Control in a living cell

Discussions on topics related to biochemistry and molecular biology, functional genomics, etc.

Control in a living cell

Postby lateralsuz on March 30th, 2019, 12:14 pm 

I was first drawn to this site by some topics, which I can no longer find, that seemed to ask about the nature of control in a living cell. It was a issue that niggled at my mind during my studies, and which has never been explained.

Cells do not have brains within them. Nor do they seem to have extensive neural networks that could act as a pseudo-brain.

Cells can also exist in isolation, so they do not need to be controlled by outside influences. Yet they are regularly seen to adapt to changing circumstances in appropriate ways.

As was pointed out in the other posts, there are many cellular functions such as adapting internal structures during the reproductive cycle, (while expanding or contracting); or DNA repair; which seem to go far beyond the inevitability of a chemical reaction.

Is anyone aware of factors that could explain what is observed?
(Sorry if this is covered by the other topics - but I can't find them)
lateralsuz
Forum Neophyte
 
Posts: 11
Joined: 19 Dec 2018


Re: Control in a living cell

Postby SciameriKen on April 11th, 2019, 3:16 pm 

Hi Lateralsuz - I was not sure what you mean by your question? Could you clarify?
User avatar
SciameriKen
Forum Moderator
 
Posts: 1442
Joined: 30 Aug 2005
Location: Buffalo, NY


Re: Control in a living cell

Postby lateralsuz on May 13th, 2019, 10:06 pm 

Hi SciameriKen

I have been ill which is why I haven't been on the forum for a while.

DNA is a mechanism which seems to initiate the production of various polymers, (principally proteins, RNA etc).

This is believed to happen because the chemical components of DNA act as a code, as well as a template. In combination with various enzymes and other chemicals, different sections of the DNA code can be switched on or off at different times, in what is believed to be a relatively fixed sequence, in order to produce a living being. The development of that sequence is believed to be the result of trial and error by natural mechanisms over millions of years until a working version emerged.

As some books have pointed out, there is a difference between these 'structural' mechanisms / processes and those which 'react to the moment' - which cannot be pre-coded in the same way because they represent dynamic circumstances that require actions to resolve issues, not just construct things to a fixed template. There's a long list of these activities within individual cells.

By focussing on individual cells rather than an entire body we see the real difficulties with these matters when we try to explain such levels of control without a brain - just relying on chemical processes.

As was pointed out in the other posts, some of these processes are very involved because they do seem to 'investigate' problems before determining an appropriate solution out of many possible responses. Yet conceptually the most sophisticated chemical control mechanism we have thought of is the 'feedback loop' where concentrations of a chemical that get out of balance, can trigger a chemical-based response which regulates those concentration. That hardly seems to deal with these circumstances.

In terms of some cell processes, it has been suggested that codes are used to direct activity, and such chemical codes do seem to be observed, (say on vesicles), but a code that is used in this way suggests a level of purpose that goes beyond whether a chemical reaction occurs or not. Something has to deploy them and then respond them in different ways.

As the other posts tried to point out, we can imagine how a computer chip might regulate complex activity like this, but there is no known computer equivalent in a cell - so what is the latest thinking on how these effects are achieved?

Has there been any more progress in this research?
lateralsuz
Forum Neophyte
 
Posts: 11
Joined: 19 Dec 2018


Re: Control in a living cell

Postby edy420 on May 14th, 2019, 2:58 am 

Maybe not a computer chips equivelent, but most definitely machines.

User avatar
edy420
Active Member
 
Posts: 1330
Joined: 09 Jul 2010
Location: Fergusson st, Tokoroa, NZ


Re: Control in a living cell

Postby lateralsuz on May 18th, 2019, 11:35 pm 

I think you're right about the notion of machines in cells edy420.

Whether we consider motor proteins or ribosomes, there is a level of sophistication that goes beyond what we might expect from a chemical reaction - even with trial and error.

You went for the motor proteins (above) and how they transport cargo (vesicles) to very different but specific destinations around a cell - apparently reading and using a code. However in putting the destination code on a vesicle something must determine an end location and the code relevant to that destination. The motor proteins must also read the code and work out how to navigate the many criss-crossing pathways around the cell. How?

This goes way beyond the simple bumping of two chemicals that then react in an inevitable way.

What gives the control if there is only chemistry?

There are many other examples - and as cells can operate in isolation in a test tube, it can't be direction from a larger brain.
lateralsuz
Forum Neophyte
 
Posts: 11
Joined: 19 Dec 2018


Re: Control in a living cell

Postby TheVat on May 19th, 2019, 11:04 am 

User avatar
TheVat
Forum Administrator
 
Posts: 7264
Joined: 21 Jan 2014
Location: Black Hills


Re: Control in a living cell

Postby lateralsuz on May 31st, 2019, 7:28 pm 

Thank you for the link, but this article merely acknowledges the problem - it doesn't offer any solutions, or even pointers to solutions.

As was pointed out on the previous posts on this forum, (which I still can't find), various cell mechanisms (again - working within an isolated single cell within a 'test tube'), such as homologous re-combination, do genuinely seem to analyse a problem, search out relevant factors, and then determine and implement a complex solution out of a myriad of possible options.

This is obviously how we interpret what is happening in these chemical processes but there is every indication that problems are being worked out in a dynamic situation - which seems to be impossible on a fixed pre-coded basis, without a computer/pseudo-brain program, using just chemical reactions.

However, if we do begin to see possible solutions, could this start to give us the beginnings of an idea about the underlying nature of thought? Conversely, if thought is indeed based on quantum mechanical principles rather than 'pure chemistry' could we start to argue that it might be applicable at any level of life?

The one thing that the article didn't seem to mention were ideas based on quantum theory.
lateralsuz
Forum Neophyte
 
Posts: 11
Joined: 19 Dec 2018


Re: Control in a living cell

Postby Dave_C on June 3rd, 2019, 8:48 pm 

lateralsuz » May 31st, 2019, 6:28 pm wrote:However, if we do begin to see possible solutions, could this start to give us the beginnings of an idea about the underlying nature of thought? Conversely, if thought is indeed based on quantum mechanical principles rather than 'pure chemistry' could we start to argue that it might be applicable at any level of life?

Here’s an interesting article regarding single cellular “slime mold”. They seem to not only be capable of problem solving:

Traditionally, simple organisms without brains or neurons were thought to be capable of simple stimulus-response behavior at most. Research into the behavior of protozoa such as the slime mold Physarum polycephalum (especially the work of Toshiyuki Nakagaki at Hokkaido University in Japan) suggests that these seemingly simple organisms are capable of complex decision-making and problem-solving within their environments. Nakagaki and his colleagues have shown, for example, that slime molds are capable of solving maze problems and laying out distribution networks as efficient as ones designed by humans (in one famous result, slime molds recreated the Tokyo rail system).


They also appear to be capable of memory:
But Dussutour wanted to push further and see whether that habituating memory could be recalled in the long term. So she and her team put the blobs to sleep for a year by drying them up in a controlled manner. In March, they woke up the blobs — which found themselves surrounded by salt. The non-habituated slime molds died, perhaps from osmotic shock because they could not cope with how rapidly moisture leaked out of their cells. “We lost a lot of slime molds like that,” Dussutour said. “But habituated ones survived.” They also quickly started extending out across their salty surroundings to hunt for food.

Right away, I wonder what molecular mechanism is responsible for this 'memory'.

Some thoughts are provided on how slime mold might accomplish this but you’ll need to dig into the research papers for more:
Scientists have no idea what mechanism underpins this kind of cognition. Baluška thinks that a number of processes and molecules might be involved, and that they may vary among simple organisms. In the case of slime molds, their cytoskeleton may form smart, complex networks able to process sensory information. “They feed this information up to the nuclei,” he said.

Chris Reid and his colleague Simon Garnier, who heads the Swarm Lab at the New Jersey Institute of Technology, are working on the mechanism behind how a slime mold transfers information between all of its parts to act as a kind of collective that mimics the capabilities of a brain full of neurons. Each tiny part of the slime mold contracts and expands over the course of about one minute, but the contraction rate is linked to the quality of the local environment. Attractive stimuli cause faster pulsations, while negative stimuli cause the pulsations to slow. Each pulsing part also influences the pulsing frequency of its neighbors, not unlike the way the firing rates of linked neurons influence one another. Using computer vision techniques and experiments that might be likened to a slime mold version of an MRI brain scan, the researchers are examining how the slime mold uses this mechanism to transfer information around its giant unicellular body and make complex decisions between conflicting stimuli.

https://www.quantamagazine.org/slime-mo ... -20180709/

Regarding thought, if neuroscience had all the answers to how phenomenal consciousness (and thought) arise in a brain, there would be an uncontroversial theory. But there is no such thing. Chalmers pointed out the hard problem, but I’d suggest the even harder problem is for everyone to understand all the issues surrounding the ‘hard problem’… As Chalmers puts it, why don’t all the neuron interactions and chemical reactions simply occur WITHOUT any experience or feeling or whatever? Clearly, there’s no need to have experiences or feelings for chemical and neuron interactions to occur. In fact, the problem arises BECAUSE there’s an experience of something. This leads us to the problem of epiphenomenalism. But there are many more problems. The symbol grounding problem is a very serious issue we’ve not resolved. And counterfactual sensitivity seems to violate everything we know about physics. So the problem is not just the ‘hard problem’ of how experience arises in a brain, the really really hard problem IMHO is getting people to understand why it’s so hard. People simply don’t understand why it should be hard and what the logical problems are with the existing theory of computationalism.

If you’re interested, feel free to read and comment on a paper I’ve written (and intend to finish some day before I croak) which provides answers to these even harder problems and does seem to dovetail nicely into those mechanisms single cellular organisms might use (on a quantum scale) to do such things as learn and create memory. Long story short, I believe our experience must supervene on our DNA or something very much like it. In the nucleus of each neuron and each slime mold, the DNA reads and interprets the surroundings. Single cellular theories of mind are rare but have garnered attention from biologists and neuroscientists. There are a few out there. And I think they make sense. Neurons had to evolve somehow. If things such as thoughts and qualia were in fact phenomena that could be ‘discovered’ by cells/DNA rather than some sort of phenomenon that was ‘created’ (think of math being discovered or created) then we should expect cells to discover these phenomena long before brains develop.
viewtopic.php?f=39&t=34944

Per the above link:
But some mainstream biologists and neuroscientists are critical of the results. “Neuroscientists are objecting to the ‘devaluing’ of the specialness of the brain,” said Michael Levin, a biologist at Tufts University. “Brains are great, but we have to remember where they came from. Neurons evolved from nonneural cells, they did not magically appear.”
User avatar
Dave_C
Member
 
Posts: 331
Joined: 08 Jun 2014
Location: Allentown
TheVat liked this post


Re: Control in a living cell

Postby TheVat on June 3rd, 2019, 9:08 pm 

...in one famous result, slime molds recreated the Tokyo rail system).


Without unions, they will continue to be exploited. If the slime molds need an organizer, we have many slime balls in my country.

The cytoskeleton idea, for complex processor networks, with DNA as a central processor, is fascinating. And a bit Penrosian. Be funny if Penrose and Hamerof were onto something after all, after being poo-poohed for the last couple decades.
User avatar
TheVat
Forum Administrator
 
Posts: 7264
Joined: 21 Jan 2014
Location: Black Hills
sponge liked this post


Re: Control in a living cell

Postby lateralsuz on June 13th, 2019, 1:20 pm 

Be funny if Penrose and Hamerof were onto something after all, after being poo-poohed for the last couple decades.


There have been quite a few experiments on cognitive processes which have been shown to relate to quantum mechanical influences, (such as navigation in some birds), and there are other theories (like Pribram & Bohm's Holononmic Brain Theory) which might dove-tail into Penrose Hamerof as well. Following the links on the earlier posts I read Finipolscie's 2nd Book and found it to be an interesting summary of the options.

However, I still think the key lies in individual cells. Brains are multi-celled organs, whereas the apparent logic being applied within a single cell has to be self-contained and not part of a collaborative process.
lateralsuz
Forum Neophyte
 
Posts: 11
Joined: 19 Dec 2018


Re: Control in a living cell

Postby lateralsuz on June 13th, 2019, 1:45 pm 

Clearly, there’s no need to have experiences or feelings for chemical and neuron interactions to occur. In fact, the problem arises BECAUSE there’s an experience of something.


I totally agree.
It may be argued that an 'occurrence' generates a feedback loop, (ie. in some way adapting a chemical circumstance to an experience/occurrence), but when chemical processes seem to initiate an investigation of something, (as in the case of DNA repair), then that implies much more than a chemical response, because it is initiating something for the purpose of a recognised objective (eg. apparently working out how to fix a particular type of break while preserving and not distorting the complex code that DNA represents).

In the nucleus of each neuron and each slime mold, the DNA reads and interprets the surroundings.


I haven't read any theory about DNA which suggests that it actually thinks. It is a fixed code that essentially prescribes a relatively fixed sequence (especially when engaged in cellular reproduction). Individual genes can be triggered to generate new proteins and RNA - but that doesn't require logic. I haven't heard of any DNA-related process which indicates logic or experience.

I think Finipolscie made a valid point by distinguishing pre-determined processes (generally based around DNA), from those mechanisms which generate responses to dynamic circumstances, (which are therefore not structured and therefore less likely to be pre-coded).

Not sure about whether the slime mould experiments deal with individual cells or groups of cells.
lateralsuz
Forum Neophyte
 
Posts: 11
Joined: 19 Dec 2018


Re: Control in a living cell

Postby Dave_C on June 21st, 2019, 9:57 pm 

Paul Stamets likes his mushrooms and other fungi. He talks about the Tokyo train thing and has some film of the fungus that designed the underground (better than people could). The info about mushrooms and our evolution from them is cool too. All sorts of crazy gems in this piece. Take 11 minutes, it's worth it.
https://www.youtube.com/watch?v=Nxn2LlBJDl0
User avatar
Dave_C
Member
 
Posts: 331
Joined: 08 Jun 2014
Location: Allentown


Re: Control in a living cell

Postby Event Horizon on September 30th, 2019, 6:08 pm 

By far my favourite organelle is called the Golgi Body.
Its basically like a parcel delivery hub, packing proteins in lipids and sending them on to their destinations.
I do love cell biology. If intelligent design has but one prop, the workings of a cell would be a good shout!
User avatar
Event Horizon
Member
 
Posts: 418
Joined: 05 Mar 2018
Location: England somewhere.



Return to Biochemistry

Who is online

Users browsing this forum: No registered users and 5 guests