Annoying creationists

[cyborg]

But I still feel I had a choice if I answered this post,

I couldn't give a crap if you feel Jesus told you to create a new Christian cult - feelings are irrelevant.

Why do you seem to think how you feel overrides how it is?

 

[Kotatsu]

Are you proposing that humans and chimpanzees evolved from the primate precursor by these mechanisms?

Surely you can read? I propose that those mechanisms are possible ways by which speciation may occur. Nothing more. I have not proposed that they are necessarily part of any or all given speciation processes. In fact, I have suggested a case of speciation where neither has to occur: autopolyploidization. However, that is not to say that I would hold it impossible that one or both of those processed were involved, at least at some point.

As to your specific example, I have no idea. My area is oligochaetes. Ask me about them.

 

[Ivor the Engineer]

<snip>
You're being accused of saying that discussing the issue is a waste of time - nothing else.

Then I'm not guilty your honour. And I can prove it:

And what should we do with the knowledge that free will is an illusion on a day to day basis?

Or to put it another way, what tasks can you perform better by incorporating that knowledge?

Mercutio gave me an intelligent and sensible reply. You appear to be up for an argument and want me to bend to your (non-free) will. It isn’t going to happen.

 

[Dr Richard]

I think you are rather missing the point. Virtually all equilibrium reactions will have oscillated.

(snip)

Specifying more detailed chemistry needs model experiments and people who are funded to do them. I aim simply to lay down the architecture of the approach...

So, supposing you got some funding tomorrow from a benefactor who read your website or your posts here and was so impressed with the idea they wanted you to progress your work experimentally, to the tune of say a million dollars.

Where would you start? Which model experiments would you propose? Which chemicals would form your initial starting set and what reactions would you be looking for?

 

[Dr Richard]

[continue_thread_derail_with_free_will_debate]

“What comes before determines what comes after….”
“And just what comes before…?”
“For Men? History. Language. Passion. Custom. All these things determine what men say, think, and do. These are the hidden puppet-strings from which all men hang.”

“We seek absolute awareness, the self-moving thought. The thoughts of all men arise from the darkness. If you are the movement of your soul, and the cause of that movement precedes you, then how could you ever call your thoughts your own? How could you be anything other than a slave to the darkness that comes before? ...Only knowing the sources of thought and action allows us to own our thoughts and our actions, to throw off the yoke of circumstance.”

The Darkness That Comes Before, R Scott Bakker


[end_thread_derail_with_free_will_debate????]

 

[John Hewitt]

So, supposing you got some funding tomorrow from a benefactor who read your website or your posts here and was so impressed with the idea they wanted you to progress your work experimentally, to the tune of say a million dollars.

Where would you start? Which model experiments would you propose? Which chemicals would form your initial starting set and what reactions would you be looking for?

I did touch on this toward the end of my work.
1. Take the best current estimates for the temperature, daily, 13 hour, temperature excursion.
2. Set up an apparatus to apply those temperature cycles.
3. Add in high energy events such as UV light during the high temperature part of the cycle. Add mixing processes.
4. Add substrates - salty water, suitable igneous rocks and whatnot to provide a range of protected and unprotected environments.
5. Add suitable chemicals, possibly an approximation to the soup, possibly more specific chemicals to test specific ideas.
6. Abstract samples over time and lay hand upon a GC/MS apparatus, which can rapidly identify and measure the concentrations of a large number of different organic chemicals. Then plot variations in the composition as they develop - if they develop. If they do not, begin again at step one.
7. Use the resulting data to narrow down the range of likely pathways through which prebiotic oscillations would have evolved.

It is true that one could guess at likely reactions but, really, one would hope that the experimental data would be telling you.

 

[kleinman]

Annoying Creationists

Are you proposing that humans and chimpanzees evolved from the primate precursor by these mechanisms?

Surely you can read? I propose that those mechanisms are possible ways by which speciation may occur. Nothing more. I have not proposed that they are necessarily part of any or all given speciation processes. In fact, I have suggested a case of speciation where neither has to occur: autopolyploidization. However, that is not to say that I would hold it impossible that one or both of those processed were involved, at least at some point.

Surely you can do mathematics? If it was autopolyploidization or recombination, show us how this was done. Random point mutations is a profoundly slow mechanism for accumulating information when using realistic genome lengths and mutation rates as show by ev. So what mechanism evolved the human and chimpanzee from its ancestral predecessor? Describe to us the mechanism of selection.

So, supposing you got some funding tomorrow from a benefactor who read your website or your posts here and was so impressed with the idea they wanted you to progress your work experimentally, to the tune of say a million dollars.

Where would you start? Which model experiments would you propose? Which chemicals would form your initial starting set and what reactions would you be looking for?

I did touch on this toward the end of my work.
1. Take the best current estimates for the temperature, daily, 13 hour, temperature excursion.
2. Set up an apparatus to apply those temperature cycles.
3. Add in high energy events such as UV light during the high temperature part of the cycle. Add mixing processes.
4. Add substrates - salty water, suitable igneous rocks and whatnot to provide a range of protected and unprotected environments.
5. Add suitable chemicals, possibly an approximation to the soup, possibly more specific chemicals to test specific ideas.
6. Abstract samples over time and lay hand upon a GC/MS apparatus, which can rapidly identify and measure the concentrations of a large number of different organic chemicals. Then plot variations in the composition as they develop - if they develop. If they do not, begin again at step one.
7. Use the resulting data to narrow down the range of likely pathways through which prebiotic oscillations would have evolved.

It is true that one could guess at likely reactions but, really, one would hope that the experimental data would be telling you.

John, your proposal will encounter the same mathematical limitations that other proposals of abiogenesis have. Without a selection mechanism, the probabilities for forming the complex molecules needed for living things will be astronomically small. The miniscule probabilities occur even if you assume that the only mers in your salty solution are amino acids or RNA bases. Consider the link that Delphi provided with the self replicating ribozyme. This reaction requires a carefully controlled environment to get an results. What happens when you have a complex soup of molecules, your equilibrium equations have numerous competing chemical reactions.

And consider this, we still have a 24 hour heating and cooling cycle today. Why aren’t new life forms being generated all the time?

 

[Mercutio]

But I still feel I had a choice if I answered this post, just as I feel I have choices about what I’m going to cook for dinner tonight and what I’m going to watch on TV.

When Wilhelm Wundt, in his early psychological laboratory, introspected about the decision-making process, he deliberately started with very very simple decisions. Seeing a signal, deciding which of two signals it was, responding appropriately. And introspecting about what the processes must be that make up this chain. Perception, apperception, thought, each subjectively dissected; we have extensive writings on what this task feels like.

Modern neuroscience can trace the pathways back and forth (there are always feedback loops; it is not a one-way process) through various serial and parallel brain processes, from the retina through the LGN to the primary (V1) visual cortex, though V2, V4, on to the infratemporal cortex, up to the prefrontal, primary motor cortext, motor projection areas, spinal cord, down to the finger that presses the key. What is happening is very little like what it feels like (we have no sensory nerves in the brain, after all).

Even when we can locate the neural equivalent of "this is what making a choice feels like", we see (a la Libet) that it is effect, rather than cause. We also see (e.g., Chalmers) that conscious awareness is not necessary for many of the things we do for which we have always assumed that conscious awareness in necessary (blindsight is perhaps the most well-known counter-example, but it is not the only one).

Perhaps you are a more committed Determinist than I?

Or perhaps I have simply filled in more gaps. At some point, thinking those gaps are big enough to hide "free will" is just silly; even the defenders of free will on this forum have had to redefine it in a much more modest form than "free will" has historically taken.

 

[John Hewitt]

John, your proposal will encounter the same mathematical limitations that other proposals of abiogenesis have. Without a selection mechanism, the probabilities for forming the complex molecules needed for living things will be astronomically small. The miniscule probabilities occur even if you assume that the only mers in your salty solution are amino acids or RNA bases. Consider the link that Delphi provided with the self replicating ribozyme. This reaction requires a carefully controlled environment to get an results. What happens when you have a complex soup of molecules, your equilibrium equations have numerous competing chemical reactions.

And consider this, we still have a 24 hour heating and cooling cycle today. Why aren’t new life forms being generated all the time?

There is a selection mechanism inherent in my work and the initial environment could be essentially random with few high energy molecules present. I agree that mathematical modelling, or even computer modelling, would be waste of time without some model experimental figures to start off with and point the simulations in some kind of direction.

The careful control of conditions needed for RNA synthesis experiments is, indeed, one of several very strong reasons not to take the RNA world seriously.

On a point of detail, the prebiotic earth probably had a 12-13 hour day - the earth's spin is slowing down due to tidal friction. (This is why "leap seconds" are periodically added to days.) In principle, the mechanism I propose could still exist, though the presence of oxygen might change the details of the chemistry. In any event, and whether or not my work is correct, I think any evolutionary model implies that current life forms would be able to outcompete newly emerging competitors.

 

[kleinman]

Annoying Creationists

John, your proposal will encounter the same mathematical limitations that other proposals of abiogenesis have. Without a selection mechanism, the probabilities for forming the complex molecules needed for living things will be astronomically small. The miniscule probabilities occur even if you assume that the only mers in your salty solution are amino acids or RNA bases. Consider the link that Delphi provided with the self replicating ribozyme. This reaction requires a carefully controlled environment to get an results. What happens when you have a complex soup of molecules, your equilibrium equations have numerous competing chemical reactions.

There is a selection mechanism inherent in my work and the initial environment could be essentially random with few high energy molecules present. I agree that mathematical modelling, or even computer modelling, would be waste of time without some model experimental figures to start off with and point the simulations in some kind of direction.

I have challenged the other readers of this thread for a description of their selection mechanism that would lead to the complex molecules that are in all life forms. Do you care to take up this challenge?

How much time do you think your experiment would take before you have some experimental figures to use in a computer simulation?

The careful control of conditions needed for RNA synthesis experiments is, indeed, one of several very strong reasons not to take the RNA world seriously.

RNA proponents have not offered a description of a selection mechanism either that would form their self replicators.

And consider this, we still have a 24 hour heating and cooling cycle today. Why aren’t new life forms being generated all the time?

On a point of detail, the prebiotic earth probably had a 12-13 hour day - the earth's spin is slowing down due to tidal friction. (This is why "leap seconds" are periodically added to days.) In principle, the mechanism I propose could still exist, though the presence of oxygen might change the details of the chemistry. In any event, and whether or not my work is correct, I think any evolutionary model implies that current life forms would be able to outcompete newly emerging competitors.

You are assuming that the earth was around long enough for the slowing of the spin to give us our present day time duration, but I’ll leave that argument to the young earth geologists who seem to be coming out from under the rocks.

Do you think your experiment would run more quickly with a 12-13 hour cycle or a 24 hour cycle? Let’s say that you can generate some complex biological molecules by your heating and cooling proposal, how long do you think these molecules would stay in their complex form before they denature?

If your theory is correct, why wouldn’t we find signs of the chemicals required to generate life spontaneously around all the time even though they may not form new life because they are out competed by other competitiors.

 

[hammegk]

... Seeing a signal, deciding which of two signals it was, responding appropriately. And introspecting about what the processes must be that make up this chain. Perception, apperception, thought, each subjectively dissected; we have extensive writings on what this task feels like.

What might rote signal processing as described have to do with free will?

Even when we can locate the neural equivalent of "this is what making a choice feels like", we see (a la Libet) that it is effect, rather than cause.

Er, yes. What do you actually have to say regarding a "cause"?

We also see (e.g., Chalmers) that conscious awareness is not necessary for many of the things we do for which we have always assumed that conscious awareness in necessary (blindsight is perhaps the most well-known counter-example, but it is not the only one).

Yawn. What makes you believe free will involves any public behavior? I will ask how science samples which thought is selected from the ongoing possibilities, and why it was selected?

Or perhaps I have simply filled in more gaps. At some point, thinking those gaps are big enough to hide "free will" is just silly; even the defenders of free will on this forum have had to redefine it in a much more modest form than "free will" has historically taken.

Even if our minds are programmed automata 99.9999% of the time, why would you suggest meaningful free will has no room to operate? Are you with Schneib -- if it's 90% probable, there's nothing left to discuss?

 

[Kotatsu]

Surely you can do mathematics? If it was autopolyploidization or recombination, show us how this was done. Random point mutations is a profoundly slow mechanism for accumulating information when using realistic genome lengths and mutation rates as show by ev. So what mechanism evolved the human and chimpanzee from its ancestral predecessor? Describe to us the mechanism of selection.

So I shall conclude that you cannot read, is that correct?

I would wager that that part of evolutionary history was achieved by a combination of several mechanisms, including random point mutations, sexual selection, natural selection, and several other mechanisms which are well understood, and many of which have actually been discussed and even described earlier in this thread.

You will notice that I used "random point mutations" in my answer. This is because you have failed to show that this is too slow a mechanism when using not only realistic values of the parametres you chose to use, but also include all other known mechanisms. Well, in fact you have failed to show anything.

 

[John Hewitt]

I have challenged the other readers of this thread for a description of their selection mechanism that would lead to the complex molecules that are in all life forms. Do you care to take up this challenge?

How much time do you think your experiment would take before you have some experimental figures to use in a computer simulation?

RNA proponents have not offered a description of a selection mechanism either that would form their self replicators.

You are assuming that the earth was around long enough for the slowing of the spin to give us our present day time duration, but I’ll leave that argument to the young earth geologists who seem to be coming out from under the rocks.

Do you think your experiment would run more quickly with a 12-13 hour cycle or a 24 hour cycle? Let’s say that you can generate some complex biological molecules by your heating and cooling proposal, how long do you think these molecules would stay in their complex form before they denature?

If your theory is correct, why wouldn’t we find signs of the chemicals required to generate life spontaneously around all the time even though they may not form new life because they are out competed by other competitiors.

The selection mechanism I describe is in chapter 4 under the prebiotic evolution link of "sex and philosophy." It depends on the high energy processes such as UV exposure, lightning etc. and competition for environments that are protected from such processes. Many of the equilibrium reactions leading to oscillations are likely to include polymerization steps that might generate macromolecules.

I do not have a fairy godfather and do not anticipate doing the kind of experiment I described in response to Dr. Richard's inguiry. I do not know how many cycles one would need to use but one would not have enough time to replicate the real earth. Instead, one would try to devise conditions that would speed things up and use the results to extrapolate over longer time frames.

The word "denature" is used to describe the unfolding of a protein with consequent loss of its biological activity. Emergent macromolecules would themselves be subject to selection according to whether their physicochemical properties did or did not cause them to occupy protected niches. However, they would have no preexisting biological function and hence, the word "denature" is inapplicable.

You are correct that I have taken my estimate of the earth's age from conventional dating procedures. As I have often stressed, my work is evolutionary and it would be inconsistent to adopt any other figure. I do not think the mechanism I propose could be easily accommodated into a young earth scenario.

Modern organisms would be expected to be more efficient and to outcompete any prebiotic process. This would be expecially true of the mechanism I have suggested since it depends upon high energy processes, including those following UV exposure. UV exposure is now much lower than it would have been on the prebiotic earth due to the appearance of an oxygenated atmosphere and the ozone layer. The ozone absorbs UV and greatly reduces UV intensity at the surface. Oxygen would also tend to oxidise many organic compounds to CO2 and water. Hence, there are several reasons to expect this phenomenon to be less significant on the modern earth than it was before the emergence of life. Nonetheless, to a small extent, it may still exist.

 

[kleinman]

Annoying Creationists

Surely you can do mathematics? If it was autopolyploidization or recombination, show us how this was done. Random point mutations is a profoundly slow mechanism for accumulating information when using realistic genome lengths and mutation rates as show by ev. So what mechanism evolved the human and chimpanzee from its ancestral predecessor? Describe to us the mechanism of selection.

So I shall conclude that you cannot read, is that correct?

You draw so many illogical conclusion, why not one more?

I would wager that that part of evolutionary history was achieved by a combination of several mechanisms, including random point mutations, sexual selection, natural selection, and several other mechanisms which are well understood, and many of which have actually been discussed and even described earlier in this thread.

The difference between Dr Schneider and you is that Dr Schneider performed mathematical computations with his slogan. His mathematical computations show that random point mutations do not get anywhere close to showing how macroevolution could have occurred. You reiterate and discuss the slogans but do not show how mutations of any kind and selection can evolve a gene from the beginning. Without a selection mechanism there is no mathematics of mutation and selection.

You will notice that I used "random point mutations" in my answer. This is because you have failed to show that this is too slow a mechanism when using not only realistic values of the parametres you chose to use, but also include all other known mechanisms. Well, in fact you have failed to show anything.

Ask Paul whether I have shown anything as his description of ev goes from a model of reality to it models a small part of the evolutionary landscape to it is a stylized model…

Unless you can present a realistic description of how selection works to evolve a gene from the beginning, your explanation for the theory of evolution collapses to mutation without selection.

I have challenged the other readers of this thread for a description of their selection mechanism that would lead to the complex molecules that are in all life forms. Do you care to take up this challenge?

The selection mechanism I describe is in chapter 4 under the prebiotic evolution link of "sex and philosophy." It depends on the high energy processes such as UV exposure, lightning etc. and competition for environments that are protected from such processes. Many of the equilibrium reactions leading to oscillations are likely to include polymerization steps that might generate macromolecules.

UV exposure can be destructive to organic molecules. Look what happens to the tires on you automobile if it is parked in the sun for long periods. Perhaps you can get polymerization in the experiment you prepose but how do you get the unique sequences of mers necessary to generate life?

How much time do you think your experiment would take before you have some experimental figures to use in a computer simulation?

I do not have a fairy godfather and do not anticipate doing the kind of experiment I described in response to Dr. Richard's inguiry. I do not know how many cycles one would need to use but one would not have enough time to replicate the real earth. Instead, one would try to devise conditions that would speed things up and use the results to extrapolate over longer time frames.

You can make rough estimates for the number of cycles. For example, if it took 100,000,000 years to spontaneously generate life, that would give approximately 2 * 365 * 100,000,000 cycles. I included the factor of 2 since the earth was rotating twice as fast. I don’t know of anyone since the Miller experiment of the 1950’s who tried to demonstrate chemically how life could have formed. What kind of polymer do you believe was the initial source of life?

Do you think your experiment would run more quickly with a 12-13 hour cycle or a 24 hour cycle? Let’s say that you can generate some complex biological molecules by your heating and cooling proposal, how long do you think these molecules would stay in their complex form before they denature?

The word "denature" is used to describe the unfolding of a protein with consequent loss of its biological activity. Emergent macromolecules would themselves be subject to selection according to whether their physicochemical properties did or did not cause them to occupy protected niches. However, they would have no preexisting biological function and hence, the word "denature" is inapplicable.

I use the term “denature” in a more general sense and include unfolding of a molecule or mechanism of altering a molecule from its original state. For example, iodine disinfects by attaching to the proteins of a cell which in turn changes the folding of that protein and its enzymatic properties.

Biologic molecules such as proteins, DNA and carbohydrates are very reactive molecules and don’t remain in their original condition for very long when exposed to the wide array of chemicals you would find in the primordial soup. Even if you manage to generate biologic polymers, how long do you think they would remain in that state before react with other chemicals in the primordial soup?

You are assuming that the earth was around long enough for the slowing of the spin to give us our present day time duration, but I’ll leave that argument to the young earth geologists who seem to be coming out from under the rocks.

You are correct that I have taken my estimate of the earth's age from conventional dating procedures. As I have often stressed, my work is evolutionary and it would be inconsistent to adopt any other figure. I do not think the mechanism I propose could be easily accommodated into a young earth scenario.

That’s fine, I have used the “conventional” age of the earth in these discussions since ev is so slow at converging that the age of the earth doesn’t have to enter the debate.

If your theory is correct, why wouldn’t we find signs of the chemicals required to generate life spontaneously around all the time even though they may not form new life because they are out competed by other competitiors.

Modern organisms would be expected to be more efficient and to outcompete any prebiotic process. This would be expecially true of the mechanism I have suggested since it depends upon high energy processes, including those following UV exposure. UV exposure is now much lower than it would have been on the prebiotic earth due to the appearance of an oxygenated atmosphere and the ozone layer. The ozone absorbs UV and greatly reduces UV intensity at the surface. Oxygen would also tend to oxidise many organic compounds to CO2 and water. Hence, there are several reasons to expect this phenomenon to be less significant on the modern earth than it was before the emergence of life. Nonetheless, to a small extent, it may still exist.

UV light is used as a disinfectant. If I understand this mechanism, the high energy UV photons knock off electrons making free radicals which are more chemically reactive. You believe you can make biologic polymers this way? I think you could set up an experiment fairly easily to try and demonstrate if this happens. A UV light, a heater, a timer, a flask and some raw chemicals. What chemicals would you put in the flask?

 

[kjkent1]

Gee, if I'd known you were going to start adding "stylized," I would have said "stylized to demonstrate one particular thing." Then you would say:

No one said science is finished, only that the theory of evolution is finished, it is mathematically impossible, your own (stylized to demonstrate one particular thing) computer model shows this.

Then your statement would be even more clearly and self-evidently ludicrous.

~~ Paul

Paul, have you ever run Unnamed's selection function past Dr. Schneider to see if he found it a reasonable response to the allegation that ev's original selection method is unrealistically slow?

 

[Schneibster]

The oscillation is the entity that evolves.

John, when evolutionary biologists talk about the evolution of the common ancestor of chimps and people into chimps and people, they don't talk about evolution of oscillations.

Let's try this again. Perhaps I wasn't specific enough. When a living creature on Earth, that is, a single- or multicellular life form that uses DNA, evolves, what precisely evolves?

BTW, it is not my intent to be obtuse. I can see where you want to go with the conversation, and if you'll humor me for a little while, we'll go there. I just want to establish some common ground so that I'm sure we're communicating on the same terms.

ETA: I forgot to answer your question. I'll get to how earlobes get into it when we've established that common ground.

 

[articulett]

The problem with the creationists is they want everybody to spend time proving each of their individual pet hypotheses wrong when we have a great framework that is amassing data and furthering understanding. It always sounds to me like someone trying to reorganize the periodic chart because of something they feel they can explain better or something that doesn't make sense to them.

I don't care why John uses the term "free will"--it's just not scientific or scholarly--it's obfuscating. As is his refusal to say whether he believes in an "intelligent designer" or rather his theory sticks to naturalistic explanations.

As for his pre-biotic theory...it never links up to the facts we have. Yet there is so much more that does. Like this information, which Hewitt dismissed. Why is he not interested? Why does he not want to illustrate how his "hypothesis" is better or more useful or where it dovetails.

http://www.physorg.com/news82299861.html

David Deamer, professor of chemistry and biochemistry at U.C. Santa Cruz, commented that "Bob Hazen is boldly asking a fundamental question related to the origin of life. We know that organic compounds were present in the early Earth environment, but as dilute solutions of thousands of different species in the global seas. How were specific kinds of organics selected to assemble into the first forms of life, and by what process were they sufficiently concentrated to initiate a primitive version of metabolism? We now know that minerals select specific organic compounds out of solution, and can even distinguish between subtle properties such as chirality, binding a left-handed amino acid in preference to one that is right handed. These are very significant results that are guiding my own research as well as many other investigators in the field."

Yes, energy going into the system is a major component in life formation--energy from the sun and movements...and also energy from the core of the earth--which may be the most important energy source at the bottom of the "primordial soup"--but the article above actually links the input of energy with the output of certain kinds of molecules sticking together--the kinds of molecules associated with life-- ribonucleic acids. When does John's theory get to the nucleic acids? And how can he keep insisting that the cell is the true replicator when we know that both RNA and DNA can replicate outside of a cell with the right catalyst. Denucleated cells can't--nor can prokaryotic cells without DNA. Or can they under his hypothesis.

 

[Yahzi]

Facts are anathema.

That's all I needed to hear.

 

[The Atheist]

That's all I needed wanted to hear.

Fixed it for you!

 

[Yahzi]

Eventually they evolve to self-oscillating biochemical pathways that resemble Eigen's hypercycles; and yes Schneibster, biochemical pathways do self-oscillate - not widely known that but they do.

If the RNA world was too chaotic to allow RNA to reproduce, how could it have been stable enough for your pathways to maintain an oscillation?

Shouldn't there be some calculations about binding strengths here?