Theories - Origin of Life

[AstraSequi]

...are you going to reply to the second half of my post?

I believe you refer to your final point of your post of Sun Feb 19, 2012 12:08 am. Page 39

...Actually, no. I refer to the second half of my post, like I said in the question. I did not refer to one specific point near the end of my post.

I am asking you for the fifth time to complete your response, or to concede points. Conceding points is not conceding the entire discussion, and I will not treat it that way. In fact, it will give the impression that you are a thoughtful person who is actually engaging seriously in the discussion. However, if you simply do not answer, that gives the impression that you are simply refusing to admit that you cannot. If you need time to think, then it would be polite to specify that. If you cannot respond and are still trying to maintain the same position without making any changes, I suggest that you ask yourself why that might be.

Furthermore, please do not use responding to me as an excuse to avoid responding to Luxorien.

[Luxorien]

AstraSequi

My apologies,
Luxorien's interjection somewhat hijacked me, quite challenge to deal with matters on different fronts.

Anyhow I will return to you now, and ask Luxorien to be a little patient. I am sure he would appreciate the rest from parading his developmental potential to his principle.

No problem, man. I got time.

I don't understand any part of that last sentence except the pronoun, so I might as well take this opportunity to mention that I have girl parts. I don't mean that as a reprimand - just stating a fact.

Good luck.

[scottie]

AstraSequi

It seems to me that you are being quite evasive here.
I believe I have responded to all the points you have made. If I have missed any then please be courteous enough to specify what I have not responded to.

Also I have no intention of avoiding a response to anyone, nor have I even suggested that as an excuse. I will simply put your last comment down to a misunderstanding.

It is noticeable to me that you have not responded yourself to the points I have raised in rebuttal. Are you then conceding those points?
If not perhaps, could you in in turn address the issues I have raised.
You do appear to be getting a bit rattled.


Luxorien
Sorry,
Thanks for the gender correction.
I have a very busy life at the moment and cannot devote all the time I would wish to this forum, so I appreciate your patience.

I will go over your last post point by point as far as possible, and will start later on this evening.

[AstraSequi]

I would call it frustration than being "rattled," thank you - it's now been a month that I've been trying to get you to answer. If you were uncertain about anything, it would only have taken a couple of minutes for you to check, and I was assuming you could do that without me reposting it (although of course I would have, if you had asked). You were certainly able to find the comment about speciation which is within said post.

I will, of course, start replying when you have finished. If I think I have points to concede, I will do so at that time. Since you say you have no intention of evasion, I will give you the benefit of the doubt, at least for now.

The sections for which I see no response are as follows. If you actually did reply to any of it (besides the speciation comment containing the Wikipedia link, which I already know about), then please give me the page and post number.

According to the theory, the mutations upon which this process rests is Random. To expect, as you suggest that changes will probably be in similar ways, is to support my view that the change is not random. You can't have it both ways. Either change is random or it is not.

This is essentially the same point. As long as you have enough chances, the "correct" mutations will be able to occur, and then natural selection will be able to act.

For example, if we put some bacteria in nutrient-rich media, they will always start to grow faster after some time. This experiment only takes about a week to run, and the change will always be in the same direction.

That is to say, we observe that natural selection produces the same result. This will happen for almost any bacteria we can grow - the new environment favors those bacteria that grow the fastest, so long as we allow enough time to pass.

Natural Selection is not a force but simply the naturally selected result of random forces.
The driving force in darwinian theory is the random mutations that allow nature to select from.

I think this is semantics. Both stages, the mutations and the selection, are required for species to adapt. If there are no mutations, no variation is generated and no change can occur. If there is no selection, only random change can occur.

The enviromental stress in three different continents are not the same. What the researchers noted was that the climate/latitude was the common factor. That is why they made the link with global warming.

That is why I said:

In the most charitable interpretation I can think of, I suppose it is possible to make some assumptions and then say that their data is consistent with a completely deterministic model. However, you cannot say that it is evidence for such a model against natural selection, because natural selection can account for the same results quite well, and without the extra assumptions.

Camille Parmesan at the University of Texas in Austin, US, who has carried out similar research, says these new findings are a warning that species may only have limited capacity within their own genomes to adapt to climate change.

If the capacity for change is limited as this researcher warns, then what happens to the theory?
After all climate has always been on the change throughout life's history.

Natural selection does not say that the capacity for change is unlimited. It might perhaps be the case, but only given enough time - the rate of change over any particular time scale is limited by the amount of pre-existing variation in the population, and the rate of production of new variation (that is, the rate of mutation).

If the rate of change is too fast, the species is unable to adapt and goes extinct. Climate has never changed as fast as it is now in any point in Earth's history (save perhaps the mass extinctions, and of course they didn't go too well for life!)

Are you sure you can't think of another reason why someone would be disturbed by the observation that climate change is causing animals to undergo dramatic genetic changes?

Well actually I cannot think of any reason why Dr Huey would be disturbed, other than this change does not sit well with evolutionary theory.

Very well - it is related to what you said above. Drosophila is a highly successful species, with a very short generation time and the ability to adapt very quickly to new environments. When we see such a species changing very rapidly, it means that it needs to change that fast in order to stay adapted to the environment. (Or, in an even worse case, that its rate of change is at maximum, and it would be changing even faster if it could.)

This means that any less successful species, which cannot adapt as fast as Drosophila is adapting now (and which does not have other options such as migration), is likely to be in great difficulty.

In fact, I can tell you what the authors of the paper say, in their concluding paragraph:

The increasing numbers of examples documenting genetic (2–5, 8, 10, 11), as well as phenotypic (1, 2) responses, to recent climate change are not surprising from an evolutionary perspective, but nonetheless are disturbing from ecological or economic ones, because such changes signal inevitable disruptions in the distributions, population dynamics, and community interactions of organisms (1, 2).

(My emphasis.)

I definitely agree with you that the authors know more about this topic than us. However, you will then need to accept these statements as well.

Also, observing rigorous data contradicting evolution would not be disturbing to scientists in the same way - it would be interesting.

Species change is the product of random (unguided with no goal) mutations with nature selecting any functional changes that present themselves.
In other words the functional variation is already there for nature to select.

I agree with your first statement. The second is not true in all cases, since mutations can and do continue to occur at about the same rate, whether selection is happening or not.

In this case, the functional variation was indeed already there, and all three populations already had the capacity (a low level of pre-existing inversions) for that change, because they shared a common ancestor which already had that capacity, and none of them lost it in the intervening generations. I suppose you might call this "programmed," insofar as all DNA is a cellular program, but there is nothing in this that contradicts natural selection.

Actually - what do you mean when you say "programmed"? A definition might help to clear up any misunderstanding.

If the change is dramatic (as you are suggesting) then new species would be expected to arise.

Speciation requires a) differential selection on different parts of the population, b) very low gene flow between those two parts of the population, and c) the low gene flow to be maintained until enough change has occurred to prevent any future interbreeding. (There are other types of speciation, but they are not as well understood.) The authors point out in the paper that criterion b is not met - in fact, that the gene flow is unusually high. As a result, criterion c cannot be met either.

Why would that be disturbing?
Surely this is the natural way, according to the theory.

As mentioned above - the authors say it quite well. Of course, it is not as disturbing for the future of life on earth as a whole, which will probably carry on no matter what we do.

What evidence is there for Speciation through Natural Selection?
It is after all the corner stone of evolutionary theory.

I would say the "cornerstone" is in fact the logical argument I mentioned above. (See below for my answer.)

Darwin's own words
http://www.jstor.org/pss/187407 (please note my good form in naming my source )

Thank you.

Has this situation changed since Darwin's day?
Can someone help with some evidence.

Most definitely. I suggest you read http://en.wikipedia.org/wiki/Speciation, and also any included citations if you want to investigate further. Please note in the opening paragraph, "Observed examples of each kind of speciation are provided throughout."

Lets try and make the question a little easier.

What evidence is there that random mutations and natural selection can produce new functional biological information.

This is not the same question. I will answer you if you can demonstrate that you understand why that is.

[scottie]

AstraSequi
This is going to be a long one, so take your time.

I would call it frustration than being "rattled," thank you - it's now been a month that I've been trying to get you to answer. If you were uncertain about anything, it would only have taken a couple of minutes for you to check, and I was assuming you could do that without me reposting it (although of course I would have, if you had asked). You were certainly able to find the comment about speciation which is within said post. 

Yes you are right it has been a month, but what have you contributed in that time? What response have I had from you?
However I don't get frustrated, I have just learned to cope.

I will, of course, start replying when you have finished. If I think I have points to concede, I will do so at that time. Since you say you have no intention of evasion, I will give you the benefit of the doubt, at least for now. 

Now now, I don't need you to give me the benefit of any doubt, whether you harbour any doubts really is your concern.

The sections for which I see no response are as follows. If you actually did reply to any of it (besides the speciation comment containing the Wikipedia link, which I already know about), then please give me the page and post number. 
According to the theory, the mutations upon which this process rests is Random. To expect, as you suggest that changes will probably be in similar ways, is to support my view that the change is not random. You can't have it both ways. Either change is random or it is not.

This is essentially the same point. As long as you have enough chances, the "correct" mutations will be able to occur, and then natural selection will be able to act.

I would have thought my response on the wiki link along with the probability point was sufficient to answer most of your questions, but it seems not, so I will deal with all your points even though I will find myself going over the same ground again'

So, how many “chances” are enough? And what are “correct” mutations.
The “Chances” question can only be answered with probability theory. I have already dealt with that aspect of this subject see scottie » Sun Mar 04, 2012 7:42 pm page 41

The question of “correct” mutations being random makes no sense when we are dealing with for example proof reading. This type of process requires some template to compare with in order to be “correct”.
How about checkpoint systems during cell division. Here again there must be some template by which the process is able to determine when the process is ready to move on to the next stage.
In other words there must be some body plan by which these mutations can be compared in order to make any determinations as to whether to continue or abort.
No one as far as I am aware has even adequately addressed the how cell differentiation can be the result of random mutations to the genome.

For example, if we put some bacteria in nutrient-rich media, they will always start to grow faster after some time. This experiment only takes about a week to run, and the change will always be in the same direction.

That is to say, we observe that natural selection produces the same result. This will happen for almost any bacteria we can grow - the new environment favors those bacteria that grow the fastest, so long as we allow enough time to pass. 

The question is not whether the bacteria grow any faster, the question is does this produce any new species.
The Lenskie experiment has clearly shown that no new species has emerged despite all the mutations that occurred.
May I refer you to the previous discussions on this subject
about14351-60.html
Page 6  scottie » Mon May 02, 2011 7:10 pm
For a start there has not been enough time in earth's history for any probability theory to be used in connection with these ideas.

Natural Selection is not a force but simply the naturally selected result of random forces.
The driving force in darwinian theory is the random mutations that allow nature to select from.

I think this is semantics. Both stages, the mutations and the selection, are required for species to adapt. If there are no mutations, no variation is generated and no change can occur. If there is no selection, only random change can occur. 

This is not about semantics. Random Mutations are the driving force in Darwinian processes. The problem is that you have to rely on such vague terms as “enough chances” to try and justify the hypothesis.

The enviromental stress in three different continents are not the same. What the researchers noted was that the climate/latitude was the common factor. That is why they made the link with global warming.

That is why I said:
In the most charitable interpretation I can think of, I suppose it is possible to make some assumptions and then say that their data is consistent with a completely deterministic model. However, you cannot say that it is evidence for such a model against natural selection, because natural selection can account for the same results quite well, and without the extra assumptions.

Well you are right. You can suppose its possible to make any manner of assumptions if you wish to be charitable.
It may not refute NS but it is certainly evidence against as I stated

Camille Parmesan at the University of Texas in Austin, US, who has carried out similar research, says these new findings are a warning that species may only have limited capacity within their own genomes to adapt to climate change.

If the capacity for change is limited as this researcher warns, then what happens to the theory?
After all climate has always been on the change throughout life's history.

Natural selection does not say that the capacity for change is unlimited. It might perhaps be the case, but only given enough time - the rate of change over any particular time scale is limited by the amount of pre-existing variation in the population, and the rate of production of new variation (that is, the rate of mutation).

I haven't suggested that NS in unlimited, however it is attributed with going from Amoeba to Man. That's a very bold claim, so what is the evidence to back it up.

If the rate of change is too fast, the species is unable to adapt and goes extinct. Climate has never changed as fast as it is now in any point in Earth's history (save perhaps the mass extinctions, and of course they didn't go too well for life!)

It's not a question of whether the species goes extinct. Species do go extinct. The point is whether they change into new species, That is what Natural selection is supposed to accomplish.

Are you sure you can't think of another reason why someone would be disturbed by the observation that climate change is causing animals to undergo dramatic genetic changes?


Well actually I cannot think of any reason why Dr Huey would be disturbed, other than this change does not sit well with evolutionary theory.

Very well - it is related to what you said above. Drosophila is a highly successful species, with a very short generation time and the ability to adapt very quickly to new environments. When we see such a species changing very rapidly, it means that it needs to change that fast in order to stay adapted to the environment. (Or, in an even worse case, that its rate of change is at maximum, and it would be changing even faster if it could.)

This means that any less successful species, which cannot adapt as fast as Drosophila is adapting now (and which does not have other options such as migration), is likely to be in great difficulty.

In fact, I can tell you what the authors of the paper say, in their concluding paragraph:
The increasing numbers of examples documenting genetic (2–5, 8, 10, 11), as well as phenotypic (1, 2) responses, to recent climate change are not surprising from an evolutionary perspective, but nonetheless are disturbing from ecological or economic ones, because such changes signal inevitable disruptions in the distributions, population dynamics, and community interactions of organisms (1, 2).


(My emphasis.) 

I am aware of their “ not surprising from an evolutionary perspective” view but are they speaking from the perspective of speciation? The fact is they are not. The variations they are referring to are variation within species that appear to be governed by cellular responses to climate change. If natural selection was at work (in other words if NS was causing these changes) why would they be disturbing?
After all is it not expected that natural selection will result in changes such as these.
They are disturbing because they don't sit very well with Natural Selection expectations.

I definitely agree with you that the authors know more about this topic than us. However, you will then need to accept these statements as well.

 
I accept their data not their “disturbing” perspective.

Also, observing rigorous data contradicting evolution would not be disturbing to scientists in the same way - it would be interesting.

So scientists are now relying on symantics are they?
You are going around in circles here How then did the program arise?

The common ancestor argument is an assumption. The creationists argue that the data this argument rests on is equally applicable to the creation argument. So this is no different to the “God did it argument” except in your case you are only moving the problem back.
The method by which the common ancestor arrived is no different to how  Drosophila arrived.
Ernst Mayr one of the fathers of the Modern Synthesis in his Crafood Lecture put it this way.
http://www.biologie.uni-hamburg.de/b-on ... luence.htm

A most important principle of the new biological philosophy, undiscovered for almost a century after the publication of On the Origin of Species, is the dual nature of biological processes. These activities are governed both by the universal laws of physics and chemistry and by a genetic program, itself the result of natural selection, which has molded the genotype for millions of generations.

According to Mayr, God didn't do it. Natural Selection is what did it via common ancestory. That was his philosophy as he himself has put it.
But you eventually get back to the single cell. He provides no explanation any more than Darwin himself did.
How did the cell emerge? There is no plausible answer that scientists can envisage other than by some outside agency.
My argument is simple. The same process that caused the cell to emerge is the one that has caused the different species to emerge and that is by an outside agency.
Craig Venter has shown that an outside agency (his team) have managed to demonstrate proof of concept. Albeit not in the creation of life but how an existing life form can be changed by design.

However In his intellectual arrogance Ernst Mayr classically contradicted his own argument.
His philosophy as he states it, is “governed both by the universal laws of physics and chemistry by a a genetic program (his words).
Every scientist knows that a program be it genetic or otherwise does two things.
1) It uses natural forces which are governed by universal laws
2) It injects decision nodes into the process to over ride that natural progress and directs (governs) towards a specified goal.
He then goes on to state as if it were a fact that it was natural selection that created this program.
What decision node has natural selection injected into a process governed by the universal laws that has resulted in this genetic program?
Natural Selection has to work on what is already there, that is why is regarded as a selective process.
It does not create anything let alone inject decision nodes into any process.
For example how is the genetic code(s) the result of natural selection. There is no answer yet according to Mayr and all those who follow his philosophy, natural selection has somehow done just that. It is a dogma nothing else.

Actually - what do you mean when you say "programmed"? A definition might help to clear up any misunderstanding.

Yes I did use the term programmed. I am not alone am I?

If the change is dramatic (as you are suggesting) then new species would be expected to arise.

Speciation requires a) differential selection on different parts of the population, b) very low gene flow between those two parts of the population, and c) the low gene flow to be maintained until enough change has occurred to prevent any future interbreeding. (There are other types of speciation, but they are not as well understood.) The authors point out in the paper that criterion b is not met - in fact, that the gene flow is unusually high. As a result, criterion c cannot be met either. 
Why would that be disturbing? 
Surely this is the natural way, according to the theory.

As mentioned above - the authors say it quite well. Of course, it is not as disturbing for the future of life on earth as a whole, which will probably carry on no matter what we do.

Your assumption is that climate change is man made. You appreciate that the debate around this is quite vigorous.  

What evidence is there for Speciation through Natural Selection? 
It is after all the corner stone of evolutionary theory.

I would say the "cornerstone" is in fact the logical argument I mentioned above. (See below for my answer.)

Logic does not necessarily reflect reality as I have pointed out to you before. It can only be used if it is based on evidence, and with respect that is where your problem is

Darwin's own words
http://www.jstor.org/pss/187407 (please note my good form in naming my source )

Thank you. 
Has this situation changed since Darwin's day?
Can someone help with some evidence.


Most definitely. I suggest you read http://en.wikipedia.org/wiki/Speciation, and also any included citations if you want to investigate further. Please note in the opening paragraph, "Observed examples of each kind of speciation are provided throughout."
Lets try and make the question a little easier.

What evidence is there that random mutations and natural selection can produce new functional biological information.

Well we are back to the Wiki argument which I have dealt with.

This whole post has really been an exercise in futility as I have gone over the same ground before and with others, however I don't get frustrated as this is the price one has to pay for dealing with what is essentially
a philosophical position trying to pose as science.

[wbla3335]

This whole post has really been an exercise in futility

Finally. Something we can agree on. Have you ever looked into the extensive research on the origin and evolution of religion and the psychology of religious belief? Doing so might be more fruitful than continuing with your misunderstandings and misrepresentations of biological evolution.

[scottie]

Luxorien

Actually, I mentioned HIV immunity and antibiotic resistance as examples of beneficial mutations. I brought up sickle cell anemia as an interesting example of how the term beneficial can be relative. I said all this before, and you still keep talking about sickle cell anemia as though the existence of beneficial mutations stands or falls on this example.

You mentioned sickle as your favourite that is why I went on to analyse it in the way I did.
I also said I am quite happy to respond to your HIV and antibiotic resistance examples as well if you wished, so I don't “keep talking about sickle cell anemia as though the existence of beneficial mutations stands or falls on this example.”

If you recall I wrote

Now do you really want me to respond to all the other examples you have enumerated, because I can if you really wish to extend this periphery point.

I hope you are not deliberately trying to misquote me and introduce straw man arguments.
My point was and is, if you wish to point to “beneficial examples” then keep them in the context they appear.

The simple fact remains that beneficial mutations exist. That is the only point that I am making. Your argument against the efficacy of natural selection relies on the premise that a random mutation cannot be beneficial. This premise is demonstrably false.

This is what I wrote on page 41
 scottie » Sat Mar 03, 2012 5:23 pm

The reality is that most genetic changes occur as a result of cellular processes in response to stress, damage and copying errors and are rectified in various ways, (I have not taken account of the developmental changes that occur) while most other mutations which for some reason not corrected, are deleterious to the organism. I haven't even begun to talk about transposons and their part in genome restructuring. All these processes are under the control and regulation of the cell as it responds to stress and the maintaining of it's own equilibrium.

(my emphasis)
I have not argued as you are suggesting, since when does “most other mutations .. are deleterious” some how translate into, as you put it “the premise that random mutations cannot be beneficial”
Perhaps rebutting what I actually say would be helpful

Further My point

If Natural Selection acting on random mutations is responsible for the fetal hemogoblin (which it has to be for the theory to be intact) and this hemogoblin protects against sickle cell, what is the process that removes this protection?

Your response

This argument fails on two levels. The first is that it assumes that fetal hemoglobin was originally produced throughout the life of the organism. This does not necessarily have to be true, and indeed is not true. So there was no protection that was subsequently removed.The second level at which this argument fails has to do with its relevance to the topic at hand. The fact that a single point mutation confers malaria resistance does not somehow go away because there is another mutation that can mitigate the effects of sickle cell anemia.

Your first point is somewhat bizarre. Are you actually suggesting that fetal hemoglobin was not produced first?
I would have thought it was obvious that fetal hemoglobin had to be produced first if as you claim sickle cell is a random mutation. What on earth was it a mutation of, if fetal hemoglobin was not there in the first place.
(or have I missunderstood you somehow?)
Your second point is also somewhat curious.
Fetal hemoglobin actually protects against malaria, it is when that protection is removed as part of the development process, that children become exposed. So the mutation is initially deleterious and then some protection is offered in the hetrozygote.
This is what I mean when I suggest that you report on these matters in context.

And again I remind you that the whole point of this discussion is about NS being the process of speciation.

You then go on :-

I can explain why your example of fetal hemoglobin is not evidence against natural selection:
In the course of the (random) gene duplications that led to the present series of hemoglobin genes, certain sequences were positively selected for, or achieved fixation through genetic drift. A mutation in the fetal hemoglobin's regulatory sequences can cause this hemoglobin to be produced throughout one's life, but this mutation has not occurred often enough, or has not been selected for strongly enough, to become very common.

What evidence do you produce, that the course of the (random) gene duplications is what led to the present series of hemoglobin genes?
I understand the hypothesis you are presenting and trying to explain, however what evidence do you call on that shows these random mutations have in fact produced the “present series of hemoglobin”
I appreciate you actually believe this, but you have to do more than state a belief if you are going to present it as a fact, and an empirical one at that.
As indeed you believe what you further go on to say

Even if only a tiny portion of mutations are beneficial, that's enough genetic novelty to fuel speciation.

Again I appreciate you actually believe that, however you have to provide the evidence to support that statement if you are presenting it as having any empirical support? Are you able to do that?

However we are all agreed on this point, as you put it, “

From a molecular standpoint, most changes in DNA will be harmful. Hence the repair mechanisms.

( well almost agreed I would add most random changes..)
You appear not to have thought through the natural implications of the statement.
If random and unguided mutations produce speciation and as molecular evolution puts it

DNA replication is remarkably accurate. The DNA copying machinery in eukaryotes usually makes a mistake less than once in every million nucleotides. This incredible copy fidelity is achieved by a sophisticated error-checking system involving base selection, proofreading and post replication repair.

What has produced the incredible copy fidelity achieved by a sophisticated error-checking system involving base selection, proofreading and post replication repair.

Are you seriously suggesting that this same process of a tiny portion of random and indeed unguided mutations has also produced the sophisticated error-checking, proofreading and post replication repair.
Are you not aware that in order to proof read, or repair the entire process must have some template or body plan to check against.
The rest of your rather long essay stands or falls on these statements if it to be empirically sound.
From a philosophical standpoint it may come over as sound, but we are dealing with reality.

Finally as regards Shapiro's essay.

As I said before, I do not necessarily question the scientific conclusions of the papers you cite. I question your ability to understand their meaning. As we saw earlier, you quoted from a paper that directly contradicts your argument. You went so far as to include in your quote a sentence that clearly stated that beneficial mutations exist. You ignored that sentence and bolded the part about most mutations being deleterious.

Actually Shapiro rejects neo darwinian or the standard hypothesis. His view is that there is a third way that is neither Darwinian nor ID. He calls it Natural Genetic Engineering.
He is not able to explain how this cellular engineering actually got started except that it was not through some Darwinian process.
Since you are not necessarily questioning the scientific conclusions of his paper, perhaps you better read it more carefully, because he is actually arguing against your clearly stated views.
I do really understand the papers I cite.

Now you bring up the Molecular Evolution quote I presented.
You appear once again to be misrepresenting my position, and then arguing against that misrepresentation.
This straw man argument is a debating tactic that you probably are aware of, but I hope you are not using it as a strategy.
It is quite clear I did not quote from Molecular Evolution because I agreed with the premise of the paper, as it is clearly one that tries to explain evolutionary theory which I disagree with.

That quote was in the context of what constituted a mutation, as not all mutations are random or randomly neutral if any change in genetic sequence is regarded as a mutation.
Many biologists hold the view that any change in genetic information is a mutation.
I quoted it to show that even evolutionary biologists recognise that most random mutations are deleterious to the organism. These researchers themselves recognise that and so do you, as I have previously shown.

My whole point is really quite simple.
I am arguing that it is the cell with it's built in systems, that responds to the environment and not the other way around as you argue in the case for natural selection.
Random mutations that the cell for some reason cannot correct, debilitate the cell's response to that pressure.

So to be clear, let me remind you of what I actually wrote as a direct quote from Molecular Evolution.

All models recognize that most random changes to the genome are deleterious, because they will tend to disrupt highly organized genetic information. It is the relative proportions of mutations that are advantageous, neutral or nearly neutral that is debated.

The question of what categorises a mutation is perhaps better left to another post.
Do you wish me to respond to your HIV and antibiotic examples?

May I request however before you feel the need to respond to any of my arguments please present an argument against what I actually write.

[AstraSequi]

Thank you for the reply. I will reply in kind (for all of your posts, of course, not just the most recent one) by next week.


In the meantime, I will point out:

Yes you are right it has been a month, but what have you contributed in that time? What response have I had from you? However I don't get frustrated, I have just learned to cope.

Now now, I don't need you to give me the benefit of any doubt, whether you harbour any doubts really is your concern.

I think that anyone who reads the discussion since page 39 will see my responses. I suppose I assumed it was understood that I didn't really want to reply until you had responded point by point, which I suppose I might have made clearer. (You appreciate that someone not arguing in good faith could take advantage of this to drop points they didn't want to answer, not that I'm imputing this to you.)

I would also like to mention that the quoted statements above came across as quite condescending. Of course I'm sure this was not your intent, and it doesn't make much difference to me personally either way, but I thought I would let you know.

I'd rather not comment on this again, since the issue is over now that you've finished the reply.


Also,

Actually - what do you mean when you say "programmed"? A definition might help to clear up any misunderstanding.

Yes I did use the term programmed. I am not alone am I?

is not an answer to the question.

I know that you might think there is a standard definition, but if so please quote it to me. I think that your use of the word may not be what I am understanding from it.


Finally, you seem to have left my final point out of your reply - I assume this is an oversight.

The question was, do you understand the difference between speciation and production of new biological information? If so, please humour me and give an answer, since I think this might be an important point.

[Luxorien]

I hope you are not deliberately trying to misquote me and introduce straw man arguments.
My point was and is, if you wish to point to “beneficial examples” then keep them in the context they appear.

I'm not sure what you mean by keeping things in "context." I guess you're saying that any example of beneficial mutation is, in a sense, taken out of context because you think I'm not representing the full complexity of the issue?

I agree that I left out a lot of detail, but as I said before, nothing I left out was relevant. You offered some assorted statements about sickle cell anemia that had nothing to do with the fact that sickle cell anemia is caused by a random mutation and that it does confer an advantage, albeit one that is highly situational.

I have not argued as you are suggesting, since when does “most other mutations .. are deleterious” some how translate into, as you put it “the premise that random mutations cannot be beneficial”

Since the statement I was responding to read as follows:

Where are the functional phenotypes that random mutation is supposed to have produced in order for NS to select from?

-March 3rd, pg. 41

As I have said many times before, my only contention is that random mutations can produce beneficial mutations. Your statement from March 3rd appears to contradict that. Much of what you've said in response to my first post has been irrelevant to the question of whether there is such a thing as a random mutation that can produce an advantageous phenotype.

In one of my previous posts I explained that I took your statement to mean that a beneficial mutation could not be produced randomly, and you neither confirmed nor denied this interpretation. Based on your most recent foray, it sounds like you wish to deny this interpretation. If that is the case, the prosecution rests.

Your first point is somewhat bizarre. Are you actually suggesting that fetal hemoglobin was not produced first?

I think perhaps I did not make myself clear. Yes, I am actually suggesting that fetal hemoglobin was not produced first. But I'm talking on an evolutionary time scale, not during the life of a single organism. Our (reptilian) ancestors had normal adult hemoglobin before they had fetal hemoglobin.

I would have thought it was obvious that fetal hemoglobin had to be produced first if as you claim sickle cell is a random mutation. What on earth was it a mutation of, if fetal hemoglobin was not there in the first place.
(or have I missunderstood you somehow?)

You have misunderstood me so severely that I'm unsure how to proceed. I'm not sure why it would be "obvious" that fetal hemoglobin was produced first if sickle cell is a random mutation. There is no logic in that statement. Fetal hemoglobin and adult hemoglobin are not produced by the same genes. A mutation in the gene that codes for adult hemoglobin will have no effect on fetal hemoglobin production. Nor will a mutation in fetal hemoglobin affect adult hemoglobin production. They are two separate molecules, with different structures. They are produced by different genes. There's a good diagram of the gene clusters here.

Your second point is also somewhat curious.
Fetal hemoglobin actually protects against malaria, it is when that protection is removed as part of the development process, that children become exposed. So the mutation is initially deleterious and then some protection is offered in the hetrozygote.
This is what I mean when I suggest that you report on these matters in context.

I'm confused by this. Are you saying that the sickle cell mutation causes the cessation of fetal hemoglobin production? Are you arguing that the mutation is occurring as the child develops? I still don't get what fetal hemoglobin has to do with anything.

What evidence do you produce, that the course of the (random) gene duplications is what led to the present series of hemoglobin genes?

Evolution by gene duplication is old news. As far as I know, researchers still regard the origin of hemoglobin clusters by duplication as a matter of fact. That article is not very recent, but it has the advantage of being available in full text for free. A search of more recent papers turns up a lot of abstracts that seem to treat this as a matter of course.

I'll stop there for now, because it's almost time to go to work.

[wbla3335]

Evolution by gene duplication is old news.

Creationists have not managed to come up with viable arguments against the evidence for evolution, particularly for gene duplication, even more particularly for polyploidy, and most particularly for allopolyploidy (verging on the perverse). Maybe the creator had the hiccups or just ran out of ideas.

[JorgeLobo]

Evolution has nothing to do with creation of life - only modification after the event.

Science is not driven by "argument" and even if there were data generated that impeached the thery of evoluton, it would not de facto establish some religious concept as its replacement.

[AstraSequi]

I’ve been thinking about the comments earlier, and I realized while writing it that the discussion has started to get less useful for me as well – not least because of how much time it’s taking (this reply took ~12 hours to make, including all the researching, and it is ~26 pages long in Word). As a result, I’ll make this my last response.

However, I still suggest you read it carefully, and try to make sure you understand my points. If you have a few questions about the scientific content, I can probably still find some time, but try to make sure you actually understand what the question is first and have tried to understand the scientific opinion on it (for example, on Wikipedia or TalkOrigins, or in a science textbook). Of course, when looking for evidence, I would suggest you make sure you understand this link as well: http://en.wikipedia.org/wiki/Confirmation_bias.

Anyways, I hope this is useful to you. I have divided up my discussion into posts based on how you divided yours ‒ approximately 1:1, but I split a couple of them for consistency of post length.

Then what is your objection?
The occurrence of natural selection is based on a logical argument, with four premises. (Can you reconstruct the argument?)
- the offspring of animals are never exactly the same as their parents, but rather have small variations.
- some of this variation gives an advantage to an animal that possesses it
- these variations can be passed down to the next generation
- in each generation, not all animals survive.

If you wish to dispute the occurrence of natural selection, you have to deny one of the premises.

I understand the logic of the argument and I have no problem with it.
This logic is perfectly acceptable.
The problem is in how the variation arises.

Yes, but the fact that variation does arise is the important point (and it is very easy to observe). The mechanism by which it occurs is irrelevant to the original argument. It turned out that the mechanism was mutation, but their discovery only strengthened the original argument instead of being required for it.

So just to be clear (since you have “no problem with it”), you agree that natural selection occurs, and that changes occur in species over time as a result?

Remember, if you want to say that change does not occur, you must say that one of the four premises is false. Again – can you reconstruct the argument? If so, please humour me and demonstrate your understanding.

However I believe the question of definitions is important here.
...
So, to understand NS is it not first necessary to get clear what a mutation is and then determine how it is regarded as random, because it appears according to berkley edu, that all genetic variations are random.

What a mutation actually is, needs to be determined, since there are those who have a different description of mutations.

Again, the appearance of genetic variation is random, and natural selection is not random. The two are separate processes; natural selection acts only after the genetic variation is generated.

The first process is random, and the second is not. This means that after natural selection, the variation within the population is also not random, although it is constrained by what the first process generates.

I apologize if you already understand this, but I don't see what it is that you're not getting.

You gave these three descriptions:

The genetic variation that occurs in a population because of mutation is random-but selection acts on that variation in a very non-random way: genetic variants that aid survival and reproduction are much more likely to become common than variants that don't. Natural selection is NOT random!

The term mutation can refer to any process that changes the genetic information in the genome, including DNA insertions, deletions and rearrangements.

Genetic variation is generated continuously by the mutational process, but its persistence in the genome is determined by different historical and genomic factors.

...and you said that the first contradicted the other two. As I already mentioned, I see nothing in any of these quotes which implies any contradiction between them, or with my own understanding of mutations or natural selection. Again, it would be helpful if you could specifically identify what you think the contradiction is.

I would also point out that of the three quotes, only the second is actually a specific definition – the others are descriptions. For example, the only thing the third description really implies about mutations is that they continuously generate genetic variation.

If you go to the Berkeley website and look at their definition of mutations (the quote you have taken is from their natural selection page), you get this definition:

Mutation is a change in DNA, the hereditary material of life.

Again, I don’t see the contradiction. The second of your quotes is somewhat more advanced, referring to the process causing the change rather than the change itself, but the end result of what the DNA sequence is afterwards is the part that is relevant to natural selection.

Also when berkley edu sets out to describe what a Random mutation is, notice what it states

Mutations are "random" in the sense that the sort of mutation that occurs cannot generally be predicted based upon the needs of the organism.

So therefore, before a mutation can be classified as random or not, (although berkley seems to suggest that all mutations are random) we have to determine what the needs are of the organism. How then is that achieved?

Mutations are random. Some kinds are more likely than others (sometimes much more likely, as you correctly point out below), and there are also some things that can cause mutations with very high probability (like UV light). However, there is no guarantee that any particular mutation will be observed.

The “needs” of the organism are only important in the second stage, natural selection. So I suppose that if you constrained “mutation” to refer to only the changes that persisted in the population, then you would only see those which corresponded to the “needs” – that is, the beneficial ones (or at least, the ones that are not detrimental) – because otherwise they would have disappeared.

Is this what the misunderstanding is? If you observe a mutation that has spread within the population, then it is highly likely to be beneficial. That doesn’t mean that all mutations are beneficial, because natural selection filters them (we don’t see any mutations that caused the animal to die as an embryo, for example).