Theories - Origin of Life

[scottie]

AstraSequi

I have tried to catch up with the postings, now I am not sure but is this the question you wish me to address.

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.

However I believe the question of definitions is important here.
According to berkley edu NS is described thus:-
http://evolution.berkeley.edu/evolibrary/article/evo_32

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!

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.

For instance Lindell Bromham, Centre for Macroevolution and Macroecology, School of Botany and Zoology, Australian National University, Canberra, Australia describes mutations this way

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

http://www.tempoandmode.com/wp-content/ ... oels08.pdf

Alan F Wright, MRC Human Genetics Unit, Edinburgh, UK has this to say

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

http://evolution.unibas.ch/teaching/evo ... ations.pdf

It would be good if we can, as a start, agree on what we mean a mutation actually is.

My own understanding of mutation harmonises with the two descriptions I have cited ( Bromham and Wright) and not that of berkley edu.
So which definition do you understand to be the correct one?

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?
Can you help out here?

[AstraSequi]

I have tried to catch up with the postings, now I am not sure but is this the question you wish me to address.

...I was hoping that you would address the entire post, not just one part of it.

[scottie]

yes I intend to address your entire post.
But I do have to start somewhere don't I?

So can we agree on what each of us means when we use the term mutations. As I have demonstrated there are differing views on what constitutes a mutation.
The talkorigins essay by Richard Harter states that :-

It is important to realize that mutations do not occur in response to the environment. They simply happen.

http://www.talkorigins.org/faqs/mutations.html
This appears to agree with berkley edu.
I have given you my understanding, could you let me know what your understanding is, so at least we don't get to talk across each other.

[AstraSequi]

yes I intend to address your entire post.
But I do have to start somewhere don't I?

I can wait for you to finish; in attempting to devise answers, I think you will be able to get closer to resolving any confusion. I see no contradictions or "differing views" in any of the phrases you have quoted - for example, as you think, you might try to specifically identify what you think the difference is.

[LeoPol]

So, Origin of Life.
In order for a origin of membrane - much organic matter is not necessary - only the membrane lipids of different isoforms, it is necessary also to a weak emission core of the star created a flow of heat through the surface phase transition, and yet not interfere with a certain oscillation - vibration … In general, all this is difficult to discuss now, not yet studied the process of emergence and functioning in a natural cell membrane of this very … - Active situational model - a kind of natural intelligence and personality!! But when it all becomes clear, then we can speculate about the conditions and awakening him to the protostar, or on some planet out there.

So. Life has two interacting components. One component - natural intelligence. The second component - the polypeptide-nucleic technology - a self-contained database on DNA, which is implemented through the input-output - RNA into the polypeptide interface. What comes first? I believe that natural intelligence is primary, and polypeptide-nucleic technology - is secondary. In this sense, the theory of “Evolution of the primary replicators to Homo Sapiens” should be replaced by a theory of “Abiogenesis, and social development of the primary natural intelligence”, which later created and developed polypeptide-nucleic technology. http://richarddawkins.net/articles/6435 ... egin#page4

But there is an interesting aspect! Scientists can learn everything you can observe and verify, and Theologysts - thinking about the else far that beyond the border of observable reality. Here, for example, the active situational model is on the cell membrane, and that this membrane? Interacting electromagnetic fields of electronic orbitals. Hence, the intellect - the active situational model in the electromagnetic field. And what is the electromagnetic field? What, in general, the continuum? Yeah … Theologians would say - it is a membrane of Spirit! Well, ok! It does not contradicts the rational science! http://spacenoology.agro.name/?page_id=5519

I adhere to the hypothesis that the engineering design occurred during the rare periods when the developed technological civilizations. This has happened very rarely. But for a very long interim periods ran the Darwin’s Natural Selection, as well as Dawkins’s His Majesty the Selfish Gene! At the same time created by the engineering design technologies were degenerative effects of natural selection. As a result of species to varying degrees, lose universalism, but due to hypertrophy of various technological relics specialize in different biological niches.

[scottie]

AstraSequi

I can wait for you to finish; in attempting to devise answers, I think you will be able to get closer to resolving any confusion. I see no contradictions or "differing views" in any of the phrases you have quoted - for example, as you think, you might try to specifically identify what you think the difference is.

Since you see no difference in the views I have presented, you have answered my question.
I can therefore move on and respond with perhaps more freedom than I had anticipated.

There are random mutations that rearrange the DNA of the cell. These mutations are invariably the result of copying errors, breakdown in regulating functions like error correction, and DNA damage from environment like from chemical or UV radiation sources.

There are also more mutations in DNA, by orders of magnitude, as a result of regulated cell processes, than those that are random in nature.

The random mutations that do occur are invariably deleterious to the organism and are quite naturally the subject of intense study to solve or prevent health problems like cancers.

Now
Back in 1983 in her Nobel laureate lecture Barbara McClintock described various ways that an organism uses to respond to stress, among them by altering its own genome. This is what she said.

“Some sensing mechanism must be present in these instances to alert the cell to imminent danger, and to set in motion the orderly sequence of events that will mitigate this danger. The
responses of genomes to unanticipated challenges are not so precisely programmed. Nevertheless, these are sensed, and the genome responds in a descernible but initially unforeseen manner.

She ended her address this way

In the future attention undoubtedly will be centered on the genome, and with greater appreciation of its significance as a highly sensitive organ of the cell, monitoring genomic activities and correcting common errors, sensing the unusual and unexpected events, and responding to them, often by restructuring the genome. We know about the components of genomes that could be made
available for such restructuring. We know nothing, however, about how the cell senses danger and instigates responses to it that often are truly remarkable.

(my emphasis)
http://www.nobelprize.org/nobel_prizes/ ... ecture.pdf
It was also her foresight was actually quite remarkable.

For instance here then is an interesting review of some genomic changes(variations) found in nature. (1 December 2010)
http://www.nature.com/nrg/journal/v11/n ... g2883.html
note what it says

Genomic rearrangements are associated with many human genomic disorders, including cancers. It was previously thought that most genomic rearrangements formed randomly but emerging data suggest that many are nonrandom, cell type-, cell stage- and locus-specific events. Recent studies have revealed novel cellular mechanisms and environmental cues that influence genomic rearrangements.

(again my emphasis)
I could ofcourse go on citing research after research paper endorsing these observations, if necessary.
The point I make is this.

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.

In the light of all this actual evidence (and with respect, not logic that you appear to rely upon) what does Natural Selection actually have to do?
Where are the functional phenotypes that random mutation is supposed to have produced in order for NS to select from?
It is no wonder that Darwin himself acknowledged he could recount no evidence for species change
by NS.
The reality is that NS has very eloquently described how species may survive but has nothing to say about how they arrived.
Molecular biology was the great hope in answering the question of arrival, but it is only confirming
what many have instinctively known, that this is not the answer.
Neo darwinism is stuck in the Neanderthal period of last century biology and (I am sorry to be blunt about this) no amount of huffing and puffing is going to alter that. (I am not suggesting that you are doing this, but others certainly are)

btw I use the term "evidently" meaning “According to the evidence available” a conclusion is drawn.

I won't go on to make this post any longer but I will continue with my response (i.e your third logic point that you feel is the most likely) in the next one.

[scottie]

AstraSequi

Again, the possibilities are:
- the mutations might be common enough that they happen all the time
- the mutations might occur once or twice and then spread through the population by interbreeding
- the mutations might have already been present in the ancestral population

From my post above, I think it should be fairly clear that the third option is the most likely. However, even if it is incorrect, the others are still quite possible. 

Sorry but the third possibility( the existing mutation) still has to deal with the actual issues of cell processes that researchers have identified and that I have already pointed to in my last post.

I suppose most things are possible, it is possible that pigs will fly, but is that what we are discussing here, possibilities?
I would argue not.

The interpretation "developed" is an inference that is not part of the data. Nobody has observed any population with no inversions. 

Yes of course it's an inference, that is what data does. It helps us to draw conclusions. Do not most research papers have a conclusion section.
Also I have not made any statement about populations without inversions.

I will also point out that changes can indeed happen quite fast, so long as the environment also changes fast - it is mainly the major innovations (like fins turning into legs) that take large amounts of time. 

You are right variations can happen quite fast.
However what is the data for “fins turning into legs” Please remember that this is also an “inference” but from what data is that inference drawn?
Darwin couldn't find it in his pre molecular days, hence my question again, what has changed since then?

The next part of your questions is a serious one that deals with probability theory so I will respond to that separately.

[Luxorien]

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

I should think that the frame shift mutation that resulted in bacteria that could metabolize the byproducts of nylon manufacture would be an example of this. As would be the several mutations that seem to confer immunity to HIV. Or the mutation that causes sickle cell anemia (my favorite example of how relative the terms "beneficial" and "deleterious" are - it all depends on the environment). Or are you arguing that these mutations were non-random events controlled by transposable elements?

[AstraSequi]

While I'm waiting for you to finish, I thought I would just clarify this:

Since you see no difference in the views I have presented, you have answered my question.

Actually, I can't figure out what the views you have presented are. I only said that among the statements that you quoted, I did not see anything contradictory to my own understanding of mutations and natural selection. (And of course, I only hold one viewpoint - the commonly accepted scientific one. )

[wbla3335]

Actually, I can't figure out what the views you have presented are.

scottie has difficulty communicating but has just the one view: everything is programmed by his god. So everything that enters his brain has to pass through the god filter. But at least he's learning, and education is a good thing. We can only hope that a day may come when, like looking at a Necker cube, everything will flip and he'll get it.

[scottie]

Luxorien
Some parts of human population have a mutation to their hemoglobin. This is the protein in the red blood cell that carries oxygen. Often people from sub-Saharan African origins have two copies of this mutated gene, which leads to severe sickle cell disease.
Individuals with that disease suffer quite badly
However on the other hand, this trait is beneficial because it prevents the most severe symptoms of malaria, including death.
Now is sickle cell a random mutation, we actually don't know how it got into the human population but let's assume that it is.
Having two copies of the gene leads to severe sickle cell disease. Individuals with this disease suffer greatly.
Untreated this disease often leads to death.
http://www.ncbi.nlm.nih.gov/pubmed/14531921
Does it prevent them from succumbing to malaria.?
Well this trait can be beneficial to humans because it prevents the most severe symptoms of malaria, including death. 

So the result is that people with this level of immunity from malaria because of carrying the sickle cell mutation are better off are they?
Do they not still have the problem of sickle cell disease?
And you refer to this as

(my favorite example of how relative the terms "beneficial" and "deleterious" are - it all depends on the environment)

Try convincing a sufferer of sickle cell of the cleverness of these so called relative terms.

The choice seems to be, suffer with malaria or sickle cell. I would call it being between a rock and a hard place for those unfortunate ones.
What on earth is favourable about having to have sickle cell disease to prevent contracting malaria?
Which way is Natural Selection working then?
And finally this supposed to be your favourite argument for NS selecting from random mutations to produce new species is it?
You need to try a bit harder.
Now I will deal with your other points but please get in the queue, I am still dealing with the AstraSequi questions. But rest assured I will get back to you.

[scottie]

AstraSequi
(continued)

It depends what you mean by "unlikely." While any individual mutation is unlikely, that doesn't mean that it will not happen on a regular basis if you give it enough chances. 

So the question therefore must be, how many chances does “enough” mean?
(no need to answer )

Suppose there is a mutation that has a one in a million chance of happening - you can call this unlikely. However, if a million fruit flies are born, then it will probably happen around once. If you then wait for a thousand generations, it will probably happen around a thousand times. 

You are missing your own point here.
The problem is that the second mutation has by necessity, have to build on the first for some fitness function to begin to arise.
This is where your probability analysis falters.
Your analogy refers to the same mutation arising. (the point you are making for your analogy)

In order for an improved fitness/function to arise, the mutation must be different but also it has to add to the function of the previous mutation.

The probability for every mutation, by nature of it's randomness, has to start from scratch every time.
So by your analogy of a thousand generations, the progressive mutation towards fitness/function will not occur around a thousand times. It will be orders of magnitude more.

Also please remember that mutations are invariably deleterious to the organism.
Take for example the mutation that causes Cystic fibrosis.
As I understand it, this is a mutation caused by the deletion of three nucleotides. This is a fairly common mutation and deleterious, it is in the nature of most random mutations.

For NS to select for survival or “fitness” whatever that should mean, the mutation needs to be a positive one. Now since most of these mutations are deleterious, any positive one, has to not only evolve for greater fitness or function, but it also has to offset the downward pull of the many harmful mutations that are also taking place.

Your probability idea (although in terms of logic is possible) in reality is now far more remote than your simple calculation suggests.

Another thing to please keep in mind, these examples of random mutations provide evidence of what is termed micro evolution and in a negative way at that, the deterioration of the organism. (Nobody as far as I am aware denies that these changes take place.
The point is do these changes lead to new species formation.
And this of course leads to another related question.
What evidence do we have of the positive effects of any random micro evolutionary mutations?

(I will also point out that for a fruit fly, a thousand generations is only about 40 years.)

I would ask, what evidence that the segmented nature of the body plan of the fruit fly has changed throughout it's existence, regardless of how rapid its generation time may be.
The body plan must be altered in some way for speciation to happen.

Recall Richard Lenskie's 22 year experiment with bacteria (I have covered this before). After over 50,000 generations in each of 12 populations (600,000 generations) no new species of bacteria arrived.

I think this might be an important point that you're missing - in statistics, this is called a Bonferroni correction. If you roll a pair of dice, your chance of a double 6 is quite low (1/36). However, if you try twice, your chance doubles - and if you try a hundred times times, your chance of getting it at least once is very high - in fact, it would be more surprising if you didn't get it at least once. The probability of something happening increases as the number of times it is possible to occur increases. 

I don't know much about the Bonferroni correction, but on what you appear to have indicated, there is an obvious flaw in trying to connect this with biological mutation.
Your last sentence reveals the flaw.

The probability of something happening increases as the number of times it is possible to occur increases. 

This is with regard to the same thing happening again and again.
But for a new mutation to provide a positive outcome it must add to a previously positive one and in a positive way, to succeed. In other words ( as I have previously stated) it must be a different type of mutation.
Take the cystic fibrosis mutation (the 3 nucleotide deletion), it can repeat itself over many generations in a population, but it is the same mutation.
It doesn't add anything.
Also in addition to this one that I have cited, I am informed that there are some 200 other mutations of this gene that have been documented. So mutation of this gene is fairly common. Only a few lead to the severe form of this disease while others cause lesser problems, but, there are no beneficial results.

Systems biologists are increasingly recognising the robustness of cellular processes. Mutations (of all kinds) produce little phenotypic variation. If the mutation is serious enough the organism either becomes diseased or it dies.

Your roll of dice analogy simply does not apply.

Finally on what is the “scientific” view of mutations? Are they all random or are they also non random.
Let me answer since you appear to be somewhat coy over the subject.

Mutations originate both randomly, and also as a result of cellular processes, non randomly.

Actually the interjection by  Luxorien moves this subject on a bit as he raised an interesting side to this discussion.

But before going on I am going to take a break.
Be back in the morning UK time.