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I've spent a great deal of time wondering why biological systems are so complex. Seeing this videos leads me to ponder this question yet again. I keep coming ba

by jostmey 13y ago

I've spent a great deal of time wondering why biological systems are so complex. Seeing this videos leads me to ponder this question yet again. I keep coming back to the same answer. Evolution as a process proceeds forward without regard for complexity. In other words, the outcome of an Evolutionary does not have to be simple - it just has to work. I fear that most biological systems are in many ways unnecessarily complicated, which makes research in Biology and Medicine even more difficult.

agumonkey 13y ago
Maybe that is 'simple' when solving the problem nature had, it's just that we're not used to this kind of problems.
- yeison 13y ago
  That's a really great way to look at it. Thanks for sharing your perspective.
- pointernil 13y ago
  That's really a very profound way to see it! Thanks. I'd add to that: there is even a chance (quite high btw) we are not yet seeing all the problems nature solves AND maybe we never will even though we are constantly and exponentially growing our understanding... always, forever, now.
- cristianpascu 13y ago
  Nature does not solve problems. Molecules bump into each others. There's no purpose in their doing so. There is not simple for nature and complex for us. If you want a scientific approach to complexity, you would not insert a term in the definition that reads as 'us', or 'nature', or frogs.
  - agumonkey 13y ago
    Alright, there is no inherent purpose (something I always say to others and here I am giving the opposite impression :) but if we agree that things 'are' because they sustain some abstract structure in some context then can't we allow saying 'to sustain' is a problem to solve ? and if the context is very diverse thus high in complexity. And as we lack information, the observed structure will elude our understanding, 'complex for us'. From my very limited point of view, I'd believe nature follow some sort of simplest path possible (~lagrangian) law, hence my 'simple for nature' expression. Feel free to correct me further.
    - cristianpascu 13y ago
      Living organisms are not structures. Not sure if that's what you say, but I have heard this many times, in the context of origin of life. Where life is seen as self-replicating structures. The complexity of a geometrical structure (like a cube, or a protein) is one thing. The complexity of a process that fulfills a function (engine of a car) is another thing. One is static, the other is dynamic. One just sits there. Like a pile of rocks. The other one takes an input and process it into an output, in a specified, repeatable manner. A pile of rocks, in a particular context, solves the problem of surviving the surrounding conditions. Is it the simplest solution? Who cares! DNA replication on the other hand? What did Mother Nature drink to come up with this problem and try to solve it?
      - agumonkey 13y ago
        That's why I added 'abstract' it's not fixed, things move underneath but the abstract properties remain. Funny about the rock thing, I never know what to make about them, I would need to add an 'adaptability' rule to my core ones. DNA replication did not emerge from the early organisms. Before replication, we could investigate about DNA or prototypical forms of DNA as forms of variable input transformation. This kind of meta-encoding (sorry programmer POV leaking) of input tranformation is probably not the first minimum but pressure + time pushed the versatility needs up (again programmer POV).
        cristianpascu 13y ago
        I'm a programmer too, but also a physicist, and it's also hard for me to read through explanations/narratives that use a lot of metaphorical language. And there's a lot of that in evolutionary narratives.
atmosx 13y ago
I believe the exact opposite: Biological systems are extremely optimized and add complexity only when needed. Of course, in order to proceed in a meaningful way this conversation we should first establish what exactly complexity and optimization means, in this context. So if you feel like it, please share a specific example.
- jostmey 13y ago
  The mere presence of Junk DNA represents a potential layer of unnecessary complexity. This makes the job of deciphering the function of each gene just a little harder. While there is much debate about how much of our own DNA is junk, there is little doubt that a considerable amount of it is just junk. There are also cases where molecular machinery in our cell is repuprosed to carry out novel tasks unrelated to its design. The first example that comes to mind are the voltage-gated potassium channels. These proteins are usually involved in the electrical signalling of the nervous system. Why the voltage-gated potassium channel Kv1.3 functions as part of the immune response in T-cells makes no sense to me. Yet this voltage-gate potassium channel is an indispensable part of the cascade of events underlying the immune response. Another example of a protein with numerous and possibly unrelated functions is p53. And then there is of course the example of the laryngeal nerve. This nerve makes an unnecessary loop down the neck and then back up to the larynx. This odd quirk is especially exaggerated in the giraffe. Why this is so makes no sense. The best explanation I have to such weird design quirks, which exaggerate the complexity of biological systems, is that Evolution as a process has no regard for complexity.
  - pixl97 13y ago
    Why the laryngeal nerve is the way it is makes much more sense if you look at is as a series of trillions and trillions of little tiny steps. At some point a very long time ago vertebrates had very different designs from the contemporaries. As they evolved from strange filter feeders in to jawed creatures, this nerve extended itself longer and longer as creatures with a neck came in to existence. The important thing to see here is the lengthening of this nerve didn't cause selection pressure against it. If any vertebrate animals did develop other, more efficient, nerve routing, it did not give them an advantage to survive unto this day. None of the things we are calling quirks were quirks far back in the past. They have been 'stretched' by billions of iterations. It would be complex, by all definitions of the term, if not impossible to put DNA and all the cellular functions in any semblance of order that would make sense to a person. If evolution has regards for anything, it is survival. No other metric, be it efficiency or complexity, matters unless you produce offspring that produce offspring.
alok-g 13y ago
This is what makes the concept of junk DNA [1] non-surprising [2]. Often complexity would come at a cost though, and evolution would automatically end up optimizing for it. Such costs may include energy costs, vulnerability to faults/diseases, etc. With such elaborate mechanisms for DNA wrapping, replication, etc., I wonder how much cost junk DNA brings to the system (vs. benefits in terms of fault-tolerance and evolution). [1] http://en.wikipedia.org/wiki/Junk_DNA#Junk_DNA http://en.wikipedia.org/wiki/Junk_DNA#Junk_DNA [2] I am not making any assertion here about the percentage of junk DNA in the human genome, and am unqualified to do so.
tokipin 13y ago
Well there's all sorts of issues. But what it essentially comes down to is that evolution works in tiny steps, not in great leaps. When "trying to achieve" goal X, adding a tiny bit of complexity is simply much more likely than a simplifying "refactoring". And then in terms of the biology itself, you will run into things that we might think of as "complications" but which are actually for the sake of redundancy/fault tolerance, etc. I remember watching a series of biology videos where a particular messaging pathway was explained. It had at least 5 or 6 proteins. But then the lecturer described that by having so many proteins in the chain, the messaging is exponential. So what initially might seem like a complex way of sending messages is actually an amplifier!
jballanc 13y ago
Evolution proceeds without regard for complexity, efficiency, or anything else for that matter, except survival. I think the most common misconception about evolution is that it is not a system of "best" but rather "just good enough". For example, do you like your lungs? They work pretty well, right? But how long can you hold your breath under water? Obviously cetaceans have much better lungs that humans, but that's because our lungs are just good enough for running around on a savannah. If we were forced to dive to incredible depths to search for our food, we'd need to evolve better lungs, as the cetaceans have done. Before the dolphins get to smug, though, they don't have the best lungs either. The title of best lungs goes to the birds. Whereas all other air breathing animals have bidirectional flow in their lungs, birds have evolved a system of continuous unidirectional flow. Turns out that bidirectional flow is not good enough at high altitudes with an extremely high metabolic rate. As for what makes Biology and Medicine difficult, I think the answer is: time. That is, aside from dealing with systems composed of more moving parts than physics or chemistry, biology is also less open to direct manipulation and experiments take, on average, much longer for the amount of information gained. Eventually, though, I don't doubt that we will understand biology as well as we understand the other two. At the moment we're in the "alchemy" stage of biological research. We have a sense that there are units of action and rules governing these units, but we don't know what those units are or how they interact. A rock you dig up from the ground is, also, a rather complex system difficult to understand until you have knowledge of chemicals, molecules, bonding, etc. We just need to figure out what the "atoms" of biology are.
cristianpascu 13y ago
Evolution DOES proceed with a lot of regard for complexity. Evolution is not a person. The processes by which the evolution is supposed to go about are very much complex. Complexity is something that can be clearly defined in terms of probabilities and hence measurable. If it's stated that these complex (made of {large number of} parts) molecules _work together_ with these others complex (also very large) molecules, than this all process, in order for it to fulfill a function, requires a set of very specific values for very specific parameters. This is measurable complexity. And if one says that in time evolution will solve a problem, you can make the liaison with the complexity of the process through the probability of its occurrence.

by jostmey 13y ago

agumonkey 13y ago

Maybe that is 'simple' when solving the problem nature had, it's just that we're not used to this kind of problems.

yeison 13y ago
That's a really great way to look at it. Thanks for sharing your perspective.
pointernil 13y ago
That's really a very profound way to see it! Thanks. I'd add to that: there is even a chance (quite high btw) we are not yet seeing all the problems nature solves AND maybe we never will even though we are constantly and exponentially growing our understanding... always, forever, now.
cristianpascu 13y ago
Nature does not solve problems. Molecules bump into each others. There's no purpose in their doing so. There is not simple for nature and complex for us. If you want a scientific approach to complexity, you would not insert a term in the definition that reads as 'us', or 'nature', or frogs.
- agumonkey 13y ago
  Alright, there is no inherent purpose (something I always say to others and here I am giving the opposite impression :) but if we agree that things 'are' because they sustain some abstract structure in some context then can't we allow saying 'to sustain' is a problem to solve ? and if the context is very diverse thus high in complexity. And as we lack information, the observed structure will elude our understanding, 'complex for us'. From my very limited point of view, I'd believe nature follow some sort of simplest path possible (~lagrangian) law, hence my 'simple for nature' expression. Feel free to correct me further.
  - cristianpascu 13y ago
    Living organisms are not structures. Not sure if that's what you say, but I have heard this many times, in the context of origin of life. Where life is seen as self-replicating structures. The complexity of a geometrical structure (like a cube, or a protein) is one thing. The complexity of a process that fulfills a function (engine of a car) is another thing. One is static, the other is dynamic. One just sits there. Like a pile of rocks. The other one takes an input and process it into an output, in a specified, repeatable manner. A pile of rocks, in a particular context, solves the problem of surviving the surrounding conditions. Is it the simplest solution? Who cares! DNA replication on the other hand? What did Mother Nature drink to come up with this problem and try to solve it?
    - agumonkey 13y ago
      That's why I added 'abstract' it's not fixed, things move underneath but the abstract properties remain. Funny about the rock thing, I never know what to make about them, I would need to add an 'adaptability' rule to my core ones. DNA replication did not emerge from the early organisms. Before replication, we could investigate about DNA or prototypical forms of DNA as forms of variable input transformation. This kind of meta-encoding (sorry programmer POV leaking) of input tranformation is probably not the first minimum but pressure + time pushed the versatility needs up (again programmer POV).
      - cristianpascu 13y ago
        I'm a programmer too, but also a physicist, and it's also hard for me to read through explanations/narratives that use a lot of metaphorical language. And there's a lot of that in evolutionary narratives.

atmosx 13y ago

I believe the exact opposite: Biological systems are extremely optimized and add complexity only when needed. Of course, in order to proceed in a meaningful way this conversation we should first establish what exactly complexity and optimization means, in this context. So if you feel like it, please share a specific example.

jostmey 13y ago
The mere presence of Junk DNA represents a potential layer of unnecessary complexity. This makes the job of deciphering the function of each gene just a little harder. While there is much debate about how much of our own DNA is junk, there is little doubt that a considerable amount of it is just junk. There are also cases where molecular machinery in our cell is repuprosed to carry out novel tasks unrelated to its design. The first example that comes to mind are the voltage-gated potassium channels. These proteins are usually involved in the electrical signalling of the nervous system. Why the voltage-gated potassium channel Kv1.3 functions as part of the immune response in T-cells makes no sense to me. Yet this voltage-gate potassium channel is an indispensable part of the cascade of events underlying the immune response. Another example of a protein with numerous and possibly unrelated functions is p53. And then there is of course the example of the laryngeal nerve. This nerve makes an unnecessary loop down the neck and then back up to the larynx. This odd quirk is especially exaggerated in the giraffe. Why this is so makes no sense. The best explanation I have to such weird design quirks, which exaggerate the complexity of biological systems, is that Evolution as a process has no regard for complexity.
- pixl97 13y ago
  Why the laryngeal nerve is the way it is makes much more sense if you look at is as a series of trillions and trillions of little tiny steps. At some point a very long time ago vertebrates had very different designs from the contemporaries. As they evolved from strange filter feeders in to jawed creatures, this nerve extended itself longer and longer as creatures with a neck came in to existence. The important thing to see here is the lengthening of this nerve didn't cause selection pressure against it. If any vertebrate animals did develop other, more efficient, nerve routing, it did not give them an advantage to survive unto this day. None of the things we are calling quirks were quirks far back in the past. They have been 'stretched' by billions of iterations. It would be complex, by all definitions of the term, if not impossible to put DNA and all the cellular functions in any semblance of order that would make sense to a person. If evolution has regards for anything, it is survival. No other metric, be it efficiency or complexity, matters unless you produce offspring that produce offspring.

alok-g 13y ago

This is what makes the concept of junk DNA [1] non-surprising [2]. Often complexity would come at a cost though, and evolution would automatically end up optimizing for it. Such costs may include energy costs, vulnerability to faults/diseases, etc. With such elaborate mechanisms for DNA wrapping, replication, etc., I wonder how much cost junk DNA brings to the system (vs. benefits in terms of fault-tolerance and evolution). [1] http://en.wikipedia.org/wiki/Junk_DNA#Junk_DNA http://en.wikipedia.org/wiki/Junk_DNA#Junk_DNA [2] I am not making any assertion here about the percentage of junk DNA in the human genome, and am unqualified to do so.

tokipin 13y ago

Well there's all sorts of issues. But what it essentially comes down to is that evolution works in tiny steps, not in great leaps. When "trying to achieve" goal X, adding a tiny bit of complexity is simply much more likely than a simplifying "refactoring". And then in terms of the biology itself, you will run into things that we might think of as "complications" but which are actually for the sake of redundancy/fault tolerance, etc. I remember watching a series of biology videos where a particular messaging pathway was explained. It had at least 5 or 6 proteins. But then the lecturer described that by having so many proteins in the chain, the messaging is exponential. So what initially might seem like a complex way of sending messages is actually an amplifier!

jballanc 13y ago

Evolution proceeds without regard for complexity, efficiency, or anything else for that matter, except survival. I think the most common misconception about evolution is that it is not a system of "best" but rather "just good enough". For example, do you like your lungs? They work pretty well, right? But how long can you hold your breath under water? Obviously cetaceans have much better lungs that humans, but that's because our lungs are just good enough for running around on a savannah. If we were forced to dive to incredible depths to search for our food, we'd need to evolve better lungs, as the cetaceans have done. Before the dolphins get to smug, though, they don't have the best lungs either. The title of best lungs goes to the birds. Whereas all other air breathing animals have bidirectional flow in their lungs, birds have evolved a system of continuous unidirectional flow. Turns out that bidirectional flow is not good enough at high altitudes with an extremely high metabolic rate. As for what makes Biology and Medicine difficult, I think the answer is: time. That is, aside from dealing with systems composed of more moving parts than physics or chemistry, biology is also less open to direct manipulation and experiments take, on average, much longer for the amount of information gained. Eventually, though, I don't doubt that we will understand biology as well as we understand the other two. At the moment we're in the "alchemy" stage of biological research. We have a sense that there are units of action and rules governing these units, but we don't know what those units are or how they interact. A rock you dig up from the ground is, also, a rather complex system difficult to understand until you have knowledge of chemicals, molecules, bonding, etc. We just need to figure out what the "atoms" of biology are.

cristianpascu 13y ago

Evolution DOES proceed with a lot of regard for complexity. Evolution is not a person. The processes by which the evolution is supposed to go about are very much complex. Complexity is something that can be clearly defined in terms of probabilities and hence measurable. If it's stated that these complex (made of {large number of} parts) molecules _work together_ with these others complex (also very large) molecules, than this all process, in order for it to fulfill a function, requires a set of very specific values for very specific parameters. This is measurable complexity. And if one says that in time evolution will solve a problem, you can make the liaison with the complexity of the process through the probability of its occurrence.