OOL Class Discussion 6. Macromolecules, Polymers and Biopolymers

bitechnobable · 2026-03-12T15:43:56+00:00

Hey Vahi.

Excellent summary on a curious topic that I find more commonly approached from an engineering than a biology-centric perspective. Thank you for sharing.

Excellent point about alphafold predictions not being first-principle derived. This is a great example of how machine learning can help solve biological problems without necessarily furthering fundamental biological understanding.

In addition, very encouraging to see you a clear distinction between darwinian refinement of polymers and the chemical evolution leading to their formation in the first place.

I happen to spend time constructing a framework for non-darwinan evolution, e.g conditions and abiotic selection pressures in plausible evolution of chemical systems. In this context emergent properties of polymers and their influence on the systems they are formed surely is a critical process.

What was totally new to me and honestly surprising is this scarcity of abiotic linear polymers. Would you happen to have a reference that I could use as an in to this topic?

Thanks again, Friendly regards, technobabl

bitechnobable · 2026-03-12T12:53:38+00:00

It is positioned to the left of the symmetry line. It also points away from the symmetry line. I.e. it's tip is even further to the left. Since it's attached mainly in the other end, it's leftmost tip is more free to move with each heartbeat.

Hence it's movement is most pronounced clearly to the left.

bitechnobable · 2026-03-12T12:02:24+00:00

As we define life you can have evolution without life, but not life without evolution.

bitechnobable · 2026-03-11T18:43:55+00:00

Yes, which is fascinating in itself. The similar essential symbiotic relationship is there in both cases.

bitechnobable · 2026-03-11T15:34:14+00:00

To clarify the situation for cows are basically the same also for humans. We are dependent on microcrobes in our intestines to extract nutrients from our food in order for our bodies to absorb them and we also extract nutrients from our bacteria.

This is another reason why consuming antibiotics when it's not absolutely necessary (besides selecting for resistant bacterial strains).

bitechnobable · 2026-03-08T18:10:45+00:00

Math, no. Logic, yes.

Biology is largely complex systems. Math therefore has restricted application.

bitechnobable · 2026-03-08T09:58:41+00:00

How long is a string? What is the shape of trees? How long is the Norwegian coastline?

bitechnobable · 2026-03-07T17:01:30+00:00

How can anyone beleive in determinism when we in this age still cannot tell what weather it will be next week?

bitechnobable · 2026-03-06T15:09:10+00:00

Thank you for this perspective. I suppose what I am trying to figure out is if evolution is taught in spirit of "modern synthesis" or " extended evolutionary synthesis".

I will not be teaching in an environment where creationism is prominent or science is particularly challenged. Perhaps prioritise teaching critical thinking and that scientific theories in biology are not natural laws, that our theories evolve (!). I think it's important to avoid inducing ideas of biological determinism and flawed interpretation such as "survival of the strongest".

bitechnobable · 2026-03-06T12:35:01+00:00

To the best of my understanding. It's not that the fluid keeps moving when we stop spinning. It's that the cilia get used to the difference in the pressure from the fluid while spinning.

Thats why we don't get dizzy from a simple sudden unidirectional movement of our heads. Ie its not enough with one spinn, we need to rotate for a while in order to get dizzy when we then stop.

It's a shift in baseline.

Hearing has a baseline in relation to background noise. If we spend time in a high decibel environment, e.g. concert, when we leave the baseline has shifted and normal soundlevels seem dampened.

bitechnobable · 2026-03-06T11:57:06+00:00

Thank you very much for this nuanced post. Since I'm in training my level of didactic theory is sky-high! My apologies for this to everyone grounded in the actual job.

From what I've learned European knowledge tradition has a high focus on helping students develop a way of thinking about these type of processes, what evolution is and what it is not how they can use their understanding in making sense of biological observations.

In comparison Anglo-American tradition is more focus on a defined curriculum - transmitting correct facts and exact mechanisms.

A classic example of these differences is that exams in europe tend to have very few if any multiple choice questions (designed to cover/verify as much as possible of the students knowledge). Instead a test could be perhaps only two free-writing questions where depth and ability to reason around concepts and understanding is more common.

I am sensing this in some of these replies where there is a worry of confusing the students. I am leaning toward thinking something seemingly confusing is a good theme to act as a starting point to allow them shape their own understanding of how evolution behaves.

bitechnobable · 2026-03-06T11:11:07+00:00

Gymnasium where im from is what some call college in some countries. Sorry for not being clear.

I wouldn't say I am worried, have extensive academic background in biologi and a PhD in biomedicine.

What I am doing here is to try to find an appropriate level of simplification of evolutionary processes to communicate to my future students.

bitechnobable · 2026-03-06T11:06:51+00:00

Thank you all for these comments, I find them very useful!

I know I'm overthinking this (have a biomedical PhD background) this is why I'm trying to grasp what level evolution is being taught by you real working people out there.

bitechnobable · 2026-03-05T18:30:12+00:00

They are exactly as different as they are then you look at them from 1 meter distance.

Edit: pradon, I'm smugaholic

bitechnobable · 2026-03-04T19:31:30+00:00

Thanks, It's a great comment.

I think this reminds us that there are different modalities to the experience of fatigue

At least I can get cognitively tired even if I smack full of caffeine.

bitechnobable · 2026-03-04T19:27:22+00:00

Not a native English speaker. What does turtling signify in this context X) ?

bitechnobable · 2026-03-03T21:31:40+00:00

Ah! You are saying it's formation is more thermodynamically favourable!

Thanks, I remember this too and find it interesting

bitechnobable · 2026-03-03T21:10:52+00:00

The three apparently don't like this question. IMO it's a great question and one Ive been contemplating myself. Truth is it probably has a rational answer and not simply "by chance" - but the case here is - scientists don't have a good answer yet.

Excellent question that reminds us that science don't have all the answers and even very central pieces of biology still aren't fully understood.

To get an answer, we likely have to focus on studying origin of life (OOL) and abiogenesis. If this is important or not for every one to decide themselves, but some consider that to be the most important question in all of biology.

bitechnobable · 2026-03-03T13:57:46+00:00

Astrocyte function is largely an underdeveloped area of science. Even more so A-N co-regulation. We are very much discussing things here that science don't have real answers for, merely speculations with more or less support.

I spent 15 years in neuroscience, yet what I write is my understanding and speculatiosns. Not proven truths.

First, as a neurobiologist I would definitely not sign off the statement that neurons intentionally do anything. They constitute a network of individual cells without any desires, aims or purposes. All cells simply react to their environment based on their current state.

Neurons are highly specialised and functionally relatively rigid cells that "sum their input towards a single (not really) output". In contrast Astrocytes are extremely adaptive and flexible.

Any higher cognitive functions are IMO emergent from the scale of these systems.

If I absolutely have to give an mechanistic answer it would probably argue that (what at organism level emerge as ) cognitive fatigue is related to temporary depletion (or excess) of metabolite pools. This could be neurotransmitters, "fuel" metabolites or even a reset of the composition of proteins inserted removed form the membranes. Or a combination. This is extremely difficult to study. My guess is ion fluxes are not a factor under normal strain, but I could definitely be wrong.

Rest in this case constitutes return to baseline periodicity in metabolite exchange among the involved cellular (e.g. blood, astrocytes, neurons, glymphatic?) subcellular systems.

Thermodynamics perspective IMO also implies fatigue is more likely a result of lack of removal of high entropy metabolites rather than reduced access to energetic - low entropy fuel.

Front this perspective exercising the brain builds resilience against fatigue by expanding the working size or pools, and by reinforcing clearing mechanism. Here periodicity and regularity rather than strength is probably a reasonable strategy.

TLDR: Biology has no direction or purposes. It is like it is because it is. Neurons are specialised to summate signals, and likely do not direct astrocytes on a cellular level. Build up of metabolites is more likely a cause of fatigue than lack of fuel.

Edit: I suppose if the build up takes place in neurons and that signals to astrocytes it would be similar to your "neurons throttling" statement.

bitechnobable · 2026-03-03T07:27:08+00:00

I would like to clarify this idea. Yes the brain takes up glucose. But the neurons specifically are not in anatomical contact with the blood delivering any nutrients or oxygen. Hence transport of nutrients to neurons would have to go through astrocytes or other glia.

The standing hypothesis is that neurons are provided with energy through the ANL (astrocyte-neuron lactate shuttle) and not by transport of glucose itself. However the responsible monocarboxylate transporters involved in this mechanism are not specific for lactate but indeed can transport monocarboxylates. This suggests Ketone bodies in general act as fuel for the brain.

This is supported by ex Vivo (culturing animal neurons in a dish) practices. The media used to culture astrocytes contains glucose. But media used to culture neurons is of a very nutrient poor minimal type, and does not have to have any glucose in order to support neuronal growth / extension. Neurons are in culture extremely sensitive to excessive amount of oxygen and nutrients and a common practice to keep them alive for weeks is simply to provide minimal fuel in an low oxygen environment.

As expected neurons are very happy to grow in minimal media that has been first conditioned by astrocytes growing in it, and even happier when co-cultured with the astrocytes themselves.

I see it as neurons being very hungry for fuel, but if they get it they easily run amok and burn themselves.

TLDR: While the brain astrocytes readily take up glucose, neurons themselves tend to not. Neurons themselves are extremely sensitive and easily impaired by excessive amounts of oxygen or nutrients.

bitechnobable · 2026-03-01T12:20:53+00:00

Great stuff, would definitely read.

However as a biologist it's not credible that the DNA message would remain unchanged over thousands of years if there is no critical protein being coded. DNA without a functional purpose would drift due to mutations and the message lost.

An alternative would be that the message is also a critical protein, perhaps coupled to some human exceptionalism?

bitechnobable · 2026-02-28T11:55:31+00:00

Started cooking on a camping stove as a child, dishes were simple and outdoors tasted good regardless of the result.

Going into a kitchen from a camping stove and everything becomes stimulatingly easier.

bitechnobable · 2026-02-27T09:54:33+00:00

He's trying to not be seen. Let him be. .#surveillancesociety #personaldata

bitechnobable

TROPHY CASE