How to picture the cell?

Ryan_m_b

A quick piece of advice; when learning about a topic it is best to not making conclusions that contradict what is already known. It doesn't give the impression of a good attitude for learning and in the case of something relevant to evolution may get you branded as a creationist with an agenda.

Whilst many molecules such as proteins have multiple roles they generally have very specific active sites. With regards to assembly look into chaperone proteins.

Diderot

First of all, please excuse me for my bad English writing. It is not my intention to make a creationist point here. I'm trying to imagine how diffusion can contribute to order. All sorts of possibilities for chemical bonds seemed like an obvious threat to order to me, so I’m arguing for highly specified parts that can fall in their unique places in a specific sequence.
Unfortunately my knowledge of biology is also extremely poor so it’s no surprise that my statements contradict what is already known.
I would appreciate it very much if someone points out where I go wrong.

Darwin123

I am not sure what you are asking. The way you write English makes it appear as though you are pointing out something you think is wrong. I don't really know what issues to address.
One problem with the English is that you are excessively anthropomorphizing everything. For instance, you say that "all sorts of possibilities for chemical bonds seems like an obvious threat to order to me." Are the chemical bonds really threatening order? Is it obvious that the chemical bonds are threatening? Furthermore, you are "trying to imagine how diffusion can contribute to order." Did anyone say "diffusion is contributing to order"? You seem to think that diffusion is countering the threat of the possible chemical bonds.
Maybe you are asking what reduces the probability of most chemical bonds forming, and why some chemical bonds are likely to form anyway. With that:
In what are called living things, there are these large molecules with specific shapes. This simplified model is called "lock and key theory." The shape of the molecule makes certain chemical bonds unlikely to form after collision with other molecules. The shape of the molecule allows certain bonds to for after collision with other molecules.
The selectivity is 80% of the time determined just by the geometry (shape) of the molecule. There are also electrical and magnetic forces involved. Quantum mechanics is also involved. What is important is that some chemical reactions are more likely than others for certain molecules. I will dump all these different properties into the word "shape". The randomness of the collision is greatly reduced by the shape and properties of the molecules.
Now, maybe you want to know how the shape of the molecule got that way.
The shape of each molecule is copied with high fidelity from generation to generation. However, high fidelity doesn't mean infinite fidelity. Some cells in each generation have a molecule or two which is slightly different. These are called inherited variations. Most mutations increase the probability of the cell dying or not reproducing in a certain environment. Some inherited variations improve the probability of the cell dying out in that environment. The cells with the improvements eventually outnumber the ones that remained the same or decreased the chance of survival. This is natural selection.
Natural selection together with inherited variation supposedly determined the current shape of the molecules. Hypothetically, the molecules in the first generations of life did not have the specific shapes they had now. However, generation after generation of variation and selection has resulted in molecules of very specific shape.
Now, what in my description can't you imagine?
There was an article in the Washington Post on 20 September 2012 (Wedsday) in the Politics and Nation section. Some scientists kept a colony in a bacteria (E. coli) in bottle for 25 years. This corresponds to 50,000 generations of bacteria. The PI was Richard Lenski of Michigan State University. The full experiment is described in a recent issue of Nature. Alas, I don't have the original article in Nature.
Every 500 generations, a sample from the colony was frozen as a record of changes. Some challenge was given every day to the flask. Every day, part of the colony was transferred to a new sugar solution. However, there was no exotic manipulation of the bacteria.
The bacteria in the flask now have different molecules and different chemical reaction chains then their distant ancestors.
The current bacteria now can digest citrate, something their distant ancestors could not do. This took about 30,000 generations of bacteria. Some of these chemical reaction chains seem very specific and rather complex.
Yet at no time did any scientist "design" the molecules or reactions. The shape was not directly controlled except by providing that very general "challenge". There was no guidance to the shape. They just moved the bacteria into a new flask with fresh sugar every day. Yet, the new molecules have to have a really complex and specific shape to digest citrate. There are several other "unlikely" changes that have occurred over the 50,000 generations.
Now, what do you think happened in that flask over 25 years and 50,000 generations?
Please answer without anthropomorphizing anything. The E. coli may be insulted.

atyy

Yes, this is essentially correct. There are also various ways of preventing and undoing errors.
http://www.ncbi.nlm.nih.gov/books/NBK26850/
http://www.ncbi.nlm.nih.gov/books/NBK26829/
http://en.wikipedia.org/wiki/Kinetic_proofreading

Pythagorean

This, I think, is the problem statement (especially in the context of your quotes). In the first place, Legos are a bad example because they have very limited degrees of freedom for coupling (there's very few ways you can put Legos together). The building blocks of life, on the other hand, are rather "sticky" (they stick together in all kinds of different ways).

But more importantly, your statement opposes the view that these sticky pieces can, indeed, through random motion, form functional structures. You have to remember the age of Earth and how many chances it's had to perform random trials. Even with legos, if you jumble them around in a box enough times, there is a chance they will eventually make some simple structures (even a car, though the chance is very very low). In none of these examples would you be able to commit enough trials in your lifetime... but life exceeds many lifetimes; billions of years of trials. It's not really surprising that all these sticky components had a chance to stick together in complicated ways.

And remember that they didn't start out quite as complicated, it's been a very long period of emergence. There's a point at which early Earth chemistry becomes "life" through these small, random changes. Self-organized complexity.

Here's a very simple example:



notice that the system does require perturbation from time to time, but the perturbations for life would be found in the geophysics of the Earth (currents, heat vents, sun rising/setting, etc.). The only "order" is in the laws of physics that govern the particle interactions. All the other (macroscopic) "laws" are emergent and statistical in nature: they depend on the particular configuration of the ensemble of particles (including, in the above example, the red, blue, and bar magnets, the dish, and the water. For life, it could be the monomers, the heat vents, the lipid layer, and the ocean.)

gravenewworld

Have fun

http://www.sigmaaldrich.com/etc/medi...ays_poster.pdf

atyy

Could you also address that "random" may mean essentially deterministic? For example, can the second law of thermodynamics be violated? Theoretically yes, practically no. So it would not be wrong to say that there are emergent laws that are essentially deterministic.

Pythagorean

When I use random in this context, I mean in the noise sense. We can use a random distribution to model noise, but the noise could have easily come from several unrelated deterministic processes. The "random" terminology illustrates that aspect: that the sources are uncorrelated.

atyy

Hmmm, would "1/f noise" be noise then, since it would have correlations on all time scales?

Darwin123

No, not all chemical reactions, No, there doesn't have to be an "exact" amount of everything. Obviously, there is a great amount of variation in the amounts of different chemicals in the body.
No. Small mutations do not destroy the balance. Obviously, there is a lot of variation within a species and even in an individual. Obviously, small variations in chemistry don't shatter the "coincidental" cooperation of parts. Mind you, I don't know what you mean by coincidental.
Yes. I think so. I don't know what you mean by unsupported. However, there are a lot of people who have hypothesized that life is unsupported. As Job said, the foundations of the earth are not supported !-)
If you mean conscious interest, then no.
The statistics of "natural selection" can be said to support any balance there is, delicate or not.

Diderot

There is a language barrier here, due to my poor English of course, but I will try my utmost to be clear. I’m thinking of the car workshop where all the parts of a car are floating around (diffusion) and ‘miraculously’ fall into the right place and so build a car. Out of chaos comes order. To explain this ‘miracle’ I think we must assume that every piece has a right place to fall into. Maybe some parts have multiple right places, but If the driving wheel also fit on the bumper and on the headlights it will have a negative impact on the probability that the car can be assembled by diffusion. This is what I meant when I said: "all sorts of possibilities for chemical bonds seems like an obvious threat to order to me”. I understand that my choice for ‘threat’ is clumsy; maybe I should have said ‘problem’? By ‘order’ I mean the correct assembling of the car.
So to explain the ‘miracle’ of assembling by diffusion we need parts with specific shapes otherwise there is no 'falling into its right place'. This movie gives a very simple example of ‘falling into its right place’:

Every part is falling into its right place. Unfortunately the parts in the movie all have the same shape which seems to contradict my reasoning. But I don’t think it does.
“Lock and key theory”, I like that analogy. Thank you, I will study this.
I also think that there has to be a sequence in the assembling of the car. So highly specified part A must have just one right place B at moment C and highly specified part A’ must have just one right place B’ at moment C’ … etc.
The parts in the cell are like pieces of an constantly changing puzzle.
I do have a problem understanding it. For me this is not so simple.

Pythagorean

I typed up a big response, then realized it was kind of derailing, so I tried to pm you my response, but you don't have pm set up, but I guess the bottom line is that a lot of metaphysics come into play.

I'm also imaging a statespace bigger than just time; spatial correlation is just as important as temporal correlation. Sometimes 1/f dependency is happenstance too (as an over-simplified example, big waves travel further than little waves, so sampling ambient acoustics might yield pink noise, you'll be getting more global data in low frequencies and more local data in higher frequencies; once you adjust your system a posteriori for that bias, you have white noise again.)

atyy

How did they test for the distant ancestors not having this ability at a low level?

atyy

If whether a process is random or not by your definition (zero correlations) depends on a prior, then isn't it subjective? Consequently, couldn't the OP's use of "random" be justified under a different prior? To go back to the example of entropy - I don't think it is misleading to say that entropy always increases, although strictly speaking that seems to be only a probabilistic law. Similarly, we can predict using free energies what reactions will occur in cells, even though we are only using thermodynamics. Let me try to use your language: couldn't a non-flat free energy landscape be considered non-random, relative to a "flat" prior? In my language, I would say that macroscopic deterministic laws can emerge from random processes. So a clarification of the OP's question would not necessarily involve negation, but the statement of specific probability models and the relations between them, macroscopic and microscopic observables, error bounds, and regimes of validity.

atyy

I don't think one has to have a "creationist agenda" to ask such a question. The question is very similar to "Levinthal's paradox".

http://chemistry.caltech.edu/courses/ch110/lecture3.pdf

Ygggdrasil

Actually, this is demonstrably false. The chemical and physical principles underlying self-assembly in biological systems are well understood and many experiments have demonstrated the ability of highly ordered structures to arise from random (Brownian) motion. Of course, the formation of these ordered structures do not violate the second law of thermodynamics; their formation is driven by binding interactions that convert chemical potential energy into heat, thereby counteracting the entropy lost by ordering the individual components into an assembly.

Here's a paper (citaiton below) on this topic that you may be interested in taking a look at. The paper describes various chemical systems that mimic the self-assembly of the icosahedral poliovirus capsid. Of particular interest, the authors constructed a toy capsid that self assembles when shaken in a container:

"By appropriate placement of oriented magnets as analogs to the electrostatic complementarity, we produced a model that mimics the self-assembly of the [poliovirus] from twelve pentameric assembly intermediates. Placing 12 of these tiles in a container and shaking with the appropriate strength results in a stable closed shell, usually within 1–2 min. The key aspects of this model were the fivefold symmetric tiles, the appropriate curvature at the tile interfaces, and the geometric and magnetic complementarity of the interfaces. Although intellectually we knew that this type of self-organization occurs spontaneously, watching it happen from random shaking on the macroscopic scale was inspirational."

The videos of the process (freely available movie 1, and movie 2) are, as the authors say, inspirational. Movie 2 is especially impressive because it shows that two different capsids (colored red and green) with the same shapes but reversed magnet polarity can self-assemble in the presence of each other without the formation of misfolded states. So yes, you can put a collection of lego-like bricks in a tube, shake it up, and get a complex self-assembled structure.

You can access the full paper at the PNAS website for free by following the link below:
Olson, Hu, and Keinan. 2007. Chemical mimicry of viral capsid self-assembly. Proc. Natl. Acad. Sci. USA 104: 20731-20736. doi:10.1073/pnas.0709489104.


On the topic of "delicate balance" and homeostasis, there is a good amount of scientific literature that has explored the effect of stochastic noise in protein and mRNA levels on the regulation of biological processes. I'll have to look up some good papers later, but Jonathan Weissman at UCSF and Erin O'Shea, formerly at UCSF now at Harvard, are two scientists who have done some of the key studies in this area. There's even an example of how bacteria take advantage of stochastic noise in order to produce pheotypic variability in a population of genetically identical cells (http://www.ncbi.nlm.nih.gov/pubmed/18927393).

Pythagorean

Many things in science are subjective. We arbitrarily draw lines in a continuous spectrum. We can't prove a negative, but we'll take it for granted if we haven't proved its positive after several attempts.

The point is simply that there's not a master control system guiding each process. In the context of previous posts by the OP (some of which have been deleted) there seems to be an agenda for strong emergence (not particularly creationism). Perhaps it's all a big misunderstanding, but it's not getting cleared up in the month it's been shrinking in growing in size as posts are deleted and reworded.

What you seem to be proposing is weak emergence, which doesn't seem contradictory to my point. Whether you want to call consistent trends that emerge in the macroscopic world "laws" or not is not going to affect the science itself, it's just going to affect what aspects of the science you're emphasizing. So different research approaches are going to treat entropy differently. As long as we accept the map is not the territory, than we have to accept degeneracy between maps and territory. Some maps are going to describe different components differently. The strong emergence map doesn't tell you anything about the territory (except maybe hic sunt dracones).