Evolution: the Facts.

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.
So what you're saying is that as less DNA is found to be apparently nonfunctional, that dilutes one piece of strong evidence (though frequently replacing it with another piece of pretty strong evidence)?
But surely you acknowledge that evolution didn't require the existence of 'junk' DNA for people to be convinced it was correct, and that before any 'junk' was found, biologists weren't actually doubting evolution because of the lack of it?

It may be that large amounts of noncoding DNA was one more big nail in the coffin of creationism/ID scientific credibility, but pulling that nail out and hammering a slightly smaller one in nearby (and possibly some extra ones derived from what biologists have learned in understanding the functions of things thought nonfunctional) doesn't result in the lid being meaningfully less firmly nailed down, or ID's credibility being any less dead.

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.
So you're claiming that there was a unified creationist/ID voice claiming that DNA couldn't possibly be nonfunctional, since nonfunctional DNA couldn't be part of a creator's plan?
 
It's simple. Evos had arguments based on DNA being non-functional, and they were wrong just as IDers and others predicted, and no, the arguments don't work any more now that they are functional.

Another failed evo prediction.....as expected.
 
None of this has anything to do with the claim that the groupings aren't what the theory of evolution would predict. Let's stick to one claim at a time, shall we? You've made the claim that the groupings of species aren't what the theory of evolution would predict. You've been quoted as saying this seveal times now, so you're not going to get anywhere by trying to brush this statement under the carpet. I can quote you saying it again, if you like.

Now what evidence do you have with which to substantiate this claim? Be specific. Kotatsu has given you several excellent protocols by which you could support your assertion. I suggest you follow one of those, or suggest a variation of one of them if the protocols themselves aren't to your liking, rather than repeatedly ignoring them. If you can do this and actually back up what you're saying with real evidence, then everybody who has thus far disagreed with you will have no choice but to acknowledge you're right.

What reason, other than being unable to support your assertion with evidence, do you have for continually refusing to do so? Surely, if you've been debating this very subject for more than 20 years, as you claim, and if your conclusions are based on scientific evidence, as you also claim, you'll be able to do so with ease. As it is, all your ducking and diving and trying to change the subject just makes it look like you know yourself that you can't back up your assertion, but that you don't have the courage to admit that you were wrong on that point.
Yes, I have made the claim they are not what evo theory aka Neo Darwinism would predict, but since you don't even know what ND is after pages of trying to explain it to you, why waste any more time trying to explain it to you.
 
This is not true. Or, rather, you are correct that you have stated that these groupings not predicted by evolutionary theory do exist, but you have not substantiated this claim.

Ok, so I point to data, and you say no, you did not point to data, and back and forth and we waste time.

Maybe you don't get the difference between merely reiterating something and citing specific characteristics of something in support of a point.
 
This is not true. Or, rather, you are correct that you have stated that these groupings not predicted by evolutionary theory do exist, but you have not substantiated this claim. Substantiating, rather than reiterating, these claims is what I would like you to do. I am sorry if this has been unclear.



How fortunate, then, that a consensus of all published trees is available for free online:

http://tolweb.org/Life_on_Earth/1

This link should take you to the root of the tree of life, from which you can click your way more or less anywhere you want in its various subtaxa. Granted, on a finer level, the TOLWEB tree of life often lacks details (though I was surprised to find I could get to the species level in all three genera I am working on at the moment; this was not the case when I looked last, but that was a few years ago), but the rough picture is there.

So, now that we have settled on a tree -- it being the entire tree of life, based on a conservative consensus of trees obtained by a series of analyses based on the evolutionary theory -- I ask you again to identify the groupings in this tree which "would not be predicted by evolutionary theory". Please list some groupings in these trees that "would not be predicted by evolutionary theory", your reason for believing your selected groupings "would not be predicted by evolutionary theory", and, if possible, the alternative grouping predicted by ID. If you chose to provide the latter, please also detail the reasoning behind this grouping, as well as provide a reference to the data and the analysis on which you or other ID proponents base this claim.

I will, at least until you change your opinion again, let the obvious change from "all of the trees has feature X" to "feature X is not found in any of the individual trees", which is the essence of your current position, slide.



Certainly there are cases where this is untrue. In most morphological trees, as well as in genetic trees which do character tracking, the transitions between species is clearly denoted, typically as black cross-bars. These intermediary taxa are not all named, of course, as they are typically not all known, but the transitions -- which, after all, is the most salient point, as that, not the labels, is the actual data -- are typically presented with all the clarity you may wish for. In any case, I hardly think it is a mere transition of labels that you are after, since you have stated several times that you are interested in looking at the data. That, in this case, is the distributions of characters and the transition between character states along internodes.

I can provide you with several examples, if necessary. I am confident that Dinwar, who is more familiar with the paleontological literature, could provide several more.



I cannot see how this in any way invalidates any given tree from being strong evidence for evolution. I trust you will expound on this issue when time permits.



Again, presenting data that supports your assertions in no way relies on our ability to understand this data. You do yourself a disservice if you believe the opposite to be the case, as it makes you come across as one who would rather engage in reiterations of rhetoric void of content than actually substantiating and/or validating your claims.
Kotsatu, are you just an idiot? I gave the data, specifically saying the nature of all trees. Why is that such a difficult concept for you to grasp?

Not one tree or any tree, but the nature of how all the trees fit together, and cited:

general irreversibility

the lack of macroevolution in a very long time

bacteria not evolving any new non-bacterial forms over 500 million years

nor anything else evolving itself into bacteria

the fact macroevolution appears to occur burts or pulses but no longer doing so today, etc, etc,.....

If you don't like the evidence, fine, but do not pretend I have no answered.
 
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Yes, I have made the claim they are not what evo theory aka Neo Darwinism would predict

NeoDarwinism isn't "evolutionary theory". It's a label for those scientists who heavily favor selectionism as the best way to explain certain things within evolutionary theory. But there are a lot of other scientists who favor explanations other than selectionism, and so lumping them in under the same label as the one used for the selectionists is incorrect.

It's like calling all chefs everywhere "French chefs".

Ok, so I point to data, and you say no, you did not point to data, and back and forth and we waste time.

What post number in this thread contained you pointing to the specific data asked for, and not your handwavey "you know, all of them!" nonsense?
 
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.

You are exaggerating recent findings. You claimed in your recent thread that the ENCODE project had somehow disproved any theory regarding pseudogenes as remnants of evolutionary changes in the genome. But research conducted using the ENCODE data has simply suggested that some pseudogenes may still serve some biological function.

"However, a few pseudogenes have been indicated to have potential biological roles (Ota and Nei 1995; Korneev et al. 1999; Mighell et al. 2000; Balakirev and Ayala 2003). Whether these are anecdotal cases or pseudogenes do play cellular roles is still a matter of debate at this point, simply because not enough studies have been conducted with pseudogenes as the primary subjects."

You are acting as if the matter is completely closed, but it most certainly is not.
 
It's simple. Evos had arguments based on DNA being non-functional, and they were wrong just as IDers and others predicted, and no, the arguments don't work any more now that they are functional.

Another failed evo prediction.....as expected.
There is non-functional DNA, just because some of what was thought to be junk isn't, does not mean some of it isn't.

Paul

:) :) :)
 
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.



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.



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.



Why did you say it was predicted to be complex so many times if you agree that it is not?
The LCA is now predicted to be genetically complex. I was agreeing that based on evo theory it was not expected, and that's what I am trying to get at; that it was not predicted and there are clear reasons why.

One of them you mention which is functionality. More functions in general would require a more complex genome. Genetics are connected to function and so novel genes are (or rather were) thought to arise along with novel function through Neo Darwinian means, selectionism basically.

So you wouldn't expect the LCA to be so genetically complex, but that's what molecular studies are indicating.

The LCA for plants and animals is thought to have more types of genes than are available to plants and animals today for example, which is an extraordinary conclusion. There are a number of studies showing these things, not just the one paper.
 
Randman, I do not wish to antagonise you in any way by the following, but I have now read through Davison's article "Ontogeny, Phylogeny and the Origin of Biological Information", and I recognise many of your arguments in his article. In some passages, I thought it overwhelmingly likely that you actually are Davison, but to my knowledge you have not said anything to that effect.

Everyone should read Davison's article. In fact, I should give it to my students in basic biology or basic taxonomy to read in the first few days of their courses. Certainly anyone who discusses these matters here with you should read it and see what it says, because it explains so much.

Unfortunately, it is the saddest excuse for a scientific article I have ever seen. You might as well base your arguments here on Green Eggs and Ham, for it has as much basis in reality, and as much of a place in an educated scientific discussion as Davison's crap does.

Let's focus on some general themes.

For an article of its purported weight and substance, it has a strikingly short list of references. One would expect that a serious researcher would have read up properly on the subject he discusses, mention some aspects of various competing theories, and their respective shortcomings, and that this would be properly and exhaustively cited. For instance, an article I am working on has 107 references, and this article concerns only the taxonomy of a group of bird lice, a subject that I will be the first to admit it extremely peripheral to evolutionary theory.

In contrast, Davison's article that touches on several core concepts of evolutionary theory, and which ultimately seeks to discredit it, has a total of 12 references. Of these, four are to his own previous work, one is to a popular science book by Feynman (1), one is to a popular science book by Gould (2), and of the remaining six, five are from before genetics were understood, or -- in the case of at least two of them -- even known about. The last book is an introductory book to Paleontology, and was originally published in German in 1950, but translated into English in 1993.

The introduction proclaims proudly that the theory within "incorporates the conclusions of" Schindewolf, Goldschmidt, Bateson, Broom, Grassé, and Berg. Of these, Broom and Bateson, and their conclusions, are never mentioned again in the whole body of the text, nor do anything they have written occur in the reference list. Let me repeat: apart from claiming that his views are supported by Broom and Bateson, they and their views are never mentioned in the entire text, nor is any stated reference whatsoever made to anything they have ever written. Further, both Goldschmidt and Schindewolf are mentioned precisely once more, and only in this very unhelpful manner (years excluded): "It should also be noted that Schindewolf, Goldschmidt, Berg, and Grassé all subscribed to preadaptation (preformation) during evolutionary change", but no reference to where they did so, what they said more precisely, and what they based their conclusion on is ever mentioned.

Grassé and Berg are included more frequently, however, but this still suggests that only two out of a purported six experts in the field have had their conclusions "incorporated" in any practical sense whatsoever in the article. It should also be noted that among all the experts of evolutionary theory throughout the last 200 years, Davison selects six of which five were dead before the advent of genetically based phylogenies. The sixth is Grassé, who died in 1985, which makes him only a potential borderline authority on genetic data and what they show. However, he, too, is removed from any serious consideration as to how Davison's theory should be applied to a post-genetic world, as the only reference to Grassé that Davison makes is to a book published originally in 1973, and translated into English in 1977.

And even then, Grassé is mentioned precisely twice, once for the quote: "According to Darwinian doctrine and Crick’s central dogma, DNA is not only the depository and distributor of the information but its sole creator. I do not believe this to be true." and once for "The existence of internal factors affecting evolution has to be accepted by any objective mind." That is, for Grassé, too, no mention is made of what he based his conclusions on, or any details of what his specific claims even were, apart from the sentences cited above, which are in splendid isolation. However, to Davison's credit, the former quote is actually referenced to page.

The first mention of Berg is to claim that he was "perhaps the first to indicate that evolution and the development of the individual were closely related", which to me seems to be an admission that Davison is unique among creationists -- for this is what he is, as will be obvious below -- in never having heard of Haeckel.

Let me repeat this in other words:
None of the authorities cited by Davison in support of his theory could possibly have known about the vast majority of the genetic data on which so much of modern evolutionary theory is based.

This alone should be enough to simply throw Davison's paper away and pretend it never existed, because he is actively ignoring all available research and data after 1973 apart from references to his own previous work. But sadly, the uselessness of this paper does not stop with what data Davison decided to consider before writing this nonsense.

And the nonsense never stops... I though you had just selected some unfortunate examples when I asked you, above, whether Davison was suggesting that the various organs found in Diplodinium were homologous to those in C. elegans or in humans, but it turns out that Davison's seemingly limitless ignorance of what biology actually is runs so deep that this question would have no meaning to him.

Consider, for instance, his implied suggestion that the fact that some stick insects have eggs that are similar in morphology to their host plants' seeds is because they have the same genes for egg/seed morphology which has been inherited -- without being expressed -- for countless millions of years in these two lineages, and then suddenly expressed in two ecologically correlated taxa.

This, he implies, is a more likely explanation for the data than that the eggs of the stick insects have become similar to the seeds of their host plants precisely because they are eggs, and eggs are typically extremely nutritious, and there is therefore a selection pressure to disguise them, for instance by crypsis. Even though he undoubtedly knows that there are such things as mutations -- as he mentions "micromutations" on the very first page -- he implies that a far likelier explanation is that the genes that code for egg ultrastructure of this kind has been preserved without any mutations disturbing their sequences from the last common ancestor of the stick insect and the Umbelliferous plant they live on -- and presumably we have it as well!

This continual blurring of the line between "similar" and "identical", which cuts to the heart of both my previous questions about Diplodinium, and to all that is wrong with Davison's paper, is the most glaringly idiotic part of this rambling essay. If you are in any way in contact with this misguided individual, Randman, please pass the following information on to him:

"Similar" does not equal "identical". The existance of similar organs or organs performing similar functions in distantly related taxa is of interest if and only if they are homologous. It is not a keen-eyed insight into the nature of beings to say that both velvet worms, sharks, and mammals have a structure that functions in a similar manner to our placenta if this is not actually the exact same structure. If the placenta in these animal groups are coded by the same genes, develop from the same germ layers, and in all other aspects are homologous, then you have a point. The existence of organs with a similar function but which do not share a similar genetic or developmental background is entirely irrelevant to the argument you are trying to make, as these do not show that the same genes are present in all organisms and just expressed differentially depending on what the organism is. It shows that the same function performed by vastly different organs can arise several times if this is a function that is advantageous to a general organism.

The same goes for the internal structure of the Diplodinium, the similarity of scents -- perceived by that highly flawed human nose! -- of distantly related flowers, the kidneys of Annelids and Amphioxus, the imaginal discs of "higher insects" and nemerteans, and the eggs and seeds, respectively, of the stick insects and their plant hosts.

The whole purportedly biological part of this article is based on the blurring of this line. Only by ignoring the concepts of homology and analogy -- concepts which are not even mentioned in the text -- can Davison's article make any sense at all, but then, if you ignore those concepts, why on Earth should any scientist ever take your article seriously? If I call my local soccer club and ask them to ignore for a while the fact that their game is played with two teams and a ball, because I have this fabulous, revolutionary idea about how they will win the ... well, I don't know what kinds of leagues there are. The European Great Soccer League, for instance. If I do this, how far into my detailing of my plan do you think I get before they hang up on me?

Homology and analogy are perhaps the single most important concepts you need to understand if you are to study evolution and phylogenetics in any meaningful way, and Davison elects to ignore them completely. This speaks volumes about how well founded his ludicrous ideas are, even if one discounts the fact that he spends a whole page in a seven-page article basically telling us that we should consider the possibility that Goddidit. Seen in chapters (or sections, really), a fourth of his article is an exploration of great thinkers who have mentioned God in some way. I find it very telling that an article on evolution that does not mention the concept of homology at all still takes time to point out that Galileo, Newton, Pascal, Faraday, Einstein and Feynman have referred to God in their work.

This is getting far too long for what this moronic piece of make-believe and baseless assertions deserve, and I still have not even touched on his many unsupported claims, and the very many times he puts words in the mouths of unidentified "Darwinists" without any reference to these words ever having been spoken by them, or any of the other drivel contained within this laughable essay. Still, I will end this review here, and hope that, if you are Davison, you will not see these comments as personal insults, but as constructive critic; as in, the most constructive you could do would be to do something entirely else, because you have no idea what a scientific article is. And if you want to claim to understand science, understanding what a scientific article is must by all accounts be the most fundamental of starting points.

---
(1) Referring to the fact that Feynman compared scientific discovery to a religious experience.
(2) Referring to Gould's characterisation of evolution to "a drunk reeling back and forth between the bar room and the gutter".
 
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Kotsatu, are you just an idiot? I gave the data, specifically saying the nature of all trees. Why is that such a difficult concept for you to grasp?

Not one tree or any tree, but the nature of how all the trees fit together, and cited:

general irreversibility

the lack of macroevolution in a very long time

bacteria not evolving any new non-bacterial forms over 500 million years

nor anything else evolving itself into bacteria

the fact macroevolution appears to occur burts or pulses but no longer doing so today, etc, etc,.....

If you don't like the evidence, fine, but do not pretend I have no answered.

Ah, so that is what you consider your answer. Yes, I have seen this several times, and I have commented on it several times as well. Invariably, these comments I have made have not caused you to answer them. Let me direct you to my answers, and I expect you to have some comment to make on these, or I will have to draw the conclusion that you do not care what the data shows, as your preconceived notion of what is correct will be correct no matter what:

general irreversibility

I have pointed out several times that you are simply wrong in this claim. The most recent one includes the following part on morphological and behavioural reversal:

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

And a previous post, cited in this one, discussed the same point 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.

I now expect you to either rebut these claims I make, or stop referring to the lack of reversibility as any kind of evidence against the utility of phylogenetic trees as evidence for evolution.

------------------------------

the lack of macroevolution in a very long time

I have explained this misunderstanding of yours several times, and Dinwar has posted an excellent essay which thoroughly discussed the concepts that you have got wrong, and how higher taxonomy actually works. Some recent comments on this misapprehension of yours includes:

As I have pointed out to you before, and as Dinwar so brilliantly explained in another thread, this is because these taxa do not exist in nature. There is no such thing as a "phylum". These are merely labels we attach to groupings of organisms which show certain common characteristics. The longer this group has been around, the more likely it is to have a label at a higher exclusive rank. The lack of recent new phyla is because this label is one that is attached only to groups that have a long evolutionary and geological history as an entity separate from all other phyla. Nothing that is today classified into a phylum will ever involve into something that would be classified into another phylum, because that is how taxonomy works. All Chordata will always be Chordata, even if they evolve to lose their spines.
Again, this is easy for a beginner to believe because any phylogenetic tree can give the evolutionary history of the included taxa only up until the date the oldest included individual was collected. As soon as a given individual is dead, it will no longer have further descendants, and evolution along that individual's lineage will stop there. Naturally, if an included individual had descendants before the collection date, or DNA was collected non-lethally, that individual would still have descendants, but their future evolution will not be picked up by the DNA as it is, by definition, in the future.
You will need to detail this picture more comprehensively, as I can see no such picture forming when I look at the data. Assuming I am the one with bias, I would ask you for more detail, and also to clarify what your claim actually is. As "phylum" is a label given to groups of animals which have a very long common history, and have been separated from all other groups of animals for a long time, this by necessity means that this label will be given only to groups of animals that formed a long time ago. More recent groups have other labels attached to them.

This does in no way imply that "phylum", "family" or any other taxonomic label is anything that exists in nature; these are all within-science terms used for communication, and has no external existence. However, certainly there are groupings referred to as, e.g., families that are more recent than other groupings having the same rank label. As taxon labels are only terminology, they are not comparable between higher taxa. A bird family is not necessarily as inclusive or as old as a wasp family, as the very term is just a label we use for a certain grouping we feel is significantly closely related to warrant it. How inclusive a taxon in differs widely between higher taxa, mainly because it is comparatively rare for people to work on multiple taxa, and because different taxa offer different levels of resolution, and have different number of differently skilled people working on them.

Dinwar's essay can be found here:
The concept of “higher taxa”, and how such taxa arise, is a very complicated subject, and one that deserves a better presentation that it currently is receiving. Here is my correction of Point 1 above. Please keep in mind my previous statement: Anything less than about 500 pages is necessarily incomplete, and that includes this. And to be honest, I wrote this while downloading geologic maps, so there are any number of nuances that I’ve missed; however, I believe this to be a decent summary of several summaries of summaries of where taxonomy currently stands, with sufficient personal bias (though I tried to call out where that is and why I think what I do).

I will now expect you to either address these points, or withdraw your assertion that macroevolution hasn't happened in a long time.

---------------------------------

bacteria not evolving any new non-bacterial forms over 500 million years

This has also been addressed several times. I will not repeat my answers here, as it is simpler to just reiterate them:

There is nothing in evolutionary theory that obliges an organism to change over time in a manner that is measurable to humankind. There is also nothing in evolutionary theory that obliges an organism to change over time so much that we would classify it as another higher taxon.

In addition to this, it is also important that you try to understand that it is a taxonomic impossibility that any member of the clade Bacteria in the true tree could ever evolve into something other than a member of the clade Bacteria (supposing there is such a clade). If you are a member of an inclusive taxon, you will always be a member of this taxon, no matter how much time passes. Chordates will always be Chordates, even if they lose their chorda. Bilaterians will always be Bilaterian, even if they -- like many Echinoderms could be argued to have done -- come to lose bilateral symmetry. This is a feature of how taxonomy works, and is entirely independent of evolution, but coincidentally, this is also a feature of how evolution works, which is entirely independent of taxonomy.

------------------------------------------

nor anything else evolving itself into bacteria

This has also been addressed, and I will reiterate it here:

Nothing will ever evolve into a member of the clade Bacteria (assuming there is such a clade), as any organism that is indistinguishable from another organism but which do not share a common, extended evolutionary history with it will per definition be classified as closer to those taxa with which is shares such a history. If, tomorrow, horses evolved into something indistinguishable from E. coli, they would still not become E. coli, as they would have an extended evolutionary history which is distinct from that of E. coli, and which it does not share with it.

As for something evolving into a bacteria but not being classified as one, that is not impossible, that is just extremely improbable, as it would, for instance, mean that within a few generations, mutations to the genome would both have to make sure that only one cell is produced from the egg and sperm of the last multicellular ancestor, and make sure that the new unicellular organism could survive without being multicellular.

I would suggest that in most habitats, the advantages to any extant multicellular organism of being multicellular are so great, that reverting to unicellularity will never happen. This, however, is not in any way a shortcoming of the theory of evolution, but actually evidence against your own theories. If subpopulation isolation truly does result in diminished genetic variation, then over geological time we would see exactly the pattern you propose: that multicellular organisms regularly revert to unicellularity.

I now expect you to either address my views, or withdraw this line or argument.

-------------------------------------------------

the fact macroevolution appears to occur burts or pulses but no longer doing so today, etc, etc,.....

This was dealt with, above, and I will not reiterate my points again within the same post. For details, see the second section of this post.

------------------------------------------------

So of your five arguments, two (2 and 5) turn out to be the same one, one (1) turns out to actually happen in the data, thus rendering your assertion baseless, and two (3 and 4) turn out to be based on your limited understanding of how taxonomy works.

Remarkably, none of them address your initial claim, that there are groupings in all phylogenetic trees that would not be predicted by evolutionary theory.
 
ANT, you should read the rest of his papers. His debates, though contentious, at Uncommon Descent elaborate a little more as well.

From your post, I don't think you quite get what he saying in that you emphasize homologous structures within DNA whereas he talks of chromosomes in his semi-meiotic hypothesis rearranging DNA more like an evo-devo mechanism which creates more of a saltional effect; hence the comments on lack of variation within genera for horse fossils (despite there being so many fossils I would add). He, of course, adds more substantial evidence and observations in his papers.

I think it's worth noting that if one removes the Neodarwinian lens, what we see in living biota is what we see in the fossil record, no gradual speciation leading to macroevolution.

Homology and analogy are perhaps the single most important concepts you need to understand if you are to study evolution and phylogenetics in any meaningful way, and Davison elects to ignore them completely.

analogy? what the heck?

Anyway, he does not ignore homology but specifically cites occurrences of homology as evidence for preformation rather than Neodarwinism.
 
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ANT, you should read the rest of his papers. His debates, though contentious, at Uncommon Descent elaborate a little more as well.

From your post, I don't think you quite get what he saying in that you emphasize homologous structures within DNA whereas he talks of chromosomes in his semi-meiotic hypothesis rearranging DNA more like an evo-devo mechanism which creates more of a saltional effect; hence the comments on lack of variation within genera for horse fossils (despite there being so many fossils I would add). He, of course, adds more substantial evidence and observations in his papers.

My post?

This is why you need to use the quote button, randman. It's right there under every post.
 
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Kot....

I have pointed out several times that you are simply wrong in this claim. The most recent one includes the following part on morphological and behavioural reversal:

Except you haven't. Reappearance of specific traits is not what I am talking of but the line of speciation.

I will now expect you to either address these points, or withdraw your assertion that macroevolution hasn't happened in a long time.

Neither you, nor Dinwar, addressed the point at all. Dinwar objects to the use of taxa being used in the context of the origin of higher tax through speciation events. However, this is exactly how science describes the event and peer-reviewed papers, as I have shown, use the same terms in the exact same way.

Neither of you have shown where macroevolution is still occurring today.

As for something evolving into a bacteria but not being classified as one, that is not impossible, that is just extremely improbable,

No more improbable or slightly more so than many other claims of evos such as the magical origin of the genome in the first place; that mutations via random mutation increase genetic variation over the observed loss of genetic variation due to natural selection, subgroup isolation and genetic drift; etc, etc,....

What you are doing is simply not addressing the argument raised, nor even showing a proper understanding of it.

Has it occurred to you that perhaps the reason we don't see examples of the common ancestor in any grouping by and large (can you name one for animals?) is not that the parent species went extinct? In other words, why would the parent species not also split off and reverse speciation into what it was before?

Oh yeah, the magic bullet...natural selection except selectionism across a wide field is shown to be less and less explanatory.
 
that mutations via random mutation increase genetic variation over the observed loss of genetic variation due to natural selection, subgroup isolation and genetic drift; etc, etc,....

Actually, you've twice ignored where I told you where to find (and in one case even linked you directly to) actual papers that explore that.
 
ANT, you should read the rest of his papers. His debates, though contentious, at Uncommon Descent elaborate a little more as well.

Well, of course he would elaborate more. There's hardly any alternative, is there?

From your post, I don't think you quite get what he saying in that you emphasize homologous structures within DNA whereas he talks of chromosomes in his semi-meiotic hypothesis rearranging DNA more like an evo-devo mechanism which creates more of a saltional effect;

But homology is a concept initially defined for morphology, and which works perfectly well if you consider only morphological data, and which still makes Davison's paper look like the scientific equivalent of the result of a Goodenough-Harris test.

Consider the following, for instance. Following what passes for his logic, the wings of a hummingbird and those of a bumblebee are similar, and thus they are expressions of the same preserved genes that were present in their last common ancestor. However, penguins don't have wings, they have fins, so these would have to originate in another part of the DNA that codes for fins. This would be the same region that codes for fins in seals, perches, thecosomates, plesiosaurs, and shrimp. But wait! There are several groups of birds -- like the Diving-petrels -- that use their front extremities both for flying and for diving, so by Davison's logic, we only have two choices: either wings and fins are expressed in the same way in all animals, or these birds have a mixture of both of them; put in another way, either the genes that make things that function as a wing and those that make things that function as a fin are the same, or both are expressed in the Diving-petrels, without that resulting in them having two pairs of front appendages.

This is pure insanity, but this is exactly what Davison proposes in this paper. He argues that if some part of an animal has the same function as a part of another animal, this is evidence that the genetic information for making these two parts are the same, and have been fed into the ancestral animal by God in long-lost days and remained there unmutated until they were needed several million years later. If you do not see that this is the same thing, then it is you who do not understand the implications of his paper.

hence the comments on lack of variation within genera for horse fossils (despite there being so many fossils I would add).

The words "horse", "genera", and "genus" do not occur in Davison's paper, and the word "variation" occurs only in his quote of Grassé. "Fossil" occurs only once, in an unsubstantiated assertion that there is an "absence of intermediates both in contemporary and in fossil species." I must therefore assume that you are discussing something entirely else here.

Nevertheless, lack of variation within a genus is not surprising, as a genus is per definition a construct which collects organisms that show a great deal of morphological similarity.

He, of course, adds more substantial evidence and observations in his papers.

Against my better judgment, I will download and read those other papers (I have access to the J. Theor. Biol. ones as well, including a response that was published in that journal by M. P. Maguire). This will likely take some time, as his manifesto alone is 56 pages, so I will simply stop looking into the other threads we have both participated in recently. If there is anything there you wish to continue discussing, please transfer it here instead.

analogy? what the heck?

You don't know what analogous organs are in biology? And you lecture other people on their need to learn evolutionary theory? Really, Randman, you could at least have read up and concealed your ignorance.

Except you haven't. Reappearance of specific traits is not what I am talking of but the line of speciation.

Then you will have to elaborate. Are you suggesting that the fact that it never happens that taxon X evolves into taxon Y which evolves into taxon Z which evolves back into taxon X?

If so, the fact that this never happens is precisely what evolutionary theory predicts and is as such not evidence against it. You can imagine a lineage as a train going through a landscape with a virtually unlimited amount of dimensions. At every stop (generation), the train changes direction. Its present location determines which options are available to it at that stop, but the options are still, for all practical purposes, unlimited. The probability that it will return to a previous stop is proportional to the amount of stops it has passed in between, as well as on entirely unpredictable circumstances.

If Davison is correct, then we would see lineages revert to ancestral taxa all the time, because the descendant taxon would still contain all the genetic data needed to make the ancestral taxon. All it would take would be a small change in what genes were expressed during development, and my kids would turn into monkeys. And their kids, if randomness struck again, could turn out to be frogs, or cats, or fruit flies, or velvet worms, or acorns, or bacteria, because they would all contain all the genes needed to develop all these organisms, and all it would take is a change in what genes are expressed and when.

No more improbable or slightly more so than many other claims of evos such as the magical origin of the genome in the first place;

Evolutionary theory suggests no origin of the genome in the first place. Evolutionary scientists may speculate, but the theory is silent on it, in the same way that it is silent on gravity or politics. It is a separate field which is, by definition, outside the scope of evolutionary theory.'

that mutations via random mutation increase genetic variation over the observed loss of genetic variation due to natural selection, subgroup isolation and genetic drift; etc, etc,....

Subgroup isolation, as Dinwar has told you, is not in any way correlated to statements of the genetic variation in this subgroup. A subgroup that is isolated from the mother population may have higher relative genetic variation than the mother population, it may have lower relative genetic variation, or it may have exactly the same relative genetic variation.

Random mutations do increase genetic variation in any given population that is subject to the same genetic processes as a standard population. Over time, these will give rise to genetic variation (supposing the population survives) regardless of the initial genetic variation at the isolation event.

Has it occurred to you that perhaps the reason we don't see examples of the common ancestor in any grouping by and large (can you name one for animals?) is not that the parent species went extinct? In other words, why would the parent species not also split off and reverse speciation into what it was before?

This question makes no biological sense. When a population splits, both subpopulations by definition are daughter populations. This does not work like a family, where the mother is still there after having given birth to the daughter. Phylogenetics is more or less per definition asexual, and each division gives rise to two daughter populations, one or both of which is initially largely identical to the mother population, but both of which due to known evolutionary processes over time will typically diverge.

You seriously need to sort out your terminology.
 
They don't compare the 2. But if you disagree, please cite them again with the relevant passages in quotes below.
 
Well, of course he would elaborate more. There's hardly any alternative, is there?



But homology is a concept initially defined for morphology, and which works perfectly well if you consider only morphological data, and which still makes Davison's paper look like the scientific equivalent of the result of a Goodenough-Harris test.

Consider the following, for instance. Following what passes for his logic, the wings of a hummingbird and those of a bumblebee are similar, and thus they are expressions of the same preserved genes that were present in their last common ancestor. However, penguins don't have wings, they have fins, so these would have to originate in another part of the DNA that codes for fins. This would be the same region that codes for fins in seals, perches, thecosomates, plesiosaurs, and shrimp. But wait! There are several groups of birds -- like the Diving-petrels -- that use their front extremities both for flying and for diving, so by Davison's logic, we only have two choices: either wings and fins are expressed in the same way in all animals, or these birds have a mixture of both of them; put in another way, either the genes that make things that function as a wing and those that make things that function as a fin are the same, or both are expressed in the Diving-petrels, without that resulting in them having two pairs of front appendages.

This is pure insanity, but this is exactly what Davison proposes in this paper. He argues that if some part of an animal has the same function as a part of another animal, this is evidence that the genetic information for making these two parts are the same, and have been fed into the ancestral animal by God in long-lost days and remained there unmutated until they were needed several million years later. If you do not see that this is the same thing, then it is you who do not understand the implications of his paper.



The words "horse", "genera", and "genus" do not occur in Davison's paper, and the word "variation" occurs only in his quote of Grassé. "Fossil" occurs only once, in an unsubstantiated assertion that there is an "absence of intermediates both in contemporary and in fossil species." I must therefore assume that you are discussing something entirely else here.

Nevertheless, lack of variation within a genus is not surprising, as a genus is per definition a construct which collects organisms that show a great deal of morphological similarity.



Against my better judgment, I will download and read those other papers (I have access to the J. Theor. Biol. ones as well, including a response that was published in that journal by M. P. Maguire). This will likely take some time, as his manifesto alone is 56 pages, so I will simply stop looking into the other threads we have both participated in recently. If there is anything there you wish to continue discussing, please transfer it here instead.



You don't know what analogous organs are in biology? And you lecture other people on their need to learn evolutionary theory? Really, Randman, you could at least have read up and concealed your ignorance.



Then you will have to elaborate. Are you suggesting that the fact that it never happens that taxon X evolves into taxon Y which evolves into taxon Z which evolves back into taxon X?

If so, the fact that this never happens is precisely what evolutionary theory predicts and is as such not evidence against it. You can imagine a lineage as a train going through a landscape with a virtually unlimited amount of dimensions. At every stop (generation), the train changes direction. Its present location determines which options are available to it at that stop, but the options are still, for all practical purposes, unlimited. The probability that it will return to a previous stop is proportional to the amount of stops it has passed in between, as well as on entirely unpredictable circumstances.

If Davison is correct, then we would see lineages revert to ancestral taxa all the time, because the descendant taxon would still contain all the genetic data needed to make the ancestral taxon. All it would take would be a small change in what genes were expressed during development, and my kids would turn into monkeys. And their kids, if randomness struck again, could turn out to be frogs, or cats, or fruit flies, or velvet worms, or acorns, or bacteria, because they would all contain all the genes needed to develop all these organisms, and all it would take is a change in what genes are expressed and when.



Evolutionary theory suggests no origin of the genome in the first place. Evolutionary scientists may speculate, but the theory is silent on it, in the same way that it is silent on gravity or politics. It is a separate field which is, by definition, outside the scope of evolutionary theory.'



Subgroup isolation, as Dinwar has told you, is not in any way correlated to statements of the genetic variation in this subgroup. A subgroup that is isolated from the mother population may have higher relative genetic variation than the mother population, it may have lower relative genetic variation, or it may have exactly the same relative genetic variation.

Random mutations do increase genetic variation in any given population that is subject to the same genetic processes as a standard population. Over time, these will give rise to genetic variation (supposing the population survives) regardless of the initial genetic variation at the isolation event.



This question makes no biological sense. When a population splits, both subpopulations by definition are daughter populations. This does not work like a family, where the mother is still there after having given birth to the daughter. Phylogenetics is more or less per definition asexual, and each division gives rise to two daughter populations, one or both of which is initially largely identical to the mother population, but both of which due to known evolutionary processes over time will typically diverge.

You seriously need to sort out your terminology.

Response to Kot above:


Lots of words but you'd save time not creating straw men. For example you write;

Consider the following, for instance. Following what passes for his logic, the wings of a hummingbird and those of a bumblebee are similar, and thus they are expressions of the same preserved genes that were present in their last common ancestor. However, penguins don't have wings, they have fins, so these would have to originate in another part of the DNA that codes for fins.

You veer off when saying "they are the expressions of the same preserved genes." He does not say that. Could be. But that's adding a little bit of your paradigm and making an assumption.

Btw, are they expressions of the same preserved genes?

However, penguins don't have wings, they have fins, so these would have to originate in another part of the DNA that codes for fins.

Why would they have to?

You are oversimplifying Davison's claims in ways he is not since he advocates a rearranging via the chromosomes. But if the idea was that the bee and hummingbird had to have the same preserved genes, this would also likely apply to the penguin since he is not advocating natural selection as particularly significant.

A subgroup that is isolated from the mother population may have higher relative genetic variation than the mother population,

Prove it. That's not what standard evo theory says, at least not right after the isolation. Dinwar showed no such thing.
 
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There is non-functional DNA, just because some of what was thought to be junk isn't, does not mean some of it isn't.

Paul

:) :) :)

The fact what was thought to be junk DNA turned out to be highly conserved is evidence FOR evolution, not against evolution theory. Because someone didn't or doesn't know what function that DNA serves or why it is conserved is not relevant to evolution theory. What role the DNA serves is relevant to the details of evolution theory, but not to the validity of the theory. Nothing in the junk DNA refutes the evolution process. and what people knew or didn't get right hypothesizing about that DNA is definitely not relative to the validity of evolution theory.

It's akin to saying Darwin didn't understand the role of DNA and that argues against evolution theory. It does not follow.
 
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