Evolution: the Facts.

[Kotatsu]

I apologise in advance for any disorderliness in the following post. I seem to have eaten something that doesn't agree with me, and have been running back and forth to the little boys' room to throw up while writing it.

It does change it completely. Evos claimed pseudogenes not being functional but appearing among certain groupings of species thought to have a common ancestor was "very strong evidence" for evolution. They had been told they were overstating their case. Their idea is that since the genes were not functional, similar function cannot explain similar design (similar genes) but that ONLY common ancestry could explain the appearance of homologous pseudogenes.

That is merely a repetition of your earlier point, without any attempt to actually explain it. I contend that you are wrong, and that it makes absolutely no difference for the theory of evolution whether or not we know that a gene is functional or not.

Evolutionary theory predicts changes in a given section of a DNA sequence over time regardless of if that section is used for coding a protein, is structural, or is actually just nonsense. Whether or not we know which of these (or any other categories) a given section falls into at the time they are being compared does not factor in at any point whatsoever (however, as I have stated before, if a certain gene region is known to be protein-coding and thus expected to evolve slower than a structural gene, it may not be chosen for comparison in the first place if the study undertaken requires evolution of a higher speed to test its hypotheses).

What you are claiming is that if a phylogeny is published based on what is believed to be a non-functional section of DNA, and this section is later found to have a function, the data and result of that phylogenetic study is no longer valid as evidence for the structuring within and common descent of the taxon studied. I will grant you that if the section in question is found to have a vastly different speed of evolution than previously thought, there may be problems with, e.g., long-branch attraction, however these will typically be picked up during the initial analysis, and will typically disappear in comparisons with other genes (I have this exact scenario in one of the data sets I am working on at the moment).

However, if this is the case -- and we discount long-branch attraction and similar for the sake of simplicity -- the only difference between the utility of the DNA section before and after its revelation as functional is the type of questions subsequent researchers would use this particular DNA section to try to answer. It does in no way whatsoever nullify its previous status as evidence for the obtained internal structures and hypotheses of descent. It remains the case that common ancestry and common descent is the only known robust theory for explaining the obtained pattern. It certainly does not in any way discredit or discount the initial findings.

Since we know that different groups of animals use different methods to solve the same problem on an organ level, there is no reason a priori to assume that the same does not hold true on a molecular level. Therefore, we have no reason to believe that similar function, understood as similar sequence, on a molecular level is evidence of anything other than common descent, unless other data makes this less likely.

On the phylogeny, I am talking about the overall pattern so we're talking all of them.

So if I suggest a sample of randomly chosen phylogenies from the last 10 years or so covering a random sample of animals, you will be able to show me that it contains groupings of species that would not be predicted by the theory of evolution? If so, I could provide you with a list of phylogenies tomorrow and you would have as much time as you require to look them over and present your case.

It's not a point original I have thought of. If you look at the pattern and assume common descent, it suggests a couple of things; first a process that has largely ended

This is true inasmuch as for the studied individuals, the process of evolution has ended, as they are typically dead. We have a few dozen fridges filled with biological samples from a range of vertebrate and invertebrate taxa here at my institute, and apart from the birds, of which only a few feathers are typically stored, it is true that for the individuals actually used in a phylogeny, evolution has ended. These individuals will never again contribute to evolution in any way.

It is also true to the extent that we can only use material that exists today. therefore, all phylogenies stretches only up until the date of collection for the oldest included specimen in any given clade. I collected my first clitellates in 2005, for instance, so when my latest paper on the group was published in 2009, I could only claim to have tracked the evolution of that particular group of clitellates until 2005 (well, I used some earlier material as well, so I think it is actually 2004). We cannot extrapolate into the future beyond the point of collection, and thus we are essentially looking at a process that has ended. This does not suggest, however, that the process has ended outside the laboratory.

second, evolution seeming to occur via a pulse and burst of groupings of creatures that remain largely in stasis or go extinct but evolve around a range; the common ancestor that began each of these bursts is conspiciously absent;

This is necessarily true inasmuch as these ancestors typically are not available for DNA extraction and sequencing. It does not hold true for phylogenies based on morphology or ones that actually do include so-celled "ancient DNA", such as sequences from moas and the Great Auk.

However, the way a phylogeny is usually presented could easily give the uninitiated exactly the impression you outline. This suggests exactly one thing: that any observer needs to understand how to read a tree and what the various features of a tree represent before attempting to comment on it. For a beginner like yourself, it is often easier to start with trees that do character tracking, as these will often comment on likely traits of organisms at ancestral nodes, and therefore the process of visualising, e.g., morphological change throughout a tree is easier.

a repetition of forms such as with placentals and marsupials suggesting the pattern was in some sense preformed in DNA; etc,....

Naturally some aspects of the DNA of extant marsupials and mammals were present in the DNA of their common ancestors.

It doesn't look like an unguided process.

Could you elaborate? I cannot see how a phylogeny could look like anything but an unguided process.

We haven't seen a new phyla, for example, in what 500 million years or something like that?

We have most likely not found all phyla. At least three new extant phyla have been found within my lifetime; I have no idea if there have been any discoveries of phyla that are only known from the fossil record within this time.

How long for the other taxa? Say a new kingdom in what? even longer, right?

Well, this betrays a fundamental lack of knowledge with what a taxon actually is. These limits between phyla and other taxonomic units are arbitrary distinctions, which correspond to certain basic bauplans found in nature, but which could theoretically be subdivided further. Nothing is stopping you from redefining the phylum concept so that all groups that diverged between 70-65 million years ago are separate phyla. The lack of descriptions on phylum level of taxa which diverged more recently than 500 million years ago or so has more to do with conservatism in the biological community than any feature of evolution or evolutionary theory.

New family?New genus? New species?

Examples of families, genera and species which have evolved more recently than 500 million years ago are, I think you will find, plentiful. You're holding this discussion with one, for instance.

Hopefully you get the picture? Why have bacteria with such a remarkable adaptive and mutation rate not evolved something else in the past billion years?

Why should they? There is nothing in evolutionary theory that obliges them to, so for a more serious answer to your question, you will have to ask someone who subscribes to a distinctly different theory in which they would be.

They are one of the most stable forms around. Micrevolution happens all the time there but never adds up to macroevolution.

Please provide evidence for the claim that microevolution never adds up to macroevolution.

The mammalian ear is thought to have evolved independently among mammals, not that the common ancestor of mammals had a mammalian ear.

Do you have a reference for this claim?

Take some time to look at the different "pairs' between placentals and mammals. The Darwinian answer is that a random process still produced these pairs because of environmental pressures. That's ridiculous. What environmental pressures duplicated the mammalian ear, for example.

The fact that predators, when moving on old leaves, produce sound? The fact that many prey species, when moving in similar terrain, also produce sounds? The fact that it is detrimental to the survival of the species if none of them can hear warning sounds? The need for heat regulation?

If you, by "pairs", are talking about gross morphology in comparison between placentals and mammals, then I can think of a range of environmental pressures that could modify a given common ancestor. Assuming that Australian and Eurasian soils are sufficiently similar, similar solutions and adaptation to living underneath it would likely evolve, such as strong front paws, partial or entire loss of sight, a heightened sense of smell and perhaps tactile and chemo-sensory senses, a diet of roots, tubers, seeds, insect larvae, worms, and other kinds of food available in a subterranean environment (with the necessary changes in tooth and jaw structure and intestinal morphology, if needed). This could -- and did -- result in similar groups of animals which meet the requirements of a subterranean life in similar ways.

 

[randman]

The mammalian ear is thought to have evolved independently among mammals, not that the common ancestor of mammals had a mammalian ear.

Citations and evidence that this statement was made?

Take some time to look at the different "pairs' between placentals and mammals. The Darwinian answer is that a random process still produced these pairs because of environmental pressures.

Which paris and who says what where, cite your sources, please.

That's ridiculous. What environmental pressures duplicated the mammalian ear, for example.

What claim do you think you are making, who said that the proto mammals did not have ears that led to later ears?
What claim are you trying to state?

A more likely scenario, if one assumes common descent in the first place, would be that these forms were in some sense already programmed into the DNA of the theoritical common ancestor; in other words, it's the DNA that drove the emergence of very similar "pairs", not environmental pressures.

Or that the ears already existed, what is your data for these statements? That mammalian ears arose independantly?
Common ancestor has ears, yes or no?

So you are unfamiliar with the data and arguments? Ok, some reading for you to get up to speed.

http://www.sciencemag.org/content/307/5711/861.summary

http://www.sciencemag.org/content/307/5711/910.abstract

http://www.uncommondescent.com/evolution/a-prescribed-evolutionary-hypothesis/
http://www.uncommondescent.com/evolution/a-prescribed-evolutionary-hypothesis/

 

[randman]

That is merely a repetition of your earlier point, without any attempt to actually explain it. I contend that you are wrong, and that it makes absolutely no difference for the theory of evolution whether or not we know that a gene is functional or not.

I keep repeating the point because you fail to get it. My point is that evolutionists said that pseudogenes were particularly strong evidence, and now they cannot use that as evidence. It sounds like you don't know why evolutionary biologists made these claims and don't want to learn either.

Functional DNA as evidence is a separate matter.

Got it now?

If you get that basic point, it might be worth delving into the rest of your post but you cannot seem to get past arguments about evo's use of data and whether they were right and more fundamental arguments about evolution.

It may well be finding that so-caleld junk DNA is functional is not the death-knoll for darwinism, but that doesn't change the fact Darwinist insisted IDers, creationists and others were wrong on this issue when in fact they were right and Darwinists wrong.

ID and related scenarios have often been more predictive of results than Darwinism, hence better models.

 

[randman]

Examples of families, genera and species which have evolved more recently than 500 million years ago are, I think you will find, plentiful. You're holding this discussion with one, for instance.

Not what I said. Phyla that have emerged in the past 500 million years give or take 50 say, and then look at the time periods for the last example of a taxa to emerge. A picture is formed. Evolution, if it happened, appears to be dead now.

We have most likely not found all phyla. At least three new extant phyla have been found within my lifetime; I have no idea if there have been any discoveries of phyla that are only known from the fossil record within this time.

So you think if we find some new phyla, it might have evolved, say, 10 million years ago? or 100 million years ago?

If not, why not?
Why should they? There is nothing in evolutionary theory that obliges them to,

Then maybe you guys should quit using them as examples of evolution in action which is my point and was Pierre Grasse's.

 

[Paulhoff]

For people who can think.......



Paul

 

[Wowbagger]

wowbagger, first natural selection is generally a conservative process counter to the origin of higher taxa.

That seems wrong. Natural selection is conservative, but only in as much as it generally selects the least radical or "expensive" changes, in the process of replication and survival of the genes.

I don't know what "counter to the origin of higher taxa" means. I have not heard those words coming out of any evolutionary biologists that I know. I suspect it is a Creationist invention, but I could be wrong. Can you explain that phrase better?

Second, people speak of and yes the most prominent evos even like Watson and Wilson of "random mutations" because it's a huge part of NeoDarwinian theory.

I did not say random mutations were not important. Only that they are one factor in genetic change. But, those mutations, as you might guess are not sufficient, either. That is why everything else gets studied besides them.

The idea of mutations conferring new traits

Mutations do not confer new traits - at least they are not likely to. My point is that the full process of natural selection is where such adaptation actually develops. Study the process and you study how new traits develop.

To claim evolution is faulty because changes do not seem to be driven by random mutations is to completely misunderstand the process.

By the way, what role, exactly, does the Creator or Intelligent Designer play in all of this?

That's standard evolutionary theory.

Standard evolutionary theory is the change of allele frequency over time, based on selection pressures faced. What part of that core theory is wrong? Why would discoveries about the role of random mutations change that?

The easiest way to illustrate this is to consider dog breeding. We can breed and produce an incredible level of complexity with this one species, really a subspecies since dogs can mate with wolves, but the further we evolve a breed, the less it can evolve further.

This is correct! And, a point I would like to emphasize is that you are NOT debunking the natural process of evolution by stating this. You are, in fact, indirectly arguing a good reason for the study of evolution:

By admitting that evolutionary opportunities get more limited into the future, you are conceding the point that they become less limited as you go into the past.

You are, (perhaps accidentally), implying that if you go back far enough, there was enough variety for earlier life forms to evolve into later ones: (Dinosaurs into birds, for example; or primitive apes into humans.)

This is exactly what current evolutionary theory tells us! You just clinched our argument!!

The only way out of it, now, is to find where the I.D. had to intervene.

Evos have never done any peer-reviewed studies to back up their claims that microevolutionary processes like this result in a greater rate of addition of novel genes than the rate of loss. They insist it is so as a matter of faith.

Therefore, it's not real science.

Oh yes they have. Here is one early example:

In experiments with bacteria, variation (including beneficial mutations) arises in populations that are grown from a single individual (Lederberg and Lederberg 1952). Since the population started with just one chromosome, there was no variation in the original population; all variation must have come from mutations.

(Lederberg, J. and E. M. Lederberg, 1952. Replica plating and indirect selection of bacterial mutants. Journal of Bacteriology 63: 399-406.)​

Taken from: http://www.talkorigins.org/indexcc/CB/CB110.html


Evos have done lots of peer-reviewed studies to back up their more important claims that genes change over time, through natural processes. Evos do not need an Intelligent Designer to do this. In fact, not even I.D. proponents have told us anything about the Designer, yet.

Therefore, Evolution is real science, and I.D. is not.

 

[randman]

I don't know what "counter to the origin of higher taxa" means.

Just means what it says and was pointed out by biologists a long time ago. The higher taxa need a process that increases an organisms ability to evolve further by adding genetic variability and novel genes sufficient for that to happen. You can evolve wolves into dogs into dog breeds but what is actually happening is a decrease of genetic variability within the populations, hence limiting their ability to evolve into a higher taxa, say a new Order, Family or likely even genus and maybe even species.

Mutations do not confer new traits - at least they are not likely to.

I agree that it's not likely but that's what evos posit as the means of evolving novel genes to encode for new traits. When you add the "process", the picture is even bleaker for evos as if the population is large, the mutation will not spread (something admitted to by evos), and if you have subgroups such as via inbreeding in geographically isolated populations, you lose genes through the process of being isolated from the parent group.

Standard evolutionary theory is the change of allele frequency over time, based on selection pressures faced. What part of that core theory is wrong?

See my comments above.

By admitting that evolutionary opportunities get more limited into the future, you are conceding the point that they become less limited as you go into the past.

That's a very interesting admission on your part. Will you stand by it? It would explain why we don't see new kingdoms, phyla, orders, families, genera, and maybe not even new species but just subspecies, and perhaps none will evolve further.

This is, of course, a prediction and claim of front loaders but not evos in general. You have stumbled onto one of the weaknesses of evo theory.

The other alternative is common descent never happened, but if it did (macroevolution), it seems to have stalled out long ago. Darwinism, however, cannot be true and the process stalling out because Darwinism posits a mechanism still in effect.

You admit, however, the mechanism limits in the future more evolution. That's my point.
Oh yes they have. Here is one early example:

In experiments with bacteria, variation (including beneficial mutations) arises in populations that are grown from a single individual (Lederberg and Lederberg 1952). Since the population started with just one chromosome, there was no variation in the original population; all variation must have come from mutations.

(Lederberg, J. and E. M. Lederberg, 1952. Replica plating and indirect selection of bacterial mutants. Journal of Bacteriology 63: 399-406.)

How does that in any way relate to my point?

Evos have done lots of peer-reviewed studies to back up their more important claims that genes change over time, through natural processes.

So what? That does not mean squat here. Genes are said to remain in populations through natural selection acting on new traits. This is a process of decreasing genetic variability as my dog example illustrates. Evos have never compared and quantified expected losses of through natural selection and population isolation with expected mutation rates to verify the claim that mutation rates are sufficient to overcome the loss of genes via population isolation.

If you disagree, show me the peer-reviewed study that does that?

Been asking that question for years. Never had an evo provide the study because it doesn't exist. It's a fairy-tale, an assumption which MUST BE so for evos because without it, their whole theory falls apart.

Moreover, you said yourself mutations are not likely to confer beneficial traits. I am actually given evos some leeway and saying assume that somehow some do. At what rate then compared to the loss of genes through sexual and geographic isolation? Let's stick to sexually reproducing organisms as that makes the discussion a little easier.

I'll be waiting for the study.

 

[Dancing David]

wowbagger, first natural selection is generally a conservative process counter to the origin of higher taxa.

Nice rhetorical statement, there are lots of means of natural selection, so what do you think you are talking about?

Second, people speak of and yes the most prominent evos even like Watson and Wilson of "random mutations" because it's a huge part of NeoDarwinian theory.

But it is not all there is, there are other forms of variation, and even with mutation it may effect an already developed trait, so it may be a mutation of an existing trait.

So give an example to discuss.

The idea is that mutations are necessary to add and change the genome, that genetic drift and variation alone is not sufficient, and that these mutations are not guided, directed or anything like that but are "random" within the context of potential mutations that could occur.

In soem cases mutation is more changing than others, but there is a lot of variation within genomes as well.

So who said these things?

That's standard evolutionary theory.

According to whom, no one said that mutationw as all there was, now did they?

There are a lot of problems with that, of course. The idea of mutations conferring new traits that are selected via natural selection suggests new genes emerge in conjunction with new traits over time. One would expect then for the earliest and simpler life forms to have the simplest genomes, but at least as far as molecular data and analysis indicates, the last common ancestor to animals and the LCA to plants and animals are now considered to have been incredibly complex genetically.

Citation, evidence and examples?

What exactly are you thinking about the last common ancestor to plants and animals is most likely something like fungi, or another eukaryote, so define complexity?

So what are you definitions of complex?

So the narrative didn't quite work out.

Whose narrative? Citation?

Another significant objection I noted above which is that microevolutionary processes are evolution in the wrong direction. The easiest way to illustrate this is to consider dog breeding. We can breed and produce an incredible level of complexity with this one species, really a subspecies since dogs can mate with wolves, but the further we evolve a breed, the less it can evolve further.

Citations and evidence, dogs are all the same species.

The primary way evolution is envisioned to occur is that small groups are isolated and evolve.

Nope, try again, who said that where?


I notice that all you do is assert some rhetorical arguments, no citations just a bunch of straw and more straw.

 

[Dancing David]

Just means what it says and was pointed out by biologists a long time ago.

Relevance, citations and data, what is protein folding Randman?

 

[Wowbagger]

The higher taxa need a process that increases an organisms ability to evolve further by adding genetic variability and novel genes sufficient for that to happen.

But, that is not true. Organisms only need enough genetic variability to survive changing selection forces. The drive towards more complexity is a trend, not a necessity. You seem to have those two concepts confused.

I agree that it's not likely but that's what evos posit as the means of evolving novel genes to encode for new traits.

No they do not. They posit mutation as a means of gaining genetic variety. That is an important distinction, and one that is important to understand. But, I know it is difficult to grasp: As I said, not even many evo fans get it right.

Videos and diagrams are often useful for demonstrating the process. Here is one video I like, if you have time to watch it: http://www.youtube.com/watch?v=mcAq9bmCeR0
It describes how a simulation of the process can generate the traits necessary to create a working watch.

The random mutations only provide variety. The selection process is what builds the watches. You can ask further questions if there is anything you still do not understand.

When you add the "process", the picture is even bleaker for evos as if the population is large, the mutation will not spread (something admitted to by evos), and if you have subgroups such as via inbreeding in geographically isolated populations, you lose genes through the process of being isolated from the parent group.

The process is not perfect, you mean?

That is hardly debunking its existence nor its overall power. Why would we expect anything better from a natural process?

That's a very interesting admission on your part. Will you stand by it? It would explain why we don't see new kingdoms, phyla, orders, families, genera, and maybe not even new species but just subspecies, and perhaps none will evolve further.

My "admission", if you will notice, implies an evolutionary process took place. It does NOT imply an Intelligence was needed.

You are the one who keeps trying to imply that an Intelligence is needed. And, yet, you cannot tell us how or why or who or what. Not even in the form of a testable hypothesis.

You even admitted, to a certain degree, that an evolutionary process took place: Your statements implied that it gets more limited over time. If an Intelligence was really necessary, what role would it play in the process?!

This is, of course, a prediction and claim of front loaders but not evos in general. You have stumbled onto one of the weaknesses of evo theory.

If that is the case, then how come the empirical facts about it were discovered by evos, and not by front-loaders?

How come evos developed all of the nitty-gritty observational and mathematical facts surrounding limitations in the scope of evolutionary variety? How come their works more-precisely predicted the outcomes of experimentation in these directions?

Not even today, now that we have the details, can the concept Front-Loading be used as a framework for finding out more details about life. It does not make any precision predictions about life, the way evolutionary frameworks do.

Even if they did make such a prediction, it does not imply what role a Designer would need to play. The Designer remains a superfluous entity, even in the "strongest" if I.D. arguments. Isn't that weird?!

How does that in any way relate to my point?

You claimed "Evos have never done any peer-reviewed studies to back up their claims that microevolutionary processes like this result in a greater rate of addition of novel genes than the rate of loss..."

So, I cited an early peer-reviewed study showing an example of how a microevolutionary processes can result in a greater rate of additional or novel genes than a rate of loss. In this case, the generation of new genes in a species of bacteria.

Evos have never compared and quantified expected losses of through natural selection and population isolation with expected mutation rates to verify the claim that mutation rates are sufficient to overcome the loss of genes via population isolation.

The study of "pseudogenization" goes into some of the specifics about this.

Here are is an example of a paper that show how a proper understanding of genetic loss and gains can help us understand more about specific details about life. The loss of teeth in whales inferred a genetic advantage, and this paper examined how that happened:
http://rspb.royalsocietypublishing.org/content/278/1708/993

More generally, there is the widely studied concept of extinction. Many of the details about how and why extinction occurs rest on discoveries made about rates of gene loss over gains.

I remind you that everything we are discussing, so far, is about how genes change over time: Therefore in the realm of natural evolution. Not about what the Intelligent Designer needed to do. You will need to do more than deny the existence of evolutionary forces to get out of that. You still have to answer to my type of challenge, if I.D. is going to be taken seriously as a science:

What does an Intelligent Designer add to the equation?!!

I'll be waiting for the study.

Here are a few random papers describing specific genes in the evolution of the eye, for example:
http://www.ncbi.nlm.nih.gov/pubmed/15950457
http://genome.cshlp.org/content/14/8/1555.full
http://rstb.royalsocietypublishing.org/content/364/1531/2819.full

Here are few describing specific genes involved in flight, to name another example:
http://www.ncbi.nlm.nih.gov/pubmed/20421465 (bats)
http://www.nature.com/nature/journal/v375/n6526/abs/375058a0.html (insects)
http://physiologyonline.physiology.org/content/14/3/87.full (insects, integrates genes with other factors)
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003325 (birds, in relation to alligators of all things)

There are not mere "just so" stories. We know enough about these processes, that we can name specific names, and point to specific genes. Front-Loaders, despite their claims, would never be able to do that!

 

[Dinwar]

Moreover, you said yourself mutations are not likely to confer beneficial traits. I am actually given evos some leeway and saying assume that somehow some do. At what rate then compared to the loss of genes through sexual and geographic isolation? Let's stick to sexually reproducing organisms as that makes the discussion a little easier.

You are obsessed with the loss of genes. Evolution discusses the frequency of traits (including genes). The loss of a trait does not equal the loss of a gene--my line could easily loose blond hair by switching from a blond allele to a brunette allele, and the number (and even type) of genes would be the exact same. When you care to acknowledge that point you may have something interesting to say about evolution; until then you are attacking straw men.

By the way, the eye is in those books I referenced. Still haven't read them, I see. And you have the audacity to call US ignorant.

 

[randman]

The drive towards more complexity is a trend, not a necessity.

Ok, so you admit there should be a trend towards more complexity (genetic complexity), right?

The random mutations only provide variety. The selection process is what builds the watches.

I understand that. But that doesn't explain how the loss of genes via subgroup isolation compared to rates of proposed beneficial or surviving mutations.

If that is the case, then how come the empirical facts about it were discovered by evos, and not by front-loaders?

This is demonstrably false and shows a lack of understanding of the history evolutionary discoveries. But in general, evos will do more studies than others because there are more of them and they control and limit the agenda to crowd out their critics. Just look at what happened with one of the first ID papers at the Smithsonian. He got fired over it but more have come out, and during the 20th century, non-Darwinian scientists did a ton of research and published their findings.

How come evos developed all of the nitty-gritty observational and mathematical facts surrounding limitations in the scope of evolutionary variety? How come their works more-precisely predicted the outcomes of experimentation in these directions?

They didn't. You just aren't aware of the history of evolutionary science and thought. As far as ID paradigms, you can go to the Discovery Institute site and read papers explaining how ID including front loading paradigms are more predictive and useful in a lot of areas.

You claimed "Evos have never done any peer-reviewed studies to back up their claims that microevolutionary processes like this result in a greater rate of addition of novel genes than the rate of loss..."

So, I cited an early peer-reviewed study showing an example of how a microevolutionary processes can result in a greater rate of additional or novel genes than a rate of loss. In this case, the generation of new genes in a species of bacteria.

Show where the paper does that? I don't think you understand the question. It's not whether mutations can add beneficial genes, it's the issue of the loss of genes through subgroup isolation.

This same point goes for the papers you cited.

I remind you that everything we are discussing, so far, is about how genes change over time:

But that's not everything we are discussing. That's the point. Genes changing over time doesn't address the issue by itself.

 

[Wowbagger]

You are obsessed with the loss of genes.

There are worse things to be obsessed about, you know.

What I find amusing is his obsession with Front-Loading: The implication that an Intelligent Designer was necesary, without telling us the need for an Intelligent Designer.

Go figure that one out!

 

[Sideroxylon]

They didn't. You just aren't aware of the history of evolutionary science and thought. As far as ID paradigms, you can go to the Discovery Institute site and read papers explaining how ID including front loading paradigms are more predictive and useful in a lot of areas.

Could you please give some examples here?

 

[Dancing David]

So you are unfamiliar with the data and arguments? Ok, some reading for you to get up to speed.

http://www.sciencemag.org/content/307/5711/861.summary

http://www.sciencemag.org/content/307/5711/910.abstract

http://www.uncommondescent.com/evolution/a-prescribed-evolutionary-hypothesis/
http://www.uncommondescent.com/evolution/a-prescribed-evolutionary-hypothesis/

Thanks, I am familiar with the ToE, you are propsing the aletrnative, so thank you.

 

[Paulhoff]

You can evolve wolves into dogs into dog breeds but what is actually happening is a decrease of genetic variability within the populations, hence limiting their ability to evolve into a higher taxa, say a new Order, Family or likely even genus and maybe even species.

You can limit the genes within a population with breeding, but that do not mean that is what happens in the wild.

Paul

 

[Dinwar]

Ok, so you admit there should be a trend towards more complexity (genetic complexity), right?

Nope. This is what we see--it could very easily have not been so.

I understand that. But that doesn't explain how the loss of genes via subgroup isolation compared to rates of proposed beneficial or surviving mutations.

Flawed premise (that loss of genes is somehow of prime importance).

They didn't. You just aren't aware of the history of evolutionary science and thought.

Says the one who can't be bothered to even learn that history himself.

Show where the paper does that? I don't think you understand the question. It's not whether mutations can add beneficial genes, it's the issue of the loss of genes through subgroup isolation.

An issue you've blown out of all proportions.

But that's not everything we are discussing. That's the point. Genes changing over time doesn't address the issue by itself.

Again, this is evolution. Evolution deals with genes through time.

As far as ID paradigms, you can go to the Discovery Institute site and read papers explaining how ID including front loading paradigms are more predictive and useful in a lot of areas.

If you consider the DiscoTute to be a legitimate source it's no wonder you've been seduced by fringe lunatics.

By the way, have you provided any evidence of fraud yet? Or have you appologized? Because you really need to do one or the other after making accusations of fraud.

Wowbagger: I agree. However, it's impossible to talk about evolution with randman because he insists on discussing the addition and subtraction of genes. He equivocates constantly between accumulation of genetic changes and accumulations of genes, despite people trying to correcting him for several pages. Because he refuses to accept even basic definitions conversation more or less shuts down immediately. If he fixed this problem we may be able to actually begin having a serious conversation (though his citation of the DiscoTute makes me doubt that).

 

[randman]

Let's try to clear up some misconceptions one by one before we move on. First on how evos envision evolution occurring.

The primary way evolution is envisioned to occur is that small groups are isolated and evolve.

Nope, try again, who said that where?

Hardy, Weinberge and population geneticists are the ones saying this.

Hardy, Weinberg, and the population geneticists who followed them came to understand that evolution will not occur in a population if seven conditions are met:

1. mutation is not occurring
2. natural selection is not occurring
3. the population is infinitely large
4. all members of the population breed
5. all mating is totally random
6. everyone produces the same number of offspring
7. there is no migration in or out of the population

http://anthro.palomar.edu/synthetic/synth_2.htm

I think the use of the word "infinitely" is a bit ridiculous, but they did it illustrate the math. Nevertheless, you can see via the bolded parts what they are getting at. There has to be some migration (subgrouping; there cannot be mating across the whole population, etc,....I don't really like the word "random" there but what they are getting at is there must be either geographic or sexual isolation of a subgroup for evolution to occur. Otherwise, the mutation would be washed out in the larger population.

And yes, there is variation, etc,....The main point and what population genetics show is that mutations would be washed out unless they occur in a small, isolated sub-group.

Here's a wiki article that you may find useful.

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

Edit add: this should help clarify what I am talking about in terms of isolation.

Speciation involves the genetic change in a subgroup of a population that renders the new population incapable of reproducing offspring with the original population. If a reproductive barrier occurs because of isolation by a physical barrier, the isolated population can evolve and develop into a new species. This process is termed allopatric speciation. This has been considered for a long time to be the primary mode of speciation.

Speciation can also occur when a subpopulation migrates into a new niche. This is termed parapatric speciation, and this process seems to have been used by some annual plants.

The final form of speciation is called sympatric speciation. This type of speciation occurs when a subpopulation that occupies the same niche as the remainder of the species develops a unique mutation that prevents it from mating with the original population.

http://www.ndsu.edu/pubweb/~mcclean/plsc431/popgen/popgen6.htm

So can you see where the concept of isolation is critical to the whole foundation of NeoDarwinism since evolution is considered to advance through speciation?

It's really a simple but sometimes overlooked point.

 

[Nonpareil]

Hardy, Weinberge and population geneticists are the ones saying this.

Hardy, Weinberg, and the population geneticists who followed them came to understand that evolution will not occur in a population if seven conditions are met:

1. mutation is not occurring
2. natural selection is not occurring
3. the population is infinitely large
4. all members of the population breed
5. all mating is totally random
6. everyone produces the same number of offspring
7. there is no migration in or out of the population

http://anthro.palomar.edu/synthetic/synth_2.htm

I think the use of the word "infinitely" by the website author's a bit ridiculous, but you can see via the bolded parts what they are getting at.

Which explains why you misunderstood what was being said. The use of "infinitely" is important. Scientists and mathematicians do not say "infinitely" when they mean "really, really big". They say "infinitely" when they mean infinitely - as in, "there is no limit".

So as long as the population size is not infinite, and there is no migration in or out, et cetera, evolution does not occuroccurs. Nowhere in that list does anyone state that evolution only occurs in small, isolated populations. In fact, they are doing quite the opposite from stating where evolution does occur: they are defining the areas where it does not occur.

Beyond that, the area they have defined can exist only theoretically. In short, these men are saying that there is no situation where evolution does not occur.

There has to be some migration (subgrouping; there cannot be mating across the whole population, etc,....I don't really like the word "random" there but what they are getting at is there must be either geographic or sexual isolation of a subgroup for evolution to occur.

No, it isn't. See above.

EDIT:

Edit add: this should help clarify what I am talking about in terms of isolation.

Speciation involves the genetic change in a subgroup of a population that renders the new population incapable of reproducing offspring with the original population. If a reproductive barrier occurs because of isolation by a physical barrier, the isolated population can evolve and develop into a new species. This process is termed allopatric speciation. This has been considered for a long time to be the primary mode of speciation.

Speciation can also occur when a subpopulation migrates into a new niche. This is termed parapatric speciation, and this process seems to have been used by some annual plants.

The final form of speciation is called sympatric speciation. This type of speciation occurs when a subpopulation that occupies the same niche as the remainder of the species develops a unique mutation that prevents it from mating with the original population.

http://www.ndsu.edu/pubweb/~mcclean/...en/popgen6.htm

So can you see where the concept of isolation is critical to the whole foundation of NeoDarwinism since evolution is considered to advance through speciation?

It's really a simple but sometimes overlooked point.

Ah, no, I see what the issue is. You are confusing speciation with evolution. Speciation is something that evolution leads to, not what evolution is.

Hope that helps.

 

[Dinwar]

Which explains why you misunderstood what was being said. The use of "infinitely" is important. Scientists and mathematicians do not say "infinitely" when they mean "really, really big". They say "infinitely" when they mean infinitely - as in, "there is no limit".

Hey, wow, randman! You took a concept that NO ONE BELIEVES CAN HAPPEN and have shown that no one believes it can happen! Therefore, magic.

So as long as the population size is not infinite, and there is no migration in or out, et cetera, evolution does not occur.

So long as any of the assumptions of HWE are violated evolution must occur--it can only NOT occur when the population is in equilibrium. Which means, practically speaking, never. HWE is typically used as a test for why a population is evolving--you can determine which assumption(s) is(are) violated, and thereby make predictions about future evolutionary trends.

As for mutations, if they're neutral it's random. If they're not, it depends. Nothing in HWE says that they'll necessarily be washed out