Evolution: the Facts.

[randman]

At this point, you should be able to predict the response. Come on now. Say it with me:

Evidence?

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.

 

[randman]

Ah, so you can't back your assertion up at all, then? Seems not.

If there is something in phylogeny which is not as the theory of evolution would predict, then you should be able to demonstrate what that is.



Not the claim you made. Your assertion was: "[...]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[...]". Now, can you substantiate that claim or not? Either substantiate it or retract it. This thread, after all, is concerned with science. And, as I've pointed out to you before, if you're making statements that even you realise you have to qualify with an "imo", then what you're posting is opinion, not science.

So, can you show scientific evidence that phylogeny contradicts the theory of evolution by natural selection, or are you going to retract that statement?

Already substantiated it but it went right over your head. Not my fault at this point. You aren't even trying to understand.

 

[randman]

Hybredization in plants often adds whole genomes to the plants. This is obviously added information (and, incidently, one of the reasons why randman's definition of species is horribly, horribly insufficient).

First off, I have never presented my own definition of species. Species and higher taxa are evolutionist terms, just in case you failed to grasp that.

Under all definitions of species used by science, sequential speciation is what Neodarwinism says happened.

 

[randman]

Natural selection often acts as a stabilizing force. As Gould and Eldretch put it, "Stasis is data"-

So when an evo says "stasis is data" but when someone else says "stasis is data", it's not.

And you guys call that science?

 

[randman]

Has anyone mentioned the Long Term Evolution experiment yet?

Randman, this can demonstrate how quickly evolution can happen. There has been a long time for evolution to occur.

Yea, bacteria evolve very quickly, or microevolve very quickly, but has been a stable form for over 500 million years according to evos.

Pierre Grasse used this point to show how silly NeoDarwinism is, and one reason he called it "the myth of evolution."

 

[ehcks]

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.

The chance of any specific mutation event is incredibly low. The chance of a second mutation event exactly inverse of the first is incredibly low squared.

 

[Sideroxylon]

Randman, could you please use the quote button. It would make following this thread a lot easier.

 

[Kotatsu]

Already stated.

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.

The "pattern" refers to the whole pattern, not just single "trees."

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.

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.

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.

Second, subgroup isolation (microevolution) entails a decrease in genetic variability.

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.

But since you yourself haven't grasped that sequential speciation is the process of how evos claim the higher taxa evolved, it's not worth taking the time to go further. You'd have to understand that's basic evo theory and haven't seen you do that yet.

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.

 

[Dinwar]

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

A great link, but I will say that it's not complete as of yet. I know a few people still working on the arthropod side of the tree.

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.

Mostly because it's an overly generalized statement which is unsupportable. The thing is, genetic isolation says NOTHING about diversity. An isolated population can have more, less, or an equal amount of variation, because there's no causal connection between the concepts.

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.

Thank you! Also, the first chapter of "The Origin of the Phyla", but Dr. Valentine, is devoted to this exact concept.

 

[randman]

Guess who said this Dinwar (without googling it).

As you'll see ..., both types of transitions often result in a new "higher taxon" (a new genus, family, order, etc.) from a species belonging to a different, older taxon. There is nothing magical about this. The first members of the new group are not bizarre, chimeric animals; they are simply a new, slightly different species, barely different from the parent species. Eventually they give rise to a more different species, which in turn gives rise to a still more different species, and so on, until the descendents are radically different from the original parent stock.

So sequential speciation is how evos think the higher tax evolved.

 

[randman]

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.

I have already substantiated it. You just don't seem capable of grasping the basic concepts involved. Sequential speciation is how evos imagine the higher taxa involved. This involves subgroup speciation, which decreases genetic variability. Genetic variability is considered by evos themselves to be critical to an organisms ability to survive and evolve further.

Evos have never shown the rate of decrease of genetic variability through sub-group isolation is lower than beneficial mutation rates and if you'd take a step back and consider the slow rates of mutation, even the highest estimates, you'd see why this point is valid.

There are other reasons. Macroevolution, if it occurred, seems to be an irreversible process buy allelic mutation being random has no direction. Macroevolution does not appear to be happening any more. I could go on but you'd have to get some basic concepts on what NeoDarwinism says and does not say in order to continue.

 

[randman]

The chance of any specific mutation event is incredibly low. The chance of a second mutation event exactly inverse of the first is incredibly low squared.

So how do you explain convergent evolution since the probability is so low for mutations to repeat?

 

[randman]

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.

Take a look a map of phylogenetic trees carefully. First note the common ancestor is always missing. Second, macroevolution appears to have stopped. No new kingdoms and phyla for a long time. No duplicates of a bacteria evolving again from a different source. No reversibility. Macroevolution, and this assumes common, descent appears to happen in irreversible pulses that peter out and end.

 

[Squeegee Beckenheim]

Already substantiated it but it went right over your head.

No you haven't. Be specific. Mention specifics. Actually provide some evidence in support of your claims. Again, you claim that your opinions are based on the science, so it should be a doddle for you to actually be specific. Why are you completely unable to do so?

 

[Squeegee Beckenheim]

Take a look a map of phylogenetic trees carefully. First note the common ancestor is always missing. Second, macroevolution appears to have stopped. No new kingdoms and phyla for a long time. No duplicates of a bacteria evolving again from a different source. No reversibility. Macroevolution, and this assumes common, descent appears to happen in irreversible pulses that peter out and end.

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.

 

[randman]

Not my fault if you can't read there, bud. I give you evidence and then you say I gave no evidence without any explanation whatsoever, not even that you understood the points being made.

You guys act like you never even heard the NeoDarwinian, etc,....Learn what your side believes first; then take a little while to learn what others believe, and then we can have an intelligent discussion.

This might help you, something written by evos, not me. I am just quoting it.

As you'll see ..., both types of transitions often result in a new "higher taxon" (a new genus, family, order, etc.) from a species belonging to a different, older taxon. There is nothing magical about this. The first members of the new group are not bizarre, chimeric animals; they are simply a new, slightly different species, barely different from the parent species. Eventually they give rise to a more different species, which in turn gives rise to a still more different species, and so on, until the descendents are radically different from the original parent stock.

So sequential speciation is how evos think the higher tax evolved.

 

[Squeegee Beckenheim]

Not my fault if you can't read there, bud. I give you evidence and then you say I gave no evidence without any explanation whatsoever, not even that you understood the points being made.

You have given no evidence to support the assertion that phylogenic groupings aren't what the theory of evolution would predict. You've hand-waved around, trying to distract people (or, perhaps, trying to convince yourself), but that is the statement you made, and that is the statement you're being asked to provide evidence to support. You've been given more than one very simple way to unequivocally support your assertion with evidence, if evidence actually exists, and have thus far utterly ignored what should be a fantastic opportunity for you to demonstrate how your assertion is not only correct, but backed up by solid empirical evidence.

So sequential speciation is how evos think the higher tax evolved.

This has nothing to do with your assertion that phylogenic groupings aren't what the theory of evolution predicts. Please don't try to change the subject. Provide evidence to support your statement.

 

[randman]

As you'll see ..., both types of transitions often result in a new "higher taxon" (a new genus, family, order, etc.) from a species belonging to a different, older taxon. There is nothing magical about this. The first members of the new group are not bizarre, chimeric animals; they are simply a new, slightly different species, barely different from the parent species. Eventually they give rise to a more different species, which in turn gives rise to a still more different species, and so on, until the descendents are radically different from the original parent stock.

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

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?

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.

 

[Squeegee Beckenheim]

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?

What I do or do not understand has no relevance on whether you can post evidence in support of your assertion or not. You have been given the protocol by which you can do this.

 

[Kotatsu]

A great link, but I will say that it's not complete as of yet. I know a few people still working on the arthropod side of the tree.

Yes, I saw that Neoptera is just a hideously large polytomy, for instance, and Phthiraptera is just a list... but nevertheless, as randman is going to show us groupings in the general pattern, I think this will still be a sufficiently resolved source, as long as we keep in mind that it is a consensus tree.

Mostly because it's an overly generalized statement which is unsupportable. The thing is, genetic isolation says NOTHING about diversity. An isolated population can have more, less, or an equal amount of variation, because there's no causal connection between the concepts.

I am not convinced that his argument has any bearing on the strength of any given phylogenetic tree as evidence for evolutionary theory even if there was such a link, but at the moment it's getting to late for me to think about it properly.

I have already substantiated it. You just don't seem capable of grasping the basic concepts involved. Sequential speciation is how evos imagine the higher taxa involved.

I don't understand why you keep mentioning this, as that is nothing I am disputing. What I am disputing is your claim that you have shown groupings in any phylogenetic tree -- even the global consensus tree to which I linked -- which would not be predicted by evolutionary theory. If you have shows any such groupings, please link to them again, as I must have missed them.

This involves subgroup speciation, which decreases genetic variability. Genetic variability is considered by evos themselves to be critical to an organisms ability to survive and evolve further.

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.

There are other reasons. Macroevolution, if it occurred, seems to be an irreversible process buy allelic mutation being random has no direction.

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.

Macroevolution does not appear to be happening any more.

Would you care to support this assertion?

So how do you explain convergent evolution since the probability is so low for mutations to repeat?

This statement does not contain a contradiction. Convergent evolution does not imply that any given gene in two distantly related lineages have mutated into the same gene. It implies that two distantly related lineages show great morphological similarities, but these may have come about by vastly different genetic routes. For instance, if two groups of birds have both lost their colour and become all white, this could be because one lineage has had a mutation in the genes that produce pigment, whereas the other has one in the gene that transports the pigments from their point of manufacture to the feathers. The two would be said to have undergone convergent evolution, but their genetic sequences would still be very different.

Take a look a map of phylogenetic trees carefully. First note the common ancestor is always missing. Second, macroevolution appears to have stopped. No new kingdoms and phyla for a long time. No duplicates of a bacteria evolving again from a different source. No reversibility. Macroevolution, and this assumes common, descent appears to happen in irreversible pulses that peter out and end.

While I appreciate that you have condensed your confusion, allowing me to address all of it without having to use the quote button multiple times, I'd rather you'd forgo this service and instead expound on your novel theories on how evolution, phylogeny and taxonomy works. If I may make a suggestion, I would recommend that you answer specific points I make, rather than just sum up everything at the end. This gives at least the impression that you have read anything I write.

Now:

Take a look a map of phylogenetic trees carefully. First note the common ancestor is always missing.

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.

Feel free to show me a phylogenetic tree that doesn't include common ancestors. As I said, I have access to most of the major journals where phylogenies would be published, so even a reference would be enough. And if I can't get it, I am sure I could get help from someone else in the thread, or simply write the author and ask for it. So don't feel constrained on my behalf when selecting examples.

Second, macroevolution appears to have stopped. No new kingdoms and phyla for a long time.

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.

No duplicates of a bacteria evolving again from a different source.

You mean that no organism has ever evolved into a bacterium? Yes, that is certainly true, but it is a tautology, as a given taxonomic category ideally contains only the descendants of a single common ancestor. Even if your descendants evolve into something that for all practical purposes is indistinguishable from a bacteria, you would still not be classified as one, as you do not have a shared exclusive evolutionary history with other bacteria.

No reversibility.

There are countless examples of reversibility, if by this you mean that a certain feature is first evolved, and then lost again in subsequent generations. If you imply a different meaning, please explain.

Macroevolution, and this assumes common, descent appears to happen in irreversible pulses that peter out and end.

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 guys act like you never even heard the NeoDarwinian, etc,....

Again, you are too caught up in what others know and don't know. For the purposes of this discussion, I am entirely uninterested in knowing what Sceptic Tank, Dinwar, or anyone else arguing against you knows or doesn't know about evolution. I am interested only in what you know about it. I am a professional biologist, and work with evolutionary theory every day. You claim to be able to show that what I am doing is either fraudulent or at least pointless. I do not care to be neither a fraud, nor a waste of taxpayers' money, so if you truly have this data, you would genuinely do me a great service if you presented it, and thus allowed me to review my career choices and perhaps change tracks into something more useful. I have, for instance, recently taken up pottery, which I find very rewarding.

Why you continue to be reluctant to do me this service is beyond me. Had I known you personally, I might even have claimed it to be rude.

Learn what your side believes first; then take a little while to learn what others believe, and then we can have an intelligent discussion.

I will agree that under the circumstances, it is hard to have an intelligent discussion here.