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Author Topic:   Evolution Theory Issue - Great Debate -mindspawn and RAZD only
mindspawn
Member (Idle past 8 days)
Posts: 1015
Joined: 10-22-2012


(1)
Message 31 of 65 (689565)
02-01-2013 3:01 AM
Reply to: Message 30 by RAZD
01-31-2013 7:14 PM


Re: mutation vs selection
As I don't know what the original organism started with, I can't really say. What I can say is that the process of evolution has resulted in occasional gain in the number of genes (coding or otherwise) and occasional loss in the number of genes (coding or otherwise), and that both cases could result in novel traits\functions\features in the phenotypes within a breeding population.

I will take this as a badly communicated "YES" to my question. You truly seem to believe its possible rather than impossible that the very first organism had as many coding genes as some modern organisms like humans. I don't want to mock, but that is truly ridiculous. Utter nonsense. If your answer is "NO" then just say it. I have never heard of such an utter copout to the matter of complexity.

Understood, I spend a lot of time on my replies, and presenting information, and a lot of it seem to be ignored (or hopefully accepted without comment ). When you ignore parts of my posts, that is me talking past you - it all goes blahdeblahblahblah to you.

However, making up an acronym before you have established a need for it can interfere with communication and I would be prefer the longer sentence (less potential for confusion). The blahblah actually referred more to the definition of the acronym, btw, using terms that we haven't really addressed at this point. Your acronym seemed to me to be setting up a strawman that doesn't accurately portray how evolution necessarily works when novel features are developed.

If I ignore anything its because its repeats of detail that I thought we have already discussed and concluded and agreed, or possibly introducing new minor side issues when we already have too many side issues to deal with.

As far as introducing a strawman, I see that part of this discussion is to show you that evolution requires this process of gaining new novel coding genes. So it appears to be a strawman but the process is essential to evolution. The alternative , that the first lifeform contained as many novel coding genes as the most extensive existing today is ridiculously laughable. I have already pointed out why, because each gene contains thousands of base pairs and these are ordered in such a perfect sequence, that nearly every time the sequence breaks even slightly the organism loses fitness. Thus the thought that there could have been many coding sequences simultaneously appearing in the first organism is hilarious, and so a novel coding gene gaining process is inevitable to evolution.

Okay, so then the walkingsticks presumably lost complexity when they lost wings and gained complexity when they gained wings?

Yes, this type of complexity gain I agree with, the complexity gain that I feel we are missing evidence for is when an additional NOVEL coding gene is gained in an organism. Regaining lost complexity is observable, gaining new complexity I feel needs more evidence.

Where do the female wingless male winged walkingsticks fit into this paradigm - half complexity between winged and wingless?

Are all winged species equally complex?
Are all non-winged species equally complex?

I agree with you that complexity is difficult to measure in most circumstances, a grey area. Where it is clear that there has been gained complexity, is when there is a new, additional novel coding gene in an organism. This added complexity is essential to evolution even if appearing like a strawman argument, it is not actually one. As explained above, the alternative is laughable that the first organism had as many of these genes as modern ones.

To compare homo sapiens to amoeba dubia is missing the point that each of them evolved according to evolutionary theory. They therefore have more novel coding genes than they had before. Each has experienced its own growth in complexity if evolution is true, the alternative that they each started out with the same number of genes in the beginning is laughable so this is no strawman argument I am introducing, the growth un the number of genes is an essential process.

(in the beginning the earth was formless and empty, and nature created various life-forms spontaneously full of novel protein coding genes in perfect sequences - sounds like creation to me)

In your opinion. We know that mutations of all types can be either deleterious, neutral or beneficial, so citing only deleterious instances does not weaken the knowledge that mutations can be either deleterious, neutral or beneficial. Citing instances of black swans in one location does not weaken the position that white swans are also known in other locations.

Well you are very welcome to cite your examples or evidence that duplications can create novel coding genes that are beneficial. That is all I ask for. With one view having evidence, and the other view without evidence, the argument definitely favors the view with some evidence.

Let's not equivocate between gene and genetic sequence.

Assume a genetic sequence (whether it is a whole gene or not, or several genes is not important yet),

say ... AAGTCCGTAAGGG ... (where the ... indicate that the sequence continues to each side of the section in question),

Can you add or delete a molecule at any point in this sequence without changing the sequence?

No, but you can change a molecule, and therefore have a mutation with no change in sequence.

Indeed, whether it is a point mutation or a complete gene duplication, any change to the overall genetic sequence is a mutation, and one that did not exist in the genome before the mutation, yes?

This is true.

Not quite clear here. Changing the frequency of alleles does not change the genetic make-up of the breeding population, loss of alleles through selection or drift changes the genetic make-up of the breeding population, but this does not add new genes\features\functions\traits.

Selection, drift, etc do not develop new genes\features\functions\traits - that only occurs through mutations

You should be clear here, because I have explained it. When you have many many trillions of possible allele combinations, the amount of new traits already contained in the genetic code is huge. Unlimited. When you change a set of alleles into a new set of combinations never seen on earth before, its impossible to say there will never be a new trait expressed within that unique combination of alleles. I find your insistence on traits being caused only by mutations illogical. You could fill the planet earth shoulder to shoulder with unique humans, over a trillion earths in this universe, over a trillion universes, and not even get close to the number of different allele combinations possible in humans. I don't say that figure lightly, it really is true. There is no logic behind your insistence that not one of those unique humans would have a new trait. At ten alleles per position, and 20000 gene locations, we have 10^20000 unique allele combinations.
ie 20 000 zeros . A trillion x trillion x trillion doesn't even cover the first 100 zeros. Given enough environmental pressures humans could develop down an evolutionary path that causes humans to be vastly different to today, without the need for any mutation.

For example, the trait for ability to handle hotter temperatures is expressed in the allele frequncies in flies. There is a regular relationship between certain alleles and latitude:
http://link.springer.com/article/10.1007%2FBF00137461?LI=...

But that novel trait was not developed by selection, rather selection operated on its existence in the population to make it dominant. What made it novel was the genetic mutation/s that resulted in the selectable trait.

Not necessarily. By interbreeding those with the trait, you can emphasize the trait beyond anything seen in the original population. This is a well known breeding technique and is not associated with mutations. Its possible that nature can do the same. Lets say a leopard population finds itself isolated in desert conditions with few trees due to increased aridity in a certain region. Only the fastest survive. The fastest breed with the fastest in the next generation, the others being too weak to be good breeding partners. You can end up with a new breed of smaller desert leopards (like cheetahs) that can run faster than any individual in the original population. The trait for speed has been emphasized. There are no theoretical limits to these kinds of processes, unless you would like to introduce a limiting factor?

The new allele combinations would possibly express the traits for speed and for lung capacity and for the ability to drop temperature of the overheated animal, and it would take many generations for the best possible combinations of these alleles to express themselves and settle into a new allele frequency within the new population.

So now we add "coding gene" to our list of terms -- can we drop "intricacy" if you want to use complexity?

Yes we can drop intricacy, why not keep micro-evolution and macro-evolution, I thought we agreed on your definitions, I'm not sure why you are dropping them when we have agreement? Unless you anticipate no need for those terms in our discussion which is fine by me. Up to you.

What is a "coding gene" versus a "non-coding gene" and how do we tell them apart?

What I have in this regard is:

http://www.phschool.com/...coach/transcription/procodgn.html

Thats correct, more technically, the gene starts at the start codon.

Edited by mindspawn, : No reason given.

Edited by mindspawn, : No reason given.


This message is a reply to:
 Message 30 by RAZD, posted 01-31-2013 7:14 PM RAZD has responded

Replies to this message:
 Message 32 by RAZD, posted 02-01-2013 11:01 PM mindspawn has responded

  
RAZD
Member
Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


(1)
Message 32 of 65 (689636)
02-01-2013 11:01 PM
Reply to: Message 31 by mindspawn
02-01-2013 3:01 AM


mutation vs selection and novelty
I will take this as a badly communicated "YES" to my question. You truly seem to believe its possible rather than impossible that the very first organism had as many coding genes as some modern organisms like humans. I don't want to mock, but that is truly ridiculous. Utter nonsense. If your answer is "NO" then just say it. I have never heard of such an utter copout to the matter of complexity.

Then you are intentionally misunderstanding what I am saying.

When it is impossible to know what the first organism was like, then all you have are guesses -- you do NOT have yes or no answers with any validity.

Nor is it necessary to fixate on the possible first life to discuss novel traits/features/functions and the genetic basis for them: we can see that novel traits evolve.

What you have asserted here is the argument from incredulity, a logical fallacy. Not an evidence based conclusion.

If I ignore anything its because its repeats of detail that I thought we have already discussed and concluded and agreed, ...

This is fine, I have a tendency to overstate things to ensure we are talking about the same thing, and I do tend to be pedantic in this regard.

... or possibly introducing new minor side issues when we already have too many side issues to deal with.

Side issues can be a problem, so yes please try to keep me focused on the topic.

As far as introducing a strawman, I see that part of this discussion is to show you that evolution requires this process of gaining new novel coding genes. So it appears to be a strawman but the process is essential to evolution. ...

Curiously, I don't have a problem with evolution processes developing or losing novel traits/features/functions and the genetic basis for them via mutations and selection.

What I have some concern is with your apparent fixation on one particular mechanism to be the only way to get this result. That is the strawman issue.

... The alternative , that the first lifeform contained as many novel coding genes as the most extensive existing today is ridiculously laughable. ...

What I am saying is that discussion of the first life is unnecessary to the discussion of the evolution of novel traits/features/functions and the genetic basis for them.

We can focus on the evolution of life since the development of eukaryotes from prokaryotes for instance, as much more is known about life at that point in time, and we are still going from single cell life to multicellular life forms. Or we can focus on life since the formation of multicellular life forms. Or we can focus on later developments. There is no particular point where we absolutely need to start in discussing the formation of novel traits/features/functions and the genetic basis for them.

Is the blue-green algae alive now the same as the blue-green algae alive then? It has undergone billions of years of evolution, yes? Is it more "complex" (have more coding genes)? Is a sponge more complex than single cell life?

... Thus the thought that there could have been many coding sequences simultaneously appearing in the first organism is hilarious, and so a novel coding gene gaining process is inevitable to evolution.

More argument from incredulity. They don't all have to be in a single organism, there could have been many variations that developed life. RNA life is one theory in this regard, and may be the only remnant left from pre-DNA life forms. There could well have been others.

We also see that the formation of eukaryotes seems to be from combining two life forms into one, with the absorbed one becoming the mitochondria or chloroplasts in the cells. We also see horizontal gene transfer between single cell bacterial forms, and can logically deduce that this is not new at this level of development. One whole "coding gene" could be transfered from one bacteria to another, thus improving the fitness of the second without it needing to evolve it independently. There is evidence of this in resistance to anti-biotics in modern times.

The important thing in science is to recognize when we do not know, and be frank about it. We can hypothesize and conjecture what the hypothesis would mean, but we still don't know.

Yes, this type of complexity gain I agree with, the complexity gain that I feel we are missing evidence for is when an additional NOVEL coding gene is gained in an organism. Regaining lost complexity is observable, gaining new complexity I feel needs more evidence.

I agree with you that complexity is difficult to measure in most circumstances, a grey area. ...

I would say that the difficulty is ubiquitous, in part due to the fact that it is mostly a subjective opinion rather than an empirically developed conclusion. The evidence of the walking-sticks for instance does not tell you which ones have more "coding genes" and thus it is just assumed that the winged forms have more than the wingless ones. This is confirmation bias and opinion.

... Where it is clear that there has been gained complexity, is when there is a new, additional novel coding gene in an organism. ...

In your opinion. Are blind cave fish fit for their environment? Do they have a trait/function/feature that did not exist in ancestral populations? They are blind. Do they become blind by adding coding genetic sequences? Do they become blind by modifying an existing coding genetic sequences? Does that modification exist in the ancestral population?

... This added complexity is essential to evolution even if appearing like a strawman argument, it is not actually one. As explained above, the alternative is laughable that the first organism had as many of these genes as modern ones.

The addition of novel traits/features/functions and the genetic basis for them is necessary as part of the explanation for the diversity of life as we know it. Whether this is only due to single coding gene duplications is questionable.

To compare homo sapiens to amoeba dubia is missing the point that each of them evolved according to evolutionary theory. They therefore have more novel coding genes than they had before. ...

Excellent. Their genetic sequences have evolved independently since their last common ancestor, each adding and losing sequences in that process. We can use that information to form nested hierarchies based on their - and other organisms - hereditary history, comparing shared - homologous - genetic sequences, paralogous genetic sequences, ohnologous genetic sequences, ... and evolutionary modifications to them since a last common ancestor.

Well you are very welcome to cite your examples or evidence that duplications can create novel coding genes that are beneficial. That is all I ask for. With one view having evidence, and the other view without evidence, the argument definitely favors the view with some evidence.

There is plenty of evidence available for the formation of novel traits/features/functions and the genetic basis for them, and we will get to them once we understand each other on basic genetics and evolutionary processes.

Let's not equivocate between gene and genetic sequence.

Assume a genetic sequence (whether it is a whole gene or not, or several genes is not important yet),

say ... AAGTCCGTAAGGG ... (where the ... indicate that the sequence continues to each side of the section in question),

Can you add or delete a molecule at any point in this sequence without changing the sequence?

No, ...

Good. Those mutations change the sequence. Can you add or delete a section of molecules at any point in this sequence without changing the sequence?

... but you can change a molecule, and therefore have a mutation with no change in sequence.

So if I change a G to an A, say,

... AAGTCCGTAAGGG ...
to
... AAGTCCATAAGGG ...

-- it is the exact same sequence?

Indeed, whether it is a point mutation or a complete gene duplication, any change to the overall genetic sequence is a mutation, and one that did not exist in the genome before the mutation, yes?

This is true.

Excellent.

You should be clear here, because I have explained it. When you have many many trillions of possible allele combinations, the amount of new traits already contained in the genetic code is huge. ...

But the number for each trait is fairly limited. Alleles for eye color do not add speed for running.

... Unlimited. ...

Sadly (for you), very false.

... When you change a set of alleles into a new set of combinations never seen on earth before, its impossible to say there will never be a new trait expressed within that unique combination of alleles. ...

Change by mutation/s?

Change by mixing eye color alleles with skin color alleles with running alleles in different ways?

There are only a set number of alleles in a breeding population at any one time for any specific trait, and that limits the number of combinations within a (sexual) species to any two (parent) alleles from those in the mix. If there are 6 alleles for hair color, for example, then there are 21 pairs that can be combined in an offspring:

11 12 13 14 15 16 22 23 24 25 26 33 34 35 36 44 45 46 55 56 66

Selection cannot add any more possible variations, all it can do is select those that are best fit for survival\reproduction.

... When you change a set of alleles into a new set of combinations never seen on earth before, its impossible to say there will never be a new trait expressed within that unique combination of alleles. ...

The probability of one of these combinations not being in the general population at any generation of several hundred breeding pairs is really quite small.

... I find your insistence on traits being caused only by mutations illogical. ...

Unfortunately (for you), opinion has been demonstrated to be amazingly ineffective at altering reality in any noticeable way.

... You could fill the planet earth shoulder to shoulder with unique humans, over a trillion earths in this universe, over a trillion universes, and not even get close to the number of different allele combinations possible in humans. I don't say that figure lightly, it really is true. ...

All living humans are unique because of the mix of alleles for different traits/function/features AND because each human has new mutations (several per person) that are not from either of their parents, and yet there is still a small, limited number of combinations for hair color for selection to affect. Selection cannot cause a new hair color, mutation can.

... There is no logic behind your insistence that not one of those unique humans would have a new trait. ...

Argument from incredulity again, sorry: your insistence on omitting mutations is illogical because they have been observed to happen in individuals in each generation.

... At ten alleles per position, and 20000 gene locations, we have 10^20000 unique allele combinations. ie 20 000 zeros . A trillion x trillion x trillion doesn't even cover the first 100 zeros. ...

But still only 10 for hair color -- without mutation.

... Given enough environmental pressures humans could develop down an evolutionary path that causes humans to be vastly different to today, without the need for any mutation.

With 1 to 10 hair colors -- without mutation.

For example, the trait for ability to handle hotter temperatures is expressed in the allele frequncies in flies. There is a regular relationship between certain alleles and latitude:
http://link.springer.com/article/10.1007%2FBF00137461?LI=...

And a small set of alleles that affect this trait\feature\function (... 21? ... coincidence?)

Not necessarily. By interbreeding those with the trait, you can emphasize the trait beyond anything seen in the original population. ...

You make it more common in the population. Red hair does not become redder, blond hair does not become blonder -- without new mutations.

... This is a well known breeding technique and is not associated with mutations. Its possible that nature can do the same. Lets say a leopard population finds itself isolated in desert conditions with few trees due to increased aridity in a certain region. Only the fastest survive. The fastest breed with the fastest in the next generation, the others being too weak to be good breeding partners. You can end up with a new breed of smaller desert leopards (like cheetahs) that can run faster than any individual in the original population. The trait for speed has been emphasized. There are no theoretical limits to these kinds of processes, unless you would like to introduce a limiting factor? ...

It is still selection of available alleles, not new, and the traits/functions/features are those of the existing genetics, not new.

Curiously, horse breeders and greyhound dog breeders cannot make their breeds faster by rebreedind the same previous generation alleles.

If what you said was true then new speed records should be set every year. This is not the case. The speed is limited by the fitness of the existing alleles being selected, and without new mutations to enable increased speed the limit for those existing alleles is reached fairly quickly when selection is strong -- as in breeding situations.

The new allele combinations would possibly express the traits for speed and for lung capacity and for the ability to drop temperature of the overheated animal, and it would take many generations for the best possible combinations of these alleles to express themselves and settle into a new allele frequency within the new population.

And obviously horse and dog racing breeders are complete morons.

What selection can accomplish:

speed ability of individuals in population before new selection pressure:

       xxx
xxxxx
xxxxxxx
xxxxxxxxxxx
xxxxxxxxxxxxxxxxx

ie a bell-curve

This would include alleles for muscles, breathing and heat dissipation, because selection operates on the whole phenotype.

speed ability of individuals in population after a few generations of strong selection:

              xxx
xxxxx
xxxxxxx
xxxxxxxxxxx
xxxxxxxxxxxxxxx

ie a skew curve.

The average speed of the population increases but the maximum speed of the fastest one doesn't.

Now if selection pressure is very strong a lot of the average, mediocre and below individuals will perish before reproduction, thus reducing the number of alleles available for breeding.

ie IF there were 6 alleles for muscles, only the 2 or 3 fastest would survive selection in the first few generations. Same for all alleles that provide fitness under strong selection.

In addition, if alleles for improved lung capacity, say, were not already joined with alleles for muscles within the population, the individuals with the best lung capacity could perish before getting combined with muscles.

Yes we can drop intricacy, why not keep micro-evolution and macro-evolution, I thought we agreed on your definitions, I'm not sure why you are dropping them when we have agreement? Unless you anticipate no need for those terms in our discussion which is fine by me. Up to you.

Thats correct, more technically, the gene starts at the start codon.

Excellent.

I have no need to use either micro- or macro- and find that using macro- generally contributes to confusion.

  1. evolution (process) - yes
  2. theory (scientific) - yes
  3. hypothesis (scientific) - yes
  4. the theory of evolution - yes
  5. novel genes\features\functions\traits - yes
  6. complexity - ... maybe ...
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis - (dropped for now)
  10. hidden gene hypothesis - (dropped for now)
  11. micro-evolution (= 'a' above) - (dropped for now)
  12. macro-evolution - (dropped for now)
  13. intricacy (= complexity) - (dropped for now)
  14. coding gene - yes

Note that I am keeping "complexity" in the "maybe" state, as I don't think it really provides a measure of what you seem to be meaning when you use the term, and I don't see that your requirement for coding gene duplication is required for new traits/functions/features to evolve. I'd rather use "increase in coding genes" than "complexity" as there is less chance of confusion on the part of readers in what you mean.

Enjoy

Edited by RAZD, : clrty


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This message is a reply to:
 Message 31 by mindspawn, posted 02-01-2013 3:01 AM mindspawn has responded

Replies to this message:
 Message 33 by mindspawn, posted 02-02-2013 2:52 PM RAZD has responded

  
mindspawn
Member (Idle past 8 days)
Posts: 1015
Joined: 10-22-2012


(1)
Message 33 of 65 (689679)
02-02-2013 2:52 PM
Reply to: Message 32 by RAZD
02-01-2013 11:01 PM


Re: mutation vs selection and novelty
Then you are intentionally misunderstanding what I am saying.

When it is impossible to know what the first organism was like, then all you have are guesses -- you do NOT have yes or no answers with any validity.

Nor is it necessary to fixate on the possible first life to discuss novel traits/features/functions and the genetic basis for them: we can see that novel traits evolve.

What you have asserted here is the argument from incredulity, a logical fallacy. Not an evidence based conclusion.


I'm not intentionally misunderstanding what you are saying. I asked you to admit its impossible for nature to create the first organism with 20000 coding genes. By your inability to admit that it is impossible you are implying that it is actually possible. You emphasize this view by repeating that we do not know what the first organism is like. without actually saying it, you have left open the possibility that its possible. This is incredulous.

You refer to an argument from incredulity. Well if you have no evidence that any organism can be created from nothing, even a simple organism, its not a valid hypothesis. How would one test to see if its possible for the first life-form to have many many more coding genes than observed in a prokaryote fossil?

A hypothesis (plural hypotheses) is a proposed explanation for a phenomenon. For a hypothesis to be a scientific hypothesis, the scientific method requires that one can test it. Scientists generally base scientific hypotheses on previous observations that cannot satisfactorily be explained with the available scientific theories

Those prokaryote fossils look like today's prokaryotes, your proposed hypothesis that they could have had a lot more coding genes is an absolutely ridiculous speculation, and you are using this proposal to avoid facing the fact that many evolutionists WILL admit:
Most of today's life-forms have more coding genes than the oldest observed fossil life-forms most likely had, and therefore a process that involves gains in novel coding genes has to be part of evolutionary theory for it to stand. This is no strawman argument, it is essential to evolution.

If you refuse to admit this , then we have nothing further to discuss, this thread is about the lack of evolutionary processes to explain additional novel coding genes.

More argument from incredulity. They don't all have to be in a single organism, there could have been many variations that developed life. RNA life is one theory in this regard, and may be the only remnant left from pre-DNA life forms. There could well have been others.

Are you a creationist? If your argument against increased complexity is that abiogenesis created many complex organisms and there has been losses of complexity since, this is very close to creationism. You then don't have to justify increased complexity, because you are also believer in miracles. The spontaneous creation of complex life containing many thousands of novel coding genes is in the realm of miracles and fantasy, welcome to the supernatural club!

If what you said was true then new speed records should be set every year. This is not the case. The speed is limited by the fitness of the existing alleles being selected, and without new mutations to enable increased speed the limit for those existing alleles is reached fairly quickly when selection is strong -- as in breeding situations.

I agree that what you are saying is generally observed, but there could be a few alleles in a separate population that could again accelerate a trait once bred in. I also agree with the bell curve, the reality is a slowdown in improvements over time as the new allele frequencies are settling. Regardless, allele combinations are infinite and can affect traits. You seem to feel that the number of genes per trait (eg eyes) are limited, but there are some genes that are more relevant to chemical balances, size of organs, hormones, digestion of specific foods that can help that organ. So the number of varied genomic regions affecting a trait could be numerous, not isolated to the obvious region in the genome.

I believe an organism like a Tasmanian wolf can be evolved from a kangaroo without the need for mutation. Its just a few adjustments to teeth, digestion, limbs, all the variety contained within existing alleles, and possible under strong environmental pressure for a predator. Who is right and wrong on this particular issue can only be decided when there is more genome sequencing of animals, if completely differing species are found to have nearly matching genomes, I will be right. Until then we are both speculating without evidence.

So if I change a G to an A, say,

... AAGTCCGTAAGGG ...
to
... AAGTCCATAAGGG ...
-- it is the exact same sequence?

Depends on how you define "sequence", maybe, maybe not, let's go with your definition, is this really relevant?

Note that I am keeping "complexity" in the "maybe" state, as I don't think it really provides a measure of what you seem to be meaning when you use the term, and I don't see that your requirement for coding gene duplication is required for new traits/functions/features to evolve. I'd rather use "increase in coding genes" than "complexity" as there is less chance of confusion on the part of readers in what you mean.

I have been pretty clear in my agreement on most evolutionary processes. I have absolutely no idea why you are saying that I have a "requirement for coding gene duplication is required for new traits/functions/features to evolve". I have been repeatedly and clearly saying the opposite, and this is central to my argument.

For the record I will explain it again:
A) I do not believe coding gene duplication is required for new traits/functions/features to evolve. They evolve through many other observable processes, devolving, deletions, changed allele frequencies, gene disabling.
B) I believe gains in novel coding genes are absolutely essential to the theory of evolution as an explanation for the observation of most modern organisms that have many novel coding genes. I believe these gains need some evidence. (The alternative that organisms started out with many novel coding genes is so akin to creationism, we would be on the same side: the spontaneous and miraculous appearance of organisms with many novel coding genes)


This message is a reply to:
 Message 32 by RAZD, posted 02-01-2013 11:01 PM RAZD has responded

Replies to this message:
 Message 34 by RAZD, posted 02-03-2013 5:00 PM mindspawn has responded

  
RAZD
Member
Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


(1)
Message 34 of 65 (689714)
02-03-2013 5:00 PM
Reply to: Message 33 by mindspawn
02-02-2013 2:52 PM


mutation vs selection and the causes of novelty
I'm not intentionally misunderstanding what you are saying. I asked you to admit its impossible for nature to create the first organism with 20000 coding genes. By your inability to admit that it is impossible you are implying that it is actually possible. You emphasize this view by repeating that we do not know what the first organism is like. without actually saying it, you have left open the possibility that its possible. This is incredulous.

And I find your fascination with first life bewildering in the extreme.

We don't know. It doesn't get simpler than that.

The first life we have any record of is the blue-green algae at some 3.5 billion years ago, iirc, and even then we cannot tell how similar it is to blue-green algae today, other than leaving mats of strands of cells and making stromatolites. We do not know if it has coding genes that life today does not have, and we do not know if it has the same coding genes as modern blue-green algae.

http://en.wikipedia.org/wiki/Blue-green_algae

quote:
Scientific classification
Domain: Bacteria
Phylum: Cyanobacteria

I would be extremely surprised if those ancient blue-green algae would be classified in one of the species living today.

We have no record of earlier life, and thus any speculation is just that: speculation, not hypothesis, not educated guess, but pure speculation.

You don't test theories with speculations.

We don't know what first life involved, and speculation here gets into the side topic of "what is life" and where you draw an arbitrary line between speculation about chemical processes and evolutionary life.

You refer to an argument from incredulity. Well if you have no evidence that any organism can be created from nothing, even a simple organism, its not a valid hypothesis. How would one test to see if its possible for the first life-form to have many many more coding genes than observed in a prokaryote fossil?

I don't know that it can, I don't know that it can't, and I don't know how many variations on a theme of replication may have been involved such that many near-life systems could come together in a variety of ways.

Further I consider it absolutely pointless and away from the topic at hand to pursue.

A hypothesis (plural hypotheses) is a proposed explanation for a phenomenon. For a hypothesis to be a scientific hypothesis, the scientific method requires that one can test it. Scientists generally base scientific hypotheses on previous observations that cannot satisfactorily be explained with the available scientific theories

All true, the problem is that we do not know enough at this time to do more than speculate, and one person's speculation is as (in)valid as any other person's speculation.

Those prokaryote fossils look like today's prokaryotes, your proposed hypothesis that they could have had a lot more coding genes is an absolutely ridiculous speculation, ...

Can you falsify the speculation that early life had coding genes that are no longer in the population?

... and you are using this proposal to avoid facing the fact that many evolutionists WILL admit:
Most of today's life-forms have more coding genes than the oldest observed fossil life-forms most likely had, ...

But now you are no longer talking about first life. The "oldest observed fossil life-forms" is an entirely different discussion point from first life, as it is an already evolved fully functional life form.

And again, we do not have DNA evidence so there is no way to tell for sure whether or not

  • all coding genes in all cells of the "oldest observed fossil life-forms" are present in current life forms, or
  • all cells of the "oldest observed fossil life-forms" all had exactly the same mix of coding genes ...

And I would be extremely surprised to find that either of these were the case. If I am going to speculate it would be that things we see in life today occurred in the past: that some coding genes are lost (via selection and drift etc), some coding genes are gained (via mutation), and that individuals in a breeding population have different mixes of coding genes, such that the number of genes in the population is greater than the number of genes in any one individual, and that we just do not know what coding genes were or were not in the population of the "oldest observed fossil life-forms" - capice?

... and therefore a process that involves gains in novel coding genes has to be part of evolutionary theory for it to stand. This is no strawman argument, it is essential to evolution.

And again, it is completely and totally unnecessary to speculate about early life to reach this conclusion.

If you refuse to admit this , then we have nothing further to discuss, this thread is about the lack of evolutionary processes to explain additional novel coding genes.

And this is why it is a straw man argument.

If you want agreement that novel gene sequences, and the expression of them in the novel traits\functions\features that result, are necessary to explain the diversity of life as we know it then there is absolutely no argument there at all.

However, the argument that novel gene sequences are necessary to explain novel traits/functions/features can be made from any point in the natural history of life on earth where novel traits/functions/features have been observed:

  • the transition from prokaryote to eukaryote
  • the transition from single cell life to colony/multi-cellular life
  • the transition from colony/multi-cellular life to division-of-labor-multi-cellular life
    ...
  • the transition from fish fin to tetrapod foot and leg
    ...
  • the transition from reptilian jaw and ear to mammalian jaw and ear
    ...
  • the transition from one variety of greenish warble to another where interbreeding does not occur
  • etc etc etc

Are you a creationist? If your argument against increased complexity is that abiogenesis created many complex organisms and there has been losses of complexity since, this is very close to creationism. You then don't have to justify increased complexity, because you are also believer in miracles. The spontaneous creation of complex life containing many thousands of novel coding genes is in the realm of miracles and fantasy, welcome to the supernatural club!

Is this supposed to scare me or something? The argument from consequences is another logical fallacy ...

I am a Deist. I do not fantasize that "complexity" means anything of value in evolutionary biology. I do not fantasize about things I don't know. I do not fantasize that speculation about the first life is the only basis for logical discussion of the evolution of novel traits.

I agree that what you are saying is generally observed, but there could be a few alleles in a separate population that could again accelerate a trait once bred in. ...

And selection would then be limited to what they can provide, however they would not be novel traits for the imported individuals from that separate population, as they would already have evolved there, and you end up with the same questions for that population.

... I also agree with the bell curve, the reality is a slowdown in improvements over time as the new allele frequencies are settling. Regardless, allele combinations are infinite ...

Wrong. There are a finite number of alleles for any one trait in an existing population. Without mutations adding new alleles there is necessarily a finite number of combinations. Even if every individual in a breeding population had different alleles from the others there is a limit to the number of alleles due to there being a fixed number of individuals in that population.

What we see is a process of mutation adding alleles and selection reducing alleles, and that the number of alleles for any trait is fairly limited.

... and can affect traits. You seem to feel that the number of genes per trait (eg eyes) are limited, ...

In any one breeding population, without mutation adding new alleles. Amusingly this is what the objective empirical evidence in all the research papers on the numbers of alleles for traits in populations show.

... but there are some genes that are more relevant to chemical balances, size of organs, hormones, digestion of specific foods that can help that organ. So the number of varied genomic regions affecting a trait could be numerous, not isolated to the obvious region in the genome.

And different combinations of those different traits/functions/features occur through the mutations involved in reproduction, not through selection. The genetic sequences of the offspring are different from those of either parent due to gene mixing (in sexual reproduction). Selection does not cause this.

Curiously, the breeders for the fastest horses and dogs appear to be totally incompetent at being able to search these out and gather them into new winning breeds, even though they have been trying for thousands of years of intense breeding to get even a 1% increase.

I believe an organism like a Tasmanian wolf can be evolved from a kangaroo without the need for mutation. Its just a few adjustments to teeth, digestion, limbs, all the variety contained within existing alleles, and possible under strong environmental pressure for a predator. Who is right and wrong on this particular issue can only be decided when there is more genome sequencing of animals, if completely differing species are found to have nearly matching genomes, I will be right. Until then we are both speculating without evidence.

No, you will still be wrong, because you apparently don't understand the difference between mutation and selection. Rearranging genetic sequences is mutation, adjustments to "teeth, digestion, limbs, (etc)" would be mutation. You would need many mutations to the genetic sequences to get a Tasmanian Devil from a Kangaroo ... in fact you would need mutations to get from one species of Kangaroo to another species of Kangaroo.

New combinations of alleles for different traits in offspring (ie muscles from one parent and hair color from the other parent) is due to the mutations that occur during the sexual reproduction processes, not selection.

Depends on how you define "sequence", maybe, maybe not, let's go with your definition, is this really relevant?

Yes:

Any change to the genetic sequence is a mutation by definition. Some are deleterious, some are neutral and some are beneficial.

http://en.wikipedia.org/wiki/Mutation

quote:
In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, ...

Any change in the genetic sequence is a mutation, every change in the genetic sequence is a mutation, and when the total sequence in an offspring is not the sequence in a parent ... it is due to mutation/s.

I have been pretty clear in my agreement on most evolutionary processes. I have absolutely no idea why you are saying that I have a "requirement for coding gene duplication is required for new traits/functions/features to evolve". I have been repeatedly and clearly saying the opposite, and this is central to my argument.

No you haven't been clear, obviously, if I have it wrong. This is why we need consistent terminology and understanding.

For the record I will explain it again:
A) I do not believe coding gene duplication is required for new traits/functions/features to evolve.
They evolve through many other observable processes, devolving, deletions, changed allele frequencies, gene disabling.

ie through new mutations, ... and also through gene duplicating mutations ...

... They evolve through many other observable processes, devolving, deletions, changed allele frequencies, gene disabling.

Wrong. Selection does not cause new traits/functions/features ... it selects new traits/functions/features when provided by new mutations.

Selection is incapable of changing the genetic sequences.

B) I believe gains in novel coding genes are absolutely essential to the theory of evolution ...

This is your straw man again. It is not absolutely essential, because the only thing evolution needs is the appearance of novel traits/features/functions in the phenotypes of a breeding population so that selection operates on those new traits/features/functions in addition to the previously existing ones to find those that are best fit for the ecological challenges and opportunities that each organism faces.

Selection does not operate at the genetic level, but on the combined expressions of the genotype in the phenotype.

... as an explanation for the observation of most modern organisms that have many novel coding genes. I believe these gains need some evidence. (The alternative that organisms started out with many novel coding genes is so akin to creationism, we would be on the same side: the spontaneous and miraculous appearance of organisms with many novel coding genes)

Selection mechanisms and any change to the frequency of alleles within a population by other means (drift etc) do not create novel traits/functions/features.

It does not matter what you believe. What matters is what the objective empirical evidence shows. What the evidence shows is that evolution occurs via mutation and selection:

Mutation occurs in the genotype (upper left box), selection occurs on the phenotype (lower right box).

Do you AGREE or DISAGREE that:

Any change in the genetic sequence is a mutation, every change in the genetic sequence is a mutation, and when the total sequence in an offspring is not the sequence in a parent ... it is due to mutation/s.

  1. evolution (process) - yes
  2. theory (scientific) - yes
  3. hypothesis (scientific) - yes
  4. the theory of evolution - yes
  5. novel genes\features\functions\traits - yes
  6. complexity - ... maybe ...
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis - (dropped for now)
  10. hidden gene hypothesis - (dropped for now)
  11. micro-evolution (= 'a' above) - (dropped for now)
  12. macro-evolution - (dropped for now)
  13. intricacy (= complexity) - (dropped for now)
  14. coding gene - yes
  15. mutation - ... (new)

A proper discussion of novel traits/features/functions cannot be made without understanding the difference between mutation and selection and the different effects of mutation and selection on the breeding population/s.

Enjoy

Edited by RAZD, : link cyano

Edited by RAZD, : roo

Edited by RAZD, : clrty,


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
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This message is a reply to:
 Message 33 by mindspawn, posted 02-02-2013 2:52 PM mindspawn has responded

Replies to this message:
 Message 35 by mindspawn, posted 02-04-2013 2:17 AM RAZD has responded
 Message 36 by mindspawn, posted 02-04-2013 5:55 AM RAZD has responded

  
mindspawn
Member (Idle past 8 days)
Posts: 1015
Joined: 10-22-2012


Message 35 of 65 (689724)
02-04-2013 2:17 AM
Reply to: Message 34 by RAZD
02-03-2013 5:00 PM


Re: mutation vs selection and the causes of novelty
And I find your fascination with first life bewildering in the extreme.

We don't know. It doesn't get simpler than that.

The first life we have any record of is the blue-green algae at some 3.5 billion years ago, iirc, and even then we cannot tell how similar it is to blue-green algae today, other than leaving mats of strands of cells and making stromatolites. We do not know if it has coding genes that life today does not have, and we do not know if it has the same coding genes as modern blue-green algae.

http://en.wikipedia.org/wiki/Blue-green_algae

Ok we are both repeating ourselves here , its due to a complete stalemate.

The fact that you are a deist and also like me believe its possible that DNA started out with long strands of many thousands of novel coding genes, means we are actually in near complete agreement. I believe in stasis or reduced novel coding genes over time, you believe in reduced or increased novel coding genes over time, the increases not being central to your view.

Frankly I don't see you as a true evolutionist, if evolutionists are now admitting that the full genome size could have been there from the start, this is the creationist view too. From an empirical view, neither of us was there to see how the DNA strand came into being, I believe it was created supernaturally, you through abiogenesis?

I personally think any informed neutral party would be more aware than you of the complexity involved in sequencing a set of codons in such an order as to not damage an organism, and to do this repeatedly over 3 billion or more base pairs is impossible without an intelligent designer or a believable process. The slow process of evolution from simplicity to complexity is far more believable than your proposed possible sudden complexity view of evolution.

I believe observers would be extremely amused to see evolutionist's convergence with creationists on this sudden appearance of complexity, and it reminds me of the creationist's catastrophic view on the fossil record, and how mainstream science has adapted from uniformitarianism to include some catastrophism as predicted by creationism.

Can you falsify the speculation that early life had coding genes that are no longer in the population?

I don't need to , its an untestable and ridiculous concept that early life had complex genomes, and this is not even a valid hypothesis that should enter into the arena of respected scientific debate. Why debate ridiculous concepts that are untestable? That is why only accepted hypotheses and theories are subjected to falsification, they have to first reach that status of being a hypothesis.

Mutation occurs in the genotype (upper left box), selection occurs on the phenotype (lower right box).

Do you AGREE or DISAGREE that:

Any change in the genetic sequence is a mutation, every change in the genetic sequence is a mutation, and when the total sequence in an offspring is not the sequence in a parent ... it is due to mutation/s.

This may be true for asexual organisms but not true for sexual organisms. The offspring in sexual organisms are a combination of the alleles in both parents. Thus the sequences in the offspring differ to each parent every time even if there are no mutations involved. The offspring shows different combinations of genes to the parent.

If you want agreement that novel gene sequences, and the expression of them in the novel traits\functions\features that result, are necessary to explain the diversity of life as we know it then there is absolutely no argument there at all.

Ok this is significant, I have to rush off, will deal with this in my next post.

Edited by mindspawn, : No reason given.

Edited by mindspawn, : No reason given.

Edited by mindspawn, : No reason given.


This message is a reply to:
 Message 34 by RAZD, posted 02-03-2013 5:00 PM RAZD has responded

Replies to this message:
 Message 37 by RAZD, posted 02-05-2013 5:34 PM mindspawn has responded

  
mindspawn
Member (Idle past 8 days)
Posts: 1015
Joined: 10-22-2012


Message 36 of 65 (689726)
02-04-2013 5:55 AM
Reply to: Message 34 by RAZD
02-03-2013 5:00 PM


Re: mutation vs selection and the causes of novelty
Wrong. There are a finite number of alleles for any one trait in an existing population. Without mutations adding new alleles there is necessarily a finite number of combinations. Even if every individual in a breeding population had different alleles from the others there is a limit to the number of alleles due to there being a fixed number of individuals in that population.

What we see is a process of mutation adding alleles and selection reducing alleles, and that the number of alleles for any trait is fairly limited.

If only 20 genes of 20000 genes in an organism affect a trait, and each gene average ten alleles, the number of allele combinations is 100 000 000 000 000 000 000. Fairly limited?? No

No, you will still be wrong, because you apparently don't understand the difference between mutation and selection. Rearranging genetic sequences is mutation, adjustments to "teeth, digestion, limbs, (etc)" would be mutation. You would need many mutations to the genetic sequences to get a Tasmanian Devil from a Kangaroo ... in fact you would need mutations to get from one species of Kangaroo to another species of Kangaroo.

New combinations of alleles for different traits in offspring (ie muscles from one parent and hair color from the other parent) is due to the mutations that occur during the sexual reproduction processes, not selection.


Let's agree to disagree unless you have proof rather than opinion based on observations of selective breeding of horses for speed. I believe in the next few years one of us will be proved wrong. Let's watch genome sequencing of marsupials in Australia. I don't mind being wrong here, but I'm sure I'm right, just by the sheer number of combinations possible.

No you haven't been clear, obviously, if I have it wrong. This is why we need consistent terminology and understanding.

Since when is lack of comprehension "obviously" the writer's fault? It could be the reader, or the writer, or both.

If you want agreement that novel gene sequences, and the expression of them in the novel traits\functions\features that result, are necessary to explain the diversity of life as we know it then there is absolutely no argument there at all.

Good, but I am referring to gains in novel coding genes, not just changes. (Increased no. of novel coding genes). Its funny that the peanut gallery has picked up on this, agrees that increased numbers of novel coding genes are essential to evolution, and are already posting evidence for the evolutionist position on this. I may never get there in this thread, being bogged down into a mire of semantic distractions (feel the frustration!) and copouts based on unlikely scenarios about evolution being unrelated to increased complexity. No hard feelings RAZD, the undercover creationist - lol

When we eventually get there, you have a cool head start of peanut gallery studies that purportedly support the evolutionist position. But just remember if you ever get around to posting your evidence for gene-adding processes, its the theory of evolution that is being challenged. Thus to use circular reasoning of the assumption of evolution to prove evolution, is illogical. When confronted with two populations (human/ape or rare ape/hominid) it would be essential to eliminate the possibility that both populations had the duplicate first, and the one population was subsequently selected for not having the gene. Alternatively it would also be essential to eliminate the possibility that both populations were always like that, to do this unfortunately requires a genetic analysis of the original population which is impossible with the alleged evolutionary time frames. These type of studies can be done within fast breeding laboratory populations where the original population is completely devoid of duplications, and then beneficial coding duplications are subsequently detected. The general principle precluding this type of beneficial duplication event, is my proposed hypothesis that genes already are optimized for protein production, and in natural conditions can never duplicate protein production across an entire gene without damaging fitness. (hence all the observed medical problems related to increased protein production). I believe that unlike other proposals in this thread, this hypothesis is falsifiable yet has a record of supporting evidence.

Edited by mindspawn, : Editing out my repetitiveness, I have been saying the same thing the whole thread!

Edited by mindspawn, : No reason given.

Edited by mindspawn, : No reason given.

Edited by mindspawn, : No reason given.


This message is a reply to:
 Message 34 by RAZD, posted 02-03-2013 5:00 PM RAZD has responded

Replies to this message:
 Message 41 by RAZD, posted 02-07-2013 5:18 PM mindspawn has responded

  
RAZD
Member
Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


(1)
Message 37 of 65 (689888)
02-05-2013 5:34 PM
Reply to: Message 35 by mindspawn
02-04-2013 2:17 AM


time wasted, and revisiting mutations again
First off, would you agree that this is an accurate quote of your position:

quote:
Message 1:

mindspawn has stated a concern that:

"... recent DNA sequencing is not providing enough support for the hypothesis of evolution. (ie increased DNA complexity of new and uniquely functional active coding genes within an organism is not observed to add fitness)."

and

"I have been looking ... for some evidence that a gene can duplicate, and then produce a novel function in the duplicated coding gene that adds fitness. Haven't seen it yet, this basic process of evolution remains unproven. Without it we would just have bacteria on earth, mutating and evolving into alternative forms but never gaining in complexity."

Fitness is determined by selection mechanism, for a genetic change to improve fitness it must be expressed in the phenotype, and it must be tested by selection to show a benefit for the individual/s with the genetic change.

If it does not involve novel traits/functions/features then it can't increase fitness (at best it would be neutral), so this process must involve novel traits/functions/features to affect fitness to meet your criteria.

I've stricken out comments that I feel are not appropriate for debate (incendiary or trolling comments) or that don't contribute to the debate (get off into side topics) and comments where you are making assumptions about my positions that are incorrect and irrelevant.

The fact that you are a deist and also like me believe its possible that DNA started out with long strands of many thousands of novel coding genes, means we are actually in near complete agreement. I believe in stasis or reduced novel coding genes over time, you believe in reduced or increased novel coding genes over time, the increases not being central to your view.

You would be wrong.

Frankly I don't see you as a true evolutionist, if evolutionists are now admitting that the full genome size could have been there from the start, this is the creationist view too. From an empirical view, neither of us was there to see how the DNA strand came into being, I believe it was created supernaturally, you through abiogenesis?

I believe we don't know. We don't have enough evidence to know.

Looking at the experimental results for abiogenesis, it appears that early life may have included a number of different nucleotide replicating molecules, of which RNA and DNA are the survivors. The first DNA may have been single stranded. I would be surprised if the first coding genes were not rather haphazard and inefficient compared to modern evolved (and refined by evolution) genes. It may have taken several steps to make some proteins for instance. There is also the possibility that repetition was used to provide both redundancy and increased production from less efficient production systems, and this would naturally lead to long strands of DNA, but length does not equate to having more variety in coding genes. Selection at that time could be rather simplistic and not affect things like overly long nucleotide strands. I would also be surprised if many of the original coding genes survived billions of years of evolution intact and in their original configuration and be unchanged today.

But this is speculation, opinion, and certainly not a basis for testing the theory of evolution.

I personally think any informed neutral party would be more aware than you of the complexity involved in sequencing a set of codons in such an order as to not damage an organism, and to do this repeatedly over 3 billion or more base pairs is impossible without an intelligent designer or a believable process. The slow process of evolution from simplicity to complexity is far more believable than your proposed possible sudden complexity view of evolution.

Words used in pseudoscience appear to have meaning, but on closer inspection are not defined in a way that is useful.

The word "complexity" has no real meaning to me, to say that something is "more complex" does not provide any predictive quality regarding fitness or evolution. At most it is an emergent facet that is 99% in the eye of the beholder. You have defined it to be additional coding genes, but you don't use it that way, and it has connotations that distract from the debate. Nor can you predict when such duplications occur.

A much more useful term would be variety. Variation has usefulness for evolution, and it can be readily determined. You cannot tell from looking at this diagram which species is more "complex" than the others without making assumptions:

But anyone can look at that diagram and see that the walking sticks evolved from one common ancestor population to 39 different species, that each wing loss or wing gain event adds variation to the amount of variation then existing, and increases the total diversity. The species with wingless females and winged males is another additional variation adding diversity.

We can also predict that variations will occur via mutations in breeding populations, and that they can then be subject to selection when expressed in the phenotype.

We can also look at that diagram and see that the two Embioptera species Oligotoma nigra and Teratembia n.sp retain the most ancestral traits, and would be classified as having plesiomorphic traits, while the species Lopaphus parakensis has the most apomorphic, or derived, traits. These terms are used in cladistics as descriptors for the branches of a nested hierarchy (such as is shown with the walking sticks).

Variation within a breeding population also predicts greater likelihood that some will survive changing ecological conditions.

I believe observers would be extremely amused to see evolutionist's convergence with creationists on this sudden appearance of complexity, and it reminds me of the creationist's catastrophic view on the fossil record, and how mainstream science has adapted from uniformitarianism to include some catastrophism as predicted by creationism.

Which just shows that you do not understand what uniformitarianism means in geology in specific and science in general. This is a typical misunderstanding\misrepresentation of creationism and creationists. But are you trying to GishGallop on the topic now?

I don't need to , its an untestable and ridiculous concept that early life had complex genomes, and this is not even a valid hypothesis that should enter into the arena of respected scientific debate. Why debate ridiculous concepts that are untestable? That is why only accepted hypotheses and theories are subjected to falsification, they have to first reach that status of being a hypothesis.

What I have said is that we do not know what the original life form DNA was like -- and that makes any concept about what was or was not included untestable.

Could it have had long strands? yes
Could it have had short strands? yes

We don't know.

But I would be surprised if genes that evolved recently would have been around, or that any genes that have survived from that time remain unchanged.

This may be true for asexual organisms but not true for sexual organisms. ...

It is true for all organisms.

... The offspring in sexual organisms are a combination of the alleles in both parents. ...

Which did not occur in either parent, and are thus mutations, by definition, as was noted in Message 34:

quote:
Any change to the genetic sequence is a mutation by definition. Some are deleterious, some are neutral and some are beneficial.

http://en.wikipedia.org/wiki/Mutation

quote:
In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, ...

Any change in the genetic sequence is a mutation, every change in the genetic sequence is a mutation, and when the total sequence in an offspring is not the sequence in a parent ... it is due to mutation/s.


If you want we can use the term "genetic change" instead of mutation. The scale of the change is irrelevant to the fact that any change in the total genetic sequence is defined as a mutation. Polyploidy is a mutation.

... Thus the sequences in the offspring differ to each parent every time even if there are no mutations involved. The offspring shows different combinations of genes to the parent.

That you don't understand that these are still mutations is part of your problem in understanding selection in specific and evolution in general.

If you want agreement that novel gene sequences, and the expression of them in the novel traits\functions\features that result, are necessary to explain the diversity of life as we know it then there is absolutely no argument there at all.

Ok this is significant, ...

Which is why the obsessive fascination with speculating about the first life forms in irrelevant to the discussion of novel traits\features\functions, and has waste way too much of our time already.

... have to rush off, will deal with this in my next post.

And I too.

Enjoy


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

This message is a reply to:
 Message 35 by mindspawn, posted 02-04-2013 2:17 AM mindspawn has responded

Replies to this message:
 Message 38 by mindspawn, posted 02-06-2013 11:32 AM RAZD has responded

  
mindspawn
Member (Idle past 8 days)
Posts: 1015
Joined: 10-22-2012


Message 38 of 65 (689914)
02-06-2013 11:32 AM
Reply to: Message 37 by RAZD
02-05-2013 5:34 PM


Re: time wasted, and revisiting mutations again
Fitness is determined by selection mechanism, for a genetic change to improve fitness it must be expressed in the phenotype, and it must be tested by selection to show a benefit for the individual/s with the genetic change.

If it does not involve novel traits/functions/features then it can't increase fitness (at best it would be neutral), so this process must involve novel traits/functions/features to affect fitness to meet your criteria.


No problem with this.

The word "complexity" has no real meaning to me, to say that something is "more complex" does not provide any predictive quality regarding fitness or evolution. At most it is an emergent facet that is 99% in the eye of the beholder. You have defined it to be additional coding genes, but you don't use it that way, and it has connotations that distract from the debate. Nor can you predict when such duplications occur.

I may have used it in its wider sense once or twice, but generally I have been pretty consistent in my use of the word complexity.

What I have said is that we do not know what the original life form DNA was like -- and that makes any concept about what was or was not included untestable.

Could it have had long strands? yes
Could it have had short strands? yes

We don't know.

But I would be surprised if genes that evolved recently would have been around, or that any genes that have survived from that time remain unchanged

Ok so you are admitting that its likely that evolution would involve additional coding genes over time? Great! Or is this still a strawman? I'm not sure? Anyway let's use that as a basis for further discussion and get on with it.

That you don't understand that these are still mutations is part of your problem in understanding selection in specific and evolution in general.

I'm no expert in genetics, only recently learning this stuff, but what you are saying about allele combinations being mutations is frankly, very wrong, and we should have concluded on that basic point many many posts ago:
http://en.wikipedia.org/wiki/Mutation
In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element.
(if the nucleotide sequence is identical to one of the alleles of a parent, there is no mutation)

http://biology.about.com/...glossary/g/Genetic-Variation.htm
Genetic variation occurs mainly through DNA mutation , gene flow (movement of genes from one population to another) and sexual reproduction.
(you see that, mutation OR sexual reproduction cause variation)

http://evolution.berkeley.edu/evolibrary/article/evo_17

Without genetic variation, some of the basic mechanisms of evolutionary change cannot operate.

There are three primary sources of genetic variation, which we will learn more about:

Mutations are changes in the DNA. A single mutation can have a large effect, but in many cases, evolutionary change is based on the accumulation of many mutations.
Gene flow is any movement of genes from one population to another and is an important source of genetic variation.
Sex can introduce new gene combinations into a population. This genetic shuffling is another important source of genetic variation


(you see that, mutation OR genetic shuffling cause variation. Gene combinations is not seen as mutation)

http://evolution.berkeley.edu/evolibrary/article/evo_25

If you have variation, differential reproduction, and heredity, you will have evolution by natural selection as an outcome. It is as simple as that

Simple as that! Variation can occur through mutation or new gene combinations, either will lead to evolution. You do NOT need mutation to get evolution.

Could we kindly conclude on the word "mutation", that its a different process to new gene combinations inherited from the alleles of the two parents? Mutations are changes within nucloetide sequences. The new sequences are not found in the alleles of either parent.

Please read the following carefully for signs of allele combinations being mutations
http://en.wikipedia.org/wiki/Mutation


This message is a reply to:
 Message 37 by RAZD, posted 02-05-2013 5:34 PM RAZD has responded

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 Message 39 by RAZD, posted 02-07-2013 12:22 PM mindspawn has responded

  
RAZD
Member
Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


Message 39 of 65 (689996)
02-07-2013 12:22 PM
Reply to: Message 38 by mindspawn
02-06-2013 11:32 AM


... revisiting mutations genetic change once again
I may have used it in its wider sense once or twice, but generally I have been pretty consistent in my use of the word complexity.

Again, I suggest that we use "variation" or "variety" as this is much more applicable to the issue at hand: adding a new variety of coding gene that improves fitness in the breeding population.

This is much more concise and precise in terms of conveying the meaning intended without confusion, yes?

Simple as that! Variation can occur through mutation or new gene combinations, either will lead to evolution. You do NOT need mutation to get evolution.

Could we kindly conclude on the word "mutation", that its a different process to new gene combinations inherited from the alleles of the two parents? Mutations are changes within nucleotide sequences. The new sequences are not found in the alleles of either parent.

They are still mutations in my book, but if you want we can use the term "genetic change" as proposed in Message 37:

If you want we can use the term "genetic change" instead of mutation. The scale of the change is irrelevant to the fact that any change in the total genetic sequence is defined as a mutation. Polyploidy is a mutation. It also becomes a tautology that genetic change is genetic change.

There are advantages to using "genetic change" in terms of general understanding. Mutation carries a lot of baggage/misunderstanding/connotations (organisms mutating into something else is a common lay person misunderstanding -- see Lack of random environments Message 1 for example), and "genetic change" avoids this.

Again, this is more concise and precise in terms of conveying the meaning intended without confusion, yes?

Now in the diagram above we have genetic change in the upper left (formation of new individuals), and selection (of individual fitness) in the bottom right.

Selection still does not contribute to making novel traits/features/functions ... it only selects traits/features/functions that allow the organisms to survive and reproduce. Those variations in traits/features/functions have to already be in the population to be subject to selection, and new traits/features/functions are caused by genetic change/s.

  1. evolution (process) - yes
  2. theory (scientific) - yes
  3. hypothesis (scientific) - yes
  4. the theory of evolution - yes
  5. novel genes\features\functions\traits - yes
  6. complexity - ... use "variation" instead
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis - (dropped for now)
  10. hidden gene hypothesis - (dropped for now)
  11. micro-evolution (= 'a' above) - (dropped for now)
  12. macro-evolution - (dropped for now)
  13. intricacy (= complexity) - (dropped for now)
  14. coding gene - yes
  15. mutation - ... use "genetic change" instead

Ok so you are admitting that its likely that evolution would involve additional coding genes over time? Great! Or is this still a strawman? I'm not sure? Anyway let's use that as a basis for further discussion and get on with it.

Next issue after resolving use of "genetic change" and understanding that selection does not contribute to making novel traits/features/functions ... it only selects novel traits/features/functions when they allow the organisms to survive and reproduce.

Enjoy.

Edited by RAZD, : link


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This message is a reply to:
 Message 38 by mindspawn, posted 02-06-2013 11:32 AM mindspawn has responded

Replies to this message:
 Message 40 by mindspawn, posted 02-07-2013 2:09 PM RAZD has responded

  
mindspawn
Member (Idle past 8 days)
Posts: 1015
Joined: 10-22-2012


Message 40 of 65 (690010)
02-07-2013 2:09 PM
Reply to: Message 39 by RAZD
02-07-2013 12:22 PM


Re: ... revisiting mutations genetic change once again
Again, I suggest that we use "variation" or "variety" as this is much more applicable to the issue at hand: adding a new variety of coding gene that improves fitness in the breeding population.

This is much more concise and precise in terms of conveying the meaning intended without confusion, yes?

Your only objection to the use of the word "complexity" was that its subjective, difficult to measure. I introduced the thought that if an organism gains one coding gene this could be a measurable form of increased complexity. I therefore felt I have successfully dealt with the objection to using the word complexity, and haven't seen any points from you to the contrary. Until you deal with this, you are bringing up unnecessary additional topics. Anyway I'm willing to compromise, let's just not use the word complexity and I will try not to use alternative words like intricacy. Drop "complexity" from your list. However "variation" is not an adequate substitute, it conveys a completely different meaning to "complexity" and should be used for its own meaning.

They are still mutations in my book, but if you want we can use the term "genetic change" as proposed in Message 37:

In "your book"? Try reading up on basic genetics. If you want us to struggle through this topic without using words that everyone else agrees on, go for it, let us drop the use of the word "mutation".

If you will not compromise on what everyone else agrees with, makes this whole discussion pretty pointless though, because if you will not agree to easy consensus issues when you are obviously wrong, how will you ever agree to more controversial points? Its all a bit pointless really if you cannot have a win-win discussion based on truth.

Again, this is more concise and precise in terms of conveying the meaning intended without confusion, yes?

I don't agree one bit, and have never come across anyone else who misunderstands the word "mutation". It is one of the most used words in genetic literature, but if you RAZD would prefer not to use the word "mutation", let us do it your way.

By the way, please answer this, do you think that it is a reasonable assumption that the earliest organisms had relatively few coding genes compared to modern organisms?


This message is a reply to:
 Message 39 by RAZD, posted 02-07-2013 12:22 PM RAZD has responded

Replies to this message:
 Message 42 by RAZD, posted 02-07-2013 6:33 PM mindspawn has responded

  
RAZD
Member
Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


Message 41 of 65 (690018)
02-07-2013 5:18 PM
Reply to: Message 36 by mindspawn
02-04-2013 5:55 AM


Re: mutation vs selection and the causes of novelty
If only 20 genes of 20000 genes in an organism affect a trait, and each gene average ten alleles, the number of allele combinations is 100 000 000 000 000 000 000. Fairly limited?? No

When you make up numbers and do not justify them with any objective evidence you can get whatever result you want. IE - if only 3 genes contribute to trait "A" and there are 2 alleles of one, 3 of another and 6 of the third then there are only 36 possible combinations, which is fairly limited (imho) and it is also highly likely that all those variations already exist within a normal breeding population and are subject to immediate selection should the ecology change.

Traits that are highly conserved typically have few alleles, and traits undergoing strong selection typically have few alleles (as less fit ones are eliminated).

Let's agree to disagree unless you have proof rather than opinion based on observations of selective breeding of horses for speed. ...

Actually it's objective fact that racing animal speeds have not increased significantly for some time -- you can look up the times and graph them.

The other side of sexual gene mixing is that breeders don't always get the "desirable" traits/functions/features in the offspring, because the trait mixing is random. Thus breeding winning males with winning female does not alway produce winning offspring.

... I believe in the next few years one of us will be proved wrong. Let's watch genome sequencing of marsupials in Australia. I don't mind being wrong here, but I'm sure I'm right, just by the sheer number of combinations possible.

I would be extremely surprised to find that you would not need to change any of the gene sequences to get from the genome of one Kangaroo species to another, to say nothing of getting to the Tasmanian Devil genome.

Good, but I am referring to gains in novel coding genes, not just changes. (Increased no. of novel coding genes). Its funny that the peanut gallery has picked up on this, agrees that increased numbers of novel coding genes are essential to evolution, and are already posting evidence for the evolutionist position on this. ...

Which should tell you that you're position is likely untenable ... once we have sorted through the terminology to see why selection does not add novel features/functions/traits, but acts on the phenotypes of existing organisms to determine fitness within a specific ecology.

... I may never get there in this thread, being bogged down into a mire of semantic distractions (feel the frustration!) ...

And yet you clearly have not understood how selection works, and this is due to "semantic distractions" that still need to be ironed out.

... But just remember if you ever get around to posting your evidence for gene-adding processes, ...

For which there is evidence, as noted in the Peanut Gallery, the question is whether or not you will accept this evidence for what it shows, and critical to this acceptance is understanding the meanings of the words through the agreement of the terminology used.

... its the theory of evolution that is being challenged. ...

... and yet, curiously, even if your claim is true, evolution will continue to be true for the development of novel traits/functions/features, so no it is not really a challenge to the theory, per se, so at most it would need a slight adjustment for an additional mechanism to account for novel coding genes. Theories are approximations of reality and these approximations improve with each adjustment. For instance Newton's law of gravity is an approximation of how gravity works, Einsteins relativity improves the accuracy of that approximation and defaults to Newton's law in specific cases (such as we normally experience here on earth).

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
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This message is a reply to:
 Message 36 by mindspawn, posted 02-04-2013 5:55 AM mindspawn has responded

Replies to this message:
 Message 44 by mindspawn, posted 02-09-2013 2:30 AM RAZD has responded

  
RAZD
Member
Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


Message 42 of 65 (690024)
02-07-2013 6:33 PM
Reply to: Message 40 by mindspawn
02-07-2013 2:09 PM


Re: ... revisiting mutations genetic change once again
... Anyway I'm willing to compromise, let's just not use the word complexity and I will try not to use alternative words like intricacy. ...

okay let's use "coding gene duplication" seeing as that is your last definition.

... but if you RAZD would prefer not to use the word "mutation", let us do it your way. ...

I don't see any point in using a term where there is disagreement on the meaning, as that is a sure path to confusion.

So let's use "genetic change/s" to be clear. One can also use specific subcategories if greater clarity is needed.

  1. evolution (process) - yes
  2. theory (scientific) - yes
  3. hypothesis (scientific) - yes
  4. the theory of evolution - yes
  5. novel genes\features\functions\traits - yes
  6. complexity - ... use "coding gene duplication" instead
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis - (dropped for now)
  10. hidden gene hypothesis - (dropped for now)
  11. micro-evolution (= 'a' above) - (dropped for now)
  12. macro-evolution - (dropped for now)
  13. intricacy (= complexity) - (dropped for now)
  14. coding gene - yes
  15. mutation - ... use "genetic change" instead

Remember that we agreed that the process of evolution was defined in Message 1 as:

quote:
For this thread I would propose using this definition for the process of evolution:

The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities.

Change in the composition of hereditary traits occurs through genetic change/s.

Changes in the frequency of their distribution occurs through selection and genetic drift.

Note that genetic drift occurs when individuals die by stochastic events (volcanoes, earthquakes, falling trees, etc) unrelated to fitness. Like selection it only operates to remove traits from breeding populations, and thus also does not result in the development of new traits

Enjoy.

Edited by RAZD, : recap


we are limited in our ability to understand
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... to learn ... to think ... to live ... to laugh ...
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This message is a reply to:
 Message 40 by mindspawn, posted 02-07-2013 2:09 PM mindspawn has responded

Replies to this message:
 Message 43 by mindspawn, posted 02-08-2013 1:45 AM RAZD has responded

  
mindspawn
Member (Idle past 8 days)
Posts: 1015
Joined: 10-22-2012


Message 43 of 65 (690032)
02-08-2013 1:45 AM
Reply to: Message 42 by RAZD
02-07-2013 6:33 PM


Re: ... revisiting mutations genetic change once again
By the way, please answer this, do you think that it is a reasonable assumption that the earliest organisms had relatively few coding genes compared to modern organisms?

I see you ignored this question, please answer it, it is core to this debate.


This message is a reply to:
 Message 42 by RAZD, posted 02-07-2013 6:33 PM RAZD has responded

Replies to this message:
 Message 45 by RAZD, posted 02-09-2013 11:54 AM mindspawn has responded
 Message 47 by RAZD, posted 02-09-2013 8:26 PM mindspawn has responded

  
mindspawn
Member (Idle past 8 days)
Posts: 1015
Joined: 10-22-2012


Message 44 of 65 (690100)
02-09-2013 2:30 AM
Reply to: Message 41 by RAZD
02-07-2013 5:18 PM


Re: mutation vs selection and the causes of novelty
When you make up numbers and do not justify them with any objective evidence you can get whatever result you want. IE - if only 3 genes contribute to trait "A" and there are 2 alleles of one, 3 of another and 6 of the third then there are only 36 possible combinations, which is fairly limited (imho) and it is also highly likely that all those variations already exist within a normal breeding population and are subject to immediate selection should the ecology change.

Traits that are highly conserved typically have few alleles, and traits undergoing strong selection typically have few alleles (as less fit ones are eliminated).

Everything you say here makes sense. Its just that my example is more related to reality than your example: let's get educated by the Magic School Bus : MOST traits are affected by many genes:
http://themagicschoolbus.blogspot.com/...s-how-genotype.html

Due to such dramatic effects of small mutations, it was believed at the time that each gene codes for a particular trait. Today, it is possible to measure miniscule effects of multiple genes and it is well understood that the "one gene/one trait" paradigm is largely incorrect. Most traits are affected by many genes, and most genes are involved in the development of multiple traits.

And generally there are more than 6 alleles per locus across a population, so the numbers that I put forward are a lot more realistic than your "36" combinations per position. In fact, my numbers were conservative.

Actually it's objective fact that racing animal speeds have not increased significantly for some time -- you can look up the times and graph them.

The other side of sexual gene mixing is that breeders don't always get the "desirable" traits/functions/features in the offspring, because the trait mixing is random. Thus breeding winning males with winning female does not alway produce winning offspring

Its ironic that you keep using this single example to prove your point, when in message 27 you made it clear that you believe that cherry picking and confirmation bias are not sufficient evidence for making a good point. Let's just agree to disagree on this point unless you have better evidence than cherry picking or confirmation bias.

I would be extremely surprised to find that you would not need to change any of the gene sequences to get from the genome of one Kangaroo species to another, to say nothing of getting to the Tasmanian Devil genome.

(I was referring to the Tasmanian wolf - it had many kangaroo-like qualities, and its predator's jaw is comparatively weak for a predator)

We are not going to conclude this argument based on cherry picking or what would surprise you. Already I have posted evidence , and even your horse example proves that traits can be emphasized through variation and selection. Put a population together that is selected for a specific trait, and there's a chance that one of those will have a unique combination of genes that emphasizes the trait more than seen in the original population. This emphasis of traits is both logical and observed, even if its observed to taper off quite rapidly near its peak as you pointed out (bell curve).

Could we kindly drop this discussion, with either consensus of the "bell curve" of the observation of traits through selective breeding (or natural selection in nature) , or alternatively just agree to disagree until most mammals are sequenced which will conclude the argument in my eyes.

... and yet, curiously, even if your claim is true, evolution will continue to be true for the development of novel traits/functions/features, so no it is not really a challenge to the theory, per se, so at most it would need a slight adjustment for an additional mechanism to account for novel coding genes. Theories are approximations of reality and these approximations improve with each adjustment. For instance Newton's law of gravity is an approximation of how gravity works, Einsteins relativity improves the accuracy of that approximation and defaults to Newton's law in specific cases (such as we normally experience here on earth).

Its not a challenge to your theory, which includes the possibility that genes were already there from the start, which is the creationist position as well. The introduction of new additional novel coding genes would be essential to most evolutionists projection of evolutionary processes from first-life.

I agree with other processes of evolution, but not the theory of evolution's claim to explain the existence of modern life forms (that do have many coding genes)

okay let's use "coding gene duplication" seeing as that is your last definition.

Evolutionists claim its not just through duplication that novel coding genes come about, I used the words "gains one coding gene" recently, and feel that's a better definition of complexity. An organism gains complexity if it gains a coding gene.

Change in the composition of hereditary traits occurs through genetic change/s.

Changes in the frequency of their distribution occurs through selection and genetic drift.

Note that genetic drift occurs when individuals die by stochastic events (volcanoes, earthquakes, falling trees, etc) unrelated to fitness. Like selection it only operates to remove traits from breeding populations, and thus also does not result in the development of new traits

I understand what you are saying about selection, yes it can only work on the existing traits, and only variation can emphasize a trait. So we have consensus on selection.

In my defense I believe selection certainly does contribute to new traits because it causes a trait to be emphasized thoughout a population, and therefore there will be a wider variation of that trait in each subsequent generation in which the population having that trait grows. (there is more chance of variation in a large population than in a small population)

I don't see any point in using a term where there is disagreement on the meaning, as that is a sure path to confusion.

So let's use "genetic change/s" to be clear. One can also use specific subcategories if greater clarity is needed.

We can't really replace words, especially since we have no consensus of what the original word means. (that doesn't make any sense)

But we can use the phrase "genetic change" (doesn't this mean genetic variation?). Anyway let's use the term if you like. So to clarify, you are including variation through sexual reproduction (new gene combinations in the offspring) when you use the phrase "genetic change"?

Edited by mindspawn, : No reason given.

Edited by mindspawn, : clarification


This message is a reply to:
 Message 41 by RAZD, posted 02-07-2013 5:18 PM RAZD has responded

Replies to this message:
 Message 46 by RAZD, posted 02-09-2013 2:56 PM mindspawn has responded

  
RAZD
Member
Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


Message 45 of 65 (690126)
02-09-2013 11:54 AM
Reply to: Message 43 by mindspawn
02-08-2013 1:45 AM


getting ready to move on?
Power out last night just as ready to post this. Temp power now. Foot of snow outside. Fun.

By the way, please answer this, do you think that it is a reasonable assumption that the earliest organisms had relatively few coding genes compared to modern organisms?

I see you ignored this question, please answer it, it is core to this debate.

Curiously, I believe (opinion) that it is possible that many of the original coding genes have been lost or changed, and that the number of original genes is therefore rather irrelevant.

And no it isn't the core of the debate, the core of the debate is whether or not coding genes have been duplicated and then added fitness to the breeding population.

Again, I believe that gene coding duplication has occurred throughout the evolutionary history of life on earth, because it is reasonable to believe that something that occurs in the present occurred in the past as well (this, btw, is the true interpretation of "uniformitarianism" -- that the laws of nature that apply today also applied in the past ... and there is plenty of evidence that this is so).

And I repeat what I stated in Message 37:

What I have said is that we do not know what the original life form DNA was like -- and that makes any concept about what was or was not included untestable.

Could it have had long strands? yes
Could it have had short strands? yes

We don't know.

But I would be surprised if genes that evolved recently would have been around, or that any genes that have survived from that time remain unchanged.

And I also expect (opinion) the biology was different in the early years, where different coding genes could be developed in different organisms before being brought together via horizontal transfer later on. We know horizontal transfer occurs todaty. Horizontal gene transfer is like sex for single cell life.

What we do know is that the ecology was considerably different even when the blue-green algae were building stromatolites 3.5 billion years ago, due to the lower levels of oxygen in the atmosphere if nothing else.

Thus I would expect that a number of genes that were suitable for that early ecology to have been replaced or modified to fit the different ecologies we see today.

... do you think that it is a reasonable assumption that the earliest organisms had relatively few coding genes compared to modern organisms?

Let me put it this way: I believe (opinion) that few of the coding genes present in organisms alive today were extant in the earliest life forms known.

That new coding genes are produced is not a major conundrum for the theory of evolution, as this would occur through the basic process of evolution from generation to generation:

We can expand this image verbally, now that we have covered most of the basic terminology, to see if we are on the same page:

Evolution Do Loop for Living Species (ie - not extinct)

  1. A breeding population typically consist of
    1. a variety of mature adults technically capable of breeding, each with a set of hereditary traits/functions/features
      • some have more opportunities to breed and will typically produce more offspring than others
      • some have less opportunities to breed and will typically produce less offspring than others
    2. some individuals that are too old, too young or too disabled to be capable of breeding.

  2. The offspring population typically has a different variety and frequency of hereditary traits/functions/features from the parent population
    1. some existing hereditary traits/functions/features are from parent/s
      • there are more offspring with hereditary traits/functions/features of parent/s that reproduce more (increasing their frequency)
      • there are fewer offspring with hereditary traits/functions/features of parent/s that reproduce less (decreasing their frequency)
      • offspring of sexual species typically have a different mix of dominant\recessive\etc copies of genes than either parent, getting one copy from each parent (changing the frequency of expressed genes)
      • offspring of asexual species typically have the same mix of dominant\recessive\etc copies of genes as their parent, however each copy can be subject to random genetic change/s
    2. some hereditary traits/functions/features that are modified from parent/s copies by random genetic change/s.

  3. Breeding/reproduction produces added variation/s due to random genetic change/s during the reproductive process
    1. random genetic change may be due to small modifications, duplicating, adding, moving, or deleting bits of the genetic sequence/s
    2. random genetic change may be due to large modifications, duplicating, adding, moving, or deleting whole sections of the genetic sequence/s
    3. random genetic change may affect whole genes, duplicating, adding, moving, or deleting whole coding gene sections of the genetic sequence/s
    4. sexual reproduction involves additional random genetic change due to the stochastic way the gametes are formed in each parent, and the stochastic way they are then combined to form the zygotes of offspring.

  4. Some genetic changes do not affect the phenotype (ie are not expressed) and thus are neutral to selection.

  5. Some genetic changes do affect the phenotype and thus may be affected by selection
    1. some increase the survival and/or reproductive success of the organism (and thus are beneficial)
    2. some do not change the survival and/or reproductive success of the organism (and thus are neutral)
    3. some decrease the survival and/or reproductive success of the organism (and thus are deleterious)
    4. some are lethal.

  6. Selection removes the least fit individuals and thus tends to remove the least fit hereditary traits/functions/features and the genetic sequences that produce them, thereby reducing the frequency of those traits/functions/features in the population.

  7. Sexual selection can asymetrically affect individual reproduction and can increase the frequency of "sexually desirable" hereditary traits/functions/features even when deleterious for survival, or reduce the frequency of "sexually undesirable" hereditary traits/functions/features even when beneficial for survival.

  8. Drift can remove an individual or a group of individuals via stochastic accident (falling trees, earthquakes, tornadoes, etc) and thus may randomly remove hereditary traits/functions/features and the genetic sequences that produce them without regard to fitness.

  9. Sexual drift can occur in sexual species when a particular gene of the parent happens to be by-passed in reproduction due to the stochastic nature of gamete production and combination in the zygotes, a gene (beneficial, neutral or deleterious) can be randomly omitted\forgotten in the mating process (a 50:50 possibility in each mating).

  10. Of the offspring that survive to breed/reproduce
    1. individuals with beneficial hereditary traits/functions/features typically breed more than
    2. individuals with neutral hereditary traits/functions/features, which typically breed more than
    3. individuals with deleterious hereditary traits/functions/features, which typically breed more than
    4. dead individuals
    5. however, individuals can have mixtures of beneficial, neutral and deleterious hereditary traits/functions/features, so deleterious hereditary traits/functions/features can "piggy-back" on beneficial hereditary traits/functions/features and persist in the breeding population.

  11. All individuals that survive to breed form the breeding population for the next generation, starting over at step 1 ... (please notice the overlap between 10 and 1).

I've included some words here that we have not discussed yet - stochastic, gamete, zygote, for instance - but I don't anticipate any (mis)understanding problems with these words.

If you agree with this (still somewhat simplistic picture) we can move on to examples of this process.

Enjoy


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
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This message is a reply to:
 Message 43 by mindspawn, posted 02-08-2013 1:45 AM mindspawn has responded

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 Message 48 by mindspawn, posted 02-10-2013 5:07 AM RAZD has acknowledged this reply

  
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