Atheistic intelligent design

[JohnB]

Moontanman, I didn't say that it was necessary to have a designer. I was pointing out that the existence of a designer does not require or prove a prior designer. A subtle but important difference.

 

I'll explain how I think it is possible, but first the assumptions and definitions of what I mean.

 

I'm assuming that this Universe isn't the first one. I'm also assuming a purpose to this Universe and that the purpose is to have lots of places where life could evolve. By "Designer" I mean an entity that existed at the creation of our Universe that was capable of tweaking the Laws of Physics so that there would be lots of places where life could evolve. After setting up the starting perameters, the entity simply sits back and lets the experiment run its course. (Being technically immortal it has presumably learned patience.)

 

So it could play out this way.

 

In the previous Universe it wasn't as easy for life to evolve, nor was it particularly abundant. However life did evolve beginning with abiogenesis and evolving from there. This life eventually became complex enough to become sentient. Once sentient it worked to avoid its own mortality and eventually became a composite mind separated from its original physical form. (Note that there are some who don't view this ability as being too far ahead in our future.)

 

Witnessing the coming end of its Universe it decides that it will tweak the Laws of the new Universe to make it more hospitable to life. (For whatever reasons as make sense to it, but perhaps it was bored and lonely.)

 

So we have the situation where our current Universe was designed and had a Designer, however that Designer wasn't designed but evolved by chance.

 

Nothing in this idea implies or requires either omnipotence nor omniscience. It is just as possible that the designer evolved 265 Universes ago and this current designed one is just one more in a series of experiments. This could be the first one that is relatively stable and the previous 264 were complete stuff ups. Nor is it required that the Designer be all powerful, although it is "giving form" to the Universes as they begin, it is not providing the energy for that beginning.

 

Even if the above is correct, it does not confirm any particular religion, or form of religious thought, It neither implies not requires any form of devotion or worship on our part. There is nothing spiritual or metaphysical involved.

 

Atheistic Intelligent Design.

[Moontanman]

I understand exactly where you are coming from, as a matter of fact i have used the argument of alien design quite successfully in the past but it does not remove the problem of how life really began any more than panspermia removes the problems with abiogenesis. Shuffling the designer back to before the creation of the universe solves no problems what so ever and has zero supporting evidence. At some point the designer has to come into existence from non design. Unless you suppose that a designer from the future creates the universe so it can evolve and eventually create the universe, this loop would continue on and on but I am quite sure it would violate some laws of causality at least.

 

It might very well be true that the universe has a designer, i can think of many situations to explain the origin of the universe and the life in it including us but they would all be speculation with zero supporting evidence. So far there is zero evidence of any designer so why should we assume there is one? I see no reason to proclaim there cannot be a designer but also no reason to assume there is one...

 

Interesting info...

 

http://www.sciencedaily.com/news/fossils_ruins/origin_of_life/

[JohnB]

I don't see where panspermia comes into it, like evolution it requires life to already exist.

 

Nor do I see a problem with abiogenesis. Given enough time, over enough plants for the lifetimes of enough Universes, I'd be quite surprised if a full human DNA chain didn't come to exist at least once by complete random chance. Like the monkeys writing Shakespeare.

 

We aren't talking about anything remotely as complex being needed to kick the process off. I find that most people who don't get abiogenesis just don't get the numbers involved. In the Primordial sludge, we are talking about hundreds of millions of random joinings happening every second over a period of hundreds of millions of years. The totals are astronomical.

 

Looking at it another way, let's assume that you need a string of 50 predefined single digit numbers to signify a "win". You have 100 million random number generators that produce 1 number per second. Over 100 million years it becomes pretty much an odds on bet that one of those machines will generate the needed sequence.

 

A point that has just occurred to me is that the abiogenesis of life could take as long as it likes on any given planet. It can be readily demonstrated that the simple existence of life changes that biosphere of the planet. Note the dramatic change in atmospheric and oceanic chemical makeup once photosynthesis arrived. I don't think it's unreasonable to think that a planetary biosphere will remain a primordial sludge until life arrives. It would then follow that there would be planets where life got a much earlier start than it did on Earth and also planets older than Earth that are still primordial sludge. There is no time table that must be adhered to.

 

Note that in all this, the Designer is neither creating the life nor deciding on its form. The Designer is doing nothing more than arranging the Laws of Physics in such a way that there are more places where abiogenesis has the opportunity to occur than would have existed previously. After that it's all up to random chance and time.

Edited November 21, 2010 by JohnB

[mississippichem]

A point that has just occurred to me is that the abiogenesis of life could take as long as it likes on any given planet. It can be readily demonstrated that the simple existence of life changes that biosphere of the planet. Note the dramatic change in atmospheric and oceanic chemical makeup once photosynthesis arrived. I don't think it's unreasonable to think that a planetary biosphere will remain a primordial sludge until life arrives. It would then follow that there would be planets where life got a much earlier start than it did on Earth and also planets older than Earth that are still primordial sludge. There is no time table that must be adhered to.

 

I agree. Look at the Miller-Urey experiment. They made a "primordial-soup" of methane, ammonia, water, and other simple binary compounds, set it up to an electric discharge and let it sit for a few weeks. After a while they discovered lipid miscelles (organized spheres of lipids), as well as complex sugars and maybe even amino-acids, if I remember correctly, that had all formed randomly in the soup. This arrival of complex molecules facilitates more complicated chemistry occurring by sheer number of possible reactions.

 

I think in the future we will come to the realization that chemical complexity [life] tends to arise out of complex chemical mixtures over time. Before life starts to compete for food and reproductive superiority, chemicals compete for free-energy and equilibrium position.

 

The laws of physics, which translate to workings of chemistry, are so that, in my opinion, life is inevitable on any body in space with enough gravity, thermal energy, some liquid/gas interface (like the ocean and air), and a steady string of photons from the nearby star. Who knows what obscure conditions life can live under though? We would've been surprised to find archaea living at the bottom of the ocean with no light, mega-pressure, and eating hydogen sulfide seventy years ago.

Edited November 21, 2010 by mississippichem

[Ophiolite]

Unless you suppose that a designer from the future creates the universe so it can evolve and eventually create the universe, this loop would continue on and on but I am quite sure it would violate some laws of causality at least.

Laws are made to be broken. That may turn out to be humanity's destiny.

[cypress]

I agree. Look at the Miller-Urey experiment. They made a "primordial-soup" of methane, ammonia, water, and other simple binary compounds, set it up to an electric discharge and let it sit for a few weeks. After a while they discovered lipid miscelles (organized spheres of lipids), as well as complex sugars and maybe even amino-acids, if I remember correctly, that had all formed randomly in the soup. This arrival of complex molecules facilitates more complicated chemistry occurring by sheer number of possible reactions.

 

I think in the future we will come to the realization that chemical complexity [life] tends to arise out of complex chemical mixtures over time. Before life starts to compete for food and reproductive superiority, chemicals compete for free-energy and equilibrium position.

 

The laws of physics, which translate to workings of chemistry, are so that, in my opinion, life is inevitable on any body in space with enough gravity, thermal energy, some liquid/gas interface (like the ocean and air), and a steady string of photons from the nearby star. Who knows what obscure conditions life can live under though? We would've been surprised to find archaea living at the bottom of the ocean with no light, mega-pressure, and eating hydogen sulfide seventy years ago.

 

Physical laws acting on chemistry don't seem to work the way you imagine. As you are aware, chemical reactions are such that products that are more stable in the environment form with regularity, while those that are unstable degrade. Complex irregular polymers don't fit this pattern, instead they seem to require pre-existing complexity to generate them and continual repair mechanisms to maintain them. They don't seem to form the way less complex stable molecules form. This observation is consistent with probability theorem and entropy laws. there does not seem to be much interest in admitting physical chemistry laws and aplying them to the notion of life from non-life.

[Edtharan]

Physical laws acting on chemistry don't seem to work the way you imagine. As you are aware, chemical reactions are such that products that are more stable in the environment form with regularity, while those that are unstable degrade. Complex irregular polymers don't fit this pattern, instead they seem to require pre-existing complexity to generate them and continual repair mechanisms to maintain them. They don't seem to form the way less complex stable molecules form. This observation is consistent with probability theorem and entropy laws. there does not seem to be much interest in admitting physical chemistry laws and aplying them to the notion of life from non-life.

However, there are many complex molecules that are both stable and complex. The reason is that these molecules are a local energy minima, that is they fit within a stable pocket of potential interactions and it takes energy to get them out of that state.

 

they don't requier preexisting complexity as it also takes energy to get them into that state, and it is from the energy that they get their order (as they disapte the energy needed to get them into that state this is a global increase in entropy even though it is a local decrease in entropy).

 

Take lipds for example:

These molecules are fairly simple as far as organic molecules go, but they spontainiously form into bi-layered sheets in the presense of water. The formation of these chemicals take energy (and the Urey/Miller experiment produced lipids by the aplication of energy to simple chemicals), but when these chemicals join up, there is a small, but important release of energy (in terms of the lipid molecules individual motion is constrained). However, if enough energy is applied (which could be by heating up the water surounding them to well over boiling point) or by physically phushing them arround (say against rocks or such) you can disrupt the sheets of lipid and break it apart.

 

Lipid bi-layers are extremely complex and ordered and will appear to be designed, however, the processes that bind them are pure physical processes and no outside agent is necesary for them to behave like they do. Not only that, these bi-layers, because of the molecular forces (which is electromagentic forces), will curl up into spheres (called vesicles).

 

This is really complex stuff and shows quite a degree of order. Which is against what you are saying. This fact disproves your claims. Sure, there are some instances where complex chemicals are unstable (and they are quite common), but as not all complex chemicals are unstable, (and by the way these more stable ones are common in living systems) your claim is not true.

 

There are certainly many complex chemcials that are stable and have interesting behaviours (like self reproduction, self organisation, etc). Actually it is these very properties that make them stable.

[cypress]

 

I plead you to make an open analysis on that before coming to any other conclusions. I have a strange feeling that you might ignore this.

 

I finished reviewing this article and others related to it. In this article they demonstrate that a several short similar and structurally dissimilar peptides that all bind to a human AIDS antibody can be altered in stepwise fashion one amino acid at a time without loss of ability to bind to the antibody.

 

Having now thought this through for some time, I can't draw any evolutionary conclusions from it because

 

1. short peptides are not selective so chemically speaking we should expect the result that was observed. This is one reason why biological proteins are much larger to obtain selectivity.

 

2. Development of Antibody binding sites are not an analog for evolutionary derivation of binding sites. The process is completely different.

 

3. The system of antibody and peptide does not form a biologically functional system so its significance in biological development is unknown.

 

This article was offered as a possible answer to a request for an verified evolutionary pathway of 4 or more contiguous selectable steps. Despite the 70 or so years of searching for such a pathway, none have been identified, indicating that the evolutionary narrative that all diversity is explained by evolution is not validated and alternative explanations should be considered including the ones offered in this thread.

 

However, there are many complex molecules that are both stable and complex.

 

Derivation of complex biopolymers are not explained by reference to fatty acids, which are quite simple from an organization view.

 

Lipid bi-layers are extremely complex and ordered and will appear to be designed, however, the processes that bind them are pure physical processes and no outside agent is necesary for them to behave like they do. Not only that, these bi-layers, because of the molecular forces (which is electromagentic forces), will curl up into spheres (called vesicles).

 

bi-layers of fatty acids are not molecules. As you indicate they have regular ordered structures by virtue of the determinist processes that cause them to form up that way. When order is defined from a probability theory and thus from an entropy viewpoint, deterministic processes do not increase or decrease order because only one outcome is possible. Bi-layers and crystals and such are not organizationally complex from an entropy viewpoint.

 

Your example is another straw man illustrations because it is not in the same context.

 

There are certainly many complex chemcials that are stable and have interesting behaviours (like self reproduction, self organisation, etc). Actually it is these very properties that make them stable.

 

Self organization is a straw man as is your lipid example. Self-replication, however, would be a good example. The only self-replicating biomolecules I am aware of are either contained in existing biological systems or are designed. It would be interesting to discuss an analog to the irregular sequenced, but specifically shaped and highly coherent biopolymers that are also unstable in the environment outside of the cell.

[Ophiolite]

Complex irregular polymers don't fit this pattern, instead they seem to require pre-existing complexity to generate them and continual repair mechanisms to maintain them.

You don't consider polypetides generated by high speed impact of amino acid bearing ices to be an instance of complex, irregular polymers forming in a natural way?

[cypress]

You don't consider polypetides generated by high speed impact of amino acid bearing ices to be an instance of complex, irregular polymers forming in a natural way?

 

I would if they were on the same scale and character as functional proteins and they persisted. Do you have any examples of long chain (100+) chiral consistent polypeptides formed and persisting?

 

The concept being explored is of the capability for material circumstance and physical chemical processes alone to generated highly ordered systems where order is defined from a probabilistic sense as in the order measured by entropy. Clearly short peptides of 2 or 3 amino acids can and do form in natural settings by a few mechanisms but the formation is guided by the random nature of chemical equilibrium and the deterministic physical laws, and thus the products are no more ordered than the configuration of the precursors.

 

Biological systems seem to defy these processes because in contrast, they contain functional information and they contain order that represents relative (molecular and information) entropy values that are substantially lower than the precursor states presumed by natural processes. Intelligence and design is one way around this dilemma which supports the topic of this thread. Thus far, there is no alternate materialistic mechanism that can account for this observation. Thermal entropy is most frequently suggested, but it is done with hand waving. No scientific demonstration is offered to show thermodynamic entropy can substitute for molecular and information entropy.

[Ophiolite]

I would if they were on the same scale and character as functional proteins and they persisted. Do you have any examples of long chain (100+) chiral consistent polypeptides formed and persisting?.

Why are you demanding chirality be a part of the formation process, when it could be part of the selection process. You are erecting artificial barriers to exclude viable possibilities.

[cypress]

Why are you demanding chirality be a part of the formation process, when it could be part of the selection process. You are erecting artificial barriers to exclude viable possibilities.

 

It's not a demand, I did not intend to imply that it was and I am sorry it came across that way. I note it because, like the probabilistic order inherent in the irregular sequences of amino acids, chiral consistency represents higher probabilistic order, and as such, is worth mention. The only demand I am making is to offer up a validated materialistic example of increased molecular order (decreased molecular and/or information entropy, either one is fine) of a system where all inputs and outputs are properly accounted. The example does not need to have consistent chirality, it does not have to be made up of amino acids or have any artificial barriers at all, any viable demonstration that is actualized is acceptable. I have suggested biological polymers primarily because they are clearer examples of the molecular and information order I describe.

[immortal]

Having now thought this through for some time, I can't draw any evolutionary conclusions from it.

 

you can't or you don't want to draw any evolutionary conclusions.

 

1. short peptides are not selective so chemically speaking we should expect the result that was observed. This is one reason why biological proteins are much larger to obtain selectivity.

 

If this is the case then why do you think that complex functions having multicomponent proteins can't arise using natural processes.

 

And also it is natural selection which selects these peptides and conserves their selectivity by inducing normalization selection or functional constraints. I mean that out of the variety of different selectivities possible evolution by NS selects those confirmations which provide a benefit to the organism.

 

2. Development of Antibody binding sites are not an analog for evolutionary derivation of binding sites. The process is completely different.

 

The paper indicated that different antibody binding sites arised by single amino acid substituions.

Am i missing something or can you describe what process you are talking about.

 

3. The system of antibody and peptide does not form a biologically functional system so its significance in biological development is unknown.

 

Well you can not expect evo by NS to produce a mouse trap at one go. The individual subsystems are not basically designed with an intent to build the overall complete multi-molecular system. The subsystem provide an evolutionary advantage or a function to the organism priorly which is in no way related to the

evolved new function.

 

This article was offered as a possible answer to a request for an verified evolutionary pathway of 4 or more contiguous selectable steps. Despite the 70 or so years of searching for such a pathway, none have been identified, indicating that the evolutionary narrative that all diversity is explained by evolution is not validated and alternative explanations should be considered including the ones offered in this thread.

 

Well lack of evidence does'nt mean that the process does not works. No one has disproved it that it will never work by that way.

 

The article clearly indicates that there are a series of neutral muations followed by a single big substitution which changes the confirmation between the peptides and if anyone wants to look at an evolutionary pathway of 4 or more selectable steps then they need those neutral mutations as it seems that the history of the organism or a population determines its future existence. So what we only see are the snapshots of evo by NS acting on the organism and conserving or accumulating the design.

[granpa]

However, there are many complex molecules that are both stable and complex.

 

Take lipds for example:

These molecules are fairly simple as far as organic molecules go, but they spontainiously form into bi-layered sheets in the presense of water. The formation of these chemicals take energy (and the Urey/Miller experiment produced lipids by the aplication of energy to simple chemicals), but when these chemicals join up, there is a small, but important release of energy (in terms of the lipid molecules individual motion is constrained). However, if enough energy is applied (which could be by heating up the water surounding them to well over boiling point) or by physically phushing them arround (say against rocks or such) you can disrupt the sheets of lipid and break it apart.

 

there are also lipids that form one dimensional chains

http://en.wikipedia.org/wiki/PAH_world_hypothesis

[cypress]

If this is the case then why do you think that complex functions having multicomponent proteins can't arise using natural processes.

 

They don't arise by observed evolutionary processes and I think they don't because the observed processes lack the necessary capability to derive the information required to facilitate change at this scale. Other more capable processes seem to be required. I do not know if some unknown natural processes can or can't generate these systems but thus far, no natural system has been observed with this capability.

 

And also it is natural selection which selects these peptides and conserves their selectivity by inducing normalization selection or functional constraints. I mean that out of the variety of different selectivities possible evolution by NS selects those confirmations which provide a benefit to the organism.

 

The research offered did not address natural selection. All selection in the research was done by the researchers. If you meant that natural selection is known to select for alterations in the biologically active peptides, then I would not disagree since it is established that natural selection is capable of adapting existing function to environmental changes. If you are suggesting that natural selection acts on biologically active peptides to form components of the complex multicomponent protein systems, I would be suspicious of that claim.

 

 

The paper indicated that different antibody binding sites arised by single amino acid substituions.

Am i missing something or can you describe what process you are talking about.

 

If I understood the paper correctly, the substitutions were made to the peptide sequences but the antibody binding sites remained unchanged. However what I intended to say was that because the research involved an antibody and because antibodies are derived by processes that are not similar to evolutionary processes, the antibody is not a good analog to gene derived protein binding sites.

 

Well you can not expect evo by NS to produce a mouse trap at one go. The individual subsystems are not basically designed with an intent to build the overall complete multi-molecular system. The subsystem provide an evolutionary advantage or a function to the organism priorly which is in no way related to the evolved new function.

 

Yours is the traditional description of evolutionary progression which require stepwise pathways where the forward steps are advantageous over the previous steps given the environmental conditions in place when each step occurs and propagates. But if this were the case, then we should have observed several short 5-10 step evolutionary pathways in the 70 year search, and more to the point, researchers should be able to reverse engineer multitudes of these past pathways.

 

Well lack of evidence does'nt mean that the process does not works. No one has disproved it that it will never work by that way.

 

I'm not so sure. Devices that violate entropy laws also lack evidence that they function as described and those who promote them make this same argument on the basis that one cannot disprove the claim since improbable events can occur. In the evolutionary narrative, natural selection is ascribed capabilities similar to that of Maxwell's Demon. It is assigned a fitness function that slopes smoothly upward but no one ever bothers to explain what physical law allowed for this specific shape of function that allows it to override entropy laws as applied to order of all kinds.

 

The article clearly indicates that there are a series of neutral muations followed by a single big substitution which changes the confirmation between the peptides and if anyone wants to look at an evolutionary pathway of 4 or more selectable steps then they need those neutral mutations as it seems that the history of the organism or a population determines its future existence. So what we only see are the snapshots of evo by NS acting on the organism and conserving or accumulating the design.

 

Describing the alterations as an evolutionary pathway with selectable steps is incorrect since the antibody - peptide pairings do not appear to be biologically active and seem to be artifacts of the the research. Im fine with the idea of neutral steps in an evolutionary pathway but I don't know of any examples of snapshots of evolutionary progression as you have described. This article is interesting but it is clearly not an example of an evolutionary pathway.

[immortal]

They don't arise by observed evolutionary processes and I think they don't because the observed processes lack the necessary capability to derive the information required to facilitate change at this scale.

 

You can’t understand how it has evolved because your scale of how it works is wrong.

These multi-component structures require multiple neutral mutations to occur on both the interacting proteins which are very rare in nature but not so rare if we look at it in a scale of millions of years. Because most multiple mutations are screened off by NS.

 

Such a time scale is quite enough to accumulate information over time.

 

 

Other more capable processes seem to be required. I do not know if some unknown natural processes can or can't generate these systems but thus far, no natural system has been observed with this capability.

 

I do agree that self-organization is a problem in biology.

 

The research offered did not address natural selection. All selection in the research was done by the researchers. If you are suggesting that natural selection acts on biologically active peptides to form components of the complex multicomponent protein systems, I would be suspicious of that claim.

 

No I am claiming that individual subsystems evolved independently through NS and later it might be possible that they are incorporated to the genome through Horizontal Gene Transfer in which these same individual protein complexes are used in rather different ways to produce a new function in multi-component protein complexes.

 

If I understood the paper correctly, the substitutions were made to the peptide sequences but the antibody binding sites remained unchanged. However what I intended to say was that because the research involved an antibody and because antibodies are derived by processes that are not similar to evolutionary processes, the antibody is not a good analog to gene derived protein binding sites.

 

No, substitutions were made to the antibody also and their mutants were tested for different specificity. The antibody binding sites did change in some cases.

 

I think Immunoglobulins are a perfect example of multi-component proteins interacting with each other. Yes the antibodies are produced using recombination of different existing peptides but it doesn’t mean that single substitutions have no role to play; in fact these single substitutions might open a whole lot of new possibilities. The antibodies are produced by linking variable regions of different peptides and the variable regions themselves might be under single substitutions and also the peptides of antibodies may co-evolve.

 

Yes the organism which carries these genes will not have the antibody in the first place but they will have the wide range of resources to produce the required antibody

 

 

Yours is the traditional description of evolutionary progression which require stepwise pathways where the forward steps are advantageous over the previous steps given the environmental conditions in place when each step occurs and propagates. But if this were the case, then we should have observed several short 5-10 step evolutionary pathways in the 70 year search, and more to the point, researchers should be able to reverse engineer multitudes of these past pathways.

 

We can reverse engineer it only if the previous information is conserved for example in the link which I earlier gave to you showed how it was possible for insects to develop all their abdominal legs by tweaking their genome.

 

If the parts are evolved to such extent that they are co-related in such a way that removing one part makes the entire system to fail so in this case we can not do reverse engineering and know the function of the independent part as its previous information is lost or in the sense transformed.

 

And also too much selection on populations seem to indicate that it is on the verge of extinction. Do some research on Huia birds.

 

So if you want an evidence for 4 or more selectable steps in such short period of time you wouldn’t probably get it as NS will screen it off.

 

 

I'm not so sure. Devices that violate entropy laws also lack evidence that they function as described and those who promote them make this same argument on the basis that one cannot disprove the claim since improbable events can occur. In the evolutionary narrative, natural selection is ascribed capabilities similar to that of Maxwell's Demon. It is assigned a fitness function that slopes smoothly upward but no one ever bothers to explain what physical law allowed for this specific shape of function that allows it to override entropy laws as applied to order of all kinds.

 

This is in response for your request for how thermodynamic entropy substitutes for information entropy.

 

I quote since it is the collective work of many biologists.

 

“I suppose you know how neurons work. The neurons will have an active potential or the membrane potential in the form of Na+ and K+ ions. When we extract information our sense organs the nerve fibers will produce an action potential i.e. influx of Na+ and out flux of K+ ions. This action potential is coupled with Ca+ ions which activates a protein there by phosporylating some regulatory proteins which acts as a feedback given to the DNA of the neurons for the incoming signal .

 

And also these Ca+ ions stimulate the synaptic vesicles to release the neurotransmitters.

These synaptic vesicles are situated in the pre-synaptic region and they release these neurotransmitters to the receptors at the post-synaptic membrane. The action potential at the other end of the post synaptic membrane depends on the

 

1. The type of gate the neurotransmitter interacting with the receptor opens up .i.e. the type of ion entering the neuron membrane.

 

2. The number of neurotransmitters which signifies the strength of the signal.

 

The feedback signal which was sent to the DNA makes sure that these membrane proteins are synthesized and transferred to the end regions of the neuron to produce the synaptic branches or synaptic nodes or basically synaptic connections.

 

These synaptic connections determine the various ways in which the neurotransmitter reacts with the receptors in the post-synaptic membrane producing a specific signal. This is nothing but fine tuning.

 

So the neurons receive all signals which are impinged on it and transform it into a single output. This output signal’s action potential is coupled to the release of Ca+ ions which regulates the movement of contractile proteins actin and myosin and they control all your locomotion from speech to the letters which I am typing here now.

 

The incoming signal from the sense organs is fine tuned by the development of synaptic branches or synaptic connections to produce a specific output signal.

 

This is learning and this is in your terminology eliminating the other possibilities. This is acquiring information.

 

This was the work of Kandel and his researchers on learning and memory.”

 

Out of the various possible ways one can regulate the movement of actin and myosin the brain a physical device gives directions on how to regulate the movement of actin and myosin by eliminating all other possible regulations and there by generating information.

 

The thermodynamic entropy is nothing but the uncertainty in the dispersal of energy and physical devices like brain can effectively decrease the dispersal of energy of its molecules which is nothing but information represented physically by acquiring energy from outside and releasing heat to the surroundings there by increasing the net entropy of the system and the surroundings.

 

Do some research in molecular neurobiology.

 

 

 

Describing the alterations as an evolutionary pathway with selectable steps is incorrect since the antibody - peptide pairings do not appear to be biologically active and seem to be artifacts of the the research. but I don't know of any examples of snapshots of evolutionary progression as you have described. This article is interesting but it is clearly not an example of an evolutionary pathway.

 

The examples are right in front of you the fact that the information in the genomes is conserved and one can see when each genome has diversified.

 

You can see the snapshots from the development of the embryos.

[cypress]

You can’t understand how it has evolved because your scale of how it works is wrong.

These multi-component structures require multiple neutral mutations to occur on both the interacting proteins which are very rare in nature but not so rare if we look at it in a scale of millions of years. Because most multiple mutations are screened off by NS.

 

Such a time scale is quite enough to accumulate information over time.

 

I don't think my time scale is off, though I have not spoken much about it in threads where you participated. I do agree selectable mutations are rare (research seems to confirm this) and I agree that multi-component structures require multiple neutral, unfavorable and selectable mutations by known evolutionary processes (also confirmed by research). Finally, I agree that time allows for additional probabilistic resources to provide opportunities for rare combinations to occur. However, there are two problems with making an appeal for more time.

 

The first issue is that evolutionary processes are also constrained by time. The geologic clock provides standard measures of the time available for these events to occur. Humans and chimps are posited to have evolved from an ape-like ancestor around 7 million years ago. Whales from a land dwelling mammal over a period of 10 million years about 50 million years ago. Both of these transformations are thought to require many thousands of substantive simultaneous or near simultaneous (even if interdependent) evolutionary pathways of tens and hundreds of steps (neutral, detrimental and selectable) based on observed and presumed genetic differences. Do you agree with these estimates and timelines? If you do do you begin to see the issue? I will contend that even a few million years is not enough time based on the measured progression of known evolutionary processes.

 

If you don't agree with let's take some time to agree on these points before proceeding.

 

I do agree that self-organization is a problem in biology.

 

Thank-you for that, acknowledgment is rare at this site. I don't do it as often as I would like.

 

 

No I am claiming that individual subsystems evolved independently through NS and later it might be possible that they are incorporated to the genome through Horizontal Gene Transfer in which these same individual protein complexes are used in rather different ways to produce a new function in multi-component protein complexes.

 

Ok we can investigate this hypothesis as well to see if it has observable support at the level where you posit these transfers are supposed to occur.

 

 

 

No, substitutions were made to the antibody also and their mutants were tested for different specificity. The antibody binding sites did change in some cases.

 

Antibody binding sites are not derived by evolutionary mechanism though as I mentioned before. To extend it as an analog for evolutionary processes is flawed. It is an interesting study of antibody to peptide binding selectivity and may well have application in immunology but I don't find this relevant to the question we are discussing.

 

I think Immunoglobulins are a perfect example of multi-component proteins interacting with each other. Yes the antibodies are produced using recombination of different existing peptides but it doesn’t mean that single substitutions have no role to play; in fact these single substitutions might open a whole lot of new possibilities. The antibodies are produced by linking variable regions of different peptides and the variable regions themselves might be under single substitutions and also the peptides of antibodies may co-evolve.

 

Yes the organism which carries these genes will not have the antibody in the first place but they will have the wide range of resources to produce the required antibody

 

They may be interesting examples of protein interactions but the processes by which these binding sites are formed are not good analogs of evolutionary processes.

 

We can reverse engineer it only if the previous information is conserved for example in the link which I earlier gave to you showed how it was possible for insects to develop all their abdominal legs by tweaking their genome.

 

If the parts are evolved to such extent that they are co-related in such a way that removing one part makes the entire system to fail so in this case we can not do reverse engineering and know the function of the independent part as its previous information is lost or in the sense transformed.

 

And also too much selection on populations seem to indicate that it is on the verge of extinction. Do some research on Huia birds.

 

So if you want an evidence for 4 or more selectable steps in such short period of time you wouldn’t probably get it as NS will screen it off.

 

First of all I reject your supposition because it follows from evolutionary theory that properly ordered backward pathways must result in organisms that are reproductively competitive in some way, but still, surely you don't believe that all or even most pathways from the recent past as short as 4 or 5 steps should be lost.

 

 

 

This is in response for your request for how thermodynamic entropy substitutes for information entropy.

 

I quote since it is the collective work of many biologists.

 

“I suppose you know how neurons work. The neurons will have an active potential or the membrane potential in the form of Na+ and K+ ions. When we extract information our sense organs the nerve fibers will produce an action potential i.e. influx of Na+ and out flux of K+ ions. This action potential is coupled with Ca+ ions which activates a protein there by phosporylating some regulatory proteins which acts as a feedback given to the DNA of the neurons for the incoming signal .

 

And also these Ca+ ions stimulate the synaptic vesicles to release the neurotransmitters.

These synaptic vesicles are situated in the pre-synaptic region and they release these neurotransmitters to the receptors at the post-synaptic membrane. The action potential at the other end of the post synaptic membrane depends on the

 

1. The type of gate the neurotransmitter interacting with the receptor opens up .i.e. the type of ion entering the neuron membrane.

 

2. The number of neurotransmitters which signifies the strength of the signal.

 

The feedback signal which was sent to the DNA makes sure that these membrane proteins are synthesized and transferred to the end regions of the neuron to produce the synaptic branches or synaptic nodes or basically synaptic connections.

 

These synaptic connections determine the various ways in which the neurotransmitter reacts with the receptors in the post-synaptic membrane producing a specific signal. This is nothing but fine tuning.

 

So the neurons receive all signals which are impinged on it and transform it into a single output. This output signal’s action potential is coupled to the release of Ca+ ions which regulates the movement of contractile proteins actin and myosin and they control all your locomotion from speech to the letters which I am typing here now.

 

The incoming signal from the sense organs is fine tuned by the development of synaptic branches or synaptic connections to produce a specific output signal.

 

This is learning and this is in your terminology eliminating the other possibilities. This is acquiring information.

 

This was the work of Kandel and his researchers on learning and memory.”

 

Out of the various possible ways one can regulate the movement of actin and myosin the brain a physical device gives directions on how to regulate the movement of actin and myosin by eliminating all other possible regulations and there by generating information.

 

The thermodynamic entropy is nothing but the uncertainty in the dispersal of energy and physical devices like brain can effectively decrease the dispersal of energy of its molecules which is nothing but information represented physically by acquiring energy from outside and releasing heat to the surroundings there by increasing the net entropy of the system and the surroundings.

 

Do some research in molecular neurobiology.

 

I will come back to this topic as it is my second issue and we may have better dialog if we stick to one at a time.

 

The examples are right in front of you the fact that the information in the genomes is conserved and one can see when each genome has diversified.

 

You can see the snapshots from the development of the embryos.

 

Biological systems contain with them pre-existing information encoded in the DNA sufficient to account for growth, development, management of cell function and reproduction and do so without any apparent net decrease in entropy. The issue comes in when one posits that new forms are derived by increasing the order and content of older forms. I don't see how embryonic development is an analog for posited evolutionary progression, it certainly does not duplicate or follow any genetic mutation pathway. Your claim above that these past pathways are lost certainly contradicts this new posit.

[immortal]

I don't think my time scale is off, though I have not spoken much about it in threads where you participated. I do agree selectable mutations are rare (research seems to confirm this) and I agree that multi-component structures require multiple neutral, unfavorable and selectable mutations by known evolutionary processes (also confirmed by research). Finally, I agree that time allows for additional probabilistic resources to provide opportunities for rare combinations to occur. However, there are two problems with making an appeal for more time.

 

The first issue is that evolutionary processes are also constrained by time. The geologic clock provides standard measures of the time available for these events to occur. Humans and chimps are posited to have evolved from an ape-like ancestor around 7 million years ago. Whales from a land dwelling mammal over a period of 10 million years about 50 million years ago. Both of these transformations are thought to require many thousands of substantive simultaneous or near simultaneous (even if interdependent) evolutionary pathways of tens and hundreds of steps (neutral, detrimental and selectable) based on observed and presumed genetic differences. Do you agree with these estimates and timelines? If you do do you begin to see the issue? I will contend that even a few million years is not enough time based on the measured progression of known evolutionary processes.

 

If you don't agree with let's take some time to agree on these points before proceeding.

 

I have no problem with the timelines or your estimates of it but I disagree with your claim that known evolutionary processes can not account for it.

 

I think I have addressed this problem earlier in this same thread. May be you have missed it.

 

I address it again.

 

Well one reason for the increased rate of evolution in mammals is given through Wilson's hypothesis it says that there is an internal pressure in mammals which forces them to interact with the environment in rather different ways and there by increasing the fixation of alleles through out the population. So the argument that only the rate of occurences of mutations determine the rate of evolution of organisms is not true. This internal pressure in mammals is linked to large brain sizes in mammals.

 

But once Cultural evolution kicked in the internal pressure in humans reduced and the biological evolution was in almost in a statis has the internal pressure was resolved very fastly with the development of memes.

 

 

And also from your examples one can see that both the humans and whales had the opportunity to exploit new ecological niches this ability had to come from earlier slight mutations but once it was conserved or established it is very much possible for them to have accelerated progression in evolution through positive selection.

 

One more thing is that you have to see the changes from the point of chromosomes also and the new processes like genome responses to shock discovered by geneticists.

 

I don't do it as often as I would like.

 

If there is a resonable evidence against your hypothesis then you have to withdraw that hypothesis.

 

 

Ok we can investigate this hypothesis as well to see if it has observable support at the level where you posit these transfers are supposed to occur.

 

Well it is not my hypothesis. This hypothesis was claimed by biologists who discovered the evidence that many of the genes involved in photosynthesis had different evolutionary histories.

 

Antibody binding sites are not derived by evolutionary mechanism though as I mentioned before. To extend it as an analog for evolutionary processes is flawed. but I don't find this relevant to the question we are discussing.

They may be interesting examples of protein interactions but the processes by which these binding sites are formed are not good analogs of evolutionary processes.

 

Yes I never gave you an evidence for the stepwise evolution of multi-component structures but it does give us the basic glimpses of how it might happen which keeps the mechanisms of evolution based on darwinian terms unpunctured.

 

 

First of all I reject your supposition because it follows from evolutionary theory that properly ordered backward pathways must result in organisms that are reproductively competitive in some way, but still, surely you don't believe that all or even most pathways from the recent past as short as 4 or 5 steps should be lost.

 

Most biologists agree that we might never be able to show the evidence requested by Michael Behe. I suppose you understand the complexity of the task involved here.

 

We have to take this seriously and put a dynamic system under observation and see what the hell is going on here rather than just quarreling with each other.

 

 

I will come back to this topic as it is my second issue and we may have better dialog if we stick to one at a time.

 

Well it was you who raised the issue and its your claim and we are quite happy to show you that your claim is wrong or flawed. We have disproved it by giving quite reasonable arguments.

 

You can take how much ever time you want and also I don't think that discussing two issues at the same time will affect the quality of our dialog. I hope you give a quick response to it since I have time constraints.

 

 

Biological systems contain with them pre-existing information encoded in the DNA sufficient to account for growth, development, management of cell function and reproduction and do so without any apparent net decrease in entropy. The issue comes in when one posits that new forms are derived by increasing the order and content of older forms. I don't see how embryonic development is an analog for posited evolutionary progression, it certainly does not duplicate or follow any genetic mutation pathway. Your claim above that these past pathways are lost certainly contradicts this new posit.

 

Well ofcourse embryonic development doesn't invovle genetic mutation pathways and don't think that I was that stupid to give this as an evidence for an evolutionary pathway.

 

This was my response to your request for examples of snapshots of evolutionary progression.

The less developed forms of the ancestors can be seen in embryonic development

[Edtharan]

Derivation of complex biopolymers are not explained by reference to fatty acids, which are quite simple from an organization view.

 

bi-layers of fatty acids are not molecules. As you indicate they have regular ordered structures by virtue of the determinist processes that cause them to form up that way. When order is defined from a probability theory and thus from an entropy viewpoint, deterministic processes do not increase or decrease order because only one outcome is possible. Bi-layers and crystals and such are not organizationally complex from an entropy viewpoint.

 

Your example is another straw man illustrations because it is not in the same context.

I also mentioned Phosphoramidate DNA, which can spontainiously self polymerise into long chains as part of that explaination. It works a bit like lego blocks. Each component is fairly simple and they easily conect together.

 

It is the modularity that allows such complex, long chain molecules to form. Each time the molecule adds another module onto it, it is the same as when the first two modules connected together.

 

Now, if this long chain was kept confined in a safe environment where it could't easily be damaged, where it could't escape but the component modules could get in (say within a fatty acid vesicle), then this long chain molecule could develop into quite long strands.

 

Self organization is a straw man as is your lipid example. Self-replication, however, would be a good example. The only self-replicating biomolecules I am aware of are either contained in existing biological systems or are designed. It would be interesting to discuss an analog to the irregular sequenced, but specifically shaped and highly coherent biopolymers that are also unstable in the environment outside of the cell.

Not at all. Self organisation is the first step to self replication. All self replicating systems have to self organise.

 

The setps that will occur are:

 

1) Self organisation

2) Externally driven replication

3) Self replication

 

The example I provided with fatty acid vesicles and Phosphoramidate DNA is an example of firstly self organisation. This system without any other external effects will self organise. You will get the fatty acid vesicles and the polymerisation of Phosphoramidate DNA (if this polymerisation occurs within the vesicles, the polymerised Phosphoramidate DNA will be trapped within it). Phosphoramidate DNA will also spontainiously base pair (note the base pair is not a molecule, it is a hydrogen bond between molecules) and the base pair will encourage polymerisation as well.

 

However, this is also Externally driven replication as well. If this system is contained in an environmnet that has periodic fluctuation of temperature, then the Phosphoramidate DNA chains will split their base pairs forming into two Phosphoramidate DNA chains that are reverse templates of each other. When temperatures lower, then these chains will begin to base pair again, but due to fluid movements inside the vesicle, these chains will be seperated, thus the base pairing will be with indivisual Phosphoramidate DNA bases.

 

This process will create two Phosphoramidate DNA base paired chains. You will have replication driven by external influences (eg the cycleing of temperature in the external environment).

 

However, Phosphoramidate DNA is not passive. It has some enzymeatic activity. This activity can produce other molecules, such as lipid, and even produce chemicals that encourage (or directly) the creation of Phosphoramidate DNA. Also, some of these other chemicals mimic the effects of heat and cause the Phosphoramidate DNA base pairs to split apart.

 

When structures like this exist, then you have internally driven (or self) replication.

 

This shows how you go from self organisation, to externally driven replication to self replication.

[cypress]

I have no problem with the timelines or your estimates of it but I disagree with your claim that known evolutionary processes can not account for it.

 

OK, I'll begin in my next post to demonstrate where experimental evidence supported by population genetic modeling illustrates the problem. Perhaps you will be able to offer evidence that overcomes the obstacles I raise. Is we proceed you can bring in the objections you summarized in your post.

 

If there is a resonable evidence against your hypothesis then you have to withdraw that hypothesis.

 

Reasonable scientific evidence, yes, philosophical arguments, no.

 

Well it is not my hypothesis. This hypothesis was claimed by biologists who discovered the evidence that many of the genes involved in photosynthesis had different evolutionary histories.

 

Since they are not here to make their case, you will have to make it for them or agree to drop this line from your argument.

 

 

 

Yes I never gave you an evidence for the stepwise evolution of multi-component structures but it does give us the basic glimpses of how it might happen which keeps the mechanisms of evolution based on darwinian terms unpunctured.

 

Then yours is a philosophical argument. We should stick to evidence.

 

Most biologists agree that we might never be able to show the evidence requested by Michael Behe. I suppose you understand the complexity of the task involved here.

 

To posit that all observed diversity is a result of evolutionary processes is a grand claim, some say it is an incredible claim. I think I have some small understanding of the complexity of the task these bombastic individuals embraced. In science one should take care when making claims they can't demonstrate.

 

We have to take this seriously and put a dynamic system under observation and see what the hell is going on here rather than just quarreling with each other.

 

There are a lot of researchers looking into what is going on. Others are summarizing and debating what the research means. I think we are in the debate.

 

Well it was you who raised the issue and its your claim and we are quite happy to show you that your claim is wrong or flawed. We have disproved it by giving quite reasonable arguments.

 

Ok I'll address this now.

 

Arguments based on reason alone generally take place in philosophy. I have asked for evidence and demonstration. What you described from neuroscience could be processing and storage of information as opposed to generation of the information. In computers, thermal and electrical energy is used to process and store information, but the information itself is derived and inserted by the program and systems design which come from the designer. What objective process has been offered to determine if it is the material brain alone generating information from energy? The trouble with using biological systems to attempt to argue the ability of material only processes is that it has not been demonstrably established that biological systems have material as the sole source.

 

Well ofcourse embryonic development doesn't invovle genetic mutation pathways and don't think that I was that stupid to give this as an evidence for an evolutionary pathway.

 

I don't think you are stupid, or I would likely not respond to your post at all.

 

This was my response to your request for examples of snapshots of evolutionary progression.

The less developed forms of the ancestors can be seen in embryonic development

 

People see in things what they want to see. It is a form of conformational bias.

 

"It is now firmly established that ontogeny does not repeat phylogeny.", George Gaylord Simpson and William S. Beck, Life: An Introduction to Biology, 1965

 

"The theory of recapitulation has had a great and, while it lasted, regrettable influence on the progress of embryology.", Gavin R. de Beer, Embryos and Ancestors, 1951

 

 

"Surely the biogenic law is as dead as a doornail.", Keith Stewart Thomson, "Ontogeny and Phylogeny Recapitulated," American Scientist, May-June 1988

[immortal]

Since they are not here to make their case, you will have to make it for them or agree to drop this line from your argument.

 

But still you can't ignore that hypothesis.

 

Then yours is a philosophical argument. We should stick to evidence.

 

If a theory firmly accounts for the reality it claims to describe the more we try to disprove it then more is our faith towards that theory.

 

 

To posit that all observed diversity is a result of evolutionary processes is a grand claim, some say it is an incredible claim. I think I have some small understanding of the complexity of the task these bombastic individuals embraced. In science one should take care when making claims they can't demonstrate.

 

Just because we can not have an empirical evidence of the process the theory describes it doesn't necessarily mean that the process doesn't account for it. We may know it indirectly.

 

For example:- We can not see the quarks present in protons but still we can know its presence indirectly by the way the protons interact with other charged particles.

 

There are a lot of researchers looking into what is going on. Others are summarizing and debating what the research means. I think we are in the debate.

 

May be my knowledge is outdated.

 

 

Ok I'll address this now.

 

Arguments based on reason alone generally take place in philosophy. I have asked for evidence and demonstration. What you described from neuroscience could be processing and storage of information as opposed to generation of the information.

 

This was not an argument based on philosophy infact it is a process which is going on as I am typing these letters. It is a well established objective process. Do some research in molecular neurobiology.

 

According to your terminology generation of information is nothing but eliminating all other possibilities and this is exactly what the physical brain is capable of doing. Even in computers the newly generated information is stored in memory before it is sent as the output. So the newly generated information is stored in brain and it clearly demonstrates the generation of new information.

 

In computers, thermal and electrical energy is used to process and store information, but the information itself is derived and inserted by the program and systems design which come from the designer. What objective process has been offered to determine if it is the material brain alone generating information from energy? The trouble with using biological systems to attempt to argue the ability of material only processes is that it has not been demonstrably established that biological systems have material as the sole source.

 

Again this is your problem not ours it is on you to show that in some instances biological systems require information source from somewhere else. You asked for how thermodynamic entropy substitutes for information entropy and we have demonstrated it and it is on you to show the instances where it fails.

 

People see in things what they want to see. It is a form of conformational bias.

 

I don't have to be bias on one thing. I have got no problem in accepting the requirement for design processes if it really exists and accounts for the reality as it is.

[cypress]

But still you can't ignore that hypothesis.

 

If there is no one to defend it, I don't see why not.

 

According to your terminology generation of information is nothing but eliminating all other possibilities and this is exactly what the physical brain is capable of doing. Even in computers the newly generated information is stored in memory before it is sent as the output. So the newly generated information is stored in brain and it clearly demonstrates the generation of new information.

 

It has been objectively established that information is stored and recalled from the brain, but it is not established that information is generated in the brain. It is believed that information is generated by the mind but it is not known if the mind is a manifestation of the material brain or not. It is not testable.

 

Again this is your problem not ours it is on you to show that in some instances biological systems require information source from somewhere else. You asked for how thermodynamic entropy substitutes for information entropy and we have demonstrated it and it is on you to show the instances where it fails.

 

This is a joint problem. It has not been established that the mind is separate from the material brain but it is also not established that the mind is a manifestation of the material brain alone.

 

I will return to your comments in your previous post next chance I have.

[immortal]

It has been objectively established that information is stored and recalled from the brain, but it is not established that information is generated in the brain. It is believed that information is generated by the mind but it is not known if the mind is a manifestation of the material brain or not. It is not testable.

This is a joint problem. It has not been established that the mind is separate from the material brain but it is also not established that the mind is a manifestation of the material brain alone.

 

Interesting speculation but it is outside science. Therefore this can not be used as an argument against evolution by Natural selection. Science tries to make models of the physical world which can ne testified.

I always thought from the beginning of this thread that if there is indeed a intelligent design process then it should be outside of science so it is definitely absurd to argue against evolutionary processes using this argument. It doesn't mean that we know all evolutionary mechanisms and there are no loopholes here. We should allow both kind of investigations.

[Edtharan]

If there is no one to defend it, I don't see why not.

 

It has been objectively established that information is stored and recalled from the brain, but it is not established that information is generated in the brain. It is believed that information is generated by the mind but it is not known if the mind is a manifestation of the material brain or not. It is not testable.

 

This is a joint problem. It has not been established that the mind is separate from the material brain but it is also not established that the mind is a manifestation of the material brain alone.

But this is not enough to propose that the mind is non physical, even if the brain does not generate the mind. There is always the posibility that the "mind" does not exist at all and it is just an illusion/delusion (and many other posibilities that have not yet been explored).

 

So it does not follow that your conclusion is true, even if it was proved that the brain does not generate the mind.

[cypress]

Interesting speculation but it is outside science.

 

How so? While there is no known way to test the idea that the material brain causes the mind, the concept of dualism is a scientific area of research with testable activity ongoing.

 

Therefore this can not be used as an argument against evolution by Natural selection. Science tries to make models of the physical world which can ne testified.

 

True and these researchers are making use of this process.

 

I always thought from the beginning of this thread that if there is indeed a intelligent design process then it should be outside of science so it is definitely absurd to argue against evolutionary processes using this argument. It doesn't mean that we know all evolutionary mechanisms and there are no loopholes here. We should allow both kind of investigations.

 

Why should it be outside of science? Seeding from alien intelligence is one testable scientific area of study consistent with this thread just as John noted previously.

Edited December 2, 2010 by cypress