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

"... 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
   http://evolution.berkeley.edu/evosite/evo101/IIntro.shtml
   
2. U. of Michigan on-line course material
   http://www.globalchange.umich.edu/...ciation/speciation.html

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.

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Message 2 of 65 (688657) 01-23-2013 2:34 PM

Reply to: Message 1 by RAZD 01-23-2013 10:50 AM

1. The thread's title should identify a specific topic.

2. The participants names should be spelled properly in the thread's title.

3. The opening post should delineate the topic more clearly than just in effect, "Continuation of something Mindspawn and I started discussing somewhere else."

Message 3 of 65 (688658) 01-23-2013 8:54 PM

Reply to: Message 2 by Admin 01-23-2013 2:34 PM

Background

This started on Flood Geology: A Thread For Portillo when midspawn posted Message 497 with this comment:

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:

Mea Culpa, as this started several off-topic comments.

Edited by RAZD, : link

Message 4 of 65 (688659) 01-24-2013 6:54 AM

Reply to: Message 1 by RAZD 01-23-2013 10:50 AM

Maybe you meant, "A scientific theory begins as an untested scientific hypothesis..."?

Message 7 of 65 (688666) 01-24-2013 11:19 AM

Reply to: Message 1 by RAZD 01-23-2013 10:50 AM

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 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 personally think the discussion would then lead too much into semantics, completely missing my real point. I don't dispute many processes of evolution that can lead to macro-evolution , myself being a great believer in variation and natural selection. (lol I am officially an evolutionist according to your definition). 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?

Without evidence of this process, evolution as an explanation for the existence of many complex life forms that contain many novel functional coding genes is just an hypothesis. Sure evolution can explain some macro-evolutionary changes , but not the existence of complex life-forms which is the essence of the creation/evolution debate.

Edited by mindspawn, : No reason given.

Message 8 of 65 (688714) 01-24-2013 6:12 PM

Reply to: Message 7 by mindspawn 01-24-2013 11:19 AM

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.

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.

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").

Again, here we still need to define what we mean by novel and what we mean by complexity and fitness.

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.

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Message 9 of 65 (688751) 01-25-2013 3:09 AM

Reply to: Message 8 by RAZD 01-24-2013 6:12 PM

I agree, no dispute there. Variation is already visible each generation.

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. if you stick to this definition, then my original dispute stands. I believe there is insufficient support that processes of evolution can explain the current diversity of life. Based specifically on novel genes, I do believe novel features, and novel functions can be explained by evolutionary processes, but not the increasing number of new novel functional coding genes that are apparently "evolved". Evolutionary processes do not explain the full DNA as observed in species.

No problem with this. I agree on divergent speciation. The observed processes of divergent speciation are sufficient to explain some diversity and some macro-evolution, yet insufficient to explain some aspects of DNA observed in most modern species (the so-called increases in the number of functional novel unique coding genes that add fitness to organisms). Thus new species are observed, yet important aspects of the genetic complexity that is the essence of the more complex modern fauna remains unexplained.

I feel we have sufficient consesus on a-d, g I'm not anticipating a problem with h

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.

Edited by mindspawn, : No reason given.

Message 10 of 65 (688770) 01-25-2013 10:32 AM

Reply to: Message 9 by mindspawn 01-25-2013 3:09 AM

Excellent.

(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:

This keeps the reference numbers/letters in view.

So we have some issue with e: novel features\functions\traits

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.

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

Message 11 of 65 (688805) 01-25-2013 2:22 PM

Reply to: Message 10 by RAZD 01-25-2013 10:32 AM

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. I am focussing on just ONE aspect of complexity (novel genes) but the fact that this ONE aspect is observed in every organism above the very simplest, makes evidence for it essential if the theory of evolution is able to stand. Can evolution actually explain all of the relative complexity actually observed in most modern life-forms?

So complexity relates to the evolutionary process of organisms gaining productive novel genes over time, a process essential to evolution as a theory explaining modern life. This is what I wish to debate. If you wish to avoid the word "complexity" and stick to discussing genes, I'm fine with that.

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)

Agreed

Edited by mindspawn, : No reason given.

Message 12 of 65 (688931) 01-26-2013 6:21 PM

Reply to: Message 11 by mindspawn 01-25-2013 2:22 PM

Excellent, so now we have agreement on all but complexity and novelty:

And I would say that 75% agreement at this early stage of this thread is a good sign.

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:

http://www.genomenewsnetwork.org/..._01/Sizing_genomes.shtml

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.

Doesn't appear to inhibit A. dubia or affect its fitness to its ecology.

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 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.

Yes, the production of novel genes is the issue, not complexity, per se.

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

So now we can go back to novelty:

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

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Message 13 of 65 (688990) 01-27-2013 3:47 AM

Reply to: Message 12 by RAZD 01-26-2013 6:21 PM

Early stage? lol we could be nearly finished by now

Agreed about complexity

God made them all different. If you could prove the "regaining" part you have already won this debate. Can you prove the regained" portion of genes was actually from a population that never had them in any form already? Were they just dormant genes ? Inactivated genes that were already there?
This is the essence of this debate, the ability of nature to create genes with unique functions out of nothing, 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.

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.

yes, but remember I am not merely discussing novel genes. 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?

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, merely through new allele frequencies. 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.

Thus I believe new functions can be created outside of novel gene sequences, 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.

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.

Edited by mindspawn, : No reason given.

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Edited by mindspawn, : Removing redundancy regarding complexity

Message 14 of 65 (689010) 01-27-2013 12:34 PM

Reply to: Message 13 by mindspawn 01-27-2013 3:47 AM

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.

And all we have left for finding consensus is novelty.

Yes, I don't expect the discussion of novelty to be this brief, in part because misunderstanding evolution is still apparent.

Enjoy.

Message 15 of 65 (689012) 01-27-2013 12:46 PM

Reply to: Message 13 by mindspawn 01-27-2013 3:47 AM

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?

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.

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.

So I move to strike the god hypothesis from this debate, and stick to science and natural explanations:

So now we can again go back to novelty.

Enjoy.

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