Organisms and QM

[foodchain]

I am trying to define relationships between organisms and quantum mechanics, and of course I am having little to no luck overall. I got the idea watching a documentary on television about aquatic animals and such and of course the relationship these animals take to the ecology in terms of structure for instance. When I was thinking about this the thought crossed my mind that no matter where you go in the known universe, if its physical is most likely a product of matter and energy and so on, or physics in general.

 

My question basically is how much does the laws or theories of QM have in common with evolution of life? I mean a streamlined for swimming animal, like a dolphin for instance, to an octopus, or does the QM matter not deal so much directly with shape as maybe it might have to do with various functions such as sight for example. I am trying to denote how to look at life in a physics perspective, as its an interest of mine. Now I know its more easier and probably correct to say Newtonian physics applies a lot more then QM, but I don’t see how I can rule such out yet.

 

 

I posted this in this forum simply because I don’t know anything about what I am asking really.

[ajb]

If you are asking if quantum mechanics is important in the undersanding of biology, then I would say "yes".

 

It is obvious to me that if you really want to understand molecular processes and DNA etc. then quantum mechanics is needed.

 

However, as I do not work in that field I cannot say how much research has been done or how useful quantum physics has been in biology.

 

What I can say is that the average biology undrgrad student will have had no or very little training in quantum mechanics, quantum chemisty, atomic and molecular physics or anything like that. Which is strange if you want to understand molecular biology!

[foodchain]

If you are asking if quantum mechanics is important in the undersanding of biology, then I would say "yes".

 

It is obvious to me that if you really want to understand molecular processes and DNA etc. then quantum mechanics is needed.

 

However, as I do not work in that field I cannot say how much research has been done or how useful quantum physics has been in biology.

 

What I can say is that the average biology undrgrad student will have had no or very little training in quantum mechanics, quantum chemisty, atomic and molecular physics or anything like that. Which is strange if you want to understand molecular biology!

 

Well for instance the shape of a fish is one possibly best suited option for the environment, but its not as if the fish or organism in general made a conscious selection for that shape. One reason the shape could have come about in a more physical sense is energy conservation, or the most efficient way to be motile in a liquid. I mean when we develop say a torpedo or an underwater vessel, it takes on a shape familiar to a fish for instance, or we don’t produce a square and attempt to propel it through the water.

 

Its somewhat akin to birds, and of course the human version of such in planes, both of such having wings. The physical reality of such in terms of function simply exists, and in terms would naturally select based on fitness, which would also denote homeostasis, or even more simply being able to eat and contain energy enough to persist. I Don’t know of many modern animals in an environment that do not have an environmentally ergonomical design to some extent, as again in the water I don’t see a grand extent of square fish, or in the air with square birds.

 

Simply the interactions of matter and energy already exist, and its matter and energy taking a form in that which would maximize for instance entropy, or simply efficiency or a form that can persist or function. It basically allows for natural selection to be very natural, but to me it implies a very direct connection to basic physics to a certain extent.

 

Its not maybe a question of simply matter in bulk in some degree of organization, I mean you have that in anything, if the environment for instance is against selection for say a hurricane, well a hurricane does not occur, and its shape, geometry and behavior is denoted by interactions of matter and energy, which goes from the very small scale such as QM and above, I don’t only think this would apply to shape, but also the molecular basis of life.

[fredrik]

Some of my personal reflections...

 

My question basically is how much does the laws or theories of QM have in common with evolution of life? I mean a streamlined for swimming animal, like a dolphin for instance, to an octopus, or does the QM matter not deal so much directly with shape as maybe it might have to do with various functions such as sight for example. I am trying to denote how to look at life in a physics perspective, as its an interest of mine.

 

I think this is an excellent focus. Ajb says bio students might benefit from some QM studies, but I also think that physics students may also benefit from some biology studies.

 

During a typical physics education I think reductionism in absurdum is often the dominating way of reasoning.

 

So at first it's tempting to think like this

 

biology is explained by biochemsitry, and chemistry in general, which in turn is explained by physics.

 

So if you understand physics, you should understand it all. Well, now it seems that it's not quite that easy. As is well known it's always alot easier to take something given a part, than to put something that works together in a process where you need to invent the parts. It's similary far easier to "invent" a cause, when you know the history, than it is to actually PREDICT the future given a state of incompleteness.

 

So I think we still do not understand everything in depth to make the full connection here, but I think you took a first step by asking the question.

 

I do not think that ordinary or classical QM are fit to explain this connection. But perhaps once we understand the theory of QG _in depth_ more intereting insights to evolutionary mechanisms will appear. At least that's what I think.

 

/Fredrik

[swansont]

Well for instance the shape of a fish is one possibly best suited option for the environment, but its not as if the fish or organism in general made a conscious selection for that shape. One reason the shape could have come about in a more physical sense is energy conservation, or the most efficient way to be motile in a liquid. I mean when we develop say a torpedo or an underwater vessel, it takes on a shape familiar to a fish for instance, or we don’t produce a square and attempt to propel it through the water.

 

Its somewhat akin to birds, and of course the human version of such in planes, both of such having wings. The physical reality of such in terms of function simply exists, and in terms would naturally select based on fitness, which would also denote homeostasis, or even more simply being able to eat and contain energy enough to persist. I Don’t know of many modern animals in an environment that do not have an environmentally ergonomical design to some extent, as again in the water I don’t see a grand extent of square fish, or in the air with square birds.

 

Simply the interactions of matter and energy already exist, and its matter and energy taking a form in that which would maximize for instance entropy, or simply efficiency or a form that can persist or function. It basically allows for natural selection to be very natural, but to me it implies a very direct connection to basic physics to a certain extent.

 

Its not maybe a question of simply matter in bulk in some degree of organization, I mean you have that in anything, if the environment for instance is against selection for say a hurricane, well a hurricane does not occur, and its shape, geometry and behavior is denoted by interactions of matter and energy, which goes from the very small scale such as QM and above, I don’t only think this would apply to shape, but also the molecular basis of life.

 

 

You might take the approach of minimizing energy, but then you will run into a wall with sexual selection.

 

Evolution is about optimizing the passing along of genes, with a feedback loop being applied each reproduction cycle. The details of the mechanisms might deal with QM, but I think the overall problem is quite classical.

[foodchain]

You might take the approach of minimizing energy, but then you will run into a wall with sexual selection.

 

Evolution is about optimizing the passing along of genes, with a feedback loop being applied each reproduction cycle. The details of the mechanisms might deal with QM, but I think the overall problem is quite classical.

 

Actually I think a theory behind the separation of prokaryotes to eukaryotes is that sexual reproduction in eukaryotes is more optimal or efficient. I don’t know if this plays a role in the formation of the nuclear envelope or a more structured cell in general.

 

If you mean sexual selection across the board in regards to species, such as with humans, well a lot comes into play of course, a great deal of which I am sure I lack understanding of.

[goingtothedo]

I was invited onto this thread and having read my way through, here are my thoughts. Forgive me if I seem to be telling my grandmother to suck eggs, but I'm unsure of the background of the participants, so I'll labour some, perhaps obvious points.

 

I should first say that I am utterly unqualified to comment on QM. My knowledge in that area is close to nil. However, I have a fairly solid understanding in the area of natural and sexual selection and evolution.

 

If I understand the gist of the thread, and I'm not sure that I get all of it; there are two aspects to selection which, it seems to me are being confused.

 

1) The mechanism of natural selection is that in a population of individuals, there exists variety. It is this variety that makes individuals more or less fit to survive and reproduce in their given circumstances. This variety is essentially random.

 

The more fit indivuals will tend to survive and reproduce. The less fit are less likely to survive and/or reproduce. This is natural selection and it is ruthlessly non-random

 

Sexual selection was mentioned. In this case the capacity for a male to reproduce depends on his ability to win the females; either through appealing to their sense of aethetics (e.g peacocks, bowerbirds) or his ability to do battle with his other male rivals and come out victorious (e.g stags, elephant seals). In this case the winner takes all. It has been estimated that in these species, something ike 10% of the males get 90% of the matings. Again, highly non-random.

 

In neither of these cases is any of the "design" of the individual in any way a result of that individual's choice, or that of its parents. Inidividuals simply work with what nature provided them and sink or swim as a result.

 

2) The variety mentioned above bears the caveat that it ust be variety capable of being transmitted to the next generation. Losing a leg in early life does not imply that, should the individual succeed in producing offspring, those offspring would be missing a leg. However, it is taken as read that offspring will resemble parent and this is the information carried genetically in the cell nucleus in the DNA of the individuals.

 

Now, for number two, the information carried by the DNA, I daresay that QM have something to say. I'm no biochemist, but I'm sure that when trying to describe say, the folding of a protein such that it will react only with a given chemical entity, QM is probably a useful descriptive tool. I don't know; as I say, I'm unqualified to comment on this area but things are happening here at a scale where QM may well apply.

 

The variety expressed in the body and behaviour of an invidual (its phenotype) arises from variety in the details of the DNA of that individual from that of another.

 

However, this tells you nothing about the action of natural/sexual selection. It is merely describing the mechanisms at molecular level whereby variety is maintained and transmitted.

 

What is important is that the individual should be stronger/faster/more aggressive/more attractive to females/smarter etc than its rivals.

 

Look at it this way.

 

If my car breaks down, I'm not looking for an explanation in terms of particle physics and the action of electrons in the wiring or of a calculation of the speeds of individual molecules of organic and inorganic chemicals in the exhaust pipe or of quantum fluctuations in the energy flows in and out of the battery. All this may be true but that doesn't make it a useful level of explanation. I gain more understanding of my car's problems by knowing where to find the spark plugs.

 

So if discussing the shape of a fish for example, it may be true at one level that such and such a set of interactions at quantum level affect the action of hox genes in such a way as to produce an animal with a long streamlined shape, but that isn't actually telling you what you want to know. The action of a related set of hox genes has also produced the streamlined shape of dolphins or of plesiosaurs. The same could be said of the flying mechanism of birds, bats and pterosaurs. More understanding is gained for this purpose by considering how individuals living in similar environments and dealing with similar problems can be sculpted by natural selection in similar ways. e.g a long streamlined shape is advantageous in the open sea to catch prey or escape predators. Therefore holders of such a shape are more likely to survive and reproduce.

 

The detail of exactly how at a molecular/DNA level these similarities are acheived is all of course important and interesting stuff and we are learning more about this at a considerable rates of knots (I recommend "Many Forms Most Beautiful" as reading on this subject, but a thorough understanding of the mechanisms of natural selection and sexual selection will gain you more for the purpose of understanding how individuals successfully interact with their environment.

 

 

It is also worth noting that Darwin made a thoroughgoing case for natural and sexual selection a hundred year before we knew anything at all about the science of genetics.

[goingtothedo]

A point that I forgot to include in my last post.

 

One of the common dirving mechanisms in evolution is what has been described as the "arms race". e.g. the antelope develops longer legs and so becomes faster, therefore the lion that hunts it must become faster, therefore the gazelle must become faster, therefore the lion........

 

Such developments are widespread and hard/impossible to escape for the organisms and lineages involved in them. The consequences are varied. Such arms races produce anything from the breathtaking speed of the cheetah to the teeth of the sabre tooth cat. I mention predators particularly because the effect is very obvious and easy to explain in these cases.

 

However, it means that the individuals concerned are trapped in a one way race to specialisation. For the example of the sabre tooth cat; there have been a number of species of them, all extinct. In each case this specialisation arose, became more and more extreme and finally drove their possessors into extinction.

 

The relevance of this to the thread is that this kind of event occurs through a mechanism that any engineer (myslef for example) would recognize as positive feedback. Nothing mysterious and quantum mechanical about it.

 

Positive feedback is, almost without exception in engineering, a bad thing. And I only say "almost" because I'm sure that somewhere out there, there's got to be a good example of it, but I'm blowed if I can think what it is.

 

The point is that positive feedback drives a reaction out of control, and whether in engineering, physics, economics or biology, it can result in tears before bedtime.

 

Sexual selection is the other biological arena where it makes itself felt. If the only way for a male to have a female is have the biggest horns, the greatest prowess in battle, the gaudiest colours, the most gorgeously elaborate song, then the successful males with pass on these characterists and become more and more extreme in their behaviour/physique.

 

We end up with the peacock's tail (weighing down its owner), the fighting bull seal (killing their own pups in their zeal to attack their opponents), the antlers of the elk (fatally locking in battle with the opponent and dooming both).

 

So.... no need for quantum mechanics. Think simple.

[foodchain]

A point that I forgot to include in my last post.

 

Sorry to cut your post short, I just think adding it all would make my reply post probably use to much memory on a server somewhere.

 

I realize what you are saying, and to be honest I have no real clue as to what I am talking about, that’s why its posted in this particular section here on SFN.

 

I cant fully accept natural selection being 100% random. I think if it were completely random well then who knows what you would get. I know we don’t have a great deal of life outside of earth to compare this to, but we do have a good deal of life on earth to do this with. Natural selection to me basically implies survival of the fittest, where fitness matter is basically ecological. Now we have certain forms of life that persist, or continue to reproduce, survive and radiate. Through this and time we get change, but much of the form can be witnessed still. Such as a common housecat compared to say a lion or a tiger, or the idea of the liver, or blood even. So these structures make it, but why? I would suggest, that its because they can obtain the fitness required, which sounds simple but its they why its fit enough that’s not.

 

Such as my fish example. It has a form that expresses the correct fitness for survival in its ecology. Its not though as if this is something that cannot come about physically, in fact it seems to be as in more relation to human engineering in regards to vessels in the sea one of the most effective and or best forms. In this why is it the best? Uses energy the most efficiently? Allows for higher rates of speed? But a fish only does so much in regards to behavior, compared to say a octopus.

 

In short I cant see it being completely random, not as in choice was made, but that the physiochemical reality of whatever ecology never ceased to have various attributes to it, such as being a liquid in the oceans. The survival of the fittest or natural selection then would have to encompass such, and life to persist or to be the best it can could actually come to occupy such states, such as being aerodynamic.

[goingtothedo]

You are missing the point.

 

There are two parts to the process.

 

1) Variation is random

 

2) The selection process is highly non-random.

 

Natural selection is NOT random

[foodchain]

You are missing the point.

 

There are two parts to the process.

 

1) Variation is random

 

2) The selection process is highly non-random.

 

Natural selection is NOT random

 

Another aspect, simple but yet subtle would be the reaction of life to winter, or how about the dependence of life on the sun or the energy or food web. It does not directly play into my previous examples, but it yet applies a very basically physical connection to reality of course. I think I just hate how biology is separated from the physical sciences in America in many education settings, I never really understood that.

[goingtothedo]

There's no point bombarding me with examples. You have it wrong.

 

Get your head around the fact that natural selection is NOT random.

 

READ what has been posted, otherwise I am wasting my time on this thread.

[fredrik]

I think the interesting question connecting to the laws of physics, is that how can the selection mechanism be "given"? Given to whom? If it's not given, where does it come from? My thinking the selection mechanism itself is also evolving. Human sophistication in selection seems complex these days because many things take place also in the human brain. It seems to me development of technology and so on is the more important one these days, rather then evolution of the human genome itself?

 

It seems one subtle difference is that in biology it's not such hard problem to define _the population_, most people could imagine the senses of the population of a certain spieces on earth. But in physics in the various "landscape" problems, these populations are pretty fuzzy, and even ambigous, or subjective at minimum. They are not hands on options, they are only abstractions within a specific setting. And when you get into that I think more extreme care must be taken to an extent that is effectively unneccessary in picturing a population in biology.

 

I personally belive in and work on some evolutionary ideals merged with and information theoretic approch with bayesian reasoning. And I've personally gained alot of insight into reality from physics point of view, by spending a few years trying my best to understand yeast cells, and biology in general. It seems the everyday problems of a yeast cell is not that fundamentally different from mine.

 

I've always like to study in terms of "projects", because that makes it more "real". Taking a course is really different, because you are presented both the answers and the questions. But that's simply not how real problems appear in reality and it can be terribly boring. But set aside he optimum way to study, I have personally have alot of use of some brief studies in biochemistry, molecular biology and the physiology of cells. Of course I was reading all those books as someone coming from physics, so every line I read I was trying to make the connection to the bigger picture. And it's analogies at all lelves, that's my experience. The DNA stuff had lots of fascinating parallells to data compression and optimation problems and even learning models. Because DNA is basically a storage device. There are also many highly interesting problems in the complexity of regulation within the cells, with many different solutions, like coregulations of genes etc. All these I did as a three year hobby project, under the "cover name" of homebrewing. One thing just leads to the other, and trying to solve a problem originating from beer brewing, lead my back to physics.

 

/Fredrik

[fredrik]

> I realize what you are saying, and to be honest I have no real clue as to what I am talking about, that’s why its posted in this particular section here on SFN.

 

I think the way to go is to keep reflecting over this. Even though your own confidence in the question is low at this point, I think you are asking a question in the right direction, but gaining confidence in it takes time I think. If you want an opinion I think you should invest more thinking along the lines, or keep it in the back of your head during your journey.

 

/Fredrik

[lucaspa]

My question basically is how much does the laws or theories of QM have in common with evolution of life? I mean a streamlined for swimming animal, like a dolphin for instance, to an octopus, or does the QM matter not deal so much directly with shape as maybe it might have to do with various functions such as sight for example. I am trying to denote how to look at life in a physics perspective, as its an interest of mine. Now I know its more easier and probably correct to say Newtonian physics applies a lot more then QM, but I don’t see how I can rule such out yet.

 

1. You need to be careful about trying to reduce everything to physics. Yes, physics underlies all existence but there are processes operating that are not the direct result of physics.

 

2. QM comes into play when you consider the contingency of evolution. Kenneth Miller did this brilliantly in Chapter 6 of Finding Darwin's God; I will try to summarize.

 

Imagine hooking up your computer mouse to a radioactive substance. When the alpha or beta particle is emitted during decay, it is emitted in a particular direction. So hook up the mouse such that you when the decay particle goes in one direction, it is "up" for the mouse; or "left", or "right", or "down". Now the motion of your mouse makes events at the quantum level visible at the macro level.

 

Well, embryonic development in living organisms does the same thing. Many mutations are quantum events, but the process of converting the DNA to a living organism amplifies those changes so that they become visible in the traits of the animals.

 

SELECTION constrains this, because it will unerringly pick traits (designs) that work in particular environments. Let's take streamlining like in a dolphin, because that is a great example. There are only so many basic shapes for a predator moving thru water to have if it is to 1) see, grasp, and eat its prey and 2) move fast enough to catch it. Thus you have sharks, ichthyosaurs, and dolphins all having basically the same streamlined shape. BUT, the details of their shape (shape of dorsal fin, exact proportions, shape of teeth, exact shape of mouth, etc) are determined by QM and the unpredictability of QM events when mutating DNA. This unpredictability is "contingency".

 

I think the interesting question connecting to the laws of physics, is that how can the selection mechanism be "given"? Given to whom? If it's not given, where does it come from? My thinking the selection mechanism itself is also evolving. Human sophistication in selection seems complex these days because many things take place also in the human brain.

 

Let me throw something out there for you to consider: ALL design is a result of Darwinian (natural) selection. The only difference between human design and natural selection is that a lot of the process for humans occurs inside the human brain.

 

As Going pointed out, natural selection is a two step process:

1. Variation

2. Selection.

 

Selection comes about because there are more individuals born in a generation than the environment can support. Therefore there is competition among the individuals for the available resources. Some win the competition and some lose. Darwin called this the "Struggle for Existence".

 

So, individuals vary. When humans design, ideas vary. Then there is the environmment and the fact that not all individuals (or ideas) can survive. Those individuals with variations (designs) that do best in that particular environment survive -- they are "selected". As I write this I have an environment composed of 1) the idea I want to say, 2) grammar, 3) spelling. I make variations in my head of what I want to say and then select that variation that best fits the environment. I have corrected several typos because these variations did not fit the environment of correct spelling.

 

In human brains, the selecting is pretty much conscious. In nature, there is no consciousness at work (that we can detect) doing the selecting. It is analgous to a tournament and the winner survives and has more kids than the loser.

[foodchain]

Let me throw something out there for you to consider: ALL design is a result of Darwinian (natural) selection. The only difference between human design and natural selection is that a lot of the process for humans occurs inside the human brain.

 

As Going pointed out, natural selection is a two step process:

1. Variation

2. Selection.

 

Selection comes about because there are more individuals born in a generation than the environment can support. Therefore there is competition among the individuals for the available resources. Some win the competition and some lose. Darwin called this the "Struggle for Existence".

 

So, individuals vary. When humans design, ideas vary. Then there is the environmment and the fact that not all individuals (or ideas) can survive. Those individuals with variations (designs) that do best in that particular environment survive -- they are "selected". As I write this I have an environment composed of 1) the idea I want to say, 2) grammar, 3) spelling. I make variations in my head of what I want to say and then select that variation that best fits the environment. I have corrected several typos because these variations did not fit the environment of correct spelling.

 

In human brains, the selecting is pretty much conscious. In nature, there is no consciousness at work (that we can detect) doing the selecting. It is analgous to a tournament and the winner survives and has more kids than the loser.

 

In a previous post at the end you ended with a more basic tenement of QM, which is down on a QM level things seem not to make sense. Well in my regards at last they make sense enough to persist, as in you don’t have a hydrogen atom seemingly forming anti particles in you and exploding. Though that would make a serious defense mechanism and I hope ants never figure that one out:eek:

 

I should have not used QM in the title as much, as my lack of understanding overall probably produced that. More or less I guess anymore my thread is about the idea of natural selection being something that applies to more then just life, and that via evolution life can come to occupy these states which might be most fit for survival, such as being streamlined for swimming, and the reality that human engineering produced the same result. That such is just basic physics really that being universal laws and such don’t simply switch on and off over time life could come to occupy such states. Basically a quick analogy would to be looking at life sort of like a liquid attempting like a river to make it to the ocean. When the amount of liquid such as a river is attempting to do such in real life, such as river formations in the world, its not complete chance that dictates the path of the water, or such would carve through very dense material as easy as lighter material.

[lucaspa]

In a previous post at the end you ended with a more basic tenement of QM, which is down on a QM level things seem not to make sense.

 

Oh, I never said that! What I said was that some quantum events don't have a cause. I've also said that QM does not match with human common sense. Too bad for our common sense..

 

Quantum events are regular in groups. Shine any beam of photons on a mirror. ALWAYS 95% are reflected and 5% go thru. That's regular.

 

But, on the level of the individual photon, there is no "cause" that one photon is reflected and another goes thru. Take all the ones that went thru the mirror and shine them thru the same mirror and, once again, 95% are reflected and 5% go thru.

 

I should have not used QM in the title as much, as my lack of understanding overall probably produced that.

 

No, you did fine. I gave you the role of QM in evolution: contingency. Natural selection makes designs according to the demands of the non-QM parts of physics. QM and its unpredictability gives you the individual difference between species evolved to meet the same design requirements.

 

More or less I guess anymore my thread is about the idea of natural selection being something that applies to more then just life,

 

Natural selection is an algorithm. As such, it applies to ANY system where there is:

1. Variation between individuals.

2. Selection among individuals.

3. Inheritance from the selected individuals to the next "generation".

 

Within the human brain we do these steps: variation between ideas, selection of some idea, keeping the idea to the next "generation" and having new variations on it.

 

I don't know why you are trying to make this so complicated. Are you trying to introduce "direction" and "intelligence" to natural selection? Yeah, it seems so when you say:

 

Basically a quick analogy would to be looking at life sort of like a liquid attempting like a river to make it to the ocean. When the amount of liquid such as a river is attempting to do such in real life, such as river formations in the world, its not complete chance that dictates the path of the water, or such would carve through very dense material as easy as lighter material.

 

How many times do we have to say it: natural selection is NOT chance. The selection part is pure determinism.

 

As I said, the basic design of sharks, ichthyosaurs, and dolphins is dictated by the physics: there are only a very few efficient shapes for moving fast thru water AND having an optimal placement of the mouth to catch (and hold) the prey. So the body shape of all 3 is nearly identical. That's the physics. Natural selection in 3 lineages picked those individuals that had that design.

 

The details are due to QM and that you can have minor variations in the basic design -- vertical tailfin vs horizontal, different shapes of dorsal fin, etc -- and still have the same efficiency in the overal function of the design.

 

So, within the limits of the parameters, QM (in the form of "chance" mutations), provides the different details.

[goingtothedo]

 

 

 

Natural selection is an algorithm. As such, it applies to ANY system where there is:

1. Variation between individuals.

2. Selection among individuals.

3. Inheritance from the selected individuals to the next "generation".

 

Within the human brain we do these steps: variation between ideas, selection of some idea, keeping the idea to the next "generation" and having new variations on it.

 

 

 

Beautifully put.

[lucaspa]

Beautifully put.

 

Thank you. I should give credit to Daniel Dennett for writing that natural selection is an algorithm to get design in Darwin's Dangerous Idea. However, the sequence of natural selection is the human brain is mine.

[goingtothedo]

Is that right? I've got Darwin's Dangerous Idea on my bookshelf in the "not yet read section". must get around to it.

[lucaspa]

Is that right? I've got Darwin's Dangerous Idea on my bookshelf in the "not yet read section". must get around to it.

 

Yes, it's in the first couple of chapters. There's a lot about Dennett's book I don't like, particularly at the end. But his discussion that natural selection is an algorithm to get design is superb! It makes evolution and natural selection much more understandable, both as science and in the relation of Darwinian evolution to religion. Darwin discovered an unintelligent process to give the designs in plants and animals, thus negating the Argument from Design as a "proof" of deity. Didn't negate deity, but negated that particular argument as a "proof".

[foodchain]

Oh, I never said that! What I said was that some quantum events don't have a cause. I've also said that QM does not match with human common sense. Too bad for our common sense..

 

Quantum events are regular in groups. Shine any beam of photons on a mirror. ALWAYS 95% are reflected and 5% go thru. That's regular.

 

But, on the level of the individual photon, there is no "cause" that one photon is reflected and another goes thru. Take all the ones that went thru the mirror and shine them thru the same mirror and, once again, 95% are reflected and 5% go thru.

 

 

 

No, you did fine. I gave you the role of QM in evolution: contingency. Natural selection makes designs according to the demands of the non-QM parts of physics. QM and its unpredictability gives you the individual difference between species evolved to meet the same design requirements.

 

 

 

Natural selection is an algorithm. As such, it applies to ANY system where there is:

1. Variation between individuals.

2. Selection among individuals.

3. Inheritance from the selected individuals to the next "generation".

 

Within the human brain we do these steps: variation between ideas, selection of some idea, keeping the idea to the next "generation" and having new variations on it.

 

I don't know why you are trying to make this so complicated. Are you trying to introduce "direction" and "intelligence" to natural selection? Yeah, it seems so when you say:

 

 

 

How many times do we have to say it: natural selection is NOT chance. The selection part is pure determinism.

 

As I said, the basic design of sharks, ichthyosaurs, and dolphins is dictated by the physics: there are only a very few efficient shapes for moving fast thru water AND having an optimal placement of the mouth to catch (and hold) the prey. So the body shape of all 3 is nearly identical. That's the physics. Natural selection in 3 lineages picked those individuals that had that design.

 

The details are due to QM and that you can have minor variations in the basic design -- vertical tailfin vs horizontal, different shapes of dorsal fin, etc -- and still have the same efficiency in the overal function of the design.

 

So, within the limits of the parameters, QM (in the form of "chance" mutations), provides the different details.

 

I am confused as to 100% random. When I think of it such basically implies anything at any giving point. If the universe were to be 100% random all you would have would be something humans would call total chaos. For instance when I flipped a coin, in 100% randomness I doubt to get a coin back if I get anything back at all, I know it sounds rather extreme but to be utterly random applies that to me. Evolution has parameters, physical ones. I think this is why we only share a small percentage different genetically with our closet living ancestors. Then one has to look at time, I mean the T plays a big role in this for one simple reason, it takes so darn long for evolution to occur.

 

If everything really is just energy, that managed to break symmetry if it was at some point all just one thing, like a singularity, which much debate is put into, that also qualifies for us. So basically what you have then is energy evolving. From quarks to cosmopolitan cities managed by mostly hairless apes.

 

Ways to study this would simply be the conservation of energy, I mean how easy does a system encapsulate more energy into a form and how? I tried to go from a conservation of energy standpoint because to me a makes the most sense to start an idea from, and then maybe a hypothesis at some point. In life, if an animal cant get enough energy, typically from food, well it dies. So then is life "over engineered" in this aspect, or typically right at the cusp? What is the visibility of change to an organism in regards to evolution? Mutation would have it as none really, but the mutations that make it of course are not wholly random, maybe mostly but not entirely, I mean a penguin would suggest at least not totally.

[lucaspa]

I am confused as to 100% random. When I think of it such basically implies anything at any giving point. If the universe were to be 100% random all you would have would be something humans would call total chaos.

 

"100% random" is a strawman invented by creationists. No scientist says the universe is "100% random" or "due solely to chance".

 

In natural selection, "random" means only with respect to the needs of the individual or population. IOW, in a climate getting colder, just as many deer with shorter fur will be born as deer with longer fur.

 

In terms of where they happen on the genome, mutations are not random. There are "hot" spots that are more prone to mutation. There are types of mutations that are more likely.

 

But, for the effects on the phenotype in a given environment, variations are "random".

 

For instance when I flipped a coin, in 100% randomness I doubt to get a coin back if I get anything back at all, I know it sounds rather extreme but to be utterly random applies that to me.

 

In a coin flip, randomness means that, in a large number of flips, you will get an equal number of "heads" and "tails".

 

Evolution has parameters, physical ones. I think this is why we only share a small percentage different genetically with our closet living ancestors.

 

No. Evolution is gradual and "descent with modification". The reason we are only slightly genetically different from our closest relatives is that the "modification" is gradual and thus is only minor.

 

Then one has to look at time, I mean the T plays a big role in this for one simple reason, it takes so darn long for evolution to occur.

 

Sigh. Depends on what you are talking about. Evolution does take generations to occur, but for species with short generation times, you can get quite a bit of evolution in a few years. In one of my favorite experiments with Drosophila, they tested speciation by putting the flies in different environments for 5 years. That's 2500 generations for them (a generation per week). At the end they had new species and the new species were 3% different in their genes. Chimps and humans are less than 1% different. Of course, 2500 human generations would be 50,000 years.

 

It is also dependent on how severe the selection pressure is. The more severe, the faster natural selection will change a population. The less severe, the more generations it will take.

 

If everything really is just energy, that managed to break symmetry if it was at some point all just one thing, like a singularity, which much debate is put into, that also qualifies for us. So basically what you have then is energy evolving. From quarks to cosmopolitan cities managed by mostly hairless apes.

 

1. Be careful of reduction. No, you can't "reduce" evolution to energy. Any more than you can reduce evolution to "changes in allele frequencies".

 

2. Evolution only applies to populations. The evolution we are talking about is not the new general definition of "evolution" which is, essentially, "change over time". You need to be careful which type of evolution you are talking about and not mistakenly flip back and forth. Biological evolution is not the same as stellar "evolution" or cosmic "evolution". Energy itself does NOT "evolve". It changes form.

 

Ways to study this would simply be the conservation of energy, I mean how easy does a system encapsulate more energy into a form and how?

 

This approach is futile. Conservation of energy says that matter and energy are neither created nor destroyed, but change form. It doesn't tell you anything important about evolution.

 

Yes, you can track how living animals use energy. Been done. After all, we have studied photosynthesis, glycolysis, and oxidative phosphorylation. All "encapsulate energy".

 

What is the visibility of change to an organism in regards to evolution? Mutation would have it as none really, but the mutations that make it of course are not wholly random, maybe mostly but not entirely, I mean a penguin would suggest at least not totally.

 

1. Change is VERY visible to natural selection. ANY change that is selectively advantageous or disadvantageous is subject to natural selection: no matter how small. The equations of population genetics, derived from Mendelian genetics, are crystal clear on this.

 

2. By "mutations that make it", do you mean the "advantageous" mutations? Yes, they are random. They "make it" because selection is not random. Yes, even today penguins are born with less adaptation to living in the water than others. Those with less adaptation are eliminated by natural selection and those with adaptations are selected for. You seem to have forgotten all about selection.

[foodchain]

TO date in this thread I don’t think I have ever stated natural selection is 100% random, to be honest I don’t even know why its a subject at hand, I am talking about "possible" selection mechanisms in a very hypothetical sense.

 

Now obviously not every mutation makes it in life, and the ones that do make it, I mean specifically can such be mapped out as to the why part? I mean you can say natural selection, boom its a sealed deal. I don’t doubt the natural selection part, its just for every specie and I would think even down on the more fine scale of populations such as individuals, its not as a black and white as some math formation would have it, I mean if that were true, well I guess we would just know the future evolution possible of any species on any giving environment on the face of the planet and phylogeny should be so easy to solve taken into every possible aspect of it such as an organisms relationship to its environment. Not that you cant do math, more so in context of population, but for a giving mutation, what if a substitution reaction is involved in it, I mean for every parameter, it just seems a little bit to large for some nifty equation is all, or at least I have not noticed any that can be called anything more then generalities, not that such is bad its just the scope of it all, evolution that is I think is still not fully solved to say the least, or I don’t think many people would be becoming biology majors, or that research in the field would be as active.

 

One of my favorite papers on evolution is evolution induced on microbes in a lab. Each time they would run the cycle with the same amount in regards to population, or at least as close as possible, and overtime with the same variables that induced change, and each time they ran it they got a different result, different results in all different kinds of ways even.

 

Now if you want to keep telling me that I am wrong about everything, that’s fine, but I mean it really makes coming to this thread to post a reply pretty bland and pointless. I mean look at the title of the thread, and what its posted in. Its not as if I am trying to tell everyone this is the way it is, or at least that’s never the way I held it to be. I mean you are not saying anything to me that’s a revelation to be honest, I am trying to be hypothetical here, that’s my main drive for making the thread, to discuss little more then science fiction because it cant be called anything more then such currently.

 

As a side point, its not a thread on reduction. Biophysics is an existing field like biochemistry, but the chemistry alone cant detail how an eagle flies, or what weather they like to fly in. Again its on hypothetical. I don’t see however how a physical system can exist outside of physical laws, so would that be to much reduction?

[lucaspa]

TO date in this thread I don’t think I have ever stated natural selection is 100% random, to be honest I don’t even know why its a subject at hand, I am talking about "possible" selection mechanisms in a very hypothetical sense.

 

You keep raising 100% random as the standard thought but are doubting it. From your post 7-01-07

I cant fully accept natural selection being 100% random. I think if it were completely random well then who knows what you would get.

 

When you say "I can't fully accept ..." you are saying that other people are saying natural selection is 100% random. They are not. Nor are other processes random, which you implied when I quoted you as saying "the universe is 100% random". Gravity isn't "random". It ALWAYS attracts, not attracts half the time and repels the other half. Chemical reactions are not random. When you mix sodium hydroxide and hydrochloric acid, you ONLY get NaCL + H2O. You don't get a random mixture of Na2Cl2, NaCl2, Na2Cl, Na3Cl3, Na3Cl2, etc, do you?

 

Now obviously not every mutation makes it in life, and the ones that do make it, I mean specifically can such be mapped out as to the why part?

 

Some can. Remember, it's only been about 20 years that we have sequenced enough of the genome that we can correlate specific changes in the sequence of bases in the DNA to specific traits! Sheesh! Give it some time, will you? Some examples relating particular mutations to "as to the why part" are:

31. Molecular evolution of FOXP2, a gene involved in speech and language. Wolfgang Enard, Molly Przeworski, Simon E. Fisher, Cecilia S. L. Lai, Victor Wiebe, Takashi Kitano, Anthony P. Monaco, Svante Pääbo Nature 418, 869 - 872 (22 Aug 2002)

2. Evolution in E. coli: http://myxo.css.msu.edu/lenski/pdf/2003,%20JME,%20Lenski%20et%20al.pdf

Lenski RE, Mongold JA (2000) Cell size, shape, and fitness in evolving

populations of bacteria. In: Brown JH, West GB (eds) Scaling in biology. Oxford University Press, Oxford, pp 221–235

Lenski RE, Travisano M (1994) Dynamics of adaptation and diversification: 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci USA 91:6808–6814

http://myxo.css.msu.edu/lenski/pdf/1994,%20PNAS,%20Lenski%20&%20Travisano.pdf

3. Sequence of favorable mutations in E. coli http://www.pnas.org/cgi/content/full/96/7/3807

1. Birth of a unique enzyme from an alternative reading frame of the pre-existed, internally repetitious coding sequence", Ohno, S, Proc. Natl Acad. Sci. USA 81:2421-2425, 1984. Frame shift mutation yielded random formation of new protein, was active enzyme nylon linear oligomer hydrolase (degrades nylon) http://www.nmsr.org/nylon.htm

3. D. Grady, Quick-change pathogens gain an evolutionary advantage.Science, vol.274: 1081, 1996 (November 15). The primary research articleis JE LeClerc, B Li, WL Payne, TA Cebula, High mutation frequencies among Eschericia coli and Salmonella pathogens. Science, 274: 1208-1211, 1996 (Nov.15).

 

I mean you can say natural selection, boom its a sealed deal. I don’t doubt the natural selection part, its just for every specie and I would think even down on the more fine scale of populations such as individuals, its not as a black and white as some math formation would have it, I mean if that were true, well I guess we would just know the future evolution possible of any species on any giving environment on the face of the planet and phylogeny should be so easy to solve taken into every possible aspect of it such as an organisms relationship to its environment.

 

1. We don't know every "given environment". Remember, "environment" is not just climate and geographical location, but EVERYTHING that impacts the individual: predators, microbes, plants, siblings, etc. That is hugely complex and can't be projected into the future very well. BUT, that said there have been some new recent experiments in the wild where species have been put in different environments and the evolution by natural selection predicted:

2. Reznick, DN, Shaw, FH, Rodd, FH, and Shaw, RG. Evaluationof the rate of evolution in natural populations of guppies (Poeciliareticulata). Science 275:1934-1937, 1997. The lay article isPredatory-free guppies take an evolutionary leap forward, pg 1880.

1. Case, TJ, Natural selection out on a limb. Nature, 387: 15-16, May 1, 1997. Original paper in the same issue, pp. 70-73 (below). Discusses natural selection in the wild where lizards were introduced to various islands in the Bahamas. Length of limbs varied according to the plant life present on the islands.

JB Losos, KI Warheit, TW Schoener, Adaptive differentiation following experimental island colonization in Anolis lizards. Nature, 387: 70-73,1997 (May 1)

1a. JB Losos, Evolution: a lizard's tale. Scientific American 284: 64-69,March 2001. Phenotypic plasticity and evolution of Anolis lizards.

 

Natural selection has been tested:

Testing Natural Selection

http://www.tulane.edu/~eeob/Courses/Heins/Evolution/lecture9.html#DEFINS

http://library.thinkquest.org/19926/text/tour/10.htm?tqskip1=1&tqtime=0827

 

Not that you cant do math, more so in context of population, but for a giving mutation, what if a substitution reaction is involved in it, I mean for every parameter, it just seems a little bit to large for some nifty equation is all, or at least I have not noticed any that can be called anything more then generalities,

 

In Mendelian genetics we find the Hardy-Weinberg Law. This basically states that, in a population the meets certain criteria: "large size", no gene flow in or out, no natural selection, then the frequency of traits (or alleles) will be constant from one generation to the next. Frequency = the fraction of individuals with that trait or the fraction of alleles. So, if the size of the population is large enough and there is documented no gene flow in or out, then changes in frequency are due to natural selection. What is measured is the ratio of progeny actually produced to the progeny expected from Mendelian inheritance. This is "fitness". Fitness is therefore always relative (Understanding Evolution, pp. 153-154.) We can also get a selection coefficient that measures the selective advantage, or disadvantage. S = 1.0 - fitness.

 

Now, you can apply these to the population. The discipline of population genetics did the basic mathematical formulas. Remember that, in the absence of any outside influence, such as natural selection, the frequency of an allele does not change from generation to generation. That is, if you have a population and 100 and 10 individuals have allele A and 90 have allele B, the next generation will be exactly the same: 10 A and 90 B. This is called the Hardy-Weinberg Law. Frequencies are symbolized mathematically by p and q. W is the relative fitness value. So we have W(A), W(B), and W(AB). The last is the fitness of the heterozygote in a sexually reproducting population.

 

So, for the first generation the frequency p of A in the population is: p^2 +2pq + q^2. Straight Mendelian genetics.

 

The frequency of p in the next generation after selection is: p' = p^2W(A) + pq W(AB)/p^2W(A) + 2pq W(AB) + q^2 (WB).

 

Now, if W(A) and W(AB) are higher than W(B), it can be seen that p' will increase. Not chance, but pure determinism.

 

You can see all this and a lot more in Chapters 4 and 13 in Futuyma's Evolutionary Biology, 1999.

 

Remember Hardy-Weinberg. The frequency of an allele remains unchanged from generation to generation in the absence of outside influence. Therefore, the fitness of a new mutation is defined as the ratio of the number of progeny actually produced divided by the number of progeny expected by Mendelian genetics. This is going to be greater than one in the case of favorable mutations. From that we get a selection coefficient such that fitness = 1 - s.

 

Now, doing the math we find that the advantageous allele A increases in frequency, per generation, by the amount delta p = (1/2)spq/(1-q).

 

If you look at the equation, you see that delta p is positive as long as s is greater than 0, even if it is very small. Eventually p will equal 1, which means that every member of the population will have the allele. Thus, a characteristic with even a miniscule advantage will be fixed by natural selection. "Fixed" means every individual will have the allele.

 

One of my favorite papers on evolution is evolution induced on microbes in a lab. Each time they would run the cycle with the same amount in regards to population, or at least as close as possible, and overtime with the same variables that induced change, and each time they ran it they got a different result, different results in all different kinds of ways even.

 

Care to cite the paper? What do you mean by "different result" and "different kinds of ways even"? The "different kinds of ways" would be the contingency I was mentioning in evolution. HOW you get to the design solution is going to depend on what variations are presented to natural selection. You may also get a situation where there are also different general design solutions to the problems. This is what happened in the evolution of eyes: there are several different general types of eyes that will function: compound eyes, pinhole and camera eyes, cup eyes, etc.

 

Now if you want to keep telling me that I am wrong about everything, that’s fine, but I mean it really makes coming to this thread to post a reply pretty bland and pointless.

 

Foodchain, if you are mistaken about something in science, what do want me to do? Not say anything? Would that make the statements made by you correct? Much of what I have said has come in response to questions you posed. If you didn't want answers, why did you pose the questions?

 

Now, if you go back and look at my first reply to you in this thread, you had asked:

My question basically is how much does the laws or theories of QM have in common with evolution of life? ... Now I know its more easier and probably correct to say Newtonian physics applies a lot more then QM, but I don’t see how I can rule such out yet.

 

Did I say you were "wrong about everything"? NO! I said that you were correct that QM did have a role to play in evolution!

"2. QM comes into play when you consider the contingency of evolution. Kenneth Miller did this brilliantly in Chapter 6 of Finding Darwin's God; I will try to summarize."

 

I even reassured you when you mentioned in your post 07-03-07:

I should have not used QM in the title as much, as my lack of understanding overall probably produced that.

 

What was my reply? "No, you did fine"!

 

I mean look at the title of the thread, and what its posted in. Its not as if I am trying to tell everyone this is the way it is, or at least that’s never the way I held it to be. I mean you are not saying anything to me that’s a revelation to be honest, I am trying to be hypothetical here, that’s my main drive for making the thread, to discuss little more then science fiction because it cant be called anything more then such currently.

 

What can't be "called anything more then such [science fiction] currently"? Evolution? Natural selection? Quantum mechanics in evolution? What do you consider the "science fiction"?

 

As a side point, its not a thread on reduction. Biophysics is an existing field like biochemistry, but the chemistry alone cant detail how an eagle flies, or what weather they like to fly in.

 

I agree that you can't reduce everything! But look at the quotes of yours I responded to: the ones where YOU were reducing evolution to "energy".

 

I don’t see however how a physical system can exist outside of physical laws, so would that be to much reduction?

 

"Reduction" in science is trying to explain complex systems or phenomena in terms of simpler ones. As an example: all the behaviors of gasses under different pressures and temperatures can be "reduced" to the motion of the atoms of a gas. The complex motion of the planets and moons of the solar system can be "reduced" to the equations of Newtonian gravity and Kepler's Laws of Motion.

 

Sometimes complex systems cannot be reduced that way. You can't reduce evolution to "So basically what you have then is energy evolving." That won't work because "energy" is not a population of individuals. And evolution happens to populations of individuals.