Reasons Behind the Theory of Evolution by Natural Selection

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Persecrates
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Post by Persecrates » August 25th, 2010, 11:24 pm

Ok, genetics, Natural Selection, adaptation and evolution are complex matters.
Let me say that I think that evolution indeed occur(ed).
But the concepts of "adaptation", "environmental/reproductive pressure" have poor cognitive significance (even if they were properly defined, which is not the case) or are simply false/meaningless.
I also repeat that I'm an Agnostic and don't believe in God, therefore I don't believe in the ID 'theory'.

Still, I think that the NS ‘theory’ is more mystic than scientific… It seems to defend the idea that "Nature" (in opposition to humans or choice) is guiding the selective process, therefore evolution… Replace the word "Nature" by "God" and see what you obtain…

Also, please note that the questions I ask or the comments I make do NOT necessarily represent my position on the matter. I often use them to play the role of the Devil’s advocate.

For now, I will simply respond to the comments made on my last post.
I also want to say that I agree with some arguments made by Maleagar, the main ones being:

"I hardly think that the existence of extra-genomic system processes that interact with the environment, thus changing how coded sequences from the genome are interpreted, and what meta-system must exist which runs that system, [describing when and how to read sequences forward or backward, or when to change the formal order]" --this part, not being an expert, I‘m not sure about-- "can be considered "irrelevant". Such meta-interpretive extra-genomic systems increase the combinatorial problem faced by "random mutation" theorists. "
Regarding the Baldwin effect and epi-genetics.

And:"Three questions:

(1) How do scientists establish that the mutations are in fact (or at least, in principle) random?

(2) How do scientists establish that the different genomic sequences in fact (or at least, in principle) are the sufficient and necessary causation of the major taxonomic variances?

(3) How do scientists establish that the selection methodology for taxonomic success is in fact (or at least in principle) natural, and not artificial?
"

For the 3rd one, I’ll differ a bit by asking what is the definition of ‘natural’ in this context? Is it simply a negative definition: Non-artificial, non-human guided? Or is it Guided by ‘Nature‘? If so, define ‘Nature’ please.
Also, can the potential action of the organism carrier transmitting the gene(s) be considered as ‘natural’? Is it considered at all? (I’ll develop on these two questions below.)

@Wowbagger:
Your arguments have become very weak after the intervention(s) of Maleagar...

Persecrates wrote:
If there is a "reshuffling" (random), it still doesn't provide a cause for the mechanism called "environmental/reprodutive pressure".
Wowbagger wrote:Why do you bring up environmental/reproductive pressure?
These terms together are part of natural selection, which, combined with mutations, leads to adaptation (evolution).
Organisms have more offspring than needed to keep their numbers constant. Offspring varies genetically. Resources are limited, thus, it comes to competition. Because of the developing 'environmental/reproductive' pressure, on average, the better equipped organisms tend to survive.
1. I bring up "environmental/reproductive pressure" because it's an essential part (conclusions C1-3, C2-4 and C3-4 use the concept of "pressure") of Alun's demonstration (the reason for this thread to exist) and of the validity and soundness of the theory of Natural Selection (guiding adaptation and evolution).

2. "These terms are not combined with mutations", they precisely are said to explain mutations.
So, thank you but I know mutations lead to evolution, but my questions still are: "What causes these mutations to happen?" What is the definition of environmental/reproductive pressure? E.g. What mechanism(s) is described by these concepts?
You cite some causes for mutations to happen (gene transfer, viral/toxin insertions/assimilations and cosmic rays, let's put genetic engineering aside as it's not a "natural" process) but they don't explain all mutations, by far.

Meleagar mentioned the concept of "epigenetic" and even if anything non-genetic can be qualified as epigenetic, it raises an interesting question as it means that geneticists seem to know they have yet to identify other causes...
So, why keep on asserting that randomness is "guiding" NS, thus adaptation?

There is a problem of level of understanding here. At a genetic level, causes like gene transfer, viral/toxin insertions/assimilations and cosmic rays appear to occur randomly.
In fact this is not randomness but clearly what is called "unpredictability" (it doesn‘t mean unpredictable by nature, but currently unpredictable due to the complexity and number of factors that exist as causes and are being able to influence the outcome of a process), which is different.

Example of your misunderstanding:
Persecrates wrote:
So, you see there are causes. Their occurrence cannot be random then.
They are not predicted due to our current knowlege of such causes, but they are NOT unpredictable by nature though.
Wowbagger wrote:
Yeah, that's what I said. Like throwing a dice, you can't predict the outcome, but of course, it is somehow determined, or, if determinism doesn't apply (doesn't matter for that discussion), at least caused to fall a certain way. It still makes sense to call it 'random' though, as opposed to 'guided', we just have to agree on what is meant.
It is very relevant to know if determinism apply or not. You're confusing randomness (absence of causation inherent to the nature of the studied system. See Quantum Mechanics.) with unpredictability (a system too complex --for now-- to theorize the outcomes of initial events/conditions… See Chaos Theory.).

BUT, as these are CAUSES (for mutations to occur), there is NO RANDOMNESS. Randomness is NOT THE CAUSE for mutations to happen. Still, we have yet to identify them all (even if scientists seem to be satisfied with the ones they have).

So, what does it mean when the scientific community asserts that genetic mutations occur randomly?
Well, it's a lie. Pure and simple.
The cause for their occurrence is unpredictable, not random by nature.
And what about the causes for genetic mutations themselves? Geneticists are quite embarrassed as they identified some objective causes they cannot deny to exist.
Again, so much for randomness...

But they still try to invoke (like occultists would do for a supernatural entity) a vague mechanism there is no definition for (it's not at all or partially explained but omitting a number of possibilities potentially explaining mutations) called environmental and/or reproductive pressure to hide their embarrassment.
This is supposed to be the inference/link between Mutations, NS and adaptation/evolution.
Environmental pressure à Mutation à Reproductive pressure à NS à Adaptation/Evolution

Two mechanisms (environmental and reproductive pressure) yet to be defined and even yet to be considered as mechanisms… Fantastic…

But if they simply get rid of the supposed random cause (not the random/unpredictable occurrence of these causes. You understand the difference?) and try to find or recognize that they haven't identified all possible causes (some humility, maybe?), we could have a sane, healthy discussion about the causes for genetic mutations and what really mean "adaptation" and "Natural Selection".

If we can't even consider the environmental/reproductive pressure to be a mechanism (yet to be meaningfully explained though), how can we identify the cause(s) for (mechanisms that induce) environmental/reproductive pressure itself?

It lacks inferences in Alun's demonstration for these very reasons... That's why he answers "there is no evidence for the existence of such mechanism", and see no problem with it...

Persecrates wrote:
1- It doesn't suffice to claim the causes of genetic mutation may be due to cosmic rays, one has to PROVE it to make it a scientific hypothesis.
Better, one has to prove and identify ALL the causes and verify if they explain ALL mutations ("naturally") occurring.
Wowbagger wrote:
Ockham's razor.
What Ockam's razor has to do with anything here. I don't make allusion to any entity.
I simply ask for an empirical proof. Not only that cosmic rays may induce mutations but that they actually explain some.

Isn't how science is supposed to work?
A claim must be backed up with proof. Not by the mere possibility that a proof may exist.
And to do that not only with cosmic rays but for ALL (identified and yet to be identified) causes for such mutations to occur.

If not, it's an incomplete hypothesis at best, the result of divination at worst... Since probabilities and statistics don't give any cause for a phenomenon/event to happen.

Wowbagger wrote:
Direct action of the environment?


Yes direct action, like cosmic rays could have. They would have a direct effect (IF they had one) on the genome of the individual expose to , it causing mutations to happen.
So, direct causes can exist and be identified. Any cause that hasn’t a proven direct effect on the genome is not a cause, nor a mechanism. It’s unscientific to claim their role!

@Alun:

P1-3) If an organism does not reproduce itself, it will eventually die and its genetic information will not be expressed.
* I think this follows deductively.
C1-3) If a mutation does not help an organism reproduce, there will not be any pressure for that change in genetic information to promulgate.
* This is microevolution by natural selection. We see it all the time in antibiotic-resistant bacteria.

P1-4) Reproduction itself is governed by the expression of DNA.
P2-4) Two populations of organisms that do not reproduce using one another's genetic material are of different species.
C1-4) Species can diverge due to the accumulation of gradual mutations.
* This has been explored on a genetic level for past eukaryotic species divergence events [11][12].
* This has been observed in the present tense for bacteria [13].
C2-4) Species can diverge due to reproductive pressure (from C1-3).
* This has been specifically observed in the present tense in many types of organism [14].
* This is the theory of evolution by natural selection.

Inferring using this with respect to the fossil record, we can further say:
C3-4) Evolution in the past can be explained as a consequence of species divergence due to reproductive pressure.


As you don’t seem to understand the problems with your demonstration. Let me go further.

The form of your demonstration:

P1-3) If an organism does not reproduce itself (P1-3a), it will eventually die (P1-3b) and its genetic information will not be expressed (P1-3c) .

Premises and conclusions cannot be formulated using conditional(s). Your use of the preposition "if" is then incorrect.
The form of your premises (here P1-3) is also incorrect as you start the first proposition with a conditional ("if"), and then make a conclusion in your premise based on this conditional.
That’s an incorrect way to present a premise. From one part of your premise (P1-3a) you seem to deduce a second proposition (P1-3b) and then a third (P1-3c), so it’s de facto two conclusions you deduce from only one premise (P1-3a) and that is not explained with any inference.
Therefore P1-3 is an invalid "premise".
You should at least make 3 premises of P1-3, without conditional.

C1-3) If a mutation does not help an organism reproduce (C1-3a), there will not be any pressure for that change in genetic information to promulgate. (C1-3b)

Again, conditional and here a split-in-two ‘sub-conclusions’ with what should be a premise (C1-3a) and a conclusion (C1-3b).

You deduce this conclusion from only one premise, also incorrect.
You arrive to this conclusion without giving any inference (I think this follows deductively is not an inference/explanation.). And, there is no causation between P1-3 and C1-3.

So, C1-3 is invalid and unsound.

C1-4 (Species can diverge due to the accumulation of gradual mutations) cannot be deduce from P1-4 and P2-4. Also, it presents two concepts (divergence and gradual mutations which are cited for the first time without having been linked to the previous demonstration)
Therefore, your conclusion is invalid.
P1-4, P2-4 and C1-4 may be true (sound) but there is a lack of causation between these two premises, the concepts of divergence and gradual mutations, and (the statement made by) your conclusion. Your demonstration lacks of, at least, two (necessary) premises evoking gradual mutation and allowing to make a ’connection’ between P1-4, P2-4 and C1-4 and at least one inference (explaining how gradual mutations cause divergence).

C2-4 cannot be deduced from P1-4, P2-4 and C1-3 as C1-3 is invalid and unsound.
Same for C3-4.

Now, let’s evaluate the content of these "premises" and "conclusions".

P1-3: You seem to confuse the individual organism with a (sub)species of organisms . An organism (beside xxxxx) rarely reproduce itself. Plants, animals and us, humans, surely don’t.

C1-3: Do you tell me that the concept of (environmental and/or reproductive) "pressure" only means: not more likely to survive??
Pressure, definition: "not more likely to survive." It’s nonsense Alun. Why this concept even exist then?
So, C1-3 would become: "If a mutation does not help an organism reproducing, it will not be more likely to survive and that change in genetic information will be less likely to promulgate."
It isn’t much of a conclusion, Alun.
Also P1-3 and C1-3 seem to mean almost the same thing, they have the same cognitive content/significance.

It should take the form of something like this:

P1: Individuals among a given species reproduce with one another.
P2: Mutations occur among (the genome of) species.
P3: Mutations are divided in 3 kinds: impairing (I think it is a more precise term than non-beneficial as neutral mutations can be considered as non beneficial but can‘t be seen as beneficial), beneficial, neutral.

Inference: As impairing mutations induce dysfunctions of the body/organs/cells, unaesthetic changes… Carriers of these mutations are less likely to survive till the age of reproduction or to be able to find a (willing) mate to reproduce if they attain this age.

C1: Impairing mutations are less likely to allow reproduction.
C2: Beneficial mutations are more likely to allow reproduction.
(Cn: Neutral mutations are neither more nor less likely to allow reproduction. We are not interested in these, here.)

These two proven, sound and valid conclusions can now be used as premises:
P4: Impairing mutations are less likely to allow reproduction.
P5: Beneficial mutations are more likely to allow reproduction.

Inference: The genome and mutations of the dead or unfit individuals are less likely to be transmitted.

C3: Impairing mutations are less likely to subsist.
C4: Beneficial mutations are more likely to subsist: "Subspecies" are created which can reproduce with all members of the studied species and become the new ‘dominant’ (sub)species.

The term "subspecies" is not the proper one to use, but I don’t have the right one in mind.

Note that there is no certainty for the elimination of impairing mutations, they still can survive for a time, depending on the level of ‘unfitness’ (not relatively to their environment but to the efficiency of their own body) resulting from these mutations. They can also stay dormant much longer.

Neither there is certainty for the beneficial mutations to subsist... One could argue that there is a statistic certainty that they WILL disappear (given enough time)… Well… Statistics…

An impairing mutation can also become beneficial if the environment change and render this mutation beneficial by making the carrier more adapted to this change.

More, my classical logic "demonstration" doesn’t account for the causes of these mutations. It still is needed.
I make no allusion to "pressure", nor adaptation. There is NS though.
If you want to include environmental direct action through cosmic rays, assimilation of toxins, appearance of new predators, change in the climate or biotope… (no "pressure" which is an empty concept) or epigenetic factors in the process of genetic mutation, NS and adaptation… You have more work to do.

All this to show that we don’t learn much from this demonstration… And that your C1-3 is still invalid and unsound (false and not supported by facts). (reproductive) "Pressure" means nothing.

C1-4 and C2-4:
First, you’re confusing, fail to differentiate 2 epistemic/cognitive levels here.
The divergence due to reproductive pressure is (considered as) the CAUSE for the divergence due to accumulation of gradual mutations.

Also and again, were do "divergence" and "accumulation of gradual mutations" come from?
I mean they are formulated in a conclusion so they should have been presented, explained and proved before, right? They haven’t.
You still don’t even explain what "reproductive pressure" is, nor from what demonstration you come to the conclusion of its existence, role and nature.

So, C1-4 may be sound (true) but you give no demonstration other than saying "This has been specifically observed in the present tense in many types of organism".
C2-4 is unsound, undemonstrated and invalid, so it’s false and "This is the theory of evolution by natural selection." Is a meaningless, unfounded claim.

C3-4: Well, I won’t repeat the same arguments. I think you understand.
___________________________________________________________

Now, I want to point out that everyone is forgetting or doesn't see a third potential candidate (the first is "environment", the second would be a God/Designer -- whom I don't believe in --) which could ‘guide’ these genetic mutations, therefore adaptation: the organim itself!

Let's take the example of the island, as it's an easy one.
Rats tend to become bigger (gigantism) on islands, it seems logical since the bigger rats have a competitive edge on the smaller ones, even and above all when it comes to reproduction as it often entails violence between ‘suitors’ to a female.
Other animals (like horses) tend to get smaller (dwarfism) because, for example, of the lack of resources and of space.
But it doesn’t explain why these types of mutations happen more frequently or only on islands.
Why gigantism is beneficial only on islands?? Why all rats don’t become bigger. The advantages would be the same everywhere…

Then, what about birds that loose their wings, what is the objective adaptive advantage a wingless bird has over a "normal" bird?? Wings or not, it needs approximately the same amount of food. Wings would even seem to be an advantage for obtaining food, by reaching places a wingless ‘bird’ could not... Also, a "normal" bird can escape predators more easily.
What about the reproductive edge then? A bird with wings should appear more attractive, healthy... to a female as it is the norm when birds with smaller and smaller wings appear.
What about the claim that evolution can "never go down on Mount Improbable" (Dawkins)?
It would seem that adaptation (to a new environment, here an island far from any coast) can not only distance itself from the "competitive/reproductive benefit/advantage" hypothesis but act against it, against the NS theory!

Could that be because the bird, understanding the uselessness of its wings, unconsciously decide to repress the combination of genes that would give him fully operational wings? (Not taking all factors in consideration of course.)

I know... That would mean they not only have a consciousness but also a subconscious like humans do.
But it's not even the most surprising, interesting, mind blowing possibility...
It would mean that animals (all organisms, us included?) can un-consciously interfere in the mutation process by modifying their own (active) genome.

I know it's pure speculation, but a logical one.
Why assume/accept for a fact that the cause for mutations (and what we call "adaptation") can exclusively be "randomness" (no cause at all which is anti-scientific and illogical) or "guided" by extrinsic factors (environment/Nature or God)??

I know the consequences of such hypothesis (if proven true or even possible through observations, experiments and/or the use of the scientific method) are tremendous. Is it why no hypothesis of the sort has been formulated yet?

It is not so far fetched as we KNOW our brains regulate ALL our body activity at a neurological subconscious level. What are the logical implications of this fact? Well, I let you think about it...

Or how come organisms get rid of simply unnecessary features?
We're not talking of impairing ones for a new environment (neither neutral ones), only unnecessary ones (also like the sight of animals living below the surface in caves. Why not improving the night vision instead of having no sight at all?). Do organisms develop new ones to compensate (like ultrasound)? If so, can they be un-adapted for thousands, millions of years in the meantime? Then, why stay in non-fitting environment when they are clearly not suited for them and they can change of such environment?

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Post by Meleagar » August 26th, 2010, 10:23 am

Persecrates wrote: For the 3rd one, I’ll differ a bit by asking what is the definition of ‘natural’ in this context?
Natural, meaning unguided by intentional, teleological agency; artificial, meaning guided by intentional, teleological agency.
2. "These terms are not combined with mutations", they precisely are said to explain mutations.
So, thank you but I know mutations lead to evolution, but my questions still are: "What causes these mutations to happen?" What is the definition of environmental/reproductive pressure? E.g. What mechanism(s) is described by these concepts?
You cite some causes for mutations to happen (gene transfer, viral/toxin insertions/assimilations and cosmic rays, let's put genetic engineering aside as it's not a "natural" process) but they don't explain all mutations, by far.
Most mutations are supposedly just random transcription errors during the procreative process. IOW, it's like an order of monks copying a text over and over through time, each time a few random errors being made in the transcription.
Meleagar mentioned the concept of "epigenetic" and even if anything non-genetic can be qualified as epigenetic, it raises an interesting question as it means that geneticists seem to know they have yet to identify other causes...
The basic, neo-darwinist view of the gene is that it is a template for physical structure-building, and that when a beneficial mutation occurs, a useful, novel protein is "coded for" at the genetic level.

The problem is that this 1-1 template system doesn't account for the necessary infrastructure required for the new protein tool/building block to have any value. Where does it go? How does it get there? Where does it fit? How did the error-correction system of the cell become informed to allow the new protein to be built? How is it that a random error process created a matrix-system of multi-directional coding?

Coding DNA is not just read "in sequence" according to one "reading program"; different transcription and interpretive methods are used that seem to take into account the whole 3D body-plan, contextualizing the interpretation of the code. IOW, the same code produces X in a man, and Y in a potato; where are those interpretive instructions?

Also, genetic expression varies according to environmental context; environmental influences can trigger transcription and interpretation variances. Where is the control system for this?

Such hierarchical, nested control-systems are not known to be the cumulative product of random errors. In fact, it's rather absurd to believe that such nested control systems can be the product of random errors regardless of the sorting process involved.
BUT, as these are CAUSES (for mutations to occur), there is NO RANDOMNESS. Randomness is NOT THE CAUSE for mutations to happen. Still, we have yet to identify them all (even if scientists seem to be satisfied with the ones they have).

So, what does it mean when the scientific community asserts that genetic mutations occur randomly?
Well, it's a lie. Pure and simple.
An ongoing con job.
Yes direct action, like cosmic rays could have. They would have a direct effect (IF they had one) on the genome of the individual expose to , it causing mutations to happen.
So, direct causes can exist and be identified. Any cause that hasn’t a proven direct effect on the genome is not a cause, nor a mechanism. It’s unscientific to claim their role!
Claiming that random cosmic rays can produced functional, complex variations in the genetic code is akin to claiming that random drops of ink might produce functional, complex plot or character variations in the text "The Vampire Lestat". Without evidence, it's hard to see why anyone would adopt this view.
It would seem that adaptation (to a new environment, here an island far from any coast) can not only distance itself from the "competitive/reproductive benefit/advantage" hypothesis but act against it, against the NS theory!
I think that what one should really question is how the theory of natural selection, which can only account for the selection of the more fecund organism, can be called in to account for increasingly less fecund organisms - all higher life-forms. Humans produce far fewer, and far less hardy offspring than bacteria. If anything, humans and all higher life forms slipped through the cracks of natural selection; natural selection can hardly be used to explain the generation of less fecund organisms.
I know... That would mean they not only have a consciousness but also a subconscious like humans do.
But it's not even the most surprising, interesting, mind blowing possibility...
It would mean that animals (all organisms, us included?) can un-consciously interfere in the mutation process by modifying their own (active) genome.
There is some research that indicates this might be true.

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Post by Alun » September 2nd, 2010, 12:33 am

Ok, so this has been delayed, I've been busy. I'm procrastinating from other stuff I should be doing even now. I think Persecrates' challenge is effectively equivalent to what Meleagar said I was missing in my answer to his challenge, so even though I quote you two separately, this whole post is directed at both of you. I also think I'm spoiling you people by looking this up for you, but I'm feeling charitable... let's see if it lasts to the end of this post.
Persecrates wrote:(1) How do scientists establish that the mutations are in fact (or at least, in principle) random?
What do you mean by random? (Or, what do you think I mean by "random"? :) ) All mutations, as far as we know, have a specific physical (or chemical, or empirically reducible) cause. Most of the time, these causes are not related to an organism's particular needs, experiences, etc. There are trends under an organism's control, however; certain types of mutations may be protected against more or less carefully. This precision or relaxation in maintaining a genetic code could even be targeted (e.g.). But the evidence generally shows that most mutations are undirected (not by the organism and not by anything else), except in cases of e.g. human genetic engineering. (source 1 - just showing that this is what scientists actually believe; source 2 - actual evidence)
Persecrates wrote:(2) How do scientists establish that the different genomic sequences in fact (or at least, in principle) are the sufficient and necessary causation of the major taxonomic variances?
As I explained in the opening, we can take a genetic sequence, change it to our liking, put it into an embryo, and then observe the results. We can make rabbits glow in the dark (e.g.), we can make flies grow extra legs (e.g.), and we can make bacteria manufacture insulin (e.g.). In fact a major part of biological experimental method is just to force bacteria to produce proteins for study, and biologists can do this without having a clue what the protein is going to be, or what its function is, because every single different protein an organism uses is transcribed from DNA. We can identify specific disorders with specific changes in the human genetic code (e.g.). We can look at the history of species and species change, and identify changes in DNA which correspond to changes in traits (e.g.).

Satisfied? Well, it's actually not the case that DNA fully describes all taxonomic variations. RNA, and potentially a few other pieces of cellular machinery, can play an important role too (especially when you go way back in the timeline).
Persecrates wrote:(3) How do scientists establish that the selection methodology for taxonomic success is in fact (or at least in principle) natural, and not artificial?"
As I said in the OP, the main evidence is experimental. We have watched things evolve due to (simulated) environmental pressures (bacteria, eukaryotes). We can induce the statistical importance of fitness selection from these cases. Which brings me to Meleagar's challenge:
Meleagar wrote:I asked for: a formal, factual, rigorous(read: mathematical) description that shows at least in principle that RM & NS are up to the task of generating major taxonomic features (like: winged flight or stereoscopic vision) from scratch.
Once we have induced the statistical importance of fitness selection, including the speed at which it essentially directs DNA change, we can extrapolate to past conditions. Roughly, the only variables are mutation rate and the strength of selective forces--that is, if natural selection is the only thing going on. The papers I gave earlier show, theoretically, that the equation for natural selection is sufficient to explain historical DNA change. Once again, these two papers: Kimura, Akashi.

To Meleagar specifically; I presume the core of your argument is still that taxonomic features are too complicated to be generated 'randomly' and 'from scratch.' Keep in mind that I'm not actually talking about that. 'Natural selection' is the heading I use for the modern theory of evolution in general, but even in this broad sense, it cannot hope to explain life. I presume that you know what a ribosome is, but just for rhetorical purposes, it is a 'macromolecule' that can be diagrammed like this:

Image

Life as we know it cannot exist without this molecule, or something extremely similar. This is what receives mRNA, essentially a copy of DNA, and then translates it into a protein described by that DNA. In other words, its function is extremely complicated, its form is extremely complicated, and it serves a pivotal role in the fundamental operations of both the livelihood of every cell on earth, in the ability of cells to reproduce themselves, and in the ability of cells to gradually evolve via 'random' mutation.

We have almost no idea of where it came from. That molecule could nearly count as an organism itself, but the earliest organisms we know of are bacteria who already relied on it. If that molecule's predecessors occurred without direction, I think chances are good that it took practically the whole earth undergoing perfect reaction conditions for millennia to produce a handful (but the first ones would've been self-replicating). Even that is idle speculation, pretty much. Abiogenesis is far from proven. Just some food for thought.
"I have nothing new to teach the world" -Mohandas "Mahatma" Gandhi

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Post by Meleagar » September 2nd, 2010, 7:10 am

Alun wrote: To Meleagar specifically; I presume the core of your argument is still that taxonomic features are too complicated to be generated 'randomly' and 'from scratch.'"
I never made such an argument; I have only asked for rigorous research and mathematical extrapolation of such research, which demonstrates that "random" is a qualitatively accurate description of the mutation process, and that natural (unguided by intelligence) selection is a sufficient sorting process to get from A to Z.

Papers which assume that the mutation process required for that walk through the landscape is random, and which assume that the selection process used in that walk is unguided, do not demonstrate those things.
If that molecule's predecessors occurred without direction, I think chances are good that it took practically the whole earth undergoing perfect reaction conditions for millennia to produce a handful (but the first ones would've been self-replicating). Even that is idle speculation, pretty much
What theoretical framework do you use to base your opinion on that the "chances are good" for the scenario you describe? What statistical analysis of the potential for conditions, chemical interactions, likelihood of chirality, and potential combinatorial challenges does your opinion rely on? How have you evaluated the probabilistic resource of the Earth towards acquiring the target?

Or do you just assume that because it happened, and because it must have happened in an unguided fashion, then the probabilistic resources of the Earth must be sufficient to acquire the target?

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Post by Alun » September 2nd, 2010, 10:38 am

Meleagar, I said if it occurred without direction, it would have required highly favorable conditions. My point was primarily that a large amount of the complexity of biological systems is not explained by the modern theory of evolution. Theories of abiogenesis try to explain it, but they have a long way to go.

The section at the end was not directed towards your challenge, it was directed towards the separate argument from the specified complexity of biological systems. I view it to be somewhat conciliatory.
Last edited by Alun on September 2nd, 2010, 10:45 am, edited 1 time in total.
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Post by Meleagar » September 2nd, 2010, 10:44 am

Alun wrote:Meleagar, I said if it occurred without direction, it would have required highly favorable conditions. My point was primarily that a large amount of the complexity of biological systems is not explained by the modern theory of evolution. Theories of abiogenesis try to explain it, but they have a long way to go.
And I said that you have presented no evidence that "highly favorable condtions" of any sort or stripe can even begin to account for the acquisition of the target in question.

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Post by Alun » September 2nd, 2010, 10:47 am

Ok. I'm not disagreeing. My point was that, so far as we know, the predecessors of the ribosome could've come from anywhere. Again, this isn't part of my answer to your previous challenge; if anything, it's a conciliation about the limit of the modern theory of evolution.
"I have nothing new to teach the world" -Mohandas "Mahatma" Gandhi

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Post by Groktruth » August 21st, 2011, 8:06 pm

Strong inference is a highly recommended scientific method, as is Bayesian inference. These both reject the theory of evolution as scientifically sound.

1. In strong inference, we establish a theory by comparing it's predictions with those of any and all alternative hypotheses. Subjectively, religiously, or culturally defended theories will dismiss alternative hypotheses without giving them their strong inference day in court. Evolution has taken this approach with regard to, say, intelligent design. Instead of getting the idea on the table, and attempting to move on with testable predictions from both evolution and intelligent design, the evolutionists (and the creationists, to be fair) have disparaged their competing theory with "discrediting" (ad hoc, usually) explanations.

2. In Bayesian methodology, intuitive, "educated guesses" or inductively derived "prior plausibilities" of hypotheses are the starting point, and energy is invested in the most plausible (a priori) hypothesis. Darwin presented much information about artificial selection, which is commonplace. Using correct methodology, he then would have proposed "The origin of species by means of artificial selection," the artificial selector in this case being God, who he treated as a probable part of the universe. Most people intuitively think it likely that there is a "God" out there, which appears to be good Bayesian science, since every other living organism known to science had some higher beings to cope with, and there was no reason to believe that man was an exception.

So, inductively, looking at the rest of the living world, it was plausible to suppose that living beings higher than man existed, and, like man, would be messing with biological diversity using artificial selection.

Today, we have genetic engineering to add to the inductive core. All of which adds up to intelligent design.

The rest of the Bayesian approach is more difficult to apply. Can we predict measurable outcomes of the "Origin of Species by means of Artificial Selection and Genetic Engineering" to come up with predictions that are different from those we have from evolution (natural selection, random genetic mutation)? Folks are working at this, but for the most important theory in biology, if not science, where is our Hadron Collider? Simplistic assumptions about how God might or might not go about His intelligent design won't do. Everything we know about theology says that His ways are not our ways. One would have to ask Him directly, which is actually the way we would handle this in court, disputing whether a particular strain of cow came about "naturally" and could be bred freely, or was bio-engineered, and had to be bred by paying royalties. Most theologies invite such interviews with God. Those who have asked, and listened, find that the general point, but little of the creationist argument, of intelligent design, is validated.

Anyway, it is clear now that the history of the theory of evolution will be dishonorable. It may be true, but that is not why it is being defended.

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Re: Reasons Behind the Theory of Evolution by Natural Select

Post by chazwyman » July 11th, 2012, 8:56 am

Alun wrote:I think this is the first thread I've started here, so it's a shame it's derivative of two topics of which this is only an important sub-topic. If this opening post is too long for you, focus on the red conclusions, then work your way back to the premises you disagree with, don't understand, or have a comment on--if you agree with the premises, but disagree with a conclusion, then explain how you think the argument is invalid. I will frequently post supporting links [#] without referring to their content; I don't suggest reading them all unless the claim they're nearby interests you, because there are going to be a lot.

Please focus on criticizing these reasons, not arguing alternatives like Intelligent Design or talking about tangents like abiogenesis and metaphysics. I ask just because this topic is important enough to stand alone.

P1-0) The same phenomenon under the same observed conditions is usually caused by the same process in the world. * This is the basic premise of empirical inductive reasoning, and is a key to the scientific method in general. P2-0) Theories explain a phenomenon by delineating the process which causes it; a scientific theory generates predictions that can be falsified by the observation of an experiment. C1-0) Theories are more likely to be true when valid experiments do not falsify them; when they successfully predict observations.
* Note that a theory is still called a theory, even when confirmed by valid experiment hundreds or millions of times, because P1-0 does not hold as a logical truth. Note also that you trust your lungs to breathe primarily due to P1-0.


Your conclusion is actually yet another premise masquerading as a conclusion.The reason for this is that you change the goalposts from "observations of phenomena" TO "experiments". This one of the most profound problems with the scientific method; reductionism. Such a practice seeks to reduce the causality to a single identifiable phenomenon, thus masking the complexity of other possible causes. This is also particularly difficult in relation to evolutionary studies for two reason. First that no natural incidences of natural selection can be adequately simulated in experimental conditions except under the most banal experiments on micro-organisms, and second that it has a tendency to want to apply "survival" alone as the only reason for the emergence of any traits, behaviours or genes that appear in the environment.


P1-1) Fossils are remnants of organisms [1]. P2-1) Fossils formed across the last 3.8 billion years [2] as determined by our ability to date them within a substantial degree of accuracy [3]. * We can also date some types of fossils and rock absolutely with raioisotope dating [16][17][18]. C1-1) Organisms have been on earth for at least 3.8 billion years and we know roughly when many types of them lived.

No problem here. Those details might be open to change though. The dating is not absolute, but based on the best knowledge we have for decay of radioactive elements. The dates are relative, which in fact is fit for purpose.


P3-1) Fossils show specific groups living at specific times; with no fossils of humans, e.g., forming 3.8 billion years ago, and fossils of e.g. dinosaurs which are no longer extant today [2]. C2-1) Evolution, the changing and growing complexity of the form of life on earth, as well as vast extinction of life, has occurred over the last 3.8 billion years.
* Note that at this point I have made no conclusions about how evolution has happened. The groups are not necessarily natural categories but conveniences developed by biological science and collected by observable morphology usually wholly reliant on bone morphology as the vast percentage of fossilised remains are in the form of shells and bones. Bones of similar morphology might mask significant differences that would only be observable were other tissues have been preserved. This could easily go as far as missing incidences of speciation. Obviously I agree with the conclusion but as it is not falsifiable it also makes an assumption about 'evolution' of some kind.
P1-2) Organisms reproduce themselves using their genetic coding, usually DNA [4][5]. P2-2) Reproduction of DNA (and RNA) molecules in biological systems often leads to small mutations or changes in the DNA molecule [6]. P3-2) Changes in DNA can lead to changes in protein structure [6]. * This premise is often referred to as part of the "central dogma" of biology; that DNA is ultimately translated into amino acid sequences. * While "dogma" may sound like a strong term, we have actually synthesized DNA from simple compounds and given it to bacteria--who then use that DNA [7]. * It is further standard practice to give bacterial cells particular DNA sequences to have them produce the protein encoded by that DNA [8]. C1-2) When organisms reproduce, sometimes mutations occur and lead offspring to have slightly different traits than the parent.
* This is partly an explanation of microevolution--note that bacteria can evolve both without the creation of 'new' genetic information [9] and due to mutations that occur during recombination and DNA copying [10].
Yes, all sound. There are a couple of worthwhile points though. DNA is almost completely absent from the fossil record, and the emergence of Darwin's theory and the interpretation of evolution by the fossil record has preceded without the understanding or the need for the theory of DNA. The other thing that seems to be getting more interesting it that ability of the micrscopic world to acquire DNA from promiscuous sources. such that the notion of species is not so easy to pin down


P1-3) If an organism does not reproduce itself, it will eventually die and its genetic information will not be expressed. * I think this follows deductively.
The genetic information, is is thought can be acquired by another organism at the microscopic level.


C1-3) If a mutation does not help an organism reproduce, there will not be any pressure for that change in genetic information to promulgate.
The bottom line is the production of viable progeny. You express in the positive what you can only express in the negative. Whilst it is true that a negative mutation is an impediment for persistence of the genes that generate it, and a positive mutation is an advantage for its persistence; there must be a whole host of neutral traits, genes and behaviours that bear no particular advantage or disadvantage but will 'hitch a ride' on an successful organism, or fall behind on a less successful one. Due to the complexity of macrorganisms these neutral traits, behaviours and genes will represent the vast majority of the genome. This explains apparently traits who use has no bearing on survival or reproduction and hints at the missing element in evolutionary studies which reduces all to survival


* This is microevolution by natural selection. We see it all the time in antibiotic-resistant bacteria.P1-4) Reproduction itself is governed by the expression of DNA. P2-4) Two populations of organisms that do not reproduce using one another's genetic material are of different species. C1-4) Species can diverge due to the accumulation of gradual mutations.
* This has been explored on a genetic level for past eukaryotic species divergence events [11][12]. * This has been observed in the present tense for bacteria [13]. C2-4) Species can diverge due to reproductive pressure (from C1-3).
* This has been specifically observed in the present tense in many types of organism [14]. * This is the theory of evolution by natural selection.
Darwin was often criticised for basing his model of evolution on the study of domestic selection, your text relies on microscopic evolution. Clearly such questions need to be taken with care when applying such ideas to the real natural world.

Inferring using this with respect to the fossil record, we can further say:

C3-4) Evolution in the past can be explained as a consequence of species divergence due to reproductive pressure.

Obviously there's a lot more to explain; specific events that are shown by the fossil record still need to be explained. For example, why is it that change seems to occur sporadically, instead of all the time? For this particular point, there is a lot of evidence that genes are relatively stable without reproductive pressure; basically, the species under no pressure will only "wobble" genetically, on average staying the same [15]. In fact the general view is that one would only expect change when reproductive pressure is in play; that punctuated equilibrium is unsurprising. (There's also the interesting application of this theory to our own species.) However, I think this discussion would be best suited to focus on disagreements with the above argument; more detailed applications can be discussed if the basic argument is ever finished.

Edit 1: Added P2-0 and C1-0. 12-22-2009 9:49 AM GMT Edit 2: Added to P2-1 with three links about radioisotope dating. 12-26-2009 1:31 AM GMT

-- Updated Wed Jul 11, 2012 9:42 am to add the following --

Concluding remarks in new post due to persistent SERVER ERROR




Once we accept that mutations and variations do not always lead to improvements, and that not all morphological changes have to obey the law of survival in that they can be reproduced as neutral traits (see above), then all of these questions disappear in the knowledge that life is far more complex and that the infinite variety of life as described by Darwin does not have to bow down to the imaginary pressure of natural selection. It is also worth pointing out the seeming obsession with trying to understand evolution in terms of DNA or genetics. The unit of selection is the individual organism and the survival of its immediate clade. Nature does not select out genes for a particular trait, it selects any organism with the ability to persist to the next generation whatever the solution to the environmental situation or crisis it has to confront. In a sense the process of evolution would be better understood by the death of unsuccessful organisms rather than those that survive. This set of qualifications I have outlined answers the problem that some have identified as "darwinitis" - the reductionist tendency to try to account for all change in terms of the survival or especially useful and novel traits. People want everything to be neat and tidy, and explicable when the history of life on earth is chaotic and very complicated.

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Re: Reasons Behind the Theory of Evolution by Natural Select

Post by Groktruth » July 11th, 2012, 4:14 pm

"The origin of specious by the selection of natural means."

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Re: Reasons Behind the Theory of Evolution by Natural Select

Post by Gulnara » November 13th, 2012, 10:18 pm

I think devolution, extinction, and unexpressed genetic information- those are all factors supportive (and directing as well) of the evolution. Those factors are active participants in evolution, because they work like moulds, forming evolutional process, propagating the other species through outward impression of self. The result is that, like sculpture, evolution proceeds on its glorious way, while the mould that created it and was used due to it's necessity and tide relation to the outcoming forms, is discarded.

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Re: Reasons Behind the Theory of Evolution by Natural Select

Post by Marina000 » December 19th, 2012, 3:20 am

Alun wrote:I think this is the first thread I've started here, so it's a shame it's derivative of two topics of which this is only an important sub-topic. If this opening post is too long for you, focus on the red conclusions, then work your way back to the premises you disagree with, don't understand, or have a comment on--if you agree with the premises, but disagree with a conclusion, then explain how you think the argument is invalid. I will frequently post supporting links [#] without referring to their content; I don't suggest reading them all unless the claim they're nearby interests you, because there are going to be a lot.

Please focus on criticizing these reasons, not arguing alternatives like Intelligent Design or talking about tangents like abiogenesis and metaphysics. I ask just because this topic is important enough to stand alone.

P1-0) The same phenomenon under the same observed conditions is usually caused by the same process in the world. * This is the basic premise of empirical inductive reasoning, and is a key to the scientific method in general. P2-0) Theories explain a phenomenon by delineating the process which causes it; a scientific theory generates predictions that can be falsified by the observation of an experiment. C1-0) Theories are more likely to be true when valid experiments do not falsify them; when they successfully predict observations.
* Note that a theory is still called a theory, even when confirmed by valid experiment hundreds or millions of times, because P1-0 does not hold as a logical truth. Note also that you trust your lungs to breathe primarily due to P1-0.
Actually I think most of your points are not made at all.

I'll speak to the first two.

1. The same phenomenon, eg dna & morphology, under the same observed conditions, eg natural selection, are produced via the same process is incorrect and is demonstrated by terms such as homoplasy and convergent evolution. Hence different phenomenon resulted in much the same outcome but from different evolutionary paths or processes.

2. TOE predicted 'junk' dna that is non functional, and the so called empirical evidence was much research that suggested the genome was 98% junk. Recently 80% of the genome has been found to be functional with evolutionary researchers saying it is likely 100% of the genome will prove to be functional. This evolutionary prediction was falsified in favour of creationist predictions to the contrary that are now being validated in time as any prediction with merit should.

http://www.sciencemag.org/content/337/6099/1159

Modern bird footprints with a reversed hallux were dated to 212mya and more than halfway to the Devonian. Effectively this should falsify the current theory on the evolution of aves. Rather than accept their own data researchers have invented a mythical and undiscovered theropod that convergently acquired these avian feet, again making TOE unfalsifiable.

TOE remains a theory because the best test of falsifiablity researchers like Dawkins could come up with was a precambrian rabbit, effectively meaning TOE is unfalsifiable and does not qualify as a science. TOE is a philosophy that explains how life came to be without the hand of God.

-- Updated December 19th, 2012, 3:55 am to add the following --
chazwyman wrote: (Nested quote removed.)



-- Updated Wed Jul 11, 2012 9:42 am to add the following --

Concluding remarks in new post due to persistent SERVER ERROR




Once we accept that mutations and variations do not always lead to improvements, and that not all morphological changes have to obey the law of survival in that they can be reproduced as neutral traits (see above), then all of these questions disappear in the knowledge that life is far more complex and that the infinite variety of life as described by Darwin does not have to bow down to the imaginary pressure of natural selection. It is also worth pointing out the seeming obsession with trying to understand evolution in terms of DNA or genetics. The unit of selection is the individual organism and the survival of its immediate clade. Nature does not select out genes for a particular trait, it selects any organism with the ability to persist to the next generation whatever the solution to the environmental situation or crisis it has to confront. In a sense the process of evolution would be better understood by the death of unsuccessful organisms rather than those that survive. This set of qualifications I have outlined answers the problem that some have identified as "darwinitis" - the reductionist tendency to try to account for all change in terms of the survival or especially useful and novel traits. People want everything to be neat and tidy, and explicable when the history of life on earth is chaotic and very complicated.
Yes now TOE needs a bush, not a tree and is embodied in the Chaos theory of evolution.

http://www.newscientist.com/article/mg2 ... ution.html

And the end result is the deterioration of the genome and overwhelmingly negative results relating to the accumulative epiststic effects of these so called 'beneficial' mutations.

http://www.plosbiology.org/article/info ... io.0030042 http://www.sciencemag.org/content/332/6034/1190 http://www.sciencemag.org/content/332/6034/1193.short

Indeed if TOE was not unfalsifiable one would strongly suggest that such a process of deterioration could not have continued for billons of years because the 'cost' is much greater than any gain, it appears.

The ability to defer to any scenario to accommodate data in favour of creationism into an evolutionary paradigm is hardly what I would call convincing.

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Re: Reasons Behind the Theory of Evolution by Natural Select

Post by Gulnara » March 20th, 2013, 8:25 am

Actually, people even glorify certain self destructive genetic set ups of their fellow humans, for example, that cause heroic behavior, which lots of times is very detrimental to life or well being of a heroic persons. Here, an ability to glorify someones very risky behavior, gives community a better chance to survive, where hero plays role of self sacrificing power. In cases when hero did a great stunt or deed and survived, he then is used by community as living model for propagating heroism idea farther.

Another illogical way that so called evolution plays on people: one can be given several great qualities, but lacks reproductive ability, and becomes extinct to no fault of their own.

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Re: Reasons Behind the Theory of Evolution by Natural Select

Post by Londoner » March 20th, 2013, 1:55 pm

Persecrates P1-3) If an organism does not reproduce itself (P1-3a), it will eventually die (P1-3b) and its genetic information will not be expressed (P1-3c) .

Premises and conclusions cannot be formulated using conditional(s). Your use of the preposition "if" is then incorrect. The form of your premises (here P1-3) is also incorrect as you start the first proposition with a conditional ("if"), and then make a conclusion in your premise based on this conditional. That’s an incorrect way to present a premise. From one part of your premise (P1-3a) you seem to deduce a second proposition (P1-3b) and then a third (P1-3c), so it’s de facto two conclusions you deduce from only one premise (P1-3a) and that is not explained with any inference. Therefore P1-3 is an invalid "premise". You should at least make 3 premises of P1-3, without conditional.
Can't help but remark that this and the following criticisms all seem to be examples of not seeing the wood for the trees.

To take this first example, the word 'if' refers to a hypothetical organism not doing something (reproducing itself), not to the rest of the sentence. The word 'If' in 'If we go out in the rain we will get wet' is nothing to do with the nature of wetness, rain or umbrellas.

The sentence doesn't assert that 'not reproducing itself' is the cause of 'genetic information...not be(ing) expressed. Rather, it points out that the meaning of the words 'not reproducing' include 'not expressing genetic information'. It is an analytic proposition, true by virtue of its meaning.

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Re: Reasons Behind the Theory of Evolution by Natural Select

Post by Lily_Alex » July 15th, 2013, 3:56 pm

I am a Catholic although I am sceptical on the Catholic views. I agree with Darwin's theory of Natural Selection and Evolution greatly even though many theists try and argue it being an atheist approach, which is absurd, he was agnostic. There are so many arguments on this theory, some being God as the sole omni-qualified creator, that He is the cause of the Evolution process and so on. There are so many arguments that stem from it too such as the argument of Design and Paley's watch analogy. However I really liked Michael Behe's Irreducible Complexity argument providing a logical explanation for evidence of potential design in his discovery of the Bacterum Flaggellum. He being a, I believe it was a biological scientist although I may be wrong, makes it even more interesting. I believe in Evolution and the Natural Selection process, but there is also the belief that some things in existence have not evolved, which is what Michael Behe argues.

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