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Author Topic:   Evolution Theory Issue - Great Debate -mindspawn and RAZD only
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 1 of 65 (688656)
01-23-2013 10:50 AM


The evolution of novel features\functions
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."
My response is that this misrepresents or misunderstands how evolution works.
These two positions will be the focus of this debate,
mindspawn has agreed to a Great Debate on this topic (for the background see Message 3).

Beginning the Debate:

So here we are.
Let's start with these statements of yours:
  1. I find the scientific community is unfortunately biased through accepting the theory of evolution too early when
  2. recent DNA sequencing is not providing enough support for the hypothesis of evolution.
  3. I have been looking around the internet for over a year, hoping for some evidence that a gene can duplicate, and
  4. then produce a novel function in the duplicated coding gene
  5. that adds fitness.
  6. this basic process of evolution remains unproven.
  7. Without it we would just have bacteria on earth, mutating and evolving into alternative forms but never gaining in complexity.
First off, I basically agree with #7, although I would word is a little differently: without speciation we would only have one species on earth.
Second, we have a number of terms here that we should define and agree on so that we are talking about the same thing:
  1. evolution (process)
  2. theory (scientific)
  3. hypothesis (scientific)
  4. the theory of evolution
  5. novel feature\function
  6. complexity
  7. speciation
For me, basic evolution is a process, the theory of evolution is a theory involving the process, and the science of evolution is the study of the process and testing of the theory. These are three different things\aspects that the word "evolution" is used for in biology (so we are not even considering non-biological use of the term).
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.
This is my wording, however references for this definition can be found at
  1. Berkeley U. and U. of California Museum of Paleontology Teachers Guide
    An introduction to evolution - Understanding Evolution
  2. U. of Michigan on-line course material
    The Process of Speciation
When you say "evidence that a gene can duplicate, and then produce a novel function" you are talking about the process of evolution, yes?
A scientific hypothesis proposes an explanation for observations and objective evidence, and it proposes tests that distinguish it from fantasy or other hypothesis. Once an hypothesis has be adequately tested it becomes a (scientific) theory.
Thus a scientific theory is a tested scientific hypothesis. Theories are never proven, just validated or invalidated (by testing). Invalidated hypothesis are discarded or modified, while validated ones continue to be tested.
Forgive me if this seems a little pedantic and covers stuff you know, but I find ensuring a common basis for understanding and terminology benefits the debate by reducing confusion.
Your turn: I'd like to see your definition for the theory of evolution:
The Theory of Evolution (T0E) is ....
Enjoy.
Edited by RAZD, : splg
Edited by RAZD, : per admin comments
Edited by RAZD, : title tweak
Edited by RAZD, : hypother mix
Edited by RAZD, : )
Edited by RAZD, : title

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Replies to this message:
 Message 2 by Admin, posted 01-23-2013 2:34 PM RAZD has replied
 Message 4 by Admin, posted 01-24-2013 6:54 AM RAZD has replied
 Message 7 by mindspawn, posted 01-24-2013 11:19 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 3 of 65 (688658)
01-23-2013 8:54 PM
Reply to: Message 2 by Admin
01-23-2013 2:34 PM


background
See changes to Message 1.

Background

This started on Flood Geology: A Thread For Portillo when midspawn posted Message 497 with this comment:
Will get there one day, but am a little put off by your requirements for posting evidence. If you dropped your requirements to the kind of discussions that are acceptable on this thread (publications, wikipedia, deductive reasoning) then that would be easier. I find the scientific community is unfortunately biased through accepting the theory of evolution too early when 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)
I copied this post to Age Correlations and An Old Earth, Version 2 No 1 thread, Message 224, to discuss the issues of age measurements and the correlations. Unfortunately I included the whole post and not just the portion pertaining to participation on the Age Correlations and An Old Earth, Version 2 No 1 thread, and further aggravated the situation by commenting that:
... when 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)
Which, curiously, is caused more by your misinterpretation\misrepresentation of what evolution actually says should happen than by any real problem in evolution. Feel free to start a thread on this topic if you want to get straightened out on this.
Mea Culpa, as this started several off-topic comments.
Message 226: I don't remember when we have discussed this topic that you can automatically assume my lack of knowledge compared to yours. On what facts do you base this assumption that I don't know what I'm talking about? I'm just interested.
I have been looking around the internet for over a year, hoping 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.
Message 248: I based it on the statement that you made.
But this is not a topic for discussion on this thread: please start a new thread to discuss this.
Message 250: And I would prefer that you don't respond so that this thread can stay focused on the issues of correlations.
I will be marking ALL off-topic posts with jeers to emphasize this point.
Please start another topic if you want to pursue this issue.
Go to Proposed New Topics to post new topics.
Message 254: I would love to continue this discussion with you, I see you have already made some good points and I really enjoy a good debate. Unfortunately I have too much self esteem to put myself through the rudeness of your peers on this site. This site should be better moderated to encourage good discussion.
Message 256: One alternative is a Great Debate thread -- two people debate a topic, other people participate through messaging or a peanut gallery thread.
See The Great Debate forum for some existing debates.
If you want I can set it up.
Message 258: Good idea, let's do it..
Edited by RAZD, : link

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RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 5 of 65 (688660)
01-24-2013 9:26 AM
Reply to: Message 4 by Admin
01-24-2013 6:54 AM


Re: The evolution of novel features\functions
wow, did I ever mix that up. thanks.

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RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 8 of 65 (688714)
01-24-2013 6:12 PM
Reply to: Message 7 by mindspawn
01-24-2013 11:19 AM


Re: The evolution of novel features\functions
Thanks
Evolution is a process that results in heritable changes in a population spread over many generations
Except that the process of evolution can be observed in one generation.
One need only look at kittens or pups newly born and note that they are not clones of either parent, that the coloration patterns are different, for example, and that there are measurable differences in size and shape and behavior among them.
... a process that results in heritable changes ...
It's the other way around -- heritable changes result in the process of evolution occurring: no change in hereditary traits means no evolution. This backwards thinking is part of what I was getting at originally.
The process of evolution is an observed fact: it has occurred many times, and occurs regularly in all living species.
Your turn: I'd like to see your definition for the theory of evolution:
The Theory of Evolution (T0E) is ....
No problem, its good to have the same terms of reference, how about this one:
Evolution is a process that results in heritable changes in a population spread over many generations
But what I asked for was your definition of the theory of evolution, not the process. They are not the same thing, just as Gravity and the Theory of Gravity are not the same thing .
For instance I would define the theory as:
The Theory of Evolution (ToE), stated in simple terms, is that the process of evolution over generations, and the process of divergent speciation, are sufficient to explain the diversity of life as we know it, from the fossil record, from the genetic record, from the historic record, and from everyday record of the life we observe in the world all around us.
where I would then define
The process of divergent speciation involves the division of a parent population into two or more reproductively isolated daughter populations, which then are free to (micro) evolve independently of each other.
Without divergent speciation we would all be one species, divergent speciation is what introduces diversity into the mix of life. This is similar to your point #7 listed in Message 1 ("Without it we would just have bacteria on earth, mutating and evolving into alternative forms but never gaining in complexity").
... What I do see lacking is proof of a process of complexity , whereby organisms with less protein coding genes and less genes with specific functions, can evolve into more genetically complex organisms over time while maintaining or improving fitness. So I am not disputing all aspects of the process of evolution, I'm merely disputing increased genetic complexity involving additional novel coding genes with novel functions that add fitness to the population of an organism. Where's the evidence?
Again, here we still need to define what we mean by novel and what we mean by complexity and fitness.
But your one is fine too, we can use any definition you like, and its very possible that you could win this debate merely on which definition of evolution that you use.
I am not interested in winning the debate but on reaching consensus\agreement on the meanings of ...
  1. evolution (process)
  2. theory (scientific)
  3. hypothesis (scientific)
  4. the theory of evolution
  5. novel feature\function
  6. complexity
  7. speciation (divergent)
    and
    (I just noticed that I should have also included in Message 1)
  8. fitness
... and then see whether or not novel features\functions\traits have evolved.
If you agree with me so far on a, b, c, d and g we can move on to e,f and h:
Would you agree that a novel feature\function\trait would be one that did not exist in a previous generation?
Note that Taq has proposed a "peanut gallery" thread at Peanut Gallery for the debate between mindspawn and RAZD. It is normal for the participants in a Great Debate to be restricted from posting on the related peanut gallery thread, just as they are restricted from posting here.
Enjoy.
Edited by RAZD, : peanut gallery

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This message is a reply to:
 Message 7 by mindspawn, posted 01-24-2013 11:19 AM mindspawn has replied

Replies to this message:
 Message 9 by mindspawn, posted 01-25-2013 3:09 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 10 of 65 (688770)
01-25-2013 10:32 AM
Reply to: Message 9 by mindspawn
01-25-2013 3:09 AM


Re: The evolution of novel features\functions
I agree, no dispute there. ...
I agree here, no dispute, so lets stick to your definition of evolution. ...
Well I'm particularly happy to stick to this particular definition of the theory of evolution. ...
No problem with this. I agree on divergent speciation. ...
Excellent.
evolution (process) *
theory (scientific) *
hypothesis (scientific) *
the theory of evolution *
novel feature\function
complexity
speciation (divergent) *
and
(I just noticed that I should have also included in Message 1)
fitness
(Where I have marked current agreement\acceptance with an *)
NOTE: if you use the "PEEK MODE" (radio button top right corner of "message you're replying to") when copying for a reply then you can copy the coding as well as the content:
Message 8:
  1. evolution (process)
  2. theory (scientific)
  3. hypothesis (scientific)
  4. the theory of evolution
  5. novel feature\function
  6. complexity
  7. speciation (divergent)
    and
    (I just noticed that I should have also included in Message 1)
  8. fitness
This keeps the reference numbers/letters in view.
I feel we have sufficient consesus on a-d, g I'm not anticipating a problem with h
So we have some issue with e: novel features\functions\traits
Regarding novel features and functions, I don't see why you have included that in your list because I see no dispute there and do not feel it should be part of our terms of reference. I agree that novel features and functions do evolve. ...
My only problem with evolution is how does evolution explain novel genes as I have described them, without these particular genes, how would one explain a transition from a bacterial form of abut 1000 coding genes to a mammal ...
Evolutionary processes can explain some speciation, but not the genetic diversity of life as we know it, and so I'm proposing we stick to the discussion about novel genes and avoid discussing novel features/functions , a topic on which we already have consensus.
Why don't we set this aside for a moment, then and resolve complexity and fitness before coming back to this?
Complexity is, imho, a red herring. It is an emergent property of evolution, but is sometimes gained and sometimes lost as species evolve over time. Blind cave fish for instance are more adapted to dark caves, and it saves on development resources.
One can't get more simple than just surviving prokaryote single cells with minimal DNA (and first life forms were likely very simple), but there is no theoretical limit to the degree of embellishment that can occur, and it doesn't necessarily track with evolution.
... I believe the genetic combinations within each species are endless. ...
Indeed, and they are all based on various combinations of just the four basic purine and pyrimidine bases adenine, guanine, cytosine, and thymine, with no theoretical limit to how long the strands can be (yet logically there is a minimum sequence below which life would fail).
How do you measure complexity: there are yeasts with many more DNA sequences than humans, so are they more complex?
Thus I would suggest we drop complexity as irrelevant to evolution and the increase in diversity we are discussing, unless you can show some reason to discuss it.
That brings us to fitness.
Here I would say that:
The Fitness of an individual organism is the measure of the relative ability of that organism to survive and reproduce compared to other organisms within its breeding population.
It is the measure of the natural selection forces acting on the organism, where the individual that produces more offspring than others in their breeding population (either in one generation or spread out over many generations) contributes more to the gene pool of that population than the others.
Enough for now.
Enjoy
Edited by RAZD, : meas

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This message is a reply to:
 Message 9 by mindspawn, posted 01-25-2013 3:09 AM mindspawn has replied

Replies to this message:
 Message 11 by mindspawn, posted 01-25-2013 2:22 PM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 12 of 65 (688931)
01-26-2013 6:21 PM
Reply to: Message 11 by mindspawn
01-25-2013 2:22 PM


Re: The evolution of novel features\functions
The Fitness of an individual organism....
Agreed
Excellent, so now we have agreement on all but complexity and novelty:
  1. evolution (process) - yes
  2. theory (scientific) - yes
  3. hypothesis (scientific) - yes
  4. the theory of evolution - yes
  5. novel genes\feature\function - no
  6. complexity - no
  7. speciation (divergent) - yes
  8. fitness - yes
And I would say that 75% agreement at this early stage of this thread is a good sign.
The essence of the debate revolves around the current observation of organisms with DNA less simple than the first life-forms, and less simple than prokaryote single cells. The essence of the debate relates specifically to complexity. ... Can evolution actually explain all of the relative complexity actually observed in most modern life-forms?
You will need to define "complexity" then, and if you are going to compare "complexity" between organisms, then you need a way that it can be measured and properly compared.
The initial problem I have here is that I do not know of any currently known way to actually "quantify" complexity. We can look at organisms and say that one appears more complex than another, but we can't provide an objective measure that shows this to be the case. This seems to me to be just a homo-centric subjective impression in most cases, not a scientific quantity.
Certainly DNA length is no measure of "complexity" -- take the single cell amoeba:
Sizing up genomes: Amoeba is king
quote:
In the animal kingdom, the relationship between genome size and evolutionary status is not clear. One of the largest genomes belongs to a very small creature, Amoeba dubia. This protozoan genome has 670 billion units of DNA, or base pairs. The genome of a cousin, Amoeba proteus, has a mere 290 billion base pairs, making it 100 times larger than the human genome.
A Sample of Species and Genome Size (in base pairs)
Amoeba dubia
670,000,000,000
Amoeba proteus
290,000,000,000
Homo sapiens
2,900,000,000

Is A. proteus 100 times more complex than humans? A. dubia 231 times more complex?
Second, IF "complexity" could be measured, would it have any predictive power in saying how fit an organism is for the ecology it inhabits? For instance, going back to kittens and puppies, I can measure the relative amounts of black areas to white areas on the black and white individuals, but that doesn't provide me with any real information on whether ones with more black are more or less fit to their ecology than ones with more white. This measurement has no predictive power in saying how fit an organism is for the ecology it inhabits.
Nothing against this in principle, but just speculating that growth of an organism could be inhibited by the length of the DNA, through slow cell reproduction. (off-topic, I know)
Doesn't appear to inhibit A. dubia or affect its fitness to its ecology.
... Can evolution actually explain all of the relative complexity actually observed in most modern life-forms?
Throw a bunch of bricks in a field and some will end up stacked on top of others in fairly complex seeming patterns compared to the bricks sitting flat on the ground. Sometimes those stacks will be increased by later bricks, sometimes they will be knocked down. Is an accidental pyramid of three or more bricks more complex than a single brick lying on the ground? Or is it just something that happens when you throw bricks in a field, an emergent property of the action?
Apparent complexity is an emergent property of evolution, sometimes increasing and sometimes decreasing.
For instance we can look at the evolutionary history of walking sticks:
See Figure 1 from Nature 421, 264 - 267 (16 January 2003); doi:10.1038/nature01313 (reproduced below)
Walkingstick insects originally started out as winged insects (blue at start and top row). That diversified.
And some lost wings (red). And diversified.
And some regained wings (blue again). And diversified.
And one lost wings again (Lapaphus parakensis, below, red again).
And this doesn't even address the ones where one sex (usually male) has wings and the other sex doesn't (the red includes these, so it is hard to determine from this graphic how many times the female sex gained and lost wings independent of the winged males).
  • Is one with wings "more complex" than one without wings?
  • Is one without wings "more complex" than one with wings?
  • Is one with wingless females and winged males "more complex"?
Does the relative apparent differences in complexity predict which form is more fit for the ecology?
So complexity relates to the evolutionary process of organisms gaining productive novel genes over time, ...
So what you are really interested in is whether or not a novel gene sequence has appeared, and we can easily discuss that without pulling in the question of whether the organism with the novel gene is more "complex" than its ancestor.
... a process essential to evolution as a theory explaining modern life. This is what I wish to debate. ...
Yes, the production of novel genes is the issue, not complexity, per se.
... If you wish to avoid the word "complexity" and stick to discussing genes, I'm fine with that.
Actually I don't think "complexity" adds anything to the debate that is not already covered by the issue of novelty and normal evolutionary processes.
This gets us to
  1. evolution (process) - yes
  2. theory (scientific) - yes
  3. hypothesis (scientific) - yes
  4. the theory of evolution - yes
  5. novel genes\features\functions\traits - not yet
  6. complexity (drop)
  7. speciation (divergent) - yes
  8. fitness - yes
So now we can go back to novelty:
Message 8: Would you agree that a novel feature\function\trait would be one that did not exist in a previous generation?
Message 9: Regarding novel features and functions, I don't see why you have included that in your list because I see no dispute there and do not feel it should be part of our terms of reference. I agree that novel features and functions do evolve. I believe there are many ways in which this can happen but possibly the most observed processes are deletions and changes to alelle frequencies. I believe the genetic combinations within each species are endless. You just have to look at the possible alelles in each location within a population (let us say for example about 10) and the number of genes (eg about 20000 in mammals) and the result is that the number of combinations of unique individuals is already practically infinite. Just over the first ten genes the maths is 10x10x10x10x10x10x10x10x10x10 = 10 000 000 000 combinations of uniqueness in a population with 10 possible alelles per location over the first ten genes. So some within the population could have unique looks, unique features, unique functions merely by an environmental presssure that causes continuous changes to alelle combinations best suited to the new environment.
My only problem with evolution is how does evolution explain novel genes as I have described them, without these particular genes, how would one explain a transition from a bacterial form of abut 1000 coding genes to a mammal of about 20000 coding genes each with a unique fitness enhancing function. By what process do these genes increase so effectively in number. By challenging this , I am challenging your own definition on the theory of evolution (are sufficient to explain the diversity of life as we know it)
Evolutionary processes can explain some speciation, but not the genetic diversity of life as we know it, and so I'm proposing we stick to the discussion about novel genes and avoid discussing novel features/functions , a topic on which we already have consensus.
First let me rephrase my question:
Would you agree that a novel gene\feature\function\trait would be one that did not exist in a previous generation?
Second, to answer why traits and functions rather than (or in addition to) genes:
The traits and functions are the expression of the genotype in the phenotype of each individual organism. You would not have novel features and functions in the phenotype without novel gene sequences.
New sequences in the genotype are either selectable (expressed in the phenotype) or hidden (not expressed in the phenotype), selection operates on the phenotype, and thus any effect of a novel gene sequence on the fitness of an organism depends on it being expressed in the phenotype.
When Mendel did his experiments in the late 1800's the gene structure was unknown, but the hereditary traits were observable. The vast majority of his results fit the theoretical pattern of dominant and recessive genes (and use of these terms seems to be from his use in his papers). A very small minority did not. He did not know about mutations and how they could introduce novel genes\features\functions\traits, but he could observe the new features\functions\traits.
In other words, you don't get novel features\functions\traits without novel genes, so the existence of one predicts the existence of the other.
Certainly, when we come to fossil organisms where DNA is not available, what we have to observe are the novel features\functions\traits in the fossils (and even then some are not preserved, being in non-fossilized soft tissues).
Enough for now,
Enjoy
Edited by RAZD, : format
Edited by RAZD, : engls
Edited by RAZD, : db

we are limited in our ability to understand
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This message is a reply to:
 Message 11 by mindspawn, posted 01-25-2013 2:22 PM mindspawn has replied

Replies to this message:
 Message 13 by mindspawn, posted 01-27-2013 3:47 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 14 of 65 (689010)
01-27-2013 12:34 PM
Reply to: Message 13 by mindspawn
01-27-2013 3:47 AM


Re: The evolution of novel features\functions: agreement to date
I'm going to split this up into a couple of posts, the first summarizing agreement should need no reply:
Yes that is what I have been asking for from the start. As I said, we can avoid the use of the word "complexity" and just discuss this gene adding process.
Excellent.
  1. evolution (process) - yes
  2. theory (scientific) - yes
  3. hypothesis (scientific) - yes
  4. the theory of evolution - yes
  5. novel genes\features\functions\traits - not yet
  6. complexity (drop)
  7. speciation (divergent) - yes
  8. fitness - yes
And all we have left for finding consensus is novelty.
Early stage? lol we could be nearly finished by now ...
Yes, I don't expect the discussion of novelty to be this brief, in part because misunderstanding evolution is still apparent.
Enjoy.

we are limited in our ability to understand
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This message is a reply to:
 Message 13 by mindspawn, posted 01-27-2013 3:47 AM mindspawn has not replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 15 of 65 (689012)
01-27-2013 12:46 PM
Reply to: Message 13 by mindspawn
01-27-2013 3:47 AM


the god hypothesis place in science
Second regarding the god hypothesis:
God made them all different. ...
God-did-it is not science, nor is it refutation of science, it justs exhibits a failure to consider how it occurred. This is not debate it is failure to debate.
I'm a Deist: god made the natural laws that caused what you see, and out interest is not in whether he did it, but how -- what were the mechanisms?
God made them all different. ...
Through the use of natural laws of evolution, mutation and selection ... now let's investigate how he did it.
If you can provide an explanation that better fits the observations, then please post it.
God made them all different. ...
Does not explain why the genetic patterns fit the nested hierarchy shown. If god/s made them different how come he made them so similar that they fit the nested hierarchy shown? Is s/he faking evidence? There is no cause to create the nested hierarchy unless the method\mechanism used to created used the natural process of evolution and selection.
Science investigates how this occurred, not why.
Of course, if you insist on god/s did it, then there is no reason to look at evidence nor debate how evolution explains the diversity of life as we know it.
This is the essence of this debate, the ability of nature to create genes with unique functions out of nothing, ...
So I move to strike the god hypothesis from this debate, and stick to science and natural explanations:
  1. evolution (process) - yes
  2. theory (scientific) - yes
  3. hypothesis (scientific) - yes
  4. the theory of evolution - yes
  5. novel genes\features\functions\traits - not yet
  6. complexity (drop)
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis (drop)
So now we can again go back to novelty.
Enjoy.
Edited by RAZD, : list

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This message is a reply to:
 Message 13 by mindspawn, posted 01-27-2013 3:47 AM mindspawn has replied

Replies to this message:
 Message 17 by mindspawn, posted 01-28-2013 2:05 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 16 of 65 (689014)
01-27-2013 1:33 PM
Reply to: Message 13 by mindspawn
01-27-2013 3:47 AM


Novelty and Evolution
Third regarding novelty and evolution:
... If you could prove ...
Nothing is proven in science, not even that the earth orbits the sun, this is just the best explanation for the observations we have.
... the "regaining" part ... Can you prove the regained" portion of genes was actually from a population that never had them in any form already? ...
This was demonstrated by the genetic analysis to be the best explanation for the observations made from the genetic sequencing of the different species.
... you have already won this debate. ...
Again, I am not interested in winning, but in reaching consensus. In consensus we both "win"
... Were they just dormant genes ? Inactivated genes that were already there?
How is a dormant gene activated?
How is a gene deactivated?
How is an inactivated gene reactivated?
Answer: by mutation/s.
How do they become predominant in the population?
Answer: by selection, by improved fitness within the ecology.
... for you to simply describe this process as fact when this is the essence of the debate, makes me wonder if you are on the same page as me that this is what you need to prove. Your arguments will gain strength if you are able to avoid the assumption of evolution in forming your arguments.
It is what the genetic information shows.
I don't assume evolution, I assume natural processes occur and look at the analysis of the data for the best explanation for the observations.
If you can provide an alternative natural explanation that better fits the observations, then please post it.
This is where I completely disagree. I thought we had this already covered and discussed. You see its possibly for some aspects of macro-evolution to already exist within a genome,...
Please define macro-evolution so we can agree on this term. I know how science uses the term, I want to see your understanding of what the term means.
What is it, how does it occur, how do you know when it has occurred?
... merely through new allele frequencies. ...
But this would be micro-evolution yes? Note that we've already agreed on this definition for the proces 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.
This is sometimes called microevolution, however this is the process through which all species evolve and all evolution occurs at the breeding population level.
So when you talk about changing allele frequencies you are talking about the process of evolution, or micro-evolution, yes?
... Let's say fish are slowly introduced into environments where their food source is increasingly above the water instead of in the water. The population will gradually change to reflect this, but in many many areas of the genome. Fin shape and size, speed, muscles that assist jumping etc etc . Every feature that assists the survival of that species in that restricted environment will be enhanced until new allele frequencies are obtained for the new environment once the environment is stabilized. The result: jumping fish, a new function. No need for for mutations.
This would still be micro-evolution, but it is just the beginning of the process. Evolution would not stop there. Any mutation that assisted jumping would also be selected for.
Jumping ability would have already existed in the breeding population, so this would not be a novel feature\function\trait, and the height of jumping would be restricted by the existing alleles in the population if no mutations occur to improve this ability.
Small mutations could easily increase the "fin shape and size, speed, muscles that assist jumping etc etc" would be subject to positive selection pressure, as the individuals with such mutations would have increased fitness compared to those that don't. Over generations the shift in alleles within the breeding population would show increased frequency of the mutations and decreased frequency for non-modified genes until one replaces the other.
For instance Pelycodus:
A Smooth Fossil Transition: Pelycodus
quote:
The numbers across the bottom are a measure of body size. Each horizontal line shows the range of sizes that were found at that depth. The dark part of each line shows the average value, and the standard deviation around the average.
Note that the range in the population just above "P. jarovvi" lies completely to the right of the range in the population just below "P. ralstoni" -- the size alleles in the upper population did not exist in the lower population and vice versa.
This is how (micro)evolution works.
Thus I believe new functions can be created outside of novel gene sequences, ...
But curiously, your example does not show a new function, but enhancement of an existing function, enhancement by standard evolutionary processes, including mutation and selection.
... my dispute with the theory of evolution remains focused on those new functions that are specifically related to new additional coding genes, and not new functions that are attained through unique combinations of existing alleles, and some point mutations or deletions or other processes.
Again, demonstrating that you misrepresent or misunderstand evolution.
With this in mind I wish to introduce an acronym , but for the record I am not 100% sure its the perfect acronym, but at least something to use to save me typing the entire description of what I am looking for every post.
G = Gene
A = Additional (ie not a changed gene, but more genes than that organism had)
I = Instrumental - has a function
N = novel (Unique)
S = selected - gains fitness
I am therefore looking for evidence of coding GAINS in organisms, one process essential to the theory of evolution. I believe new functions/features can exist outside of mutations and/or coding GAINS.
Not sure why you differentiate additional from changed - either constitutes a mutation to the genome.
Novel would mean agreeing on the term definition.
Would you agree that a novel gene\feature\function\trait would be one that did not exist in a previous generation?
yes, but remember I am not merely discussing novel genes. ...
Excellent. We can update the list of terms:
  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 (drop)
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis (drop)
  10. micro-evolution (same as 'a' above) - yes
  11. macro-evolution - not yet
... These have got be ADDITIONAL. Not a mutated gene. NEW ADDITIONAL NOVEL genes. I have to be very careful with the wording here, because you can even have new non-coding sequences that add to an organisms fitness, and I am not referring to non-coding sequences either. Sure we can observe some complexity increasing, but can entire new functions evolve in a new gene, while retaining the gene of the original function?
The process here would be gene duplication, (mutation of the genotype) then modification of one of the duplicates (mutation of the genotype) to produce a new feature\function\trait in the phenotype.
You would not know that this occurred until you see it expressed in the phenotype.
Enjoy
Edited by RAZD, : added pelycodus

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This message is a reply to:
 Message 13 by mindspawn, posted 01-27-2013 3:47 AM mindspawn has replied

Replies to this message:
 Message 18 by mindspawn, posted 01-28-2013 2:51 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 19 of 65 (689210)
01-28-2013 7:11 PM
Reply to: Message 17 by mindspawn
01-28-2013 2:05 AM


Re: the god hypothesis place in science
The only reason I brought up the "God-did-it" is to highlight that whenever you make a claim about evolution being a fact, ...
What is fact is objective evidence and observation. Theory does not claim to be fact, but to be an explanation, and the best theory is the one that best explains all the objective evidence and observations.
... it must be compared to the God "hypothesis" to see if the evolutionary process is more likely. ...
Actually it doesn't -- the hypothesis needs to become a scientific theory before it can challenge other scientific theories.
What predictions does the god/s hypothesis make that differentiates it from evolution?
Then let us see if it pans out in the evidence.
The "hypothesis" that god made it look that way -- for every bit of evidence known and found -- does not explain anything - it's a cop-out.
The "God-hypothesis" says they were created that way, an intelligent designer created all the intricacy in each gene ...
If there is no way to distinguish creation\design from natural evolution then all you are doing is stating that creation\design looks just like evolution. You are making no prediction\test of the hypothesis but using the post hoc ergo propter hoc logical fallacy to say "me too" ...
... and nature cannot spontaneously create that intricacy found in genes.
Which, curiously, is not claimed by evolution. Nothing in evolution happens "all at once" but develops over generations.
Nested hierarchy is an assumption based on the pre-acceptance of evolutionary theory, ...
Actually it is based on the observed fact that speciation events form a branch in the hereditary lineage of organisms, and that further speciation events form more branches in nested hierarchies. This has been observed to happen, via the known mechanisms and processes of evolution.
Thus nested hierarchies are a prediction of the theory of evolution, not an assumption. The data from the walking sticks matches the pattern of nested hierarchies that is predicted from observed objective evidence. I'll go into this in more detail in the next post.
... when the entire concept of groups of similar organisms could simply be explained by the fact that God designed organisms in groups. ...
Which does not explain the specific nested hierarchy pattern found in the walking sticks.
... ie there is an overlap of genetic sequences of certain organisms due to being designed so similar. ...
So your god/s could not decide whether to have wings or no wings, and when it came to Lapaphus parakensis, they kept changing their minds? Doesn't sound like intelligent design to me.
... Intelligent designers (think cars) always use this process, never having to "re-invent the wheel"., but duplicating their basic designs and adjusting other features to produce their full range.
Curiously, I am a designer by profession. The borrowing used by designers from one product to another actually violates the nested hierarchy pattern. Rear window wipers, to use an example from cars, were originally on one model and then added to other makes and models with no original development. Chevy, Ford, Subaru, Volvo, etc all sported rear window wipers.
And I'm also a Deist that believes that what was designed were the natural laws, not the products of them. Thus evolution is the tool of creation. My god/s hypothesis therefore explains the nested hierarchy of the walking sticks via evolution as well as the rest of the diversity of life on earth.
You want to compare god/s-hypothesis or talk about evolution?
... the pre-existence of the intricacy of that gene, ...
Meaningless word salad to me. Try using terminology in evolutionary science. This just looks like pretentious pretend pseudo-intellectualism, attempting to say something meaningful.
So to conclude, any genetic evidence brought forward regarding genes evolving will be compared to the "always was there" hypothesis so we can look at the evidence in an unbiased fashion, which is the essence of the evolution/creation debate. Whether mentioned or unmentioned, the comparison has to be there the whole time.
Are we now replacing the "god-did-it" hypothesis with this "always was there" hypothesis?
And how do you test the "always was there" hypothesis against evolutionary theory mechanisms and processes?
If it "always was there" then why is the expression of this genetic sequence not in the phenotypes of the organisms carrying the hidden genes?
Does a longer genetic sequence means that there is a sequence that was not "always there" and how can you tell when it is from duplication of existing sequences?
Does a shorter sequence mean that some "always was there" genetic sequence has been lost? Seems wasteful for intelligent designing.
This seems like clutching at straws to me.
The rest of your Message 17 is included in the next reply.
Enjoy
Edited by RAZD, : the new god-did-it: hidden genes

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This message is a reply to:
 Message 17 by mindspawn, posted 01-28-2013 2:05 AM mindspawn has replied

Replies to this message:
 Message 21 by mindspawn, posted 01-29-2013 3:04 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 20 of 65 (689217)
01-28-2013 8:55 PM
Reply to: Message 18 by mindspawn
01-28-2013 2:51 AM


Nested Hierarchies and Macroevolution
Continuing reply to Message 17:
Evolutionary theory states that all modern life is a result of evolutionary processes, and due to the fact that most organisms show more coding genes than the basic organisms, evolutionary theory involves coding GAINS.
Not quite. Evolution theory states that all modern life (and all historic and prehistoric life) can be explained by evolutionary processes and mechanisms. Evolutionary theory involves occasional development of novel genes\features\functions\traits by various mechanisms.
The earliest life form we know from the fossil record is a blue-green algae, a prokaryote similar to the blue-green algae today. We do not know (yet) about any earlier life forms. The DNA of those algae may have been similar to what we see today or it may have been simpler ... or it may have been more convoluted with a lot of dead weight left over from whatever process first developed for life on earth. We don't know. We do know that some fairly simple organisms have extremely long DNA. The genetic sequences necessary for life may have been relatively simple, but there also may not have been any mechanism to reduce baggage.
We also know that for the first billion years prokaryotic life was what left evidence that we can find, and that eukaryotic life seems to have developed by combining two or more forms into a new and novel form of life before developing into multicellular life forms.
... evolutionary theory involves coding GAINS.
Evolutionary theory involves evolution of organisms, from generation to generation, occasionally involving the development of novel genes\features\functions\traits.
When looking at any genome sequencing, it is therefore essential to show that the evolutionary process is more observable than the pre-existence of the intricacy of that gene, if the theory of evolution is to be a more acceptable explanation for the existence of the gene. ...
All evolution needs to show is that in population "A" the gene did not exist but in population "B" it does exist, with population "B" being direct descendants of population "A".
Continuing from my previous reply (Message 19):
Nested hierarchy is an assumption based on the pre-acceptance of evolutionary theory, ...
Actually it is based on the observed fact that speciation events form a branch in the hereditary lineage of organisms, and that further speciation events form more branches in nested hierarchies. This has been observed to happen, via the known mechanisms and processes of evolution.
Thus nested hierarchies are a prediction of the theory of evolution, not an assumption. The data from the walking sticks matches the pattern of nested hierarchies that is predicted from observed objective evidence. I'll go into this in more detail in the next post.
This ties into the issue of what macro-evolution involves ... in scientific usage anyway.
Please define macro-evolution so we can agree on this term. I know how science uses the term, I want to see your understanding of what the term means.
What is it, how does it occur, how do you know when it has occurred?
If you wouldn't mind doing the homework yourself, and we will use your definition from now on.
Macro-evolution is likely the most misunderstood term among lay people in general and creationists in specific.
Unlike evolution\micro-evolution, macro-evolution is not a process per se, rather it is the natural history record of evolutionary processes in populations over the span of many generations. Evolutionary scientists generally draw the line between micro-evolution and macro-evolution at divergent speciation.
You have previously accepted my definition for divergent speciation (in Message 9):
No problem with this. I agree on divergent speciation. ...
Now we look at how this ties into nested hierarchies and see if we can define macro-evolution for you:
If we look at the continued effects of evolution on a breeding population over many generations, the accumulation of changes from generation to generation may become sufficient for individuals to develop combinations of traits that are observably different\modified from the ancestral parent population. This lineal change within species is sometimes called phyletic change in species, or phyletic speciation. This is also sometimes called arbitrary speciation in that the place to draw the line between linearly evolved genealogical populations is subjective, and because the definition of species in general is tentative and sometimes arbitrary.
If phyletic speciation was all that occurred, then all life would be one species, readily sharing DNA via horizontal transfer (asexual) and interbreeding (sexual) and various combinations. This is not the case, however, because there is a second process that results in multiple species and increases the diversity of life.
The process of divergent speciation involves the division of a parent population into two or more reproductively isolated daughter populations, which then are free to (micro) evolve independently of each other.
The reduction or loss of interbreeding (gene flow, sharing of mutations) between the sub-populations results in different evolutionary responses within the separated sub-populations, each then responds independently to their different ecological challenges and opportunities, and this leads to divergence of hereditary traits between the subpopulations and the frequency of their distributions within the sub-populations.
Over generations phyletic change occurs in these populations, the responses to different ecologies accumulate into differences between the hereditary traits available within each of the daughter populations, and when these differences have reached a critical level, such that interbreeding no longer occurs, then the formation of new species is deemed to have occurred. After this has occurred each daughter population microevolves independently of the other/s. These are often called speciation events because the development of species is not arbitrary in this process.
If we looked at each branch linearly, while ignoring the sister population, they would show phyletic change in species (accumulation of evolutionary changes over many generations), and this shows that the same basic processes of evolution within breeding populations are involved in each branch.
An additional observable result of speciation events, however, is a branching of the genealogical history for the species involved, where two or more offspring daughter species are each independently descended from the same common pool of the ancestor parent species. At this point a clade has been formed, consisting of the common ancestor species and all of their descendants.
With multiple speciation events, a pattern is formed that looks like a branching bush or tree: the tree of descent from common ancestor populations. Each branching point is a node for a clade of the parent species at the node point and all their descendants, and with multiple speciation events we see a pattern form of clades branching from parent ancestor species and nesting within larger clades branching from older parent ancestor species.
Where A, B, C and G represent speciation events and the common ancestor populations of a clade that includes the common ancestor species and all their descendants: C and below form a clade that is part of the B clade, B and below form a clade that is also part of the A clade; G and below also form a clade that is also part of the A clade, but the G clade is not part of the B clade.
The process of forming a nested hierarchy by descent of new species from common ancestor populations, via the combination of phyletic change in species and divergent speciation, and resulting in an increase in the diversity of life, is sometimes called macroevolution. This is sometimes confusing, because there is no additional mechanism of evolution involved, rather this is just the result of looking at evolution over many generations and different ecologies.
Macroevolution is the natural history\record of the evolution of organisms via phyletic speciation (microevolution), and divergent evolution, over many generations.
I'm going to hold off on replying to the rest of Message 18 pending acceptance of the definition of macroevolution, as most of it seems to involve this in your posting.
Nothing is proven in science, not even that the earth orbits the sun, this is just the best explanation for the observations we have.
I'm happy with "best explanation for the observations we have".
Excellent. We also determine that they are the best possible explanation known by using prediction and testing to differentiate it from other explanations.
As with complexity, I suggest that the god hypothesis and the hidden gene hypothesis be dropped from the debate unless you can provide a scientific basis for including them -- a way to test them that differentiates them from evolutionary theory:
  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 - (dropped)
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis - (drop?)
  10. hidden gene hypothesis - (drop?)
  11. micro-evolution (same as 'a' above) - yes
  12. macro-evolution - not yet
If you accept this then we can move forward on novel genes\features\functions\traits.
Enjoy.
Edited by RAZD, : added
Edited by RAZD, : 18 not 19

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This message is a reply to:
 Message 18 by mindspawn, posted 01-28-2013 2:51 AM mindspawn has replied

Replies to this message:
 Message 22 by mindspawn, posted 01-29-2013 7:06 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 23 of 65 (689310)
01-29-2013 2:09 PM
Reply to: Message 21 by mindspawn
01-29-2013 3:04 AM


pseudoscience vs science
Message 22: Have you considered that it is possible to discuss novel genes directly, without agreeing on everything else first. ...
Yes, but the likelihood that we would be talking past each other would be extremely high. By going through these definitions and agreeing on their usage and meaning then it means we have a discussion with common terminology.
I am saying that all genomes look created. They exist, they have many genes, ...
What makes you say they look created? What distinguishes created from occurring naturally?
Give me a test, a measurement, a means to distinguish one from the other.
Else all you are claiming is your opinion based on belief, rather than hypothesis based on evidence. This is pseudoscience.
... Please don't get unnecessarily nasty........ especially when unjustified.
Please don't post unnecessary twaddle and pretend it is a scientific debate.
Ok well I have to admit that I never thought of this argument, that DNA could have started out long. Yes maybe the fact that we cannot observe the unlikely event of nature adding on just one gene, is because nature did all 22000 genes at once............ (I want to burst out laughing at this concept)
A) If you do assume a long DNA, then your view is similar to mine. We started with highly involved DNA. Then you have a huge problem with credibility because how does nature do this?
B) If you do not assume a long DNA then we are back to the same problem, where did the additional genes come from?
Both ways the theory of evolution has a big problem to solve.
Duplications of gene sequences have been observed, so it is not a problem for evolution. So have random insertions and deletions, sequence rearrangements and flipping of sections of genetic code. What's to explain?
... each gene is highly intricate in structure.
Every gene is composed of sequences of four base molecules, for every living organism, yes?
DNA - Wikipedia
quote:
Deoxyribonucleic acid (DNA) is a molecule encoding the genetic instructions used in the development and functioning of all known living organisms and many viruses. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life. Genetic information is encoded as a sequence of nucleotides (guanine, adenine, thymine, and cytosine) recorded using the letters G, A, T, and C. ...
The structure of the DNA double helix. The atoms in the structure are colour coded by element and the detailed structure of two base pairs are shown in the bottom right.

Where A (adenine) is cross-linked to T (thymine), while G (guanine) is cross-linked to C (cytosine). These base pairs are then arranged in a sequence, but there are only so many variations ... if we start with A then the next molecule can be A, T, C, or G, and if we start with T then the next molecule can be A, T, C, or G, and if we start with C then the next molecule can be A, T, C, or G, and if we start with G then the next molecule can be A, T, C, or G.
Thus there are 16 variations in the bonding of any two molecules along the strand, and half of them are mirror images of the other half. The length of the strand does not change this, it just duplicates sections already included. Take any two molecules in any sequence in any strand of DNA and you will find one of these 16 possible arrangements,
Do you AGREE or DISAGREE?
Thus DNA is boringly repetitious rather than intricate (or complex ...).
The process of evolution adequately explains the boring repetition of sequences.
For instance I could theoretically take a strand of DNA from the amoeba A. dubia and select from its DNA (670,000,000,000 base pairs) the sequences that match the 2,900,000,000 base pairs necessary to form our human (H. sapiens) DNA ... would the result be an amoeba or human DNA?
Does this mean that the amoeba DNA is more intricate (or complex) than the human one?
Message 22:
It usually takes many many pages in discussions with evolutionists for them to realise to get from a simple 1000 gene organism to a 22000 gene organism, involves the evolving of genes. I will ask my three year old nephew about this, how does the basket with one apple become the basket with 22 apples? You add in 21 apples. But how? Without this process , life as we know it would not exist under evolutionary processes (the range of existing modern organisms). Or maybe 22000 gene organisms just appeared? (sounds a bit like creation to me)
All it takes is the accumulation of duplication of parts of the DNA sequence, whether by insertions of single pairs, sections of DNA or whole gene sequences. We've had a few billion years to build up the sequences in life seen today.
Mutation and selection is more than adequate to explain this.
I agree on the evolving of traits, and features, and functions. Let's discuss genes.
Easy to do once all the terminology is settled.
Macroevolution is the natural history\record of the evolution of organisms via phyletic speciation (microevolution), and divergent evolution, over many generations
No problem with this. ...
Excellent. We can update the terminology list:
  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 - (dropped)
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis - (drop?)
  10. hidden gene hypothesis - (drop?)
  11. micro-evolution (same as 'a' above) - yes
  12. macro-evolution - not yet
  13. intricacy (= complexity) - (drop?)
... I feel this definition would include extreme changes through changes to allele frequencies (continued micro-evolution of one population under continued evolutionary pressures until the two populations are so different or so separated they no longer breed)
And here we see the typical lay person \ creationist confusion with macro-evolution.
What do you mean by "extreme changes"? The evolution of a novel feature\function\trait?
I don't see this as possible, if you present evidence for evolution, and at that time I point out that the creationist view explains the evidence better, then at that time I will be providing evidence for creationism as a better explanation for what is observed. This is after all a creation/evolution debate. I reserve the right to point out the creationist explanation as a more viable one throughout this debate.
You can claim it, but for me to accept it you need to show something more than assertion. You need to tell me how a created sequence can be distinguished from a naturally occurring one.
As for the "hidden gene hypothesis" I don't know anything about that, explain more?
This is your "was already there" gene that somehow did not influence development in the phenotype until millions of years later - it lay hidden within the genome. Another assertion unsupported by evidence and with no identification test methodology proposed ... and thus not scientific, but pseudoscience.
Enjoy.
Edited by RAZD, : clrty
Edited by RAZD, : sequence
Edited by RAZD, : ...

we are limited in our ability to understand
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This message is a reply to:
 Message 21 by mindspawn, posted 01-29-2013 3:04 AM mindspawn has replied

Replies to this message:
 Message 25 by mindspawn, posted 01-30-2013 5:19 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 24 of 65 (689336)
01-29-2013 5:57 PM
Reply to: Message 22 by mindspawn
01-29-2013 7:06 AM


Re: Nested Hierarchies and Macroevolution
Ok well I have to admit that I never thought of this argument, that DNA could have started out long. ...
Early reproducing molecules could have used different nucleotides altogether. Certainly RNA shows some variation by using uracil instead of thymine, and current thinking is that life evolved from RNA pre-biotic systems (RNA world). There could have been other players in the early life mix.
Until evolution processes took over control of molecular reproduction via selection there was likely no mechanism to eliminate unnecessary material. But the issue is that we do not know what the first life forms on earth were like, whether it was long or short, circular or stranded.
A) If you do assume a long DNA, then your view is similar to mine. We started with highly involved DNA. Then you have a huge problem with credibility because how does nature do this?
B) If you do not assume a long DNA then we are back to the same problem, where did the additional genes come from?
Curiously, I don't need to assume either. Evolution still answers the issue of how life changes over time. All I need to do is look at the evidence that is available and see that evolutionary processes explain the evidence.
Both ways the theory of evolution has a big problem to solve.
The process of evolution solves those imaginary problems. Remember that evolution is a two-step feedback response system that is repeated in each generation:
Like walking on first one foot and then the next. To get any great distance you need to use both feet.
Mutations and mixing existing hereditary traits in different combinations (ie for eye color) can cause changes in the composition of hereditary traits for individuals in a breeding population. Not all mutations cause hereditary change (many are in non-hereditary areas or are neutral to selection). In addition there are many different kinds of mutations and they have different effects (from small to large), especially if they affect the developmental process of an organism.
Random mutations and sexual trait mixing affect the genotype, and any changes are subject to possible selection when they are expressed in the phenotype.
Natural Selection and Neutral Drift can cause changes in the frequency distribution of hereditary traits within a breeding population, but they are not the only mechanisms known that does so. Selection processes act on the expressed genes of individual organisms, so bundles of genetic mutations are selected rather than individual genes, and this means that non-lethal mutations can be preserved. The more an individual organism reproduces the more it is likely to pass on bundles of genes and mutations to the next generation, increasing the selection of those genes.
Selection affects the phenotype, the whole bundle of various traits expressed in each individual of the breeding population.
The ecological challenges and opportunities change when the environment changes, when the breeding population evolves, when other organisms within the ecology evolve, when migrations change the mixture of organisms within the ecology, and when a breeding population immigrates into a new ecology. These changes can result in different survival and reproductive challenges and opportunities, affecting selection pressure, perhaps causing speciation, perhaps causing extinction.
I agree on the evolving of traits, and features, and functions. Let's discuss genes.
Are you ready to drop the god hypothesis, the hidden gene hypothesis and any other appeal to belief over evidence?
Are you ready to drop "intricacy" as just as problematic as "complexity" was (and any other verbal attempts to use different terms to mean the same basic thing)?
  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 - (dropped)
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis - (drop?)
  10. hidden gene hypothesis - (drop?)
  11. micro-evolution (same as 'a' above) - yes
  12. macro-evolution - not yet
  13. intricacy (= complexity) - (drop?)
Then we can discuss what science says.
Enjoy

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This message is a reply to:
 Message 22 by mindspawn, posted 01-29-2013 7:06 AM mindspawn has replied

Replies to this message:
 Message 26 by mindspawn, posted 01-30-2013 6:01 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(2)
Message 27 of 65 (689437)
01-30-2013 6:08 PM
Reply to: Message 25 by mindspawn
01-30-2013 5:19 AM


Backing up the bus
Sadly, I had hoped that I could split off a couple of easy items that would not need further discussion, and as this doesn't appear to be the case I am combining my replies into one post. This means it is long ...
Message 25:
Yes, but the likelihood that we would be talking past each other would be extremely high. By going through these definitions and agreeing on their usage and meaning then it means we have a discussion with common terminology.
Not nearly as important as you are claiming. the word "complex" would naturally come up many times in a conversation like this, and to restrict its usage is extremely pedantic and not conducive to good communication. I therefore wish to continue the usage of this word in this thread and you can strike it off the list of consensus.
The word "complexity" and any stand-in ("intricacy" etc) is meaningless to me in this debate so far, because I cannot measure it. Thus whenever you use it you are thinking you are meaning something but it is not being communicated -- you are talking past me.
Curiously, the words I've defined can be measured, quantified and compared.
I already dealt with duplications. If they code for proteins they are damaging or neutral. This is what is observed. I posted evidence for some observed duplications that do damage. So it definitely is a problem for evolution, unless you can show how duplicated coding genes improve fitness?
Yes, you have cherry picked some examples. Mutations can be deleterious, neutral or beneficial depending on how they affect the development, survival and reproduction of the organism.
Only looking ones that are deleterious is using confirmation bias to support your arguments. We can cover this in greater detail later.
I agree that there are 4 possibilities, and agree that it is repetitive. However it is highly complex. ...
What I see:
I agree that there are 4 possibilities, and agree that it is repetitive. However it is highly gobbledygook. ...
Just like binary bits of a computer are long sequences of boring repetition, place them in a certain order (computer software) and they become highly effective codes containing processing information. This is a good analogy with DNA which has double the information per position than the binary code of computers and four times the options over two positions. This "boring repetition" encodes highly detailed production of proteins, ...
Easily assembled over millions of years with trial and error testing: those that survive to reproduce continue, those that don't die off. This is not like computer programing.
Try this analogy: there is a truck with a load of bricks, the bricks are in four different colors, and they are piled randomly in the truck; a blind worker in the truck picks up a brick and hands it to another worker outside the truck who then adds it to the line of bricks made by placing one after the other.
Is this complex? Is it intricate? Does the complexity change the longer the line gets? How complex is it?
Well your defintion of macro-evolution didi not actually require novel features/functions/traits. ...
Curiously, this is how evolutionary science uses the term. As I said, it is likely the most misunderstood term by the typical lay person \ creationist resulting in confusion about what macro-evolution involves. As such I find it better to not use this term.
... You keep saying I am confused, yet you agree that changes to allele frequencies can cause micro-evolution. You also seem to agree that continuous micro-evolution can result in macro-evolution according to your definition of macro-evolution. So I'm failing to see where I am confused? Could you explain this better? ...
All that is needed for macro-evolution to be recorded is speciation. Breeding isolation can occur without any distinctly novel feature/trait being involved, ie - when we look at the Greenish Warbler:
Greenish warblers
quote:
Greenish warblers (Phylloscopus trochiloides) inhabit forests across much of northern and central Asia. In central Siberia, two distinct forms of greenish warbler coexist without interbreeding, and therefore these forms can be considered distinct species. The two forms are connected by a long chain of populations encircling the Tibetan Plateau to the south, and traits change gradually through this ring of populations. There is no place where there is an obvious species boundary along the southern side of the ring. Hence the two distinct 'species' in Siberia are apparently connected by gene flow. By studying geographic variation in the ring of populations, we can study how speciation has occurred. This unusual situation has been termed a 'circular overlap' or 'ring species'. There are very few known examples of ring species.

This shows how little difference is needed to have breeding isolation, and this is all that is necessary to make nested hierarchies.
After many speciation events and continued divergent evolution of the daughter populations over many generations features and traits can develop that are distinctly different, but that is due to many generations of phyletic evolution in each hereditary lineage, not to any new process or mechanism.
When you trace a novel feature\trait backwards to see how it developed all that is observed is normal evolution from generation to generation, and it is only when you look at features\traits from say 10 or more generations apart that you begin to see differences enough to categorize as novel.
Back in Message 16 I posted information about Pelycodus:
http://www.don-lindsay-archive.org/creation/pelycodus.html
quote:
The numbers across the bottom are a measure of body size. Each horizontal line shows the range of sizes that were found at that depth. The dark part of each line shows the average value, and the standard deviation around the average.
Note that the range in the population just above "P. jarovvi" lies completely to the right of the range in the population just below "P. ralstoni" -- the size alleles in the upper population did not exist in the lower population and vice versa.
Would you AGREE or DISAGREE that variation in sizes from one generation to the next generations is small, with a lot of individuals having the same sizes, but when comparing P. jarovvi to P. ralstoni we see that none of them are the same size? This is macro-evolution.
Speciation does not cause novel features\traits, and novel traits\features can occur without speciation.
Macro-evolution does not cause novel features\traits. It is a record of the evolutionary history of a hereditary lineage/s.
... Would you like to use a new definition of macro-evolution that includes novel features/traits?
Why should I use a definition that isn't used in evolutionary science?
Changes to allele frequencies and some minor mutations can cause phyletic speciation and divergent evolution without the need for new coding GAINS. To always assume coding GAINS through the observation of new traits is not being true to the variety of evolutionary processes claimed by evolution.
What I see:
Changes to allele frequencies and some minor mutations can cause phyletic speciation and divergent evolution without the need for new coding blahblah. To always assume coding blahblah through the observation of new traits is not being true to the variety of evolutionary processes claimed by evolution.
More on this below.
Message 26 response:
Are you ready to drop "intricacy" as just as problematic as "complexity" was (and any other verbal attempts to use different terms to mean the same basic thing)?
No. The word "complexity" is highly relevant to this discussion and the need to use it may arise repeatedly. I see it as highly pedantic to demand that I do not use a specific word before you discuss the core issues. For the sake of discussion I have been willing to compromise, hoping you can do the same.
What I have asked is that you not use a word that is not defined in a way that it can be measured and quantified.
Is the Amoeba dubia more or less complicated than Homo sapiens? How do you know?
Are you ready to drop the god hypothesis, the hidden gene hypothesis and any other appeal to belief over evidence?
That's ironic that you refuse to discuss the topic of the thread , evidence for the theory of evolution, until I give my evidence (ironic? hypocritical?)
Nevertheless I will drop discussing this for the sake of getting on with this discussion.
A small step forward after one step back ...
We can also drop the usage of micro-evolution and macro-evolution, and focus on the evolution of novel genes\features\functions\traits:
  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 - needs to be defined or dropped
  7. speciation (divergent) - yes
  8. fitness - yes
  9. god hypothesis - (drop?)
  10. hidden gene hypothesis - (drop?)
  11. micro-evolution (= 'a' above) - (drop?)
  12. macro-evolution - (drop?)
  13. intricacy (= complexity) - needs to be defined or dropped
Back to Message 25
Changes to allele frequencies and some minor mutations can cause phyletic speciation and divergent evolution without the need for new coding ...
You keep saying this, but I don't think you really understand the process of evolution, so we should go into this in more detail:
Would you AGREE or DISAGREE that selection mechanisms only operate on the existing mixture of alleles\traits\features within the breeding populations and does not cause novel genes\features\functions\traits?
Would you AGREE or DISAGREE that any change to the genetic sequences is a mutation?
From Message 24:
... Remember that evolution is a two-step feedback response system that is repeated in each generation:
Like walking on first one foot and then the next. To get any great distance you need to use both feet.
Mutations and mixing existing hereditary traits in different combinations (ie for eye color) can cause changes in the composition of hereditary traits for individuals in a breeding population. Not all mutations cause hereditary change (many are in non-hereditary areas or are neutral to selection). In addition there are many different kinds of mutations and they have different effects (from small to large), especially if they affect the developmental process of an organism.
Random mutations and sexual trait mixing affect the genotype, and any changes are subject to possible selection when they are expressed in the phenotype.
Does not any mutation create a genetic sequence that was not in the parent population?
Enjoy.
Edited by RAZD, : rearranged
Edited by RAZD, : ...

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 25 by mindspawn, posted 01-30-2013 5:19 AM mindspawn has replied

Replies to this message:
 Message 29 by mindspawn, posted 01-31-2013 2:53 AM RAZD has replied

  
RAZD
Member (Idle past 1432 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 28 of 65 (689459)
01-30-2013 8:37 PM
Reply to: Message 26 by mindspawn
01-30-2013 6:01 AM


Re: Nested Hierarchies and Macroevolution
See Message 27
Edited by RAZD, : ..

This message is a reply to:
 Message 26 by mindspawn, posted 01-30-2013 6:01 AM mindspawn has not replied

  
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