Evolution: the Facts.

[randman]

I agree that this is generally the case, though need not be the case if subgroup isolation is the result of allopolyploidy, for instance.

However, even an isolated subgroup which has a reduced genetic variation compared to the mother population will be subject to random point mutations and other mechanisms that will serve to increase variation (supposing no extinction occurs) over time. This is called a bottle neck, and is known to have happened in a great many still extant taxa. Why, at least two species in the group of birds I work on (Calidrinae) are known to have gone through bottle necks in recent time (the Dunlin and the Red Knot), but then managed to diverge again. Remarkable, they constitute two of the three Calidrine shorebirds that show sufficient morphological variation even today to be subdivided into subspecies (the third being the Broad-billed Sandpiper.

So maybe you are beginning to see what I am talking about. Bottle-necks are real and likely means of microevolution. However, just because they theoritically diverged again does not mean genetic variability increased. Nor from before the bottleneck to later on well after the bottleneck. Unfortunately, I suspect we have no molecular studies on the birds before the bottleneck? Because that would either be an extinct species, assuming it happened?

So it's a little difficult to test but I would think studies could have been done, say comparing dog breeds or subspeciation (since we may have no real examples of speciation defined in the biological sense except perhaps with plants?).

But instead of doing the studies to see if their claims are true, evos assume the mutation rates add genetic variability faster than subgroup isolation decreases that AS A GENERAL PATTERN, which is necessary under evo theory. In other words, you may have a species that could lose genetic variability and split and evolve a bunch of times before evolution has spent itself out, maybe.

But the process overall will be one of decreasing genetic variability. It's more a breeding concept narrowing the range of potential evolution down and as such, wholly unsuitable for the origin of the higher taxa. It's "a blind alley."

 

[Kotatsu]

Do you admit sequential speciation originating the higher taxa is evo theory aka Neodarwinism?

As the originator of the challenge Sceptic Tank refers to, I claim precedence in answering this question, if that is truly everything that stands between us and the data you have. I hope you will not think this too rude of me, ST, as I intend no slight.

As such, I admit freely that in general, evolutionary theory contains the claim that sequential speciation will, given time, result in lineages that would be classified in different inclusive taxa. I admit freely that evolutionary theory claims that the higher taxa we recognise today have come about because of sequential speciation, and that continued sequential speciation (absent extinction) will continue to do so in the future.

Now that that is sorted out, please go back to the protocol I suggested for the two challenges, and see if they are acceptable to you, or if you want to propose any changes. I am aware that the protocols I suggested may have flaws (a test search of the kind proposed resulted in only two eligible taxa in the first 100 Wikipedia searches, for instance!), and am very open to suggestions for how the test can be made less biased to my point of view.

If you don't understand what evo theory is, we cannot expect to examine whether or not phylogenic groupings are consistent with it, can we?

Yes, we can. All that the test requires is that you list the groupings you believe are not predicted by evolutionary theory and your reasons for this. The challenge depends entirely on your understanding of these matters. If we find that the data we have presented is too complicated for our supposedly limited understanding of evolutionary theory, we could always just send it on to someone who has a greater understanding, or read up on the subject in sources you find would be helpful in this matter. Our current understanding plays no part in this.

So it has a great deal to do with my assertion, and I am going to keep posting this until we either agree or disagree on what evo theory is. Keep in mind I am just posting what evos themselves say Neodarwinism (evo theory aka the Modern Synthesis) say. It's really no use to talk with you on anything but this point as if you don't grasp sequential speciation, you have failed to grasp even the most basic concepts of evolution.

I look forward to your examples tomorrow, as I am off to bed now! Good night!

 

[PixyMisa]

So maybe you are beginning to see what I am talking about. Bottle-necks are real and likely means of microevolution.

They are a factor, not the means, and your use of the term microevolution is disingenuous.

However, just because they theoritically diverged again does not mean genetic variability increased.

Variation, not variability. And yes, if it diverged afterwards then by definition the genetic variation increased.

 

[Dancing David]

When you admit and understand the concept of sequential speciation so we can discuss whether the pattern fits the model.

When you show who stated the model then we can discuss that model.

 

[randman]

I don't understand why you keep mentioning this, as that is nothing I am disputing.

Glad to finally find some here admitting this is the truth of what evos claim. I thought you were one of those saying that was a lie.

The posts are getting too long so not quoting it all. Reversibility would be, for example, creatures that evolved reversing themselves and evolving back to the ancestral forms.

Btw, I am not accusing you of fraud. Unfortunately, I am running out of time here to post. What I am saying is NeoDarwinism makes unsubstantiated claims as if they are fact and asserts them to be near proven, despite not being tested for an unlikely to be true.

The reason to talk of definitions at times is to more precisely define what we are talking of. For example, say one accepts common descent. Does that make him an evolutionist in the sense of accepting evo theory today as accurate.

Pierre Grasse, for example, accepted common descent but called evolution (meaning Neodarwinism) a myth. He cited the fossil record, living biota, irreducible complexity, etc, etc,....just a like a ton of other scientists. Behe accepts common descent but is not considered an evolutionist.

There are some consistent observations among these scientists concerning the data which evos have often ignore.

Macroevolution appears to be a spent process either no longer occurring or at it's tail end.

Macroevolution is not microevolution writ large but that the mechanisms of microevolution appear to work against macroevolution.

That macrevolution as evidenced by things like placental and marsupial pairs and other evidence suggesting is internally driven and perhaps even via preformation (front loading) instead via natural selection, etc,.....It's worth noting mainstream biology is heading in the direction with areas like epigenetics and other concepts that these folks strongly advocated for a very long time.

Consider these quotes from a paper in 2000, though he wrote much the same thing in 1984 as well and cites scientists commenting on the same discoveries prior to the 80s.

I now suggest that just as ontogeny and evolution share
epigenetic features, so also may they share the characteristics we
associate with preformation. In short, I propose that the information
for virtually all of evolution may have been present from very early
in the onset of that process. I realize that this idea may seem
ludicrous at first glance, yet it remains compatible with an enormous
number of otherwise enigmatic observations from comparative biology.
It also avoids postulating Lamarckian devices for which no evidence
has been forthcoming.

....
The unicellular Amoeba is structurally one of the simplest of the
Protozoa, yet in that same phylum can be found creatures exhibiting
strikingly advanced features. One such animal is Diplodinium
(Epidinium) ecaudatum (Figure 1). This ciliate exists in huge
numbers as symbionts in the stomachs of cattle (Sharp 1914). It has
a kind of "brain" (motorium), "circumoesophageal neural connectives"
resembling those of annelids and arthropods, clearly differentiated
"muscles", a kind of "segmented skeleton" (skeletal laminae), a
"mouth", "esophagus", "rectum" and "anus" all elaborated within the
confines of a single cell. Such a creature not only demonstrates
that the information is already present for these structures, but
also casts considerable doubt on the notion that multicellularity
is a prerequisite for the division of labor. It is no wonder that
Libby Hyman described the protozoa as the acellular rather than the
unicellular animals. Why this creature should have such an array of
advanced features remains a complete mystery. Could it be there to
provide us with a clue to the nature of the evolutionary process?

.....
While we associate the placenta with the higher mammals, this
structure also is found in certain sharks. Berg (1969) discussed
this and related phenomena as examples of what he called physiological
acceleration. He noted that Peripatus also nourishes its embryos
with a kind of placenta. Thus Peripatus exhibits characters of three
taxa: the annelids, the arthropods and the placental mammals.

The primitive chordate Amphioxus (Branchiostoma lanceolatus), while
it has all three chordate features (dorsal hollow nervous system, gill
slits and notochord), has a kidney consisting of solenocytes of the
protonephridial (flame cell) type found in the Platyhelminthes, the
Aschelminthes and the polychaete Annelida. On the other hand, certain
oligochaete Annelida (earthworms) have a tubular kidney system more
like that of vertebrates. The limbless amphibia (Apoda) have large
yolk-laden eggs suspended by albuminous chalazae closely resembling
the situation in the cleidoic (shelled) eggs of reptiles and birds.
They lack only the shell. Such bizarre forms as the egg-laying
monotreme mammals (Platypus and Echidna) can suddenly seem acceptable if one simply assumes that those combinations of characters were
available when those forms evolved.

....

Considerations like these and many others prompted
Leo Berg (1969) to conclude: "Evolution is in a great measure an
unfolding of preexisting rudiments."

The same view was independently offered by Pierre Grassé (1973):
"The existence of internal factors affecting evolution has to be
accepted by any objective mind."

http://www.uvm.edu/~jdavison/ontogeny.html

 

[Squeegee Beckenheim]

No, it isn't. The common ancestor is the node where two lineages converge. This is always present, or you wouldn't have a tree. You would have a bunch of parallel lines.

Further, the use of outgroups constrains the ingroup so that the common ancestor of all studied taxa is included in the analysis. This is evident in all published and unpublished trees I have ever seen.

In morphological trees and genetic trees that include character tracking, the specifics of any given common ancestor between two lineages is clearly denoted in the tree or, at least, in the text. In some morphological trees, these internal nodes even have labels attached to them that suggest known taxa that show these characteristics and may therefore be a candidate for the direct ancestor of those lineages.

I just thought this would be an excellent time to remind everybody that randman has claimed that he knows more about phylogeny than Kotatsu does.

I hope you will not think this too rude of me, ST, as I intend no slight.

Not at all. If randman ever does post some evidence to support his assertion, it's your far superior knowledge of the subject in comparison to mine that I will be looking forwards to reading.

 

[randman]

your use of the term microevolution is disingenuous.

Just using that in the same evolutionists like Nile Eldridge and others. Funny how saying the exact same thing as an evo sounds disingenuous to you.

 

[Squeegee Beckenheim]

Glad to finally find some here admitting this is the truth of what evos claim. I thought you were one of those saying that was a lie.

The posts are getting too long so not quoting it all. Reversibility would be, for example, creatures that evolved reversing themselves and evolving back to the ancestral forms.

Btw, I am not accusing you of fraud. Unfortunately, I am running out of time here to post. What I am saying is NeoDarwinism makes unsubstantiated claims as if they are fact and asserts them to be near proven, despite not being tested for an unlikely to be true.

The reason to talk of definitions at times is to more precisely define what we are talking of. For example, say one accepts common descent. Does that make him an evolutionist in the sense of accepting evo theory today as accurate.

Pierre Grasse, for example, accepted common descent but called evolution (meaning Neodarwinism) a myth. He cited the fossil record, living biota, irreducible complexity, etc, etc,....just a like a ton of other scientists. Behe accepts common descent but is not considered an evolutionist.

There are some consistent observations among these scientists concerning the data which evos have often ignore.

Macroevolution appears to be a spent process either no longer occurring or at it's tail end.

Macroevolution is not microevolution writ large but that the mechanisms of microevolution appear to work against macroevolution.

That macrevolution as evidenced by things like placental and marsupial pairs and other evidence suggesting is internally driven and perhaps even via preformation (front loading) instead via natural selection, etc,.....It's worth noting mainstream biology is heading in the direction with areas like epigenetics and other concepts that these folks strongly advocated for a very long time.

Consider these quotes from a paper in 2000, though he wrote much the same thing in 1984 as well and cites scientists commenting on the same discoveries prior to the 80s.



http://www.uvm.edu/~jdavison/ontogeny.html

That's nice.

Now, stop changing the subject, and get down to providing evidence to support your assertion that phylogenic groupings are different to how evolutionary theory would predict them to be.

 

[ehcks]

Just using that in the same evolutionists like Nile Eldridge and others. Funny how saying the exact same thing as an evo sounds disingenuous to you.

Wrongly spelling the name of someone you bring up to make a point is a bad practice. Especially if it's twice.

 

[randman]

That's nice.

Now, stop changing the subject, and get down to providing evidence to support your assertion that phylogenic groupings are different to how evolutionary theory would predict them to be.

Obviously, you still don't grasp what I have stated. Nor do most of you seem to grasp what evo theory is in the first place. This is from the OP of mine on another thread, posted in an effort to clear up the confusion so many seem to have here.

1. The dominant theory of evolution is the Modern Synthesis also commonly referred to as NeoDarwinism. I have typically abbreviated this to Darwinism and explained why, but most here seem to insist on just calling it "evolution" despite evolution being defined as a microevolutionary process involving the change in the frequency of alleles. Of course then, a mere change in the frequency of alleles is not necessarily the origin of higher taxa, and so working with that label does not address the topic at hand.

Whatever one wants to call it (I shall use ND for brevity's sake), ND posits sequential speciation however one wants to define species as the process that occurs evolving the higher taxa. One species evolves into another and then another and so forth until you have different genera, different families and so forth. However one wants to describe the process is besides the point. There is a clear process envisioned of small genetic changes adding up over time in populations to produce new species, genera, families and so forth. We can get into that in more depth later.

 

[yomero]

...

Pierre Grasse, for example, accepted common descent but called evolution (meaning Neodarwinism) a myth.

That macrevolution as evidenced by things like placental and marsupial pairs and other evidence suggesting is internally driven and perhaps even via preformation (front loading) instead via natural selection, etc,.....It's worth noting mainstream biology is heading in the direction with areas like epigenetics and other concepts that these folks strongly advocated for a very long time.

Consider these quotes from a paper in 2000, though he wrote much the same thing in 1984 as well and cites scientists commenting on the same discoveries prior to the 80s.?

...The unicellular Amoeba is structurally one of the simplest of the
Protozoa, yet in that same phylum can be found creatures exhibiting
strikingly advanced features. One such animal is Diplodinium
(Epidinium) ecaudatum (Figure 1). This ciliate exists in huge
numbers as symbionts in the stomachs of cattle (Sharp 1914). It has
a kind of "brain" (motorium), "circumoesophageal neural connectives"
resembling those of annelids and arthropods, clearly differentiated
"muscles", a kind of "segmented skeleton" (skeletal laminae), a
"mouth", "esophagus", "rectum" and "anus" all elaborated within the
confines of a single cell. Such a creature not only demonstrates
that the information is already present for these structures, but
also casts considerable doubt on the notion that multicellularity
is a prerequisite for the division of labor. It is no wonder that
Libby Hyman described the protozoa as the acellular rather than the
unicellular animals. Why this creature should have such an array of
advanced features remains a complete mystery. Could it be there to
provide us with a clue to the nature of the evolutionary process?

http://www.uvm.edu/~jdavison/ontoge...iley.com/doi/10.1002/jmor.1050520109/abstract
http://www.sciencemag.org/content/71/1840/369.extract

The most recent work I could find was by Roth and Shigenaka published in 1964 in Journal of Cell Biology.They studied with electron microscopy filamments in diplodinium. The work was mainly on filaments during mitosis and cilia. They mention the studies of both Sharp and Rees, but make no mention of a nervous system, esophagus, rectum or skeleton.
http://jcb.rupress.org/content/20/2/249.full.pdf

What is the current consensus? Either way, I fail to see how this could disprove evolution.

 

[randman]

Kotasu, you don't seem to get the basic point I was making on phylogenies and the overall pattern, not specific clades. But maybe discussing one would be helpful in other ways as one can learn a lot by looking at the data and assessing what it can or does and does not indicate. Since we have a lot of horse fossils, why don't we look at them.

MacFadden (2005) asserted that horses are a classic study system for macroevolution. What is macroevolution? Evolutionary biologists define macroevolution as “evolution above the species level.” This generally encompasses phenomena such as the origin of higher taxa (genera, families, orders, etc., .....Macroevolution does NOT include either evolutionary change within populations (microevolution) or the formation of new species (speciation).

One important debate in macroevolution deals with the pace of evolutionary change. The traditional view, the one supported by most members of the Modern Synthesis, and the one illustrated in the only figure in Darwin’s Origin of Species is known as gradualism. This view has constant evolutionary change taking place in all species, as they adapt to small changes in the environment. An illustration of gradual change is provided below. This view of evolutionary change dominated until the early 1970’s, when Eldredge and Gould (1972) proposed the theory of punctuated equilibria. This theory postulates that species are generally stable, and change only very rarely, often at speciation events. This theory was suggested to explain the fact that, even when the fossil record is well known, there seem to be long periods of morphological stability, punctuated by rapid changes to a new stable morphology,....

.....
While paleontologists have long suggested that evolutionary changes in horses are related to a change in environment, recent data have begun to highlight inconsistencies with this hypothesis.

http://ib.berkeley.edu/courses/bio1b/labschedfall07/labexercises/MacroevolutionHorse1_3_4.pdf

Please keep in mind the comments above stem from an evolutionist. So when they say we see PE in progress, what they are saying is the fossil record exhibits statis and sudden appearance which undermines "gradualism" since species don't seem to be always evolving and we don't really see the transitions. We see "sudden appearance." PE says subgroups split off and evolved and just didn't leave any fossils.

Also, a creationist would consider horse evolving to all be microevolution though some reject some of these "horse" species as ancestral or really part of evolution of horses within a creationist paradigm and think they are just other extinct animals thrown in by evos. For our purposes, it's not necessary to go into these specific creationist arguments. In some respects, creationists and evos share a similar position although creationists likely advocate more than just Neo Darwinian means, but mainstream biology is moving in that direction as well.

Davison, whom I have linked a few of his studies, is a front loader that uses horses as evidence against Neo Darwinism and evidence of some other macroevolutionary force at work. He proposes evolution happens via the chromosomes rather than simple allelic mutation causing macroevolution, and he takes a view noted scientists did before him, that microevolution does not really add up to macroevolution at all.

As of writing this, I have not checked the facts on horse evolution, but his claim and it's not going to kill his theories either way, is that we don't see speciation with horse fossils but that every link is a new genus. PE as stated above tries to explain this a different way.

You get the sense from front loaders that jumps were bigger earlier in evolutionary history; hence Goldschmidt's famous statement that the first bird hatched from a reptilian egg. Gould of late has said Goldschmidt will likely be vindicated in many aspects, though he doesn't go as far as a reptile laying a bird egg.

Similarly, in nature, sexual reproduction seems incapable of proceeding beyond the subspecies. I am unaware of a single instance of the production of a new species through the known agency of sexual reproduction. The standard Darwinian response is that evolution takes too long to be observable, an assumption which renders that proposal untestable.

This raises the question – has evolution really been gradual? I confess that the answer to this question depends on what one might accept as an intermediate state. As an example, the horse series shows an increase in size coupled with a decrease in digits. However, this series is not linear so the intermediate organisms cannot be arranged in any certain fashion. Furthermore, they differ from one another in so many independent factors that they must be relegated to separate genera. What we actually observe is the appearance of discrete phenotypes with no evidence of what might be described as missing links. This is exactly what one sees when one observes extant related organisms.

For an amateur bird watcher, like myself, a simple key or even a picture is usually all that is needed to identify any species with certainty. Schindewolf suggested that we might as well stop looking for missing links as they never existed! If they are not present in contemporary species, why should they have been present during their evolution? Any hypothesis for evolution must recognize and offer an explanation for these morphological gaps. The semi-meiotic hypothesis, which I first proposed in 1984, does exactly that (Davison, 1984, 1998). Based as it is on the reorganization of the chromosomes, such events cannot be considered gradual since they are all-or-none events for which intermediate states are inconceivable. In short, they indicate instant evolution. There is also no compelling evidence that new information is required for the expression of such reorganizations (position effects), indicating that the necessary information was already present and only needed to be derepressed (Davison, 2000)./QUOTE]

John A. Davison Professor Emeritus of Biology University of Vermont

http://www.uncommondescent.com/documentation/Davison_IsEvolutionFinished_022204.pdf

Please note he is using the biological concept of species and is saying what we see in the fossil record is exactly what we see in living biota, and advocates that Neo Darwinian gradualistic evolution does not result in macroevolution. Gradualism in the sense he is using it includes PE. He is saying it's not a species to species gradual change but that evolution jumps and that's why we see new genera in the fossils but no small changes adding up.

PE says the small changes happened, in bursts relative to geologic time, but just didn't leave fossils as the populations were small and existed for a relatively brief time. In other words, they have an absence of evidence to explain the jumps and Davison and others are saying the links are not there because macroevolution didn't happen as Neo Darwinians propose, and he has a specific hypothesis how they could have evolved.

More comments from the paper.

For centuries man has practiced intensive selection on those life forms he has domesticated, yet he has never produced new species as a result. Luther Burbank, the great horticulturist, had some pertinent comments on the limits of selection. From his autobiography:

“I know from my experience that I can develop a plum half an inch long or one two and a half inches long, with every possible length in between, but I am willing to admit that it is hopeless to try to get a plum the size of a pea, or one as big as a grapefruit (Burbank, 1939).

Why might some insist that evolution is still in progress? I propose it is in large part due to the acceptance of authority. For centuries, Aristotelian physics was accepted because it made intuitive sense that the heavier an object was, the faster it would fall. Galileo exposed the myth with a simple experiment. ...

It was not until 32 years later when it became clear that chromosomes, like Mendel’s factors occurred in pairs, that Mendelism became established as an experimental science. When that did occur, the Darwinians immediately embraced the new science of Genetics and have attempted to explain evolution with Mendelian principles ever since.

.....
In 1924, shortly before his death, William Bateson, the
father of modern genetics, confided to his son Gregory, “that it was a mistake to have committed his life to Mendelism, that it was a blind alley which would not throw any light on the differentiation of species, nor on evolution in general.” (Davison, 1998). I wholeheartedly agree.

This paper is fairly short. He goes into more length in others. It's worth noting he's been advocating macroevolution via a mechanism involving chromosomes since back in the 80s as others did long before that, and recently it's finally become of interest to evos that are beginning to question the Neo Darwinian narrative in how "evolution" happened, and others that accept Neo Darwinism as still valid but not the only means of macroevolution.

 

[ThunderChunky]

Thank you for responding. This is an interesting comment which I think the data says is not true, but even more interesting is why this should be true.

Why do you think this is the case?

What data says it's not true? In general it should be true because genes perform functions. More functions (morphological complexity) should require more genes (or more functions per gene)... in other words more genetic complexity. Now I suspect you might throw out some "simple" organism with a large number of genes as a counter example, but that is really missing the point. Just because lots of genes are required for morphological complexity does not mean that you always observe morphological complexity with lots of genes. If you really want a counter example you need to find a morphologically complex organism with out the genetic complexity.

Is this really true, however? Why would it be so?

Simple organisms do not always need large genomes, large genomes can be a burden, so they are lost or never gained. This is a general trend, if you look at genome size of all animals or all life, but not some hard and fast rule.

2 questions related to those above before going further.

1. Do we know how new genes arise? If so, how? Can this be tested as a general pattern?

Yes, we know of many ways in which new genes can arise. Many mechanisms have been directly observed, I could outline them for you but that would require a separate post. Check out this in the meantime: http://en.wikipedia.org/wiki/Gene_duplication. These types of events can then be inferred to have occurred in the past by looking at gene sequences of various related organisms.

2. The LCA is not predicted to be genetically complex? I agree. What does that mean if it is?

Why did you say it was predicted to be complex so many times if you agree that it is not?

 

[Squeegee Beckenheim]

randman, you seem to have made a post in favour of punctuated equilibrium (which you for some bizarre reason seem to think completely contradicts the theory of evolution. Would it surprise you to find out that Darwin said almost the same thing in On The Origin Of Species?), rather than one showing how the groupings of phylogeny are not what the theory of evolution would predict. Can you please provide evidence to substantiate your claim that phylogenic groupings aren't what would be predicted by the theory of evolution.

 

[Kotatsu]

Kotasu, you don't seem to get the basic point I was making on phylogenies and the overall pattern, not specific clades.

No, but then you have to remember that I approach the field from the direction of many years of actual experience of working with the theory of evolution, and not that of discussing things on internet groups for 20 years, so it is only natural that our different experiences would lead us to misunderstand each other occasionally. I could probably quote a dozen instances where you have failed to get my point, as well!

Curiously, this is precisely why I have -- so far usually in vain -- asked you to expand on your viewpoints, to clarify your statements, and to back up your claims.

But maybe discussing one would be helpful in other ways as one can learn a lot by looking at the data and assessing what it can or does and does not indicate. Since we have a lot of horse fossils, why don't we look at them.

I am very pleased that you have finally selected a group of organisms which we can study and test your claims on. I am already late for work now, but will have a closer look at this in the afternoon.

As a declaration of bias, I feel I must state that I have never worked on mammals in my research, but that the specimen collection used for teaching at my university mainly consists of mammals, and several of the exercises in evolutionary theory I teach to the students in the basic courses in biology concern mammals, and one even includes the comparative morphology of zebras and other hoofed animals. In an attempt to convert our basic taxonomy course into something useful, I have also attempted to change the species list for the course into one that contains all important extant taxa in the world, as well as the most important ones in the fossil record, but the main teacher disagreed.

I do not think this in any way biases me, but if you feel this background gives me an unfair advantage of some sort, feel free to suggest another group of animals.

I will respond to your other points later today.

 

[Kotatsu]

Reversibility would be, for example, creatures that evolved reversing themselves and evolving back to the ancestral forms.

Precisely as I outlined, then? I refer you, again, to the following part of my previous post which discusses character reversals on a molecular level:

This statement contains no contradiction. Certainly the same position in a sequence can and does mutate multiple times within a lineage, especially in sections of the DNA that is less conservative. This is a well-known fact in evolutionary theory, and has been for at least as long as we have used genetic sequences for phylogenetic analysis. However, the chance of every single mutation in a lineage being reversed at the same time and thereby producing the exact same sequence as in a removed ancestral organism increases (linearly?) with the temporal distance between the two taxa, and (unpredictably?) with the effect the mutations of the ancestral sequence have on the biology of the organism in question. Therefore, when enough change has occurred in a lineage so that we would classify it as a different taxa from its ancestor, the chances of all these mutations being reversed at the same time in the same descendant further on is incredibly small, but certainly within the realms of possibility.

This, incidentally, is the reason why different genes are used for resolution on different taxonomic levels when we do phylogenetics. Genes known to have a high rate of mutation (i.e., genes that evolve fast) will give resolution only at low taxonomic levels, whereas more conservative ones will give resolution only at higher taxonomic levels. For instance, if I were to construct a phylogeny of the whole of Neoptera and was forced to use only one gene, I would not use COI as that has too high a mutation rate, and would result in a large polytomy. While this is, of course, also data, it is not data that can be used in any way, and thus I would chose another gene.

A quick look through the papers I have in my office and on Google Scholar gave at least two examples of supposedly advanced characters which have reversed to a previous state.

The first is the loss and subsequent gain of wings in stick insects, as proposed by Whiting, Bradler & Maxwell (2003; Nature 421, 264-267), and this is somewhat controversial (see Trueman, Pfeil, Kelchner, Yeates, 2004; Syst. Entomol. 29, 138-139, and Whiting & Whiting, 2004; Syst. Entomol. 29, 140-141). This study proposes that while the ancestor of Phasmatodea+sister groups was winged, the ancestor of Phasmatodea alone was wingless. Wings then reoccurred in some lineages at a later stage of the evolution of the modern stick insects.

The second is the reversal of direct development back to larval development in Plethodontid salamanders as proposed by Chippindale, Bonnett, Baldwin & Wiens (2004; Evolution 58, 2809-2822). I have not read this article more than the abstract and the phylogenetic trees, but will get back to this later.

In any case, reversal of the type you are after is commonplace at the genetic level, but becomes increasingly unlikely with increasing temporal distance between an ancestor and its descendant. However, if we assume (and the article does not address this) that a single change in the genes regulating wing development in the ancestor to stick insects, then a single change could very well be enough to reverse this pattern as well. This is unlikely, but certainly not impossible. Whiting & Whiting (2004) lists other proposed examples (references removed for brevity): "eyes in ostracods, ocelli in cave-crickets, wings in water striders, wings in male Philotrypesis fig wasps, and other complex features in a wide variety of taxa", pointing to a review in "Developmental Plasticity and Evolution" by M. J. West-Eberhard (2003), Oxford University Press, New York. I don't own this volume, so if you want to look deeper into this, you will have to get it yourself. The prize on Amazon is £47.50:

http://www.amazon.co.uk/Development...2356/ref=sr_1_1?ie=UTF8&qid=1300712831&sr=8-1

Btw, I am not accusing you of fraud.

Yes, you are. You are saying that the data does not support the conclusions I draw from the analyses of it, and as I use these conclusions to get funding and to earn a living, you are essentially accusing me of lying and deceiving -- perhaps unwittingly -- in order to get money, typically at the taxpayers' expense. That is fraud in my country.

Unfortunately, I am running out of time here to post.

Please don't feel that I am hurrying you. I, and also Sceptic Tank, am still asking the same questions as several days ago, and we are still patiently waiting for your answers. Hopefully, now that you have selected horses as your model taxon for supporting your assertions, we will not have to wait any further.

What I am saying is NeoDarwinism makes unsubstantiated claims as if they are fact and asserts them to be near proven, despite not being tested for an unlikely to be true.

Please list some of these unsubstantiated claims again, so that we can know if these are actually unlikely to be true, or if you are just making unsubstantiated claims as if they are facts.

Macroevolution appears to be a spent process either no longer occurring or at it's tail end.

I have already several times addressed this issue by pointing out several characteristics about phylogenies which would make a beginner believe this to be the case. You have, as far as I remember, not yet responded to this, yet you persist in making the same claim. Are you of the opinion that the explanations I have offered for this misconception of yours are wrong? If so, tell me, and I will see if I can reformulate them.

Macroevolution is not microevolution writ large but that the mechanisms of microevolution appear to work against macroevolution.

"Appear to" does not equal "distinctly and umabiguously do". The flaw could be in your perception of what the mechanisms are.

The unicellular Amoeba is structurally one of the simplest of the
Protozoa, yet in that same phylum can be found creatures exhibiting
strikingly advanced features. One such animal is Diplodinium
(Epidinium) ecaudatum (Figure 1). This ciliate exists in huge
numbers as symbionts in the stomachs of cattle (Sharp 1914). It has
a kind of "brain" (motorium), "circumoesophageal neural connectives"
resembling those of annelids and arthropods, clearly differentiated
"muscles", a kind of "segmented skeleton" (skeletal laminae), a
"mouth", "esophagus", "rectum" and "anus" all elaborated within the
confines of a single cell. Such a creature not only demonstrates
that the information is already present for these structures, but
also casts considerable doubt on the notion that multicellularity
is a prerequisite for the division of labor.

Note: I have not had time to read the text you linked to, but I have printed it and may have time to do so tonight. Meanwhile, perhaps you could answer this question: Is it Davison's contention that all these structures are homologous to those in a non-protozoan organism? That is, is it his contention that, e.g., the muscles are coded by the same genes in Diplodinium as in, e.g., C. elegans, or in us, for that matter?

If it is his contention, I would need evidence to back this up.

If it is not his contention, do you realise that his and your whole argument falls flat on its face? If one set of genes code for muscles in Metazoans and another code for "muscles" in Protozoans, this in no way implies that the genes that code for muscles (sensu Metazoa) are present in the protozoa, nor that they necessarily were present in their common ancestor.

The same goes for this statement:

While we associate the placenta with the higher mammals, this
structure also is found in certain sharks. Berg (1969) discussed
this and related phenomena as examples of what he called physiological
acceleration. He noted that Peripatus also nourishes its embryos
with a kind of placenta.

Does Davison mean that the "kind of placenta" present in Peripatus is homologous to that of placental mammals? And, regardless of what he suggests, is it? Or is it a similar structure that performs the same task, but which has a different developmental and evolutionary origin?

Otherwise -- remember, I've only read your quotes so far -- this seems to suggest that he would also consider the fact that both grasshoppers and bats have wings evidence for bats having some characteristics of grasshoppers, despite these not being homologous structures in any way.

Kotasu, you don't seem to get the basic point I was making on phylogenies and the overall pattern, not specific clades

No, the claim you made was that all phylogenies contained groupings that would not be predicted by evolutionary theory:

Even looking at phylogeny, the pattern of how species seem to be grouped together, it's not what "evolution" in the sense of Darwinism would predict, but you have to take the time to look at the patterns and consider the arguments closely.

Within the framework of phylogenetics, there is no other way to understand "groupings" than "clades", and there is no other way to understand "pattern of how species seem to be grouped together" than "nested clades". When asked to provide some evidence for this claim, you said:

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

Which can be interpreted only as that any given phylogenetic tree will contain such groupings. When prompted again to give evidence for your claim, and a method less biased to your detriment was proposed, you changed your claim to:

The "pattern" refers to the whole pattern, not just single "trees." None of the single trees are good evidence for ND due a variety of factors: first the fossil record and living biota do not show the transitions. Second, subgroup isolation (microevolution) entails a decrease in genetic variability.

And then again changed the focus of the discussion from your understanding of how the data supports your claims, to how our understanding of the data and the theory affects how the data supports your claims. I will say it again: the data that supports your assertions will be the same whether you present it to experts or to novices.

I then proposed we look at the whole tree, and gave you a link to the most complete consensus tree of all life I know of, at which point you claimed again that you had substantiated your claim, but that the data you used somehow depends on my understanding of the data and the theory.

We have not progressed an inch, and will not do so until you produce some data that supports you claim, which I suppose by now would be that in the overall patterns of the entire tree of life but not in any subsection of this tree there are groupings that would not be predicted by evolutionary theory. If you have listed some suggestions for such groupings, I have missed them, and would ask you to list them again. A handful will be enough, so it should not take too much of your time.

I will now go and do some lab work, and then return to your post where you start discussing horses.

 

[Dancing David]

Spamming by me:

I think this may be the source of most of randman's nonsense:
http://www.uncommondescent.com/

 

[Dancing David]

Precisely as I outlined, then? I refer you, again, to the following part of my previous post which discusses character reversals on a molecular level:



A quick look through the papers I have in my office and on Google Scholar gave at least two examples of supposedly advanced characters which have reversed to a previous state.

The first is the loss and subsequent gain of wings in stick insects, as proposed by Whiting, Bradler & Maxwell (2003; Nature 421, 264-267), and this is somewhat controversial (see Trueman, Pfeil, Kelchner, Yeates, 2004; Syst. Entomol. 29, 138-139, and Whiting & Whiting, 2004; Syst. Entomol. 29, 140-141). This study proposes that while the ancestor of Phasmatodea+sister groups was winged, the ancestor of Phasmatodea alone was wingless. Wings then reoccurred in some lineages at a later stage of the evolution of the modern stick insects.

The second is the reversal of direct development back to larval development in Plethodontid salamanders as proposed by Chippindale, Bonnett, Baldwin & Wiens (2004; Evolution 58, 2809-2822). I have not read this article more than the abstract and the phylogenetic trees, but will get back to this later.

In any case, reversal of the type you are after is commonplace at the genetic level, but becomes increasingly unlikely with increasing temporal distance between an ancestor and its descendant. However, if we assume (and the article does not address this) that a single change in the genes regulating wing development in the ancestor to stick insects, then a single change could very well be enough to reverse this pattern as well. This is unlikely, but certainly not impossible. Whiting & Whiting (2004) lists other proposed examples (references removed for brevity): "eyes in ostracods, ocelli in cave-crickets, wings in water striders, wings in male Philotrypesis fig wasps, and other complex features in a wide variety of taxa", pointing to a review in "Developmental Plasticity and Evolution" by M. J. West-Eberhard (2003), Oxford University Press, New York. I don't own this volume, so if you want to look deeper into this, you will have to get it yourself. The prize on Amazon is £47.50:

http://www.amazon.co.uk/Development...2356/ref=sr_1_1?ie=UTF8&qid=1300712831&sr=8-1



Yes, you are. You are saying that the data does not support the conclusions I draw from the analyses of it, and as I use these conclusions to get funding and to earn a living, you are essentially accusing me of lying and deceiving -- perhaps unwittingly -- in order to get money, typically at the taxpayers' expense. That is fraud in my country.



Please don't feel that I am hurrying you. I, and also Sceptic Tank, am still asking the same questions as several days ago, and we are still patiently waiting for your answers. Hopefully, now that you have selected horses as your model taxon for supporting your assertions, we will not have to wait any further.




Please list some of these unsubstantiated claims again, so that we can know if these are actually unlikely to be true, or if you are just making unsubstantiated claims as if they are facts.



I have already several times addressed this issue by pointing out several characteristics about phylogenies which would make a beginner believe this to be the case. You have, as far as I remember, not yet responded to this, yet you persist in making the same claim. Are you of the opinion that the explanations I have offered for this misconception of yours are wrong? If so, tell me, and I will see if I can reformulate them.



"Appear to" does not equal "distinctly and umabiguously do". The flaw could be in your perception of what the mechanisms are.



Note: I have not had time to read the text you linked to, but I have printed it and may have time to do so tonight. Meanwhile, perhaps you could answer this question: Is it Davison's contention that all these structures are homologous to those in a non-protozoan organism? That is, is it his contention that, e.g., the muscles are coded by the same genes in Diplodinium as in, e.g., C. elegans, or in us, for that matter?

If it is his contention, I would need evidence to back this up.

If it is not his contention, do you realise that his and your whole argument falls flat on its face? If one set of genes code for muscles in Metazoans and another code for "muscles" in Protozoans, this in no way implies that the genes that code for muscles (sensu Metazoa) are present in the protozoa, nor that they necessarily were present in their common ancestor.

The same goes for this statement:



Does Davison mean that the "kind of placenta" present in Peripatus is homologous to that of placental mammals? And, regardless of what he suggests, is it? Or is it a similar structure that performs the same task, but which has a different developmental and evolutionary origin?

Otherwise -- remember, I've only read your quotes so far -- this seems to suggest that he would also consider the fact that both grasshoppers and bats have wings evidence for bats having some characteristics of grasshoppers, despite these not being homologous structures in any way.



No, the claim you made was that all phylogenies contained groupings that would not be predicted by evolutionary theory:



Within the framework of phylogenetics, there is no other way to understand "groupings" than "clades", and there is no other way to understand "pattern of how species seem to be grouped together" than "nested clades". When asked to provide some evidence for this claim, you said:



Which can be interpreted only as that any given phylogenetic tree will contain such groupings. When prompted again to give evidence for your claim, and a method less biased to your detriment was proposed, you changed your claim to:



And then again changed the focus of the discussion from your understanding of how the data supports your claims, to how our understanding of the data and the theory affects how the data supports your claims. I will say it again: the data that supports your assertions will be the same whether you present it to experts or to novices.

I then proposed we look at the whole tree, and gave you a link to the most complete consensus tree of all life I know of, at which point you claimed again that you had substantiated your claim, but that the data you used somehow depends on my understanding of the data and the theory.

We have not progressed an inch, and will not do so until you produce some data that supports you claim, which I suppose by now would be that in the overall patterns of the entire tree of life but not in any subsection of this tree there are groupings that would not be predicted by evolutionary theory. If you have listed some suggestions for such groupings, I have missed them, and would ask you to list them again. A handful will be enough, so it should not take too much of your time.

I will now go and do some lab work, and then return to your post where you start discussing horses.

Thanks for putting the E in the JREF!

 

[Sideroxylon]

Thanks for putting the E in the JREF!

You and the rest, too. It's an interesting read.

 

[subterranean1]

For example, the pattern assuming common descent indicates some sort of irreversible process (with slight exceptions). There is no reason for allelic random mutation to primarily run one way.

To the extent that mutations are random, given two separate similar populations, any given mutation would tend to make them diverge simply because of the maths of the process.

Even starting (for simplicity) with a hypothetical species where the only possible mutation was a point mutation, it's pretty obvious that as long as the two populations are vaguely similar, a randomly-chosen site for mutation is likely to be one where there is currently similarity, and therefore where difference would be increased by any mutation.

To reduce difference, a mutation would have to happen where there was currently a difference, *and* it would have to be the 'right' mutation.
That's simply much less likely for two populations that are meaningfully similar.

Even considering greater or smaller degrees of conservation in different areas of a genome doesn't really change that, it pretty much just reduces number the sites where 'random' mutation can be considered.

Likewise, introducing different processes of random mutation also doesn't really change things, since those processes will also tend to increase difference.