Annoying creationists

[delphi_ote]

Could you be a "a completely successful human animal" without those things?

In the context of biology, yes. Successful would mean surviving and procreating. You can do both without any of those things (otherwise we wouldn't be here.)

 

[Apathia]

In the context of biology, yes. Successful would mean surviving and procreating. You can do both without any of those things (otherwise we wouldn't be here.)

Sad but true. The Biological Imperitive generally sweeps away any conventional cultural wisdom, good judgement, and Science anyway.

What value knowing the abstraction of Free Will is illusory may have in your daily life, is outside the subject area of this thread. Consider that it will help break the attachment to that perverse abstraction called the 'ego" and help foster tollerance and compassion.

 

[cyborg]

I don't know about you, but I think a grasp of grammar and language is pretty advanced. As are the nuances of social knowledge.

I don't.

A capacity for language is an innate thing - the complexity of modern languages did not spring up overnight.

A capacity for social behaviour is an innate thing - the complexity of modern societies did not spring up overnight.

Could you be a "a completely successful human animal" without those things?

Unless you're going to posit a Flintstones view of reality then this fact is self-evident.

 

[Mercutio]

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?

I refer you to 30 years and 39 years, respectively, of publication of the peer-reviewed journals Behavior Modification and the Journal of Applied Behavior Analysis. More recently we can include 15 years of the journal Behavior and Society, and of course decades of scholarly books. Remember that any attempt to scientifically study our behavior must rely on our behavior acting lawfully. Advances in education, behavioral medicine, industrial/organizational applications, clinical Behavior Modification, all (tacitly or explicitly) depend upon assumptions of determined behavior.

 

[Dr Richard]

I agree that the assumptions of my prebiosis work are "mundane," your word and chosen negatively I think. There is nothing exceptionable about the assumptions but I have not found them applied previously and my theory does seem to be original.

The sun would act upon any chemical equilibrium that was not thermoneutral - so there is a great variety of oscillations and selection would act upon them. The final products of selection would resemble biochemical pathways. Hence my work is a "metabolism first" theory.

Which chemical equilibria?

How would selection act upon them?

And, cruicially, how would these pathways generate a mechanism for "genetically" passing on the results of this selection?

And how would this lead to the generation of RNA/DNA?

Erm ... your facetiousness and negativeness is showing. I do not think a replicator is needed for evolution, what is needed is replicating data. I am proposing that the sun provides that until self-replicating systems emerge by evolution. I suggest you read Shapiro - what was his title "A Replicator is not Needed for the Origin of Life" - something like that.

But, as detailed above, that data needs to be recorded, stored and passed on in a reasonably faithful manner.

Again, your theory (as explained so far) seems to have no idea how this would occur.

I have had a look at Shapiro's Hypothesis paper ( I presume this is the one you mean) - essentially a critique of the RNA world hypothesis - and one that rests the majority of its case on the assumption that meteorites replicate the conditions found on prebiotic Earth. The only real discussion of absent self-replicating mechanisms comes in the last paragraph:

Several scientists have put forth theories that do not require an ordered polymeric replicator at the start of life. They propose, instead, that life began with a mutually sustaining set of catalytic reactions involving smaller molecules (see, for example, 33–35). Such theories provide a robust alternative to ideas based on a replicator. The details can differ; for example, the reaction set might be carried out on a mineral surface (36), or within a membrane-bound compartment (37–39). Insufficient experimental attention has been given to such ideas, but if the hypothesis presented here is accepted, perhaps they will move to the forefront of origin-of-life research.

But I have to say that I feel all such debate essentially ends up running down the same pathway. The "RNA world" supporters are, I would say, looking at end-stage abiogenesis, the creation of the self-replicating molecules that went on to become the first forms of "life".

I think you (and the references Shapiro cites) are looking at earlier events - what drove the chemical reactions to create the RNA (or equivalent) environment from which they formed.

You may disagree, but unless you can provide a more detailed theory of your own, I stand by my interpretation.

I haven't got the paper you cite but I collect these things so if you can get me a pdf of it that would be helpful.

Hummnnnnn... not sure what the forum rules are about distributing copyrighted material... (ahem) - PM me?

Thank you for saying that "If you can provide evidence that your own idea is more fully developed than the data presented in this paper, I would be happy to reconsider, but at the moment I view an RNA world as being the most credible explanation of early molecular evolution." There is no serious evidential support for the RNA world theory and that theory makes assumptions that are chemically unworkable. As for the above comment, I think it a one-sided prejudgement.

I feel it is a perfectly reasonable position, in that currently the RNA world hypothesis has many more adherents in the scientific community than the John Hewitt hypothesis. If you want to convince me (and them) then provide some evidence/more detailed reasoning.

I'm not sure why you have a problem with this concept (c.f. cellular motion and the cytoskeleton).

In my opinion, if a good scientist comes up with a good alternative hypothesis to that of prevailing wisdom, then it should be possible to back that claim with repeatable experimental evidence. If not, then the hypothesis has to go to the "interesting idea, but..." pile - my own is fairly considerable!

 

[kleinman]

Annoying Creationists

You all have been very busy!

That’s an interesting ribozyme these scientists developed. Would you care to describe a selective process where a molecule like this could evolve?

I wouldn't care to. Fortunately, Joyce has already done so in simple language on his website:

Just as organisms undergo Darwinian evolution in nature, molecules can be made to evolve in the test tube. This can lead to the production of molecules with interesting properties, including the ability to catalyze a particular chemical reaction. The recipe for Darwinian evolution of molecules is simple:

1) Start with a large population of molecules of varying composition;

2) Select those molecules, however rare, that have the desired chemical properties;

3) Produce many copies of the selected molecules, introducing occasional random changes in their composition;

4) Repeat as desired.

In our laboratory we have harnessed the power of Darwinian evolution as applied to populations of trillions of different RNA or DNA molecules. At their most rapid, our procedures allow us to carry out over 100 "generations" of test-tube evolution in a single day. The resulting molecules have interesting catalytic properties, teach us about evolution itself, and have potential application as therapeutic agents.

This is typical for an evolutionarian proof, superficial slogans. Do you want to describe that selection process in 2) that would make this self replicator? Feel free to use 4) when using the terminology “mutation and selection” since we all now know that it is only a superficial slogan. Do you want to comment on the following line from the abstract you linked to and how this study has any relationship with what could realistically happen outside a laboratory without intelligent scientists setting up the conditions for this reaction?

The R3C ligase ribozyme was redesigned so that it would ligate two substrates to generate an exact copy of itself, which then would behave in a similar manner.

I added the bold face and underlining. Seems your link on self-replicating ligase ribozyme is an argument for intelligent design.

Oh, I know, you have “billions of years” for it to happen. “billions of years” and “mutation and selection”, slogans that constitute an evolutionarian concept of proof for their theory.

They say we need a creator, then who made God? I think thats a pretty reasonable question to ask.

The question is off topic since I am not making a claim that I can prove creationism scientifically. We are discussing the mathematics of mutation and selection and how mathematics shows that the theory of evolution to be impossible. Would it make a difference to you if you had an answer?

Certainly I do. You can start with the results from ev computer model, a peer reviewed and published model of random point mutations and natural selection which shows this mechanism of evolution is so profoundly slow when using realistic genome lengths and mutation rates that nothing can evolve by this mechanism.

Why your maths is incorrect has been explained to you many times.

I will not take credit for Dr Schneider’s math and Paul’s computer programming.

Then you can again consider the concept of natural selection which can only operate if there is a benefit or detriment to the creature.

Selection can occur in non-living things.

We are all waiting for you to mathematically describe your sieve that can evolve a gene from the beginning. Perhaps you want to describe how the self replicating RNA molecule that is described in Delphi’s link could have evolved from the beginning?

I have shown that natural selection can not evolve a gene from the beginning. I will repeat it again since so many evolutionarians are in denial about this issue.

No, you haven't kleinman. You have made an assertion, and all 'evidence' you have provided has been shown to be wrong. More then once. Please see Dr. Adequate's sig, and the various posts responding to your mathematics.

You are going to use scatequate’s posts to support your arguments? Scatequate has done no better at describing natural selection mathematically than you have. Taffer is a laffer.

A gene is to evolve.

Can you please tell me what this means?

Unless you believe that genes are eternal, your theory requires that they had to start somewhere, somehow.

The first base in the sequence for the gene is laid down on the genome.

How is a sequence "laid down on" a genome? Genomes are sequences.

Have these sequences always existed?

One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.

This is quite simply a perfect example of you understanding little about evolution and genetics.

Feel free to tell us all how the first gene arose from the beginning.

It has never been claimed that the only benificial characteristic of a sequence of DNA is in the form of producing proteins. There are many more things that a sequence of DNA can do. That doesn't even start on RNA, and other organic molecules.

You need to get on the same page with Dr Richard.

Do you evolutionarians see the goal posts or are you so far out of the ball park you need the Hubble telescope just to see the ball park?

I have not seen a single person who understands genetics, biology and evolution move any goal posts in this thread. If you think there has been, please provide evidence.

Goal posts:
My argument is that the ev computer program shows that the process random point mutations and natural selection is so profoundly slow when realistic parameters are used in the model that macroevolution by this mechanism is mathematically impossible. In addition, Dr Schneider in his publications on ev concludes that ev demonstrates evolution by punctuated equilibrium as described by Stephen Gould. Dr Schneider’s conclusions are likewise impossible since Gould’s thesis of punctuated equilibrium states the evolution occurs over short time spans in small sub-populations. The mathematical results from the ev model directly contradict these two conditions.

In addition, there is no selection process that can evolve a gene from the beginning.

So the theory of evolution started without any mathematical foundation and continues to suffer from the same deficiency. The theory of evolution is modern mythology, not hard mathematical science.

This thread is about mathematically modeling evolution by mutation and selection. If you believe there is and was selective pressure to do this, present a description for this so that you can evolve a gene from the beginning.

As I already said, I do not have access to my research nor my papers from where I am. I am returning to university at the start of next week. I should be able to provide a better explanation then. However, I feel this has adequately been answered already.

God willing, we will be here for your answer when you get back to your papers.

Feel free not to discuss this topic if you believe that all genes formed during abiogenesis.

I never said this. Please follow along. The evolution of a novel gene has been demonstrated. Please see Dr. Adequate's sig. However, the formation of the first replicating molecules deals with abiogenesis, and not evolution. You have constantly failed to show a grasp of this point.

Taffer the laffer quotes scatequate as proof.

However, you have acknowledged the first step in disproving the theory of evolution.

What? Where have I done this?

You said the following.

You are correct that, without selection pressure, the theory of evolution is not mathematically possible.

So give us a mathematical description of the selection process that proves your theory. Oh, I forgot, you don’t have your papers.

The next step is understanding that there is no selective pressure that can evolve a gene from the beginning.

This is an assertion. Care to try to prove it?

I’ll quote my proof again for you.

A gene is to evolve. The first base in the sequence for the gene is laid down on the genome. One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.

You can refute my argument by describing a selection process that would evolve a gene from the beginning.

The only thing that natural selection can do is select for a creature with a beneficial property and select against a creature with a detrimental property.

Correct. However, selection can act on things which are not 'alive', in the biological sense. Try to understand this.

Do you want to describe selection mathematically rather than using the synonym “sieve”. Otherwise, you continue to use slogans to describe abiogenesis.

The addition of bases to a sequence which is neither beneficial nor detrimental will not alter the frequency of occurrence of that sequence in the population.

You do not understand population genetics. Try looking up 'genetic drift'.

Are you arguing that ‘genetic drift’ is how a gene evolves from the beginning or is ‘genetic drift’ your new slogan for the theory of evolution?

Without selection pressure, the theory of evolution is not mathematically possible as you so correctly have said.

Of course. But, again, there are and always were selective pressure. "Natural selection" on 'living' things, and just plain, ol' "selection" on non-living things.

You have missed an important principle that ev shows concerning selective pressures. If you have more than one selective pressure acting at a time, these pressures compete against each other and profoundly slow down the rate of information gain. The more different and varied selection pressures there are, the slower the evolutionary process. This same effect would interfere with concept of chemical abiogenesis. Consider the link that Delphi posted concerning the self replicating RNA molecule. This experiment only gets results in a highly controlled laboratory environment. In any realistic environment outside a laboratory, there would be many other chemical reactions occurring that would interfere with the RNA self replication.

Taffer, that’s a lovely semantic dance you are doing here.

Perhaps you care to explain how it is a "semantic dance"? I answered his question.

You move from one slogan to the next. We are looking for a mathematical description for a selection process that can evolve a gene from the beginning that can be put into ev and correct its and your theory of evolution’s mathematical deficiency.

I’m not talking about abiogenesis, I am talking about the evolution of a new gene from the beginning. Here are some examples to consider. The gene that codes for insulin, the gene that codes for globulin, the genes that code for the enzymes for the Krebs cycle, the genes that code for the proteins in the DNA replicase system and so on. Do you believe that all these genes arose during abiogenesis? Unless you can describe a sieve that would give rise to these genes from the beginning, you theory of evolution is mathematically impossible as you so correctly noted earlier.

This has already been answered, so I will not deal with the latter part of this paragraph. However, you are constantly dealing with both evolution and abiogenesis, and equating the two. It has been shown that novel genes evolve.

If you are talking about Dr Richard’s missed field goal of describing a classification system for insulin like genes from Zebra fish to humans, he failed to describe how the ancestral antecedent arose and he failed to give the selection process which evolve these genes from one to the next. Similarity of molecules does not constitute a proof of evolution. You have to show how mutation and selection gives rise to these molecules and how the molecules transform from one to the next. Ev shows that random point mutations and selection is profoundly slow, too slow to accomplish the evolution and transformation of these molecules you see as being so similar.

You have also not answered a number of questions of mine. But, let's stick to just one.

Can you please provide a definition of "soul"?

Why, you don’t believe you have one or do you?

What this is indicating that if you have more than a single selection condition, one may interfere with the other. If you have multiple genes evolving, each is responding to their selection pressure (whatever that may be), each is interfering with others preventing any from evolving.

You have no clue about evolutionary theory.

I do have a clue on what ev is showing and that is a peer reviewed and published computer simulation of random point mutations and natural selection. The ev computer simulation shows that when there is more than one selection process operating at a time, this profoundly slows the evolutionary process.

So, at what point does a mutation in a non-binding site region obtain greater selective value than of a mutation in a binding-site region?

That's way too complicated a question for my poor little brain.

Your Rcapacity equation appears to give a fairly accurate estimate for this.

This effect is not sudden, the generations for convergence increases with increasing genome length until you reach a tipping point where the errors in the binding site region dominate the selection process and you can no longer evolve binding sites in the binding site region.

"Not sudden" is incompatible with "tipping point."

The point is that as you lengthen the genome, the non-binding site region is being lengthened and the probability of non-binding site errors are increasing. This is what is slowing the rate of information accumulation. Counting the errors in both region will determine which errors are determining selection.

Is the Rcapacity problem related to the information content of the binding site or to the selection process?

I'm not sure what this means. The Rcapacity problem arises when the number of bits of information needed to uniquely identify the binding sites from the rest of the DNA cannot be held within the binding sites. Therefore it becomes difficult/impossible to evolve a code in the binding sites. I ran experiments that decoupled the Rcapacity problem from the size of the genome, showing that there are two different issues at play.

Is the information in a binding site dependent on the selection process? Unnamed’s selection process almost completely uncouples the selection process from the genome length by biasing selection to errors in the binding site region. This is why his selection process converges so quickly despite increases in the genome length.

I agree with you, two different selection processes in operation simultaneously would slow down the process down further. A third selection process would slow evolution even more so. Each additional selection process would continue to slow evolution further and as you said “certainly there are millions of selection pressures in the real world”.

Yes, but I did not say that all the extant genetic control mechanisms evolved at the same time, did I?

What do you think a realistic number of selection pressures that are acting at any given time? Which genetic control mechanisms evolve when and how?

Subtitle: Mountain of evidence -- meet bronze age manuscript.)

It seems that ev is less than a mole hill of evidence for the theory of evolution. And as I told Dr Schneider, once evolutionarians understood what ev is computing when using realistic mutation rates and genome lengths, that his model would be discredited.

Since your theory of evolution is based on mutation and selection, there is no other point to be made until you describe what the selection mechanism is.

"My" theory of evolution is based observations of actually occuring evolution, which are described by, among other things, mutations and selection.

The selection mechanism can be the preferance of, or disinclination to mate with, individuals displaying a certain feature or behaviour corresponding to a certain set of alleles or genes.

I don’t question your observation, I question your interpretation of your arguments. Recombination and selection can accomplish rapid changes in a species. Are you saying that recombination and selection is how speciation occurs?

A slogan does not constitute a scientific proof

Then I take it that your repeated claim of having disproved the theory of evolution mathematically does not constitute scientific proof, and should not be treated as such? Likewise with, oh, perhaps 80% of the rest of your posts?

My mathematical proof is based on results from the ev computer simulation. The author of the computer program believes this computer model simulates reality. The peer review editors at Nucleic Acids Research published this model. Not only does this model demonstrate how profoundly slow random point mutations and natural selection is at accumulating information when using realistic genome lengths and mutation rates, it shows how important the selection process is. There is no realistic selection process that can evolve a gene from the beginning and ev shows that with more than a single selection condition, evolution slows profoundly.

Please everyone, stop with the flame war, already!

Yes. Please. Let's get back to the incredibly productive discussion about ev and evolution. We were so close to a breakthrough with our creationist friends. All we need now to show them once and for all they are wrong is a time machine and a notebook big enough to write the complete history of every molecule in the universe in. Don't let personal quibbles get in the way of such reasonable evidentiary standards. We only need to know everything there is to know about everything to prove to them the world wasn't created by a giant imaginary being. That seems perfectly fair to me and has yielded such an interesting discussion so far.

The only thing that has happened in this discussion about ev is that evolutionarians have abandoned it in droves. So now you have no mathematical model for mutation and selection. You have no mathematical description of selection. The theory of evolution started without a mathematical basis and continues that way. The theory of evolution is nothing more than a slogan “mutation and selection”.

So yeah, I agree this thread has become a bit of an insult fest. Let's calm down a bit and get back to the subject(s) at hand, assuming there are any subjects anyone cares to discuss. It's also become a bit of repeat theatre.

It seems that very few evolutionarians want to discuss ev. Do think that is because the evolutionarians don’t understand Dr Schneider and your (used to be realistic but now stylized) model or they do understand the model?

That’s an interesting ribozyme these scientists developed. Would you care to describe a selective process where a molecule like this could evolve?

Hmmm... that was the last post by Doctor Kleinman: 9:00 PM ET Thursday. His last moment logged in was one minute after that. We didn't get his usual Friday "have a nice weekend." I wonder what's up. This thread will not be the same without him.

I’m still here. Care to answer the question?
quote="Mr Scott"]Hmmm... that was the last post by Doctor Kleinman: 9:00 PM ET Thursday. His last moment logged in was one minute after that. We didn't get his usual Friday "have a nice weekend." I wonder what's up. This thread will not be the same without him.

I'm sure he'll be back. Sometimes reality just takes precedence over internet discussions

[/quote]
Reality has never gotten in the way of a discussion on the theory of evolution.

The notion that every facet of human existence has been adequately explained by by natural phenomena seems to imply that all scientific problems have now been answered. That is not the case.

But the question was whether naturalism has been adequate so far. No one implied that science is finished.

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

For example, I have seen Kleinman, on this thread say "tell us how genes arose" - or words to that effect. The question is legitimate and lies at the core of any serious attempt to understand origins. What comes back, from so-called skeptics?

What comes back is mostly "don't know yet."

Ah yes, the gap theory. Your own computer model shows the mathematical problem that arises when you have multiple selection processes acting simultaneously, but I guess that is just another gap.

They are, by any standards, "extraordinary claims" and the fact that they are even present in the scientific literature seems to reflect a determination among leaders in the field never to admit that there is anything wrong with their preconceived ideas.

What? You appear to be focusing on a few ideas that people are tossing about as some sort of evidence that they are closed-minded. At the same time, you ask people to be open-minded about your ideas.

Tossing ideas about? Paul this is about your computer simulation that at one time you said modeled reality and now say it is a stylized representation of a tiny part of the evolutionary landscape. Look how your fellow believers see this computer simulation now. They try to call this my mathematics, I guess this is the evolutionarian idea of derision. I wonder what Dr Schneider would think that his computer model was attributed to a creationist. How low can his work go?

This thread is now officially crapola.

Are you annoyed?

How would selection act upon them?

And, cruicially, how would these pathways generate a mechanism for "genetically" passing on the results of this selection?

And how would this lead to the generation of RNA/DNA?

Those are appropriate questions. The value of the ev computer model is that it shows how crucial the selection process is for convergence. Not only is there no selection process that would evolve a gene from the beginning, the model also shows a severe difficulty for the theory of evolution in that competing selection processes markedly slow the rate of information gain.

 

[John Hewitt]

Which chemical equilibria?
How would selection act upon them?

All chemical equilibria that are not thermoneutral (which means virtually all chemical equilibria) shift position in response to changes in temperature. This is school level chemistry. The resulting multiplicity of oscillations are interpretations of the sun's data input and are subject to evolutionary selection.

And, cruicially, how would these pathways generate a mechanism for "genetically" passing on the results of this selection?

They do not need to inherit their data, the sun does the inherit bit for them. Selection is discussed at length on my site. I cannot repeat it here

And how would this lead to the generation of RNA/DNA?
But, as detailed above, that data needs to be recorded, stored and passed on in a reasonably faithful manner.

I took the theory to protocells containing metabolic pathways and meeting the old schoolboy criteria for life - move, (breath), feed, grow, excrete, reproduce and respond to stimuli. (The protocells would not breath and no oxygen is assumed.) I stopped there because the further away from the sun's own cycle the less compelling the arguments become.

I do intend going on, first to chirality, then to data carrying molecules. I broadly know how to do these things but, especially with data carrying, the whole thing becomes more and more of a molecular fairy tale.

But I have to say that I feel all such debate essentially ends up running down the same pathway. The "RNA world" supporters are, I would say, looking at end-stage abiogenesis, the creation of the self-replicating molecules that went on to become the first forms of "life".

There is some truth to that but, more substantially, I would say the RNA world has always been outright science fiction.
The problem I find with the people in the RNA world field is the same as with so many scientists, including cell motility - they aggrandise the evidence "for" their ideas and diminish or suppress the evidence that contradicts them. Ridiculous behaviour - some of them should just switch careers and move into advertising.

 

[Yahzi]

In some ways, culture is a large scale epigenesis...

Culture is not demonstrated to be in any way analogous to genes;

First, let me note my psychic prediction was wrong: you've actually responded to the points I made. Why it took you 65 pages to decide to actually communicate is anybody's guess, but whatever.

Yes, culture is not like a gene: I just meant that it was a method for transmitting historical data.

From your comments I take it this your actual point: that the information coded in genes is not the sole source of information that affects evolution. You feel additional data is stored in chromosomes, and in the particular choice of bases, and perhaps in other places.

What you haven't explained is how this matters. There might be some historical information in the particular set of bases, but how does that affect evolution? As an analogy, there are considerable differences between AMD and Intel processors - but this difference is virtually invisible to the software that runs on them. Why should we assume the mechanical instantiation of a data structure should affect the data in the structure? In most other cases, it doesn't. What makes genetics different?

Or, to put it another way: I don't see that your signal has risen above the noise level.

Actually, I think taking abiogenesis out of evolution is an evasive redefinition

There is a discipline that studies how genes and environment interact to produce changes in living organisms. This discipline does not care where genes came from, nor does it care about extra-genetic information that is not significant. The discipline is called "evolutionary biology." I don't see what's wrong with that.

To assert that we cannot study genetic evolution in isolation is to refute the reductive principle of science.

If you want another example of biological evolution in a none genetic context, consider the workings of the brain, which is considered a Darwinian machine that processes sensory data into knowledge, or the workings of the immune system.

I don't think that really should be called biological evolution, for much the same reasons you cited about: it's not sexually reproduced, etc. etc.

As best as I can sum up: you seem to be complaining that biologists focus their attention on genes, while ignoring the substrate in which the genes are embedded in. My question is: what percentage of the signal (the change in evolution) is attributable to these non-genetic factors?

 

[Yahzi]

There's only one rule at this forum, fit in or #### off.

I know - and I just admitted that much in the above post!

So you're admitting that you don't let facts get in the way a of a good rant.

But you wonder why people dismiss you as troublemaker with nothing signficant to say.

So many times in life, I find the choices other people make to be so utterly mystifying.

:huh:

 

[hammegk]

The problem I find with the people in the RNA world field is the same as with so many scientists, including cell motility - they aggrandise the evidence "for" their ideas and diminish or suppress the evidence that contradicts them. Ridiculous behaviour - some of them should just switch careers and move into advertising.

Did you miss this thread? The game is already afoot with a few of the usual suspects.

http://www.internationalskeptics.com/forums/showthread.php?t=74269

 

[Yahzi]

But, as detailed above, that data needs to be recorded, stored and passed on in a reasonably faithful manner.

That's my perinnial question:

But how does it work?

 

[kjkent1]

Unnamed’s selection process almost completely uncouples the selection process from the genome length by biasing selection to errors in the binding site region. This is why his selection process converges so quickly despite increases in the genome length.

Well, it's good that you admit that. What you seem to be missing is the fact that Unnamed's selection process is, if anything, more realistic than Schneider's original, because it gives little weight to mutations in the junk DNA region, which have neutral evolutionary effect on the organism.

You're not being objectively honest about your position anymore, Alan. Your original claim has been soundly refuted, though you pretend that it hasn't.

 

[Dr Adequate]

See my sig.

 

[kleinman]

Annoying Creationists

Unnamed’s selection process almost completely uncouples the selection process from the genome length by biasing selection to errors in the binding site region. This is why his selection process converges so quickly despite increases in the genome length.

Well, it's good that you admit that. What you seem to be missing is the fact that Unnamed's selection process is, if anything, more realistic than Schneider's original, because it gives little weight to mutations in the junk DNA region, which have neutral evolutionary effect on the organism.

I’m all for making the ev computer model more realistic but Unnamed’s selection process is not the way to do it. How much “junk DNA” is there in a bacterial genome?

If you want to make ev more accurate, use a realistic genome and mutations to the genome that are detrimental to the creature, select out and mutations which are beneficial select in and mutations which are neutral are neither selected for or against. But what is the selection process that would evolve a gene from the beginning? All your mutations would be neutral until you had a functional gene. What happens if you have two selection process acting simultaneously in competition with one another?

You're not being objectively honest about your position anymore, Alan. Your original claim has been soundly refuted, though you pretend that it hasn't.

Now what are you whining about?

 

[kjkent1]

I’m all for making the ev computer model more realistic but Unnamed’s selection process is not the way to do it. How much “junk DNA” is there in a bacterial genome?

If you want to argue that no prokaryotes have junk DNA, then prove it and produce a realistic selection mechanism which should be preferred to Unnamed's. Otherwise, you lose. Simple as that.

I recognize that prokaryotes usually have less than 15% junk DNA, but what of it? Suppose Unnamed's selection method uses two separate binding site regions, rather than binding and non-binding regions. The point is that any such activity shortens the length of genetic material undergoing evolutionary change, and that shreds your mathematical theory, which depends on huge gene lengths evolving all at once. You're setting up a false premise -- there's no reason why this must occur.

If you want to make ev more accurate, use a realistic genome and mutations to the genome that are detrimental to the creature, select out and mutations which are beneficial select in and mutations which are neutral are neither selected for or against.

I think ev is sufficiently accurate already. So, if YOU want to make it more accurate, then YOU do the above experiment and see what happens. Otherwise, you lose. Simple as that.

But what is the selection process that would evolve a gene from the beginning? All your mutations would be neutral until you had a functional gene.

You evidently have some definition of "functional gene" which is apparently written down and stored in a library where genes can check it out and follow the rules while they evolve.


You constantly invent premises which are self evident to you as axiomatic, as if there is a Ten Commandments which dictates the only ways that genes are allowed to evolve. You have decided, a priori, that genes must be at least a certain length, that they must compete to their mutual detriment, that a very small section of genetic material cannot possibly have any selective advantage to the host organism, that huge genes must evolve independently to their currently observed completed state, rather than as the product of many smaller evolutionary steps which may or may not have anything to do with what we currently observe, that gene fusions, recombinations, transcriptions, shifts, insertions, deletions, etc. ad infinitum, all are useless for evolution. Instead, you demand that every gene must start from a totally random point and then evolve to its currently observed state via one process: point mutation and natural selection.

But, you cannot prove that this is the requirement. It's a total strawman, Alan.


I don't think that there's a biologist/geneticist anywhere who would subscribe to the rules which you seem to view as mandatory. If there are any reading this thread, then I'd like to read their concurrence.

What happens if you have two selection process acting simultaneously in competition with one another?

Your question assumes a fact not in evidence: that the processes are necessarily competing and thus detrimental rather than beneficial or neutral. The observed reality is that two or more selection processes acting simultaneously produce a very wide diversity of life. So, unless you have some proof that multiple parts of a genome evolving separately must operate detrimentally to the organism, then the empirical evidence suggests that this doesn't occur, and thus you lose this argument.Simple as that.

If all mutations are evenly distributed (I don't know if they are or not, but you seem to suggest this as axiomatic), then any section of binding sites is equally likely to produce a functional gene (whatever the definition of that gene may be) as any other section. It's not as if there's a little sign on the molecule which says, "No evolution allowed beyond this point."

There's nothing to prevent two binding site regions being close together and separately evolving different functions. Nor is there anything to prevent the two regions from later fusing together to produce some completely different function.

Now what are you whining about?

I'm not whining at all. I'm winning this argument. Simple as that.

 

[Schneibster]

Please, I invite you, choose one item from the first paragraph of empty headed babble quoted above and explain why you think it is relevant. I am really looking forward to you explaining why you think earlobes or hair colour come into this!

Sigh. Data? Just once?

Fine. What evolves, John?

More precisely, when evolution has occurred, what has changed?

 

[Schneibster]

Oh, and worth noting that Kleinman fails on the "present data" test too. Bye Kleinman.

 

[kleinman]

Annoying Creationists

I’m all for making the ev computer model more realistic but Unnamed’s selection process is not the way to do it. How much “junk DNA” is there in a bacterial genome?

If you want to argue that no prokaryotes have junk DNA, then prove it and produce a realistic selection mechanism which should be preferred to Unnamed's. Otherwise, you lose. Simple as that.

Here is a description of a realistic selection process. This is the closest I can get to such a process and it is the reason why I think the theory of evolution is impossible.

There are three possible outcomes from any particular mutation. The mutation can be beneficial, the mutation can be detrimental or the mutation can be neutral. A benefical mutation would help the reproductivity of that creature, a detrimental mutation would hurt the reproductivity of that creature and a neutral mutation would have no effect either way. You can also put gradation on the benefit or detriment that a mutation might pose, That is a mutation my offer slight benefit or slight detriment to the creature or offer large benefit or be fatal to that creature. Where Unnamed’s selection process becomes unrealistic is in ignoring virturally all harmful mutations that occur in the non-binding site region. Unnamed’s selection process does this by using a gradation to the selection that is very beneficial to the evolution of binding sites while at the same time not identifying harmful mutations in the non-binding site region.

A more realistic simulation of random point mutations and natural selection would start with an evolved genome except for a small portion of the genome where some gene or binding site is to evolve. Then mutations in the evolved region would have to be evaluated as to whether they are beneficial, detrimental or neutral while the evolving portion of the genome can have selection benefit only when that portion evolves to some beneficial function.

This is where the argument about a partially evolved gene not having a beneficial selection effect causes trouble for the theory of evolution. Unless you can somehow show that a partially evolved gene offers some selective benefit to that creature, selection is going to be controlled by mutations in the evolved portion of the genome. If that occurs, you will have the same situation that Dr Schneider’s selection process has when the errors in the non-binding site region controls selection, that is binding sites never evolve.

I recognize that prokaryotes usually have less than 15% junk DNA, but what of it? Suppose Unnamed's selection method uses two separate binding site regions, rather than binding and non-binding regions. The point is that any such activity shortens the length of genetic material undergoing evolutionary change, and that shreds your mathematical theory, which depends on huge gene lengths evolving all at once. You're setting up a false premise -- there's no reason why this must occur.

The what of it is that prokaryotes do not have much junk DNA and mutations are much more likely to be harmful to functioning DNA than to DNA that has no function. Selection will remove those creatures who suffer a fatal mutation to an otherwise functioning gene no matter what is evolving on the “junk DNA”. Mutations in the “junk DNA” will offer no selective benefit until those mutations produce a functioning gene (or at least some form of genetic benefit) for that creature.

Even in ev’s crude form, this problem is already manifest in Dr Schneider’s selection process. Unless the mutations in the area you want to evolve is controlling the selection process, that portion of the genome will not evolve. Selection in other areas of the genome is controlling which creatures are reproducing and which ones are selected out.

If you want to make ev more accurate, use a realistic genome and mutations to the genome that are detrimental to the creature, select out and mutations which are beneficial select in and mutations which are neutral are neither selected for or against.

I think ev is sufficiently accurate already. So, if YOU want to make it more accurate, then YOU do the above experiment and see what happens. Otherwise, you lose. Simple as that.

I hope my description above illuminates why ev is not sufficiently accurate already. I also hope you can recognize why ev does not converge as you extend the genome length. In addition, natural selection can only select based on benefit or detriment. Once you come to grips with this issue, you will understand why the theory of evolution by mutation and natural selection has a fatal mathematical flaw.

But what is the selection process that would evolve a gene from the beginning? All your mutations would be neutral until you had a functional gene.

You evidently have some definition of "functional gene" which is apparently written down and stored in a library where genes can check it out and follow the rules while they evolve.

Many genes are hundreds if not thousands of bases long. Are you arguing that portions of these genes have other benefits? If you do, then I ask you what was the benefit of fragments of the DNA replicase system before they evolved to the DNA replicase system?

You constantly invent premises which are self evident to you as axiomatic, as if there is a Ten Commandments which dictates the only ways that genes are allowed to evolve. You have decided, a priori, that genes must be at least a certain length, that they must compete to their mutual detriment, that a very small section of genetic material cannot possibly have any selective advantage to the host organism, that huge genes must evolve independently to their currently observed completed state, rather than as the product of many smaller evolutionary steps which may or may not have anything to do with what we currently observe, that gene fusions, recombinations, transcriptions, shifts, insertions, deletions, etc. ad infinitum, all are useless for evolution. Instead, you demand that every gene must start from a totally random point and then evolve to its currently observed state via one process: point mutation and natural selection.

I have not invented the lengths of genes, these are measured quantities. I have not invented the lengths of genomes in living creatures, these are measured quantities. It is you who invents small genes that can perform the necessary processes that support life and tiny genomes that can reproduce and transform to larger genomes. You are seeing the theory of evolution like a computer booting up. A small amount of code in ROM allows the CPU to access the disk drive which in turn allows more information to be loaded into memory which in turn allows the CPU to access the video display, keyboard and so on but in the theory of evolution you don’t have the ROM and you only have mutation and selection to “boot up” your life forms. The mathematics is just not there for you to do this.

I don't think that there's a biologist/geneticist anywhere who would subscribe to the rules which you seem to view as mandatory. If there are any reading this thread, then I'd like to read their concurrence.

They can’t subscribe to these rules because the theory of evolution collapses under these rules. So evolutionists live in denial and extrapolate the concept of natural selection far beyond what it is capable of doing.

What happens if you have two selection process acting simultaneously in competition with one another?

Your question assumes a fact not in evidence: that the processes are necessarily competing and thus detrimental rather than beneficial or neutral. The observed reality is that two or more selection processes acting simultaneously produce a very wide diversity of life. So, unless you have some proof that multiple parts of a genome evolving separately must operate detrimentally to the organism, then the empirical evidence suggests that this doesn't occur, and thus you lose this argument.Simple as that.

There are numerous selection pressures that are acting all the time. The diversity of life you see is due to recombination and selection, not mutation and selection and I doubt there are many evolutionists who attribute speciation to recombination and selection.

What you are having trouble seeing is that ev is showing that even two selection conditions can stop an evolutionary process when one selection condition dominates the other.

If all mutations are evenly distributed (I don't know if they are or not, but you seem to suggest this as axiomatic), then any section of binding sites is equally likely to produce a functional gene (whatever the definition of that gene may be) as any other section. It's not as if there's a little sign on the molecule which says, "No evolution allowed beyond this point."

It’s not me showing this, it is what ev is showing. Competing selection conditions interfere with the evolution of binding sites.

There's nothing to prevent two binding site regions being close together and separately evolving different functions. Nor is there anything to prevent the two regions from later fusing together to produce some completely different function.

That is not what ev is showing as you extend the genome and non-binding site errors dominate the selection process and prevent binding sites from evolving.

Now what are you whining about?

I'm not whining at all. I'm winning this argument. Simple as that.

You were whining that I was not being objectively honest when from the very first post in this debate I said that ev was showing that evolution by random point mutation and natural selection was mathematically impossible when realistic genome lengths and mutation rates are used in the model. The only thing that has changed in my position is that I have added that ev shows that two competing selection conditions interfere with the evolutionary process. This is the explanation why evolution by random point mutations and natural selection is mathematically impossible.

These conclusion are based on the peer reviewed and published computer model of random point mutations and natural selection. What are your conclusions based on little gator?

 

[delphi_ote]

Here is a description of a realistic selection process. This is the closest I can get to such a process and it is the reason why I think the theory of evolution is impossible.

Even if you disagree that evolution produced the diversity of life from a common ancestor, you really can't argue that evolution and natural selection themselves are impossible. You're talking about a computer model that demonstrates exactly those concepts. You've watched it happen right in front of your eyes when you ran the simulation.

You know the concept of evolution is possible, but you keep saying you think evolution is "impossible." Why? Is there some kind of disconnect between what you witness and what you type? When you're making up your arguments here, is there a point where you stop to consider reality? Does evidence even give you pause, or is scoring points for Jesus more important than pondering obvious facts?

 

[kjkent1]

Here is a description of a realistic selection process. This is the closest I can get to such a process and it is the reason why I think the theory of evolution is impossible.

I appreciate that you're attempting to respond with what you propose as a rational argument.

There are three possible outcomes from any particular mutation. The mutation can be beneficial, the mutation can be detrimental or the mutation can be neutral. A beneficial mutation would help the reproductivity of that creature, a detrimental mutation would hurt the reproductivity of that creature and a neutral mutation would have no effect either way. You can also put gradation on the benefit or detriment that a mutation might pose, That is a mutation my offer slight benefit or slight detriment to the creature or offer large benefit or be fatal to that creature. Where Unnamed’s selection process becomes unrealistic is in ignoring virturally all harmful mutations that occur in the non-binding site region. Unnamed’s selection process does this by using a gradation to the selection that is very beneficial to the evolution of binding sites while at the same time not identifying harmful mutations in the non-binding site region.

What evidence do you have to support the conclusion that a mutation in a junk region of the genome is likely to be harmful at anywhere near the rate of a mutation in a binding-site region? Point being, if you seek realism, then someone needs to quantify the deficit/benefit/neutrality of a mutation in either region.

A more realistic simulation of random point mutations and natural selection would start with an evolved genome except for a small portion of the genome where some gene or binding site is to evolve. Then mutations in the evolved region would have to be evaluated as to whether they are beneficial, detrimental or neutral while the evolving portion of the genome can have selection benefit only when that portion evolves to some beneficial function.

This is where the argument about a partially evolved gene not having a beneficial selection effect causes trouble for the theory of evolution. Unless you can somehow show that a partially evolved gene offers some selective benefit to that creature, selection is going to be controlled by mutations in the evolved portion of the genome. If that occurs, you will have the same situation that Dr Schneider’s selection process has when the errors in the non-binding site region controls selection, that is binding sites never evolve.

I'm thinking you mean "selection is going to be controlled by mutations in the 'un'evolved portion of the genome." I won't argue against this point until I'm sure I understand your position here.

The what of it is that prokaryotes do not have much junk DNA and mutations are much more likely to be harmful to functioning DNA than to DNA that has no function. Selection will remove those creatures who suffer a fatal mutation to an otherwise functioning gene no matter what is evolving on the “junk DNA”. Mutations in the “junk DNA” will offer no selective benefit until those mutations produce a functioning gene (or at least some form of genetic benefit) for that creature.

I don't think that you will get much disagreement that prokaryotes evolve more slowly than do eukaryotes. Perhaps that is the selective advantage of junk DNA: it allows most mutations to have a neutral effect on the host.

The point is that you are attempting to imply certain required conditions, a priori, to your personal notion of a what constitutes a partially constructed gene, which prevents it from conveying a selective advantage. But, you don't know all the possible selective advantages that there are. For all you know, just storing useless base pairs provides some, as yet unknown selective advantage to the organism, because it offers the possibility of some mutation causing a new function to suddenly appear "by chance."

Obviously, some such mutations might be detrimental -- some neutral -- some beneficial. But, here again, how do we quantify the probability of a beneficial vs. detrimental mutation without knowing something about the external environment into which it is introduced? Furthermore, how do we weight that benefit/detriment?

I don't think this is possible -- or at least it would be incredibly complicated. The best that anyone would be likely to do would be to create an artificial environmental algorithm to operate while ev was doing it's RMNS trick. Or, maybe we should simply use the empirical evidence of actual change over time as a means of weighting the probability of beneficial/detrimental change.

Of course, you wouldn't go for that scenario, because your position is that the changes are supernatural. But, if you keep your scientist's hat on, you have no choice but to assume that the changes are all naturalistic and therefore statistically representative of reality.

Even in ev’s crude form, this problem is already manifest in Dr Schneider’s selection process. Unless the mutations in the area you want to evolve is controlling the selection process, that portion of the genome will not evolve. Selection in other areas of the genome is controlling which creatures are reproducing and which ones are selected out.

How do you know that the other portion of the genome which you are describing as useless except for the purpose of making evolution unreasonably slow, is not also evolving some different function in a smaller part (or many smaller parts)?

You are using ev which has fixed boundaries and definitions of and between binding and non-binding sites to suggest that reality is similar. A real DNA molecule doesn't have these fixed boundaries. It just does what it does where it does it. You could have a genome that was one million base pairs long, and every 1,000 pairs might be evolving separately. If so, then your theory fails.

I hope my description above illuminates why ev is not sufficiently accurate already. I also hope you can recognize why ev does not converge as you extend the genome length. In addition, natural selection can only select based on benefit or detriment. Once you come to grips with this issue, you will understand why the theory of evolution by mutation and natural selection has a fatal mathematical flaw.

You are creating a false premise that every huge gene must have evolved from scratch, rather than from many smaller genes with other functions. You don't know that to be true, and all of the other types of genetic changes/translations/combinations/shifts/fusions/deletions/additions/etc. could permit what you view as mathematically impossible to be true.

And, it must be true, because the alternative is supernatural intervention -- something which only occurs in places like Never Never Land.

Many genes are hundreds if not thousands of bases long. Are you arguing that portions of these genes have other benefits? If you do, then I ask you what was the benefit of fragments of the DNA replicase system before they evolved to the DNA replicase system?

This is the abiogenesis question. It’s really out of scope for the discussion, but my answer is simple: random chance created the first self-replicating life form. It doesn’t matter how “mathematically impossible” you wish to believe this occurrence to be. Either abiogenesis happened by random chance, or the universe is ruled by magic. There is no other alternative.

I have not invented the lengths of genes, these are measured quantities. I have not invented the lengths of genomes in living creatures, these are measured quantities. It is you who invents small genes that can perform the necessary processes that support life and tiny genomes that can reproduce and transform to larger genomes. You are seeing the theory of evolution like a computer booting up. A small amount of code in ROM allows the CPU to access the disk drive which in turn allows more information to be loaded into memory which in turn allows the CPU to access the video display, keyboard and so on but in the theory of evolution you don’t have the ROM and you only have mutation and selection to “boot up” your life forms. The mathematics is just not there for you to do this.

Well, unless you have some two billion year old DNA that we can examine, you don't know that your position is correct. You are claiming that your mathematics defies the reality which is observed in nature, because you want to believe it to be true. The reality proves that your mathematics are wrong -- otherwise we live in a universe where the supernatural is constantly altering the rules.

If this is true, then science is a total waste of effort -- we should just pray, because ultimately, God will fix every problem if we are sufficiently devoted.

They can’t subscribe to these rules because the theory of evolution collapses under these rules. So evolutionists live in denial and extrapolate the concept of natural selection far beyond what it is capable of doing.

You have a thing for insisting on rules. There are no "rules." There are only models of what is observed in nature.

There are numerous selection pressures that are acting all the time. The diversity of life you see is due to recombination and selection, not mutation and selection and I doubt there are many evolutionists who attribute speciation to recombination and selection.

Define "speciation," precisely otherwise no one can argue the point.

What you are having trouble seeing is that ev is showing that even two selection conditions can stop an evolutionary process when one selection condition dominates the other.

One again, you are assuming facts not in evidence. You have no proof whatsoever that two or more selection conditions are more likely to stop evolution, rather than to accelerate it.

It’s not me showing this, it is what ev is showing. Competing selection conditions interfere with the evolution of binding sites.

Assumes facts not in evidence.

That is not what ev is showing as you extend the genome and non-binding site errors dominate the selection process and prevent binding sites from evolving.

You keep falling back to the original ev algorithm. That algorithm is incredibly unrealistic, and that viewpoint was brought up by me very early in this thread. Unnamed demonstrated that the algorithm is unrealistic, and provided something considerably more realistic. You just don't like the new method, because it substantially undermines your original theory.

You were whining that I was not being objectively honest when from the very first post in this debate I said that ev was showing that evolution by random point mutation and natural selection was mathematically impossible when realistic genome lengths and mutation rates are used in the model. The only thing that has changed in my position is that I have added that ev shows that two competing selection conditions interfere with the evolutionary process. This is the explanation why evolution by random point mutations and natural selection is mathematically impossible.

You can only maintain this position with respect to the original selection algorithm. You cannot maintain the position in the face of the new algorithm.

These conclusion are based on the peer reviewed and published computer model of random point mutations and natural selection. What are your conclusions based on little gator?

This is a pure argument from authority. If you are going to continue to fall back on ev's original selection mechanism, then no one can defeat your argument, because that selection mechanism is completely unrealistic, except with extremely short genome lengths. In order for it to be realistic for longer genomes, the selection mechanism must weigh the various benefits/detriments of mutations inside and outside the binding site region. Unnamed's selection mechanism does this, and when it does, your theory fails.

Simple as that.