyzes two different aspects of biological time: first, a supplementary temporal dimension to accommodate proper biological rhythms; secondly, the concepts of protension and retention as a means of local organization of time in living organisms. Moreover, the book investigates the role of symmetry in biology, in view of its ubiquitous importance in physics. In relation with the notion of extended critical transitions, the book proposes that organisms and their evolution can be characterized by continued symmetry changes, which accounts for the irreducibility of their historicity and variability. The authors also introduce the concept of anti-entropy as a measure for the potential of variability, being equally understood as alterations in symmetry. By this, the book provides a mathematical account of Gould's analysis of phenotypic complexity with respect to biological evolution. The target audience primarily comprises researchers interested in new theoretical approaches to biology, from physical, biological or philosophical backgrounds, but the book may also be beneficial for graduate students who want to enter this field.
Owing to the complexity of neuronal circuits, precise mathematical descriptions of brain functions remain an elusive ambition. A more modest focus of many neuroscientists, central pattern generators, are more tractable neuronal circuits specialized to generate rhythmic movements, including locomotion. The relative simplicity and well-defined motor functions of these circuits provide an opportunity for uncovering fundamental principles of neuronal information processing. Here we present the culmination of mathematical analysis that captures the adaptive behaviors emerging from interactions between a central pattern generator, the body, and the physical environment during locomotion. The biologically realistic model describes the undulatory motions of swimming leeches with quantitative accuracy and, without further parameter tuning, predicts the sweeping changes in oscillation patterns of leeches undulating in air or swimming in high-viscosity fluid. The study demonstrates that central pattern generators are capable of adapting oscillations to the environment through sensory feedback, but without guidance from the brain.
Portia is a genus of jumping spider which feeds on other spiders ( araneophagic). They are remarkable for their intelligent hunting behaviour which suggests they are capable of learning and problem solving, traits normally attributed to much larger animals. Portias often hunt in ways that seem intelligent.
Mind of Plants : Documentary on The Intelligence of Plants . 2013 This documentary as well as the rest of these documentaries shown here relate to important ...
Colbert Sesanker's insight:
1. acacia trees increase tannin content to prevent overgazing. they also emit ethylene gas to communicate an overgrazed state to other trees. 2. some plants seem to need 'sleep'. If deprived, they die.
Courtship display of the Coastal peacock spider (Maratus speciosus). Hard to believe, but there is no footage of this species yet in any wildlife documentary...
Colbert Sesanker's insight:
spiders typically have poor eyesight, but jumping spiders have excellent vision (3-color + ultraviolet 360 degree) for their size. They are many variations of jumping spiders many of which display sophisticated and intelligent behaviors.