Discussion for AronRa and OFNF exclusive thread

[abelcainsbrother]

It's even more strange to assume Darwin would have returned to Lamarck's theorie when one reads to the end of the paragraph (p.153) where he writes:

... I have at least, as I hope, done good service in aiding to overthrow the dogma of separate creations.

~ greets Vivre[/quote]


Everybody is overlooking that I was right about how Darwin was trying to thwart the Gap theory that was in the church before he came along,him being a former creationist knew about the Gap theory.notice "separate creations"

 

[abelcainsbrother]

Reading through AronRa'a last comment it is clear he is just declaring evolution is true because the majority of scientists accept it and trying to make the case that creationists have no way to prove their world view,and so evolution is the only hypothesis going for us to believe.This argument does not make much sense when we already know that anybody who goes against evolution in science cannot get papers published.Every scientist must go along with it or he risks not having a scientific career.He is hiding behind science just like all evolutionists do,hide behind peer reviewed science declare it is true and bash God,the bible,faith,etc.

The jig is up either demonstrate "nature did it" or stop believing it because you're only going to show that you believe science fiction as truth that is science that is promoted as the truth but cannot be demonstrated.Alot of people have fallen for it but not those of us who know how to examine evidence and tell if something is true or false or a theory.

Even if God can't be proven like AronRa claims that in no way means "nature did it" and there is no way to demonstrate it and never will be."Nature did it" is laughably wrong and there is no reason at all to prove God exists when this science fiction is promoted in our society.We who believe "God did it" don't have to do anything but we are trying to help people learn how to examine evidence.

I would reject evolution even if I did not believe in God based on the evidence.I would probably atleast believe aliens,etc created it because there is no way that life can be produced by nature.

 

[scalyblue]

Reading through AronRa'a last comment it is clear he is just declaring evolution is true because the majority of scientists accept it and trying to make the case that creationists have no way to prove their world view,and so evolution is the only hypothesis going for us to believe.This argument does not make much sense when we already know that anybody who goes against evolution in science cannot get papers published.Every scientist must go along with it or he risks not having a scientific career.He is hiding behind science just like all evolutionists do,hide behind peer reviewed science declare it is true and bash God,the bible,faith,etc.

The jig is up either demonstrate "nature did it" or stop believing it because you're only going to show that you believe science fiction as truth that is science that is promoted as the truth but cannot be demonstrated.Alot of people have fallen for it but not those of us who know how to examine evidence and tell if something is true or false or a theory.

Even if God can't be proven like AronRa claims that in no way means "nature did it" and there is no way to demonstrate it and never will be."Nature did it" is laughably wrong and there is no reason at all to prove God exists when this science fiction is promoted in our society.We who believe "God did it" don't have to do anything but we are trying to help people learn how to examine evidence.

I would reject evolution even if I did not believe in God based on the evidence.I would probably atleast believe aliens,etc created it because there is no way that life can be produced by nature.

Aronra is not claiming that nature did it. Aronra is noting observations that nature has done it. These observations are consistent no matter who looks, and they lead to models that can be used to predict results, results which have been used to develop medications that save lives.

What is the hypothesis you have that replaces evolution?

How does it explain what can be observed in the world?

Is this explanation testable in a repeatable way?

Can you think of anything that you could be shownthat would prove your hypothesis wrong?

How does your hypothesis explain the world better than evolution?

What are the predictive powers of your hypothesis? Name any technology, medicine, therapy, or innovation that has come forth as a result of using your hypothesis to predict the future.

I don't believe you have teneble answers to any of those questions, because this is what you're doing, right now.

 

[Vivre]

It's even more strange to assume Darwin would have returned to Lamarck's theorie when one reads to the end of the paragraph (p.153) where he writes:

... I have at least, as I hope, done good service in aiding to overthrow the dogma of separate creations.

~ greets Vivre

Everybody is overlooking that I was right about how ...

How do you know?

... Darwin was trying to thwart the Gap theory that was in the church before he came along, ...

Where did you state that?
What Gap theory are you addressing?
How can an existing theorie be thwarted? (I thought theories need to be disproven.)
Did Darwin succeed? (you sound as if and I doubt this intention)
And did the church (which one?) get it back somehow later?
And if not - did they adopt or extinct due to lack of Gap?

... him being a former creationist knew about the Gap theory.notice "separate creations"

What tribe of creationism?
Maybe old-earther, as they have created a wholly Gap to excuse the imperfection of the scripture.

Oh, and by the way -"separate creations"- stands in context with Lamarck and addresses his excuse-theory he needed to fill the Gap that unfortunately followed from his main theory.

So please bridge the new gap to your posting and fill yours and mine with knowledge

 

[dandan]

fightofthejellyfish has pretty much summed up the issues with what you're saying throughout this post, but I'll add my objections.

I'm bemused by your use of labels - "selectionists" and "neutralists" - to insert a distinction where none exists.

Like creationists' use of "micro-" and "macro-".

There are no distinctions - there's only evolution.

Your problem with your explanation of the "neutralists" position is assuming that these are not equivalent. They get to "D", which is all that's required.

In your "neutralist" path, combinations of neutral mutations is the equivalent of getting from "A" to "B" in the "selectionist" path - and again from "B" to "C", so there's no difference in either path going from "C" to "D" with another combination of neutral mutations.

Remember though: the "positive" step can be either due to a beneficial mutation or a combination of two or more neutral mutations.

There's no real difference between the two: a neutral mutation in combination with one or more existing neutral mutations can do what a single beneficial mutation can do on its own.

Honestly what are you talking about? The tags “selectionists” and “neutralists” are not creationists tags, there are simply branches of evolutionism.
A selectionists is someone who claims that natural selection play a major role in change, speciation and evolution, and a neutralist is someone who believes that random genetic drift and neutral mutations are the ones that play the most important role in change, speciation and evolution. A neutralist would say that natural selection doesn´t play an important role.

Of course there are scientists that are extreme neutralist, extreme selectionists and everything in between.
I am honestly surprise to see that most of you are neutralists.

In this article you can learn more about neutralism and selectionism, but I am honestly concern about the fact that I had to explain all this to you, you are the “experts in evolution” you are supposed to know all these things.

http://mbe.oxfordjournals.org/content/22/12/2318.ful

So please learn the differences between neutralism and selectionism and tell me to what branch do you belong to. ¿how important is natural selection? How important are random mutations and random genetic drift? Based on your answer I will approach ether the problems with neutralism or selectionism.

Remember how the videos and pictures show the "cup" developing more depth? That can happen either through a single beneficial mutation or a neutral mutation in combination with a number of existing neutral mutations.

Ok, so for example, how do you get a “cup” from a light sensitive nerve? Which mutation (ether neutral or beneficial) would have to occur?

You're still asking me to come up with evidence that shows that (bio-)chemical reactions don't work. :?

That atoms can't combine to produce simple molecules - that simple molecules can't combine to form ever more complex molecules - that inorganic chemistry doesn't result in organic chemistry with the formation of the CH molecule - that the formation of ever more complex hydrocarbons doesn't result in the formation of ever more complex amino acids, and so on, and so on...

:lol: :lol:
Atoms can create complex molecules therefore the eye evolved from a “simple” light sensitive nerve ¿do you see any problems with your logic?


The mechanisms that cause an atom(s) to become a complex molecule are not the same as the mechanisms that are supposed to create eyes from proto-eyes, trust me complex molecules are not a product of random mutations and descend with modification.

Besides that is a straw-man, I asked you for evidence that would convince you that eyes can´t evolve by Darwinian mechanisms, ¿what is the point of discussing if you already decided that “evolution did it” no matter what? If you don´t what us to call evolution a religion stop trating evolution a such and answer unambiguously, WHAT EVIDNECE WOULD CONVINCE YOU THAT THE EYE COULD HAVE NOT EVOLVED BY DARWINIAN MECHANISMS?

 

[Dragan Glas]

Greetings,

It's even more strange to assume Darwin would have returned to Lamarck's theorie when one reads to the end of the paragraph (p.153) where he writes:

[...]

Everybody is overlooking that I was right about how Darwin was trying to thwart the Gap theory that was in the church before he came along,him being a former creationist knew about the Gap theory.notice "separate creations"

That is not the case.

Darwin was referring to "kinds" by use of the phrase "separate creations".

Again, you're either completely misinformed or misrepresenting what's being said.

Kindest regards,

James

 

[Dragan Glas]

Greetings,

Reading through AronRa'a last comment it is clear he is just declaring evolution is true because the majority of scientists accept it and trying to make the case that creationists have no way to prove their world view,and so evolution is the only hypothesis going for us to believe.This argument does not make much sense when we already know that anybody who goes against evolution in science cannot get papers published.Every scientist must go along with it or he risks not having a scientific career.He is hiding behind science just like all evolutionists do,hide behind peer reviewed science declare it is true and bash God,the bible,faith,etc.

A naturalistic world-view precludes super-natural explanations - if one can empirically identify and/or logically infer a naturalistic explanation for phenomena, then there's no need for a super-naturalistic explanation - and anyone who puts forth such is simply not applying the scientific method: that's why papers are found wanting during peer-review.

The jig is up either demonstrate "nature did it" or stop believing it because you're only going to show that you believe science fiction as truth that is science that is promoted as the truth but cannot be demonstrated.Alot of people have fallen for it but not those of us who know how to examine evidence and tell if something is true or false or a theory.

Again you commit the fallacy that if there isn't a naturalistic explanation known to science, the explanation must be a super-natural creator-entity.

This is simply not the case - a creator-entity is not the default position, no matter how much you believe it to be. For a creationist it may appear to be the default, but it is not.

Even if God can't be proven like AronRa claims that in no way means "nature did it" and there is no way to demonstrate it and never will be."Nature did it" is laughably wrong and there is no reason at all to prove God exists when this science fiction is promoted in our society.We who believe "God did it" don't have to do anything but we are trying to help people learn how to examine evidence.

The minimum one can say is "I don't know" to the question of how a particular process occurs - however, it is a perfectly valid logical inference to say that it is due to a naturalistic cause. It is not reasonable to posit a super-natural cause just because you don't know the answer at the moment. This is the "God-of-the-gaps" fallacy.

I would reject evolution even if I did not believe in God based on the evidence.I would probably atleast believe aliens,etc created it because there is no way that life can be produced by nature.

Really?

So, how - in that case - would "aliens" have come about??

Kindest regards,

James

 

[Dragan Glas]

Greetings,

fightofthejellyfish has pretty much summed up the issues with what you're saying throughout this post, but I'll add my objections.

I'm bemused by your use of labels - "selectionists" and "neutralists" - to insert a distinction where none exists.

Like creationists' use of "micro-" and "macro-".

There are no distinctions - there's only evolution.

Your problem with your explanation of the "neutralists" position is assuming that these are not equivalent. They get to "D", which is all that's required.

In your "neutralist" path, combinations of neutral mutations is the equivalent of getting from "A" to "B" in the "selectionist" path - and again from "B" to "C", so there's no difference in either path going from "C" to "D" with another combination of neutral mutations.

Remember though: the "positive" step can be either due to a beneficial mutation or a combination of two or more neutral mutations.

There's no real difference between the two: a neutral mutation in combination with one or more existing neutral mutations can do what a single beneficial mutation can do on its own.

Honestly what are you talking about? The tags “selectionists” and “neutralists” are not creationists tags, there are simply branches of evolutionism.
A selectionists is someone who claims that natural selection play a major role in change, speciation and evolution, and a neutralist is someone who believes that random genetic drift and neutral mutations are the ones that play the most important role in change, speciation and evolution. A neutralist would say that natural selection doesn´t play an important role.

Of course there are scientists that are extreme neutralist, extreme selectionists and everything in between.
I am honestly surprise to see that most of you are neutralists.

In this article you can learn more about neutralism and selectionism, but I am honestly concern about the fact that I had to explain all this to you, you are the “experts in evolution” you are supposed to know all these things.

http://mbe.oxfordjournals.org/content/22/12/2318.ful

So please learn the differences between neutralism and selectionism and tell me to what branch do you belong to. ¿how important is natural selection? How important are random mutations and random genetic drift? Based on your answer I will approach ether the problems with neutralism or selectionism.

The point with which I take issue is - as before - you link to scientific papers which you don't appear to understand the full implications of what it says in context.

Do you think that the author is actually up-ending the process of evolution?

You are turning this paper into an either/or scenario: it dates from 2005 - here's a article from 2008, which cites yours:

Neutralism and selectionism: a network-based reconciliation

What does this tell you?

Here's a more recent paper from 2013, which cites mine, which cited yours:

Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns

What does that tell you?

I'm not in either camp - evolution works as a combination of the two.

Remember how the videos and pictures show the "cup" developing more depth? That can happen either through a single beneficial mutation or a neutral mutation in combination with a number of existing neutral mutations.

Ok, so for example, how do you get a “cup” from a light sensitive nerve? Which mutation (ether neutral or beneficial) would have to occur?

As I said, either a single beneficial one or a neutral one in combination with one or more from the "junk drawer". The latter is statistically the more likely.

You're still asking me to come up with evidence that shows that (bio-)chemical reactions don't work. :?

That atoms can't combine to produce simple molecules - that simple molecules can't combine to form ever more complex molecules - that inorganic chemistry doesn't result in organic chemistry with the formation of the CH molecule - that the formation of ever more complex hydrocarbons doesn't result in the formation of ever more complex amino acids, and so on, and so on...

:lol: :lol:
Atoms can create complex molecules therefore the eye evolved from a “simple” light sensitive nerve ¿do you see any problems with your logic?

The mechanisms that cause an atom(s) to become a complex molecule are not the same as the mechanisms that are supposed to create eyes from proto-eyes, trust me complex molecules are not a product of random mutations and descend with modification.

You know this for a fact, do you?

Besides that is a straw-man, I asked you for evidence that would convince you that eyes can´t evolve by Darwinian mechanisms, ¿what is the point of discussing if you already decided that “evolution did it” no matter what? If you don´t what us to call evolution a religion stop trating evolution a such and answer unambiguously, WHAT EVIDNECE WOULD CONVINCE YOU THAT THE EYE COULD HAVE NOT EVOLVED BY DARWINIAN MECHANISMS?

Since you seem to be missing the point I've been making throughout our recent posts, let me ask you a question:

At what point does chemistry cease to be the ultimate process and *something else* takes over?

Kindest regards,

James

 

[dandan]

HE-WHO-IS-NOBODY

Let us see it. Provide the mutations that would be selected to turn a wolf one-step closer to a Chihuahua. I predict (much like your cake phylogenetic tree) this will not materialize.

SURE

For example if you what to turn a wolf in to a Chihuahua you would need to “evolve” a small and broad skull. This can be done in one single step that would be selected (artificial selection in this case)

MSX2 and TCOF1, which are expressed during cranial facial development, were sequenced in 10 different dog breeds that varied in cranial and face shape (Haworth et al. 2001a,b). However, only a single amino acid change in the TCOF1 protein showed an association with short and broad skulls.
http://genome.cshlp.org/content/15/12/1706.full

You also need to evolve “small size” and can be achieved (at least partly by suppressing a single gene)

Small breeds, it turns out, all have a piece of DNA that seems to repress the IGF1 gene and hence stunts their growth, researchers report
http://www.scientificamerican.com/article/what-makes-small-dogs-sma/

you would also have to evolve “friendly behavior”
In order to achieve this you need selective breading of low levels of certain hormones (maybe no random mutations involved)

The levels of the hormones decreased with advancing selection. The basal cortisol levels in the blood of the domesticated foxes in generation 20 were almost twofold lower than of the non-domesticated, and it was about 30% lower under stress.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763232/

You would also have to evolve hairlessness; there are multiple paths that could produce hairlessness in a creature, for example single mutation in the HR gene might be enough.

Mutations in this gene (HR) have been documented in cases of autosomal recessive congenital alopecia
http://en.wikipedia.org/wiki/HR_(gene)

See how easy it is to copy paste something? When you ask me for a source, I do provide such source and copy-paste the exact portions of the article that would prove my point, when you quote something all you do is quote from an article that has nothing to do with the topic, You simple assert that “article X” proves your point, but you don´t provide the portion of the article that would prove your point



Ok, obviously I did not explain how every single step took place, but atleast I provided a small sample of genetic changes achievable in one generation and that would be selected. ¿can you please do the same with the evolution of the eye? If you don´t do that I will ignore all your comments from this thread.

 

[dandan]

DRAGAN

The point with which I take issue is - as before - you link to scientific papers which you don't appear to understand the full implications of what it says in context.

Do you think that the author is actually up-ending the process of evolution?

You are turning this paper into an either/or scenario: it dates from 2005 - here's a article from 2008, which cites yours:

Neutralism and selectionism: a network-based reconciliation

What does this tell you?

Here's a more recent paper from 2013, which cites mine, which cited yours:

Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns

What does that tell you?

I'm not in either camp - evolution works as a combination of the two.

I never said that neutralism and selections are mutually nexclusive nor incompatible, a selectionists is someone who believes that beneficial mutations and natural selection play a more important role in change, adaptation, speciation and evolution, than random genetic drift and neutral mutations, selectionists don´t deny that neutral mutation play some role, but the belive that selection is more important.

Neutralist believe the opposite, they don´t deny that selection takes place, but they would say that it plays a minor role.

So are you a neutralist or a selectionist? In other words, do you believe that most mutation that created the eye where neutral or positive?
Of course you answer will be “I don’t know” because you have no idea on what mutations could have produce an eye from a proto eye, you simply state that the eye evolved, but you are unable to describe the necessary genetic steps that would have had to take place.


I see no point in this conversation if you don´t provide a potential falsification, if you don´t provide potential evidence that would falsify the idea that the eye evolved I will ignore your comments.

 

[Dragan Glas]

Greetings,

DRAGAN

The point with which I take issue is - as before - you link to scientific papers which you don't appear to understand the full implications of what it says in context.

Do you think that the author is actually up-ending the process of evolution?

You are turning this paper into an either/or scenario: it dates from 2005 - here's a article from 2008, which cites yours:

Neutralism and selectionism: a network-based reconciliation

What does this tell you?

Here's a more recent paper from 2013, which cites mine, which cited yours:

Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns

What does that tell you?

I'm not in either camp - evolution works as a combination of the two.

I never said that neutralism and selections are mutually nexclusive nor incompatible, a selectionists is someone who believes that beneficial mutations and natural selection play a more important role in change, adaptation, speciation and evolution, than random genetic drift and neutral mutations, selectionists don´t deny that neutral mutation play some role, but the belive that selection is more important.

Neutralist believe the opposite, they don´t deny that selection takes place, but they would say that it plays a minor role.

So are you a neutralist or a selectionist? In other words, do you believe that most mutation that created the eye where neutral or positive?
Of course you answer will be “I don’t know” because you have no idea on what mutations could have produce an eye from a proto eye, you simply state that the eye evolved, but you are unable to describe the necessary genetic steps that would have had to take place.

I see no point in this conversation if you don´t provide a potential falsification, if you don´t provide potential evidence that would falsify the idea that the eye evolved I will ignore your comments.

So, did you read any of the articles I posted? I gather not as you haven't inferred my answer.

You also don't seem to have gathered my possible "position" from what I've posted so far - even from the post to which you've just replied.

You also haven't explained your "trust me" assertion.

Nor have you given an alternative "pathway" that doesn't involve chemical reactions.

Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup

Kindest regards,

James

 

[Rumraket]

DRAGAN

This is why I hesitated complicating explanations because it might cause confusion.

If a beneficial adaptation occurs due to a combination of neutral mutations occurring - one followed later by another - this does not mean that yet another later neutral mutation will undo the positive step.

Remember, the environment determines which mutations are propagated and which are selected out.

Two neutral mutations which combined are beneficial in the environment will be propagated. If another neutral mutation occurred that resulted in that benefit being undone, then the organism born with that negated adaptation will be less successful than those with the beneficial adaptation, and thus be less likely to survive/propagate the negated adaptation.

Does that make sense?

Ok lets Pretend that you have to go from point A to point D.

I would protest already here because thinking like this, that you "have to" get somewhere specific from another specific place is emphatically not how evolution works. There are no goals, there are only results of a sequence of events. What happens to be the result was not a goal that needed to be reached, sometimes, in fact very often, species go extinct. I'm sure you've heard the saying that over 99% of all species that ever lived have gone extinct. Only very few of all these species lie on lineages that managed to evolve species that went on to diversify and populate the planet.

What selectionists would argue is that you can go from A to B where “B” is selectively positive then you can go from B to C where “C” is also selectively positive and finally you can Get D that would also be selectively positive.

Sure, agreed.

What neutralists like yourself would argue is that you can go from A to B then to C and finally to D eventhoug, “B” and “C” are not selectively positive.

¿Do you agree up to this point?

Disregarding the idea of goals in the sense you alluded to above, yes I agree with the general statement that evolution can cross non-adaptive valleys, up to a certain point, as long as they are not outright lethal.

As I argued in the past, your neutralist model has 3 problems

1 you would be climbing mount improbable all at once, your model it´s extremely unlikely. Even in a small population of 1,000 individuals the chances for a neutral mutation to become fixed is 1 in 2,000

Yes, sure. The probability that any specific neutral variant will achieve fixation is 1/2N.

But the rate at which neutral mutations are fixed, is:

B. Rate of fixation of new mutations

In any generation, the number of possible copies at which a new mutation could originate is 2N (i.e., new mutants could exist at any of the gene copies in the population).
The probability of getting a new mutant is thus 2Nu (i.e., the rate at which mutation occurs at any one gene copy, applied to all gene copies)
Thus, the total number of mutations that will be fixed per generation is:
(2Nu) (1/(2N)) = u
(i.e., the probability of getting a new mutant in the population and then the probability that this mutant will be fixed)
That is, the rate at which new (neutral) mutants are fixed is 1/u (i.e., the number of generations for a mutant to be fixed, which is the inverse of the number of mutants fixed per generation); this rate is INDEPENDENT of population size, N.

Source: http://www.nyu.edu/projects/fitch/courses/evolution/html/genetic_drift.html

(2Nu) (1/(2N)) = u, where u is the mutation rate.

So the rate of fixation for nonadaptive mutations is simply equal to the mutation rate.

Dispensing with the goal-biased interpretation you opened with, you can look at it this way: New mutations constantly arise in all members of the population. In humans, the number is thought to lie somewhere between 70 and 150 for every individual. The probability that any one single of these will get fixed is very unlikely as you correctly note, but the probability that some will is, well, a statistical certainty. That means between 70 and 150 new neutral variants is fixed in the human population every single generation. In this very moment, the human population is full of neutral alleles drifting around at various frequences. Some of them are just at the cusp of becoming fixed, others are on the brink of extinction. They each have their long histories of dropping and rising in frequency due to random sampling.

, having a mutation in a desired spot (for example from A to B) is already extremely unlikely (1 in 30,000,000aprox)

This after-the-fact calculated improbability is meaningless. Hundreds of neutral mutations get fixed in countless species every day. What use is it to erect such a number then? You can always go back and calculate that some specific event that happened was absurdly improbable. What is the probability that some arbitrarily picked molecule of nitrogen in my living room will find itself 30cm above the ground at some specific GPS coordinate in Japan in 6 months? Incalculable. The same goes with basically any specific area I pick now, 6 months in the future. Whether that be in Japan, Uruguay or the Ivory Coast. Are we now supposed to think that the movement of air molecules is so improbable we can simply discount that it happens, because we have erected some calculation to show how unlikely it was for some specific molecule to arrive where it did, now after the fact?

The facts are that air molecules move around and that my nitrogen is no exception, it WILL find itself in SOME specific area in 6 months, and when looked at now, out of the total space of possibilities, wherever it may end up will be unfathomably unlikely.

It's basically the same for mutations and drift. It happens, erecting arbitrary theoretical scenarios about probabilities of some specific mutation in your imagination is irrelevant. A neutral mutation will arise, it will some time in the future get fixed, and it might or might not have some later adaptive potential.

and your model would require that such an unlikely event would have had to happen 2,000.

First of all, neutral mutations are not required to become fixed in the population before being coupled to adaptive variants. You can have a neutral "potentiator" mutation arise, linger around at a low frequency for a few generations and THEN have another adaptively beneficial variant arise due to the combination of the potentiator and another mutation. Then selection would work on the combination of the two and fix them.

This is actually what happened in the Lenski long-term evolution experiment with E coli. While the exact nature of the potentiator mutation isn't actually known, what has been elucidated is that at some point a mutation arose which, in combination with the later cit+ enabling mutation(the one that initiates utilization of citrate under anaerobic conditions), produces the cit+ effect. This was actually tested in the experiment because independent lineages evolving alongside the cit+ lineage, could not utilize citrate under anaerobic conditions despite having had the cit+ mutation artifically inserted into their genome. That means there's another, non-adaptive mutation sitting in there somewhere, which has to work in concert with the cit+ variant.

So, despite these massive, unfathomable after-the-fact improbabilities you calculate for "specific" mutations, they happen in the real world.
http://sandwalk.blogspot.dk/2013/12/lenskis-long-term-evolution-experiment.html

Here's what he discovered. It was published in Nature last year (Blount et al. 2012). The phylogenetic history of the Ara-3 culture is shown in the figure on the left.

There were some early unsuccessful clades (UC) but most of the culture consisted of three main clades, C1, C2, and C3. (Remember that these are clones.) Clade 1 died out at about the same time that the first cit+ bacteria arose in clade 3. Clade 2 (cit-) persisted in the culture even after the evolution of efficient citrate utilizing bacteria. The authors do not know why the cit- bacteria continue to be present in the culture. Perhaps they contain an unidentified beneficial mutation.

The first cit+ bacteria were detected at 36,000 generations but the mutation probably occurred a few thousand generations earlier as shown in the figure. The surviving cit+ clone carries a mutation in the mutS gene (methyl directed mismatch repair) making this a mutator strain. These are fairly common in the other cultures and it's not thought to be significant in the evolution of the cit+ phenotype.

Actualization

Recall that there are three steps in the evolution of the cit+ clade: potentiation, actualization, and refinement. The actualization step involved a tandem duplication of part of the genome that included the citT gene. This is the gene that encodes the citrate transporter (citrate/succinate antiporter), the protein responsible for taking up citrate from the external medium. Normal wild-type E. coli do not express this gene under aerobic conditions so they are unable to utilize citrate. The citT gene is part of an operon that's under the control of an upstream promoter to the left of the citG gene shown in the figure below.

The duplication results in the fusion of the 3′ end of the citG gene to the 5′ end of the rnk gene. This brings the new copy of the citT gene under the control of the rnk promoter resulting in constitutive expression of CitT (citrate transporter) and uptake of citrate from the medium. Thus, the mutant bacteria are able to use citrate as a carbon source under aerobic conditions.

The selective advantage of the initial tandem duplication was weak. The new cit+ phenotype conferred only a 1% growth advantage over the parental cit- strain. Previous results from the long-term evolution experiment suggest that this is not sufficient to take over the culture under the conditions of the experiment.

Refinement

The actualization step was "refined" by additional mutations that increased the level of the citrate transporter resulting in a much bigger growth advantage. The refinement step occurred around 32,000 generations. It involved additional mutations resulting in multiple tandem copies of the new citT operon. Some clones had four copies of the citT operon and one had nine copies.

Potentiation

Blount moved the new operon into several other strains to see if it would confer a cit+ phenotype. In most cases expression of CitT did NOT result in significant use of citrate. However, when transferred into ancestors of clades 1, and 2 from the Ara-3 culture there was a weak ability to grown on citrate. The effect was even stronger in the ancestors of clade 3 from before the evolution of the Cit+ phenotype.

This indicates that earlier mutations in these clones enhanced the ability to utilize citrate. These are the "potentiators" and there had to be at least two of them; one in the ancestor of clades 1 and 2 and another in the ancestor of clade 3. These mutations, which are still unidentified, could be making chromosomal rearrangements easier leading to an increased rate of tandem duplications at the citT locus. Alternatively, they could be exerting an epistasis effect where the products of the potentiating genes interact with, or enhance, the citrate transporter.

In order to distinguish between these two possibilities, Blount et al. (2008) decided to run "replay" experiments where they took ancestral clones out of the freezer and subjected them to further rounds of evolution. The first replay experiment was started on the 3rd anniversary of Stephen Jay Gould's death (May 20, 2005) and ended on the 66th anniversary of his birth (Sept. 10, 2007) (~3,700 generations). Other replay experiments ran for shorter lengths of time. They also did plating experiments where they selected for colonies that could grow on citrate.

Blount et al. (2012) sequenced 19 cit+ clones from the replay experiments. Eight (8) of them had tandem duplications similar to the original clone but with different boundaries. Six (6) had IS3 insertions just upstream of citT creating a new promoter for expression of citT (see figure below).

Two (2) mutants had larger deletions/insertions at the same locus and two (2) others had mutations that brought citT under control of a different prompter. One mutant couldn't be resolved.

These result show that the cit+ phenotype can arise in a number of different ways providing evidence that the potentiating mutations exert an epistasis effect and not an effect on mutations.

The data shows that the evolution of the cit+ phenotype was a complex process involving a number of separate mutations. The final mutations (refinement) were contingent on earlier mutations (actualization) and the effectiveness of mutations at the citT locus was contingent on earlier potentiating mutations. These potentiating mutations occurred, by chance, in the Ara-3 culture and not in any of the other cultures.

Here's how Blount et al. (2012) summarize the results.

Before a new function can arise, it may be essential for a lineage to evolve a potentiating genetic background that allows the actualizing mutation to occur or the new function to be expressed. Finally, novel functions often emerge in rudimentary forms that must be refined to exploit the ecological opportunities. This three-step process—in which potentiation makes a trait possible, actualization makes the trait manifest, and refinement makes it effective—is probably typical of many new functions.

2 Even if you go from A to B, (solving all the problems presented above) it would be equally likely to “de-evolve” from B to A, than Evolving from B to C since all of them are neutral changes there is no selective bias to evolved from B to C rather than from B to A, all (or most) of your “evolutionists” would be canceled out by de-evolutions.

And despite all this, the effect takes place. We have direct, concrete empirical evidence.

And I am still waiting for an ambiguous answer ¿what evidence would convince you that complex organs like the eye could have not evolved through Darwinian mechanisms (mutations, selection, genetic drift etc)?

From the standpoint of population genetics, I can think of a couple of things off the top of my head that could disprove the lack of evolvability of a structure like the eye, at least in terms of how we know inheritance works: If there was a total lack of a genetic basis for inheritance for the features involved in the construction of the eyes. In other words, while eyes were heritable, they were not subject to mutability or variation at all. That would obviously make their evolution impossible.

Or how about if there was a total and absolute lack of adaptive mutations, e.g. that all mutation everywhere always and invariably were deleterious or outright lethal. That would also make it pretty hard to contend that eyes were evolvable entities, at least through mutational means.

Edit: correct attribution of quotes.

 

[MarsCydonia]

And here is what we can expect from OnceForgivenNowFree:

This is pure gold! Thanks. I think it's time I leave the thread. Aronra has obviously provided all the evidence he has! I'll just make a video summarizing it....and this video will help! Like you said, the paper actually makes my point! Catch 22 is another word for irreducible complexity! Too bad aroma only read the title! Lol

This comment on one of Equestions video (the man who says "I spoke to breeders and they said they can't breed bigger animals" is evidence creationism) shows that his current plans appear to be to run away from the discussion.

 

[Vivre]

Darwin was referring to "kinds" by use of the phrase "separate creations".

Thanks for the hint, I'll check back on that.

~ greets Vivre

 

[dandan]

Dragan

I see no point in this conversation if you don´t provide a potential falsification, if you don´t provide potential evidence that would falsify the idea that the eye evolved I will ignore your comments

 

[Dragan Glas]

Dragan

I see no point in this conversation if you don´t provide a potential falsification, if you don´t provide potential evidence that would falsify the idea that the eye evolved I will ignore your comments

What if I go with Rumraket's two hypothetical ones? Happy now?

If you're merely looking for a way to escape the questions I've put to you throughout this and other threads, it won't work.

Kindest regards,

James

 

[dandan]

Moderators, I posted a long reply like 5 minutes ago but I can´t see it, is there anyway you can recover my comment?

 

[Master_Ghost_Knight]

Moderators, I posted a long reply like 5 minutes ago but I can´t see it, is there anyway you can recover my comment?

I'm no moderator. But I don't think there is much you could do if the reply didn't manage to get up on the server. It maybe to late, but if you go back it probably should still be in your history.
It is also anoying to me when I make a long post, but it doesn't get in because my internet connection went down.Next time, if you are making a long reply, please save it first before submitting (selectin gthe entire text and doing ctrl+C should be sufficient). When you submit, wait for the message confirming that your post has been submitted, if the submission fails and you haven't saved your message do no proceed, immediately go back in the history and your message should still be there.
If you can not go back in history, and you haven't saved the message, then you are out of options other than to try and submit it again, its annoying but there isn't much you can do.

 

[Dragan Glas]

Moderators, I posted a long reply like 5 minutes ago but I can´t see it, is there anyway you can recover my comment?

If hitting your back button on your browser doesn't take you back to the "post a reply" screen with it or - as MGK suggests - recovering it through your browser's history, then it's gone.

I used to have that problem with losing posts whilst posting but I now use Lazarus to recover posts and forms (filled-in forms get reset due to browser crashes).

Kindest regards,

James

 

[Dave B.]

Moderators, I posted a long reply like 5 minutes ago but I can´t see it, is there anyway you can recover my comment?

Just cut and paste one of your other replies. They're all the same anyway...