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[Challenge Topic] Benefit and Cost

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Posted at 2012-5-9 11:30:48 | All floors |Read mode

     For a biological system, it will suffer different kinds of environment conditions, such as  different concentration of nutrients, temperature. How to response to the uncertain environment? It seems that a biological system can ‘caculate’ the benefit and cost, and then make a decision to behave in whatever way.  The ability to 'caculate' may be the product of evolution, like gene redundancy, buffer mechanisms.
       So an interesting question is that, is there universal strategies guiding biological system to behave in an optimal way? which means high benefit and low cost.
     This is My poor view about this question, and I am looking forward your suggestions. More details are needed. Let's have a discuss!  

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Posted at 2012-5-9 14:48:40 | All floors
Edited by QX_Cai at 2012-5-9 14:50

'Trade off' is a common strategy in biological species. Maybe the most plausible explanation that applies to all the species is the 'trade off' behavior that bacteria, animals and other species will use the most efficient way to reproduce themselves in a given enviroment. Because this strategy may gaurantee their survival from competition through evolution.  In this case, a population needs to use less energy to produce higher reproduction rate. It has been tested on bacteria and it seems to work and make sense to us human and other species. However, I am not sure apart from this strategy, whether their exists other universal 'trade off' behavior.I think it is hardly available. After all, not all the species live in the exactly same environment. In each environment, they must have their specific fitting function. A better way to study this problem is to narrow down this topic, focus on specific species and functions, I think.

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Posted at 2012-5-9 17:48:14 | All floors
Reply Shiwenjia Add Thread


    I'm always curious about this question:  when cell adapt to certain environment, is its response "programed" or "calculated"?

"Programed" means that the cell "remembered" all situations that it usually confronts through evolution, and has a preset solution for each situation. It means fast response, yet it is like "死记硬背" so it can not respond properly to some new or man-made conditions.

"Calculated" means that there are some well-evolved circuits inside the cell, that integrate the environmental inputs, and output corresponding response. It means the cell "learned" the principles  of optimal response, and can cope with varieties of stress even it had never confronted it before.

The later one looks smarter. How ever, it seems that at least in the response of glucose, yeast take the first strategy. May be the first one is more efficient.

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Posted at 2012-5-9 19:45:22 | All floors
Edited by QX_Cai at 2012-5-9 20:01

Reply zhiyuanli Add Thread

I prefer a combination of these two. When receiving a signal, the first thing cells need to do is to judge whether they have met this signal before. As for a familiar one, cells will switch on its memory system and response to it with their experience. This way seems to be efficent as they don't need to spare their energy on 'thinking' or 'calculating'. However, if it is a strange signal, a fatal one for instance, which they have never met it before. They must learn to calculate it out how to defend themselves from it in order to survive.
The bacteria resistance is the best example. In most cases, they died from antibiotic. However, once they calculate how to resist this attack, they store this memory in their genome and pass it through generations. So next time they will never be sensitive to this antibiotic signal. Think about our human, we have learning and memory systems which are coupled. What is the learning and memory system in E. coli? How about destroy the leaning or memory system in bacteria to resolve the problem of antibiotic resistance? While I find these have nothing to do with the topic 'cost and benefit"...

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Posted at 2012-5-9 21:07:49 | All floors
It is unlikely for bacteria to "remember" or "calculating" everything because there are too much parameters. However, to persist during the history of evolution, they might evolve their own strategies by simplify there "benefit" and "cost". For example, there are various stress conditions which are inappropriate for proliferation, and dormancy seems to be a general way to survive. In such case, only thimbleful of the population will resuscitate. Interestingly, researches suggest that it is kind of a hedge off strategy. The behavior is not uniform in spite of identical genome and environment. Possibly there isn't a universal strategy or optimal way in life.

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Posted at 2012-5-9 21:14:42 | All floors
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    The main difficulty to define "trade off" or "calculation" is the complexity of a biological network. So a simple model organism or a clear pathway is needed to check whether there exists optimization. Alon's work on lactose pathway is a good example.

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Posted at 2012-5-14 17:33:17 | All floors
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   I agree. Bacteria evolved a lot of strategies to maximize their growth-rate in a changing environment. Among those strategies, some are "Programmed" and other are "Calculated". As far as I know (but I'm not sure they have exactly the same meaning of "programmed" and "Calculated" ) some theoretical work use the words "constructive" versus "responsive" to describe the two gene expression strategy. The former strategy represents a permanent cost but provides an immediate benefit, and they found that in some cases of environment states constitutive cells will benefit while in other cases the responsive ones will outgrowth. So it seems that the cost and benefit balance are constantly changing with the environment. Thus I think is weird to say that there is a fix pattern of cost and benefit theory.

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 Author| Posted at 2012-5-15 19:28:43 | All floors
Reply QX_Cai Add Thread
Yes, you are right. This trade-off behavior is the strategy for a biological system to survive, and different systems can do specific 'calculation' during these survival. However, my question is that whether these calculations behave in any underlying universal rules? Which means whether there are any rules regulating these calculations function.

   

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 Author| Posted at 2012-5-15 20:13:02 | All floors
Reply zhiyuanli Add Thread
Actually, I prefer the latter. In my opinion, the system should firstly be able to behave in the latter way and then the previous one. Because in the consideration of evolution, the latter way should emerge first.

   

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 Author| Posted at 2012-5-15 20:20:39 | All floors
Reply Fleo Add Thread

So, if we design a certain environment, can we predict the behavior of the system? If your answer is yes, maybe there are some underlying rules regulating this "benefit and cost" procedure.


   

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 Author| Posted at 2012-5-15 20:22:51 | All floors
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Yes, I agree with you, but it is a problem. Just like the defination of function, a good proposal is the key point.  

   

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 Author| Posted at 2012-5-15 20:25:35 | All floors
Reply juexiao Add Thread
Thank you for your suggestion, is there any reference about what you mentioned above?

   

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Posted at 2012-5-15 22:56:00 | All floors
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    Hi Wenjia, if you really want this one to be a topic, what's the specific goal you think we can realize in 4 days?
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 Author| Posted at 2012-5-16 09:07:36 | All floors
Reply zhiyuanli Add Thread
Yes,I know, Thanks for your suggestion. I will think about it, and that why I posted the question here. Because I do need a specific topic, here are only general ideas. I will try, and I hope there also can be more specific suggestion on this topic from the one who have the same interest with me.

   

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Posted at 2012-5-14 18:03:30 | All floors
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I have no idea about this... What do you mean by calculating rules? Biochemical reaction? Network structure? First, calculating is based on circuits and biochemical reactions. Second, until we come up with a universal function, we can hardly study on this trade off behavior. I mean we must first know what the bacteria trades off for or calculating for--it must be a specific function universally exists. A global statement is difficult to start with...  

   

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Posted at 2012-5-15 23:03:49 | All floors
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Yes.   1. Constitutive versus responsive gene expression strategies for growth in changing enviroment. Nico Geisel 2011
2. Stochastic gene expression in fluctuating enviroments. A van Oudenaarden et al 2004
3. Stochastic switching as a survival strategy in flunctuating enviroments. A van Oudenaarden et al 2008
4. Cost-benefit theory and optimal design of gene regulation functions. Uri Alon et al 2007

    The first one is most relevant to the concepts I mentioned.
    The fourth one is about a model of cost-benefit theory. And it is a revised model based on the previous work of Uri Alon which you have read in the class "系统生物学选讲"~
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