Category Archives: Biology

The Adaptive Cycle

As we all wonder how the current world order will be transformed by the Covid-19 pandemic, perhaps now would be a good time to read up on the Adaptive Cycle. Worried about societal and economic collapse, I was originally thinking about the notion of social cycles, but came across this more general notion of cycles within ecological systems. It is also applicable to insightful investigation of social institutions and organizations.

The Adaptive Cycle is usually shown as a figure-eight loop, with four main segments (Growth, Maturity, Release, and Renewal), inhabiting a space of two or three variables (Potential, Complexity, and Resilience):

  • Growth or Exploitation: (r)
  • Maturity or Conservation: (K)
  • Release or Collapse: (Ω)
  • Renewal or Reorganization: (α)

Thus these charts indicate a closed trajectory of a system’s state within a state space over time. This concept was originally applied to cycles within ecological systems, measuring certain attributes of systems in order to predict their ability to handle, recover, and adapt from significant disruptive changes in environment, species populations, genetic landscape, etc.

These cycles can form steps on chains of greater systems where an individual cycle is a quasi-stable element but the overall state can jump and grow to higher forms of complexity and potential, or indeed collapse and fall to lower forms if the resilience is weak. As well, the multiplicities of cycles can represent a range of spacial scales for systems that have smaller cycles nested within them, operating concurrently.

This greater notion of change within systems has been called Panarchy. In contrast to hierarchy or even anarchy, Panarchy is neither the top-down or bottom-up of the other two. Panarchy tries to describe how actual ecological and social systems can change and transform yet endure and return to similar states, across scales of space and time.

Further Reading:

View at

Images of the Adaptive Cycle:

Images of Panarchy:

Social Cycle Theory



The Genetic Code

There are many ways to show the genetic code, the map between triplets of nucleotides and the amino acids of proteins. Here is one that may be a bit awkward to understand, but other more standard ones are easily found.

 First, here are the codes for the four nucleotides:

  • U = Uracil
  • C = Cytosine
  • A = Adenine
  • G = Guanine

As well, let

  • $ = U or C
  • % = A or G
  • & = U or C or A
  • * = U or C or A or G

And so, here are the amino acids and their nucleotide codes

A = Ala = Alanine = GC*
C = Cys = Cysteine = UG$
D = Asp = Aspartic Acid = GA$
E = Glu = Glutamic Acid = GA%
F = Phe = Phenylalanine = UU$
G = Gly = Glycine = GG*
H = His = Histidine = CA$
I = Ile = Isoleucine = AU&
K = Lys = Lysine = AA%
L = Leu = Leucine = UU% + CU*
M = Met = Methionine = AUG
N = Asn = Asparagine = AA$
P = Pro = Proline = CC*
Q = Gln = Glutamine = CA%
R = Arg = Arginine = CG* + AG%
S = Ser = Serine = UC* + AG$
T = Thr = Threonine = AC*
V = Val = Valine = GU*
W = Typ = Tryptophan = UGG
Y = Tyr = Tyrosine = UA$
# = Stop = UA% + UGA

Note that some letters encode both nucleotides as well as amino acids, which might be confusing.

Further Reading:

[*10.146, *10.147]


A Crystal Structure of the Main Protease of COVID-19

One can gain knowledge from words, but wisdom only from things.

— George Wald, Harvard biochemist and 1967 Nobel Laureate

Many images of the coronavirus SARS-CoV-2 (a.k.a. 2019/nCoV a.k.a. COVID-19) are in the media, with the colorful spiky ball motif being the most frequent. Above is a representation of one of its proteins, its main protease, which allows the virus to process the proteins created after it splices its own RNA genetic material into your cells.

The larger three lobed spiky proteins from which these types of viruses gets the name “corona” are responsible for grabbing onto and opening up the surface of (in this case) lung cells, so that this smaller protein can perform its function within the cell. In more detailed images, you may have seen it as small pairs of spheres on the viral surface.

Several different crystal structures of  various proteins of COVID-19 have been solved and released recently, including this main protease and the spiky protein peplomers. Studies of these structures will hopefully lead scientists to discover inhibitors to their functions and thus treatments and preventive measures. Go science!

Unfortunately, these results will come much too late for many of us. Science could have also helped us with the initial defense against this deadly virus, but the powers that be deigned to consider the gravity of our plight. And even today many such leaders and spokespersons are ignoring important information and spreading misinformation.

Further Reading:




The Frauchiger-Renner Paradox

“The new experiment shows that, in a quantum world, two people can end up disagreeing about a seemingly irrefutable result, such as the outcome of a coin toss, suggesting something is amiss with the assumptions we make about quantum reality.”

— From the Quanta article by Anil Ananthaswamy

As above, so below.

As we face the deadly onslaught of electron-microscopy-sized agents, remember to wash your hands for twenty seconds, follow physical distancing rules of six feet or more, and please be safe.

Further Reading:



The Four Lobes of the Cerebral Cortex

The brain, the brain, the center of the chain…

— The Babysitter’s Club

The cerebral cortex is the outside part of the human brain’s cerebrum, with the cerebrum consisting of two hemispheres connected to each other by another structure called the corpus callosum. Each hemisphere’s cerebral cortex is traditionally divided into four main lobes, which loosely manage specific brain functions and specifically all voluntary actions of the body.

Because each side of the cerebral cortex has four lobes, I guess you could say that the cerebral cortex has eight lobes. Interestingly, each hemisphere is a bit functionally different in its operation, so perhaps those eight lobes are indeed distinct: left frontal lobe, right frontal lobe, left parietal lob, etc.

There has been research over the years about the functional differences in the hemispheres. Roger Sperry won a Nobel prize in 1981 for his pioneering work on split-brain research, although some of those findings are now known to be much more nuanced than before. Psychiatrist Iain McGilchrist has written a interesting sounding book on the differences between the two hemispheres, that is high on my to-read list!

  • Frontal Lobe: attention, planning, deciding, movement
  • Parietal Lobe: language, taste, touch, temperature
  • Temporal Lobe: hearing, emotion, smell, memory
  • Occipital Lobe: sight, vision

Further Reading:



Combogenesis and Evolution

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

— Charles Darwin, from The Origin of Species

Another important part of Tyler Volk’s theory of combogenesis that I didn’t mention previously is the role that evolution plays in the dynamical realms of biology and culture. He even illustrates evolution as a three-part braid where the strands are the processes of propagation, variation, and (natural) selection. He argues that these processes are fundamental to an abstract notion of meta-evolution that can be seen working to cause change in both of these different domains.

I don’t think that there is anything controversial in listing these three processes as being essential for biological evolution. Other diagrams and schemas available on-line also mention overproduction or fecundity, or having more off-spring than is strictly needed to continue the population, and heredity or heritability, or the ability to pass on special traits from parents to children.

Overproduction not only allows for greater survival chances for the organism but also gives genetic variation a better chance at producing something beneficial or interesting. This depends on what your chance of variation is, of course, but it seems that it is just a facet of propagation. Likewise, heredity seems like it is also included in propagation, as the continuance of the same or similar attributes to one’s descendants.

I previously proposed that four processes were essential to the workings of evolution: generation, variation, selection, and speciation. Generation is basically another word for propagation, although propagation might more clearly suggest having same or similar dependents, whereas generation just means having descendants. Overproduction can also be combined into either of these aspects if so desired. But I’ll say that (at least in my mind) generation and propagation are roughly the same.

But what about the process of speciation? Is it as fundamental to biological evolution as we see it working on our planet today as the other three processes? Speciation only means the formation of new and distinct species by evolutionary process. So generation, variation, and selection don’t really allow for the “endless forms most beautiful” in the famous quote of Darwin, or do they? Speciation also implies the heritability attribute of evolution, so maybe both generation and speciation subsume the aspect of propagation in most biologists or at least Volk’s mind.

But an important question is, is specification implied by the other three, like three mathematical axioms implying a theorem, or is it independent of them? If you don’t have speciation, don’t you essentially just have one type of organism? Or would you just have a continuum of variation within the population, without any barriers for reproduction between them? I’ll admit that these questions are too complicated for me to answer at this time.

Getting back to Volk and combogenesis, he and others have argued that cultural change is an evolutionary process as well. Another important question then is, if speciation is fundamental to evolution, then is the differentiation of cultures fundamental to the evolutionary process of culture? If so, culture may never be ‘one thing’, and we will always have different cultures competing for dominance.

The competition of different cultures isn’t necessarily a bad thing, as perhaps they can also be pluralistically cooperative. And perhaps having multiple cultures are best in case the society heads down an evolutionary dead-end, longevity-wise. But still, this might be the reason that we will always have multiple cultures that just can’t agree, can’t get along, and can’t really live together.

You might hope that by language and reason, different societies and ideologies can bridge gaps in understanding. You might hope that good-will and morality might win out, and destructive vitriol will be held in check. You might indeed hope. But research has shown that people are very resistant to changing their minds once they think they are right. I think it has been shown that new types of media (I’m looking at you, internet) has exacerbated this problem to the n-th degree.

There is the fourfold Means and Ends (of course there is) that includes cooperation and competition, as well as conflict and coalition. It is based on looking at the compatibility and incompatibility of different means and ends. Even if you can’t have full cooperation, perhaps you can have (mere) competition or coalition within cultures, instead of out-and-out conflict. Perhaps the key is to find those common goals, and even those common values that might allow our factious society to move forward. But many others have said these types of things.

Interestingly, there are also four types of geographic biological speciation, so looking at these might give us clues as to what might be occurring for our speciation in cultural evolution (there’s a nice diagram at the Wikipedia entry). Do the same processes that produce species in the biological world also produce societal divergences in the cultural world? Are these processes the origins of tribes, nations, and even wars? Are there analogues of allopatric, peripatetic, parapatric, and sympatric speciation when considering different cultures and their conflict and cooperation?

Further Reading:

Continue reading Combogenesis and Evolution

Combogenesis: a constructive, emergent cosmos

I just finished reading Tyler Volk’s “Quarks to Culture: how we came to be”. In this book Volk outlines an interesting model for what he calls combo-genesis, a “great chain of being” leading from basic physical law up through the highest organizational structures that we know of, human societies. He traces a path through human knowledge: physics, chemistry, biology, zoology, sociology, etc., and I am reminded of E. O. Wilson’s “Consilience: the unity of knowledge” that argued for some of the same things.

But Volk’s work has some good new ideas. He details twelve hierarchical levels, where each level is constructed on a “lower” previous level, and the new “higher” level has new things and different abilities than its predecessor. These levels range from the level of fundamental quanta (the quarks of the title), to geo-political states (the culture of the title).

  • QUA: fundamental quanta
  • PRO: nucleons, which are protons and neutrons
  • NCL: atomic nuclei
  • ATM: atoms
  • MOL: molecules
  • PCL: prokaryotic cells
  • ECL: eukaryotic cells
  • ANI: multicellular organisms, including animals
  • ASG: animal social groups
  • HUM: human tribal meta-groups
  • AGR: agro-villages
  • STA: geo-political states

These levels are within three dynamical realms, the first realm being of physical laws and then those realms of biological and cultural evolution. Each of these realms has a base level that has a capability for great constructive and emergent potential via an “Alpha-kit”. An alpha-kit has two facets, an element set and a cornucopia set, that operate like an alphabet and the myriad combinations that that alphabet can produce.

Dynamical realms:

  • Realm of physical laws: QUA -> MOL
  • Realm of biological evolution PCL -> ASG
  • Realm of cultural evolution HUM -> STA

Base levels and their Alpha-kits:

  • QUA, means for chemistry and molecules (atomic)
  • PCL, mechanisms for biology and its evolution (genetic)
  • HUM, faculty for culture and its evolution (linguistic)

As Volk’s model has each higher level based on or constructed from the previous lower one, I make the following suggestion utilizing my four-fold Structure-Function. The structures of each lower level serve as the parts of the next higher level, and the functions of each lower level serve as the actions of the next higher level. In this way a chain of actions and parts, structures and functions are built giving different entities and capabilities to different operational domains.

In the diagram shown, the sets of structures (S) and functions (F) of level i are used for the sets of parts (P) and actions (A) of level i+1, so S(i)=>P(i+1) and F(i)=>A(i+1). Not all structural information or functional abilities are necessarily accessible in the higher level of parts and actions, similar to the information and method hiding in object-oriented programming, and so reducing overall complexity. And as I have argued before, parts are combined to create the structures and actions are combined to create the functions of each level, so P(i+1)=>S(i+1) and A(i+1)=>F(i+1). In this way we have a bottom-up combo-genesis leading from quarks to culture.

Are we now entering another dynamical realm, perhaps based on some technological or computational alpha-kit? But, unfortunately we have to ask, will it take us forwards or backwards?

Further Reading:

Tyler Volk / Quarks to Culture: how we came to be

Tyler Volk and Robert Wright discuss:


Edward O. Wilson / Consilience: the unity of knowledge

[*11.98, *11.99]



Four New Synthetic Base Pairs Added to DNA

All life on earth uses DNA with four types of base molecules arranged in a “double helix” to encode information as sequences of Adenine-Thymine (A-T) and Cytosine-Guanine (C-G) pairs. Because A pairs only with T and C only pairs with G, DNA can be split into two halves and then each half may be completed so that two double helices with the same information can be obtained. Nature also uses the “genetic code” to translate the information in DNA into specific amino acids via its molecular machinery that assembles proteins in the correct sequence.

Now scientists have doubled the number of base pairs of DNA by adding four synthetic ones to the original four natural ones. Four new base molecules S (a Pseudo-T), B (a Pseudo-B), Z (a Pseudo-C), and P (a Pseudo-G) have been created so that S only pairs with B and Z pairs only with P. Now you have twice as many options as you had before and so this “hachimoji” (eight letter) DNA can have much greater information density. Plus if you re-engineer the molecular machinery to use these new bases you can have a brand new extended genetic code to build all sorts of synthetic proteins.

Further Reading:



The Brain with David Eagleman

sq_whowhatSpeaking of brains, “The Brain with David Eagleman” by neuroscientist and author David Eagleman is currently showing on PBS. The first episode “What is reality?” was pretty good, showing reasons why what we think of as an objective reality is really just a temporally delayed and conceptually constructed neurological fabrication.

The six episodes are titled:

  1. What is reality?
  2. What makes me?
  3. Who is in control?
  4. How do I decide?
  5. Why do I need you?
  6. Who will we be?

I wonder if the answers to these questions will pretty much be “the brain, the brain, the brain…”. Check your local listings and tune in to find out!


David Eagleman / The Brain: the story of you

David Eagleman / Incognito: the secret lives of the brain

David Eagleman / Sum: forty tales from the afterlife

David Eagleman / Why the Net Matters: six easy ways to avert the collapse of civilization


[*9.56, *9.57]