Vanderzyden

Doubting Didymus has taken it upon himself to make the outrageous and grossly inaccurate accusation of libel. 'Tis a serious charge.

I wonder, why is he so bent on these accusations? Perhaps he feels he must defend science. Or, could it be yet another way to avoid discussing difficult issues?

To avoid fragmenting this <a href="http://iidb.org/ubb/ultimatebb.php?ubb=get_topic&f=58&t=001379&p=2" target="_blank">thread</a>, I'm starting another.

So, taxonomy = phylogeny. Is that what you're saying?

You are so very wrong. You don't know me. You don't have a pattern. You don't even have a case. And yet all this distracting comes from your direction.

No, I used the quotations to demonstrate the confusion that is prevalent in phylogeny studies. The sources are reliable, and the context still holds. No matter how you read those papers, the confusion and disagreement is crystal clear. Phylogeny is an utterly ridiculous enterprise. Naturalists would do better to develop another heuristic, since it doesn't comport with all available evidence.

Now, in regard to your vitriol: why do you get so upset? I see that you have made some good points, but then you go ballistic over something that is a non-issue, anyway. Your gross presumptions give way to the shameful tone you continue to maintain.

You seem to be the type who gets bogged down in legalistic details. Just because I don't quote the entire article doesn't mean I am committing a false representation. You are simply upset because I demonstrate that there is rampant disagreement in phylogeny, despite its use as a major pillar of Darwinism.

Let me ask you: are you the judge of who has a good or bad name? Have you been designated the ethics police in these forums? Do you think I care about my reputation in the way you apparently do? No, I care about the truth. I want to face things. I want to uncover confusion and disarray and misunderstanding and narrow thinking. I am not afraid of the consequences of searching ernestly for the truth. Part of that task involves exposing problems.

This is the extent of all I need to say. My intent with the comments directed at you in the other thread was to show an inconsistency (which still remains). Furthermore, DD, if you choose to take the insulting tone again, you will understand why I withdraw from you yet again.

Vanderzyden

Doubting Didymus

So, to be clear: you claim that the quotes you use were used in good faith, in true context, are completely applicable to phylogenetic trees at the eukaryotic level and higher, and accurately represent the opinions of those who wrote them?

Doubting Didymus

Those readers who are interested may look <a href="http://scienceweek.com/search/reports1/gastamp.htm" target="_blank">here</a> for one of the articles vander quoted from. Vander quoted point 2, except for the part about "the clonal theory began to crumble when..."

Vander, I consider that you are now cleared of deliberate misrepresentation. It is obvious to me that you simply did not understand the context. I apologise formally for being vitriolic, but your persistance in not adressing this issue caused suspicion. (not just in me, I should add, but in a variety of other posters, most of whom gave up after you would not contribute to the last thread about this issue.)

What this article is really saying is that Rna phylogenetic trees can not apply to early prokaryotic organisms, simply because they are constantly exchanging genetic material. This is not anything to do with traditional phylogeny at the level of more complex organisms, such as animals, who do not exchange genes other than to breed a new organism.

The 'clonal theory' referred to in this case is simply the theory that eukaryotes evolved directly from prokarotes via ordinary asexual reproduction, selection, and mutation. (This is not to be confused with the clonal selection theory, which is to do with immune systems, I think). Phylogeny, in this case, is what disproved the clonal theory. It is the clonal theory that was disproven, not phylogeny.

Basically, we now know that phylogeny is not applicable to many prokaryotes, because they do strange and unusual things like exchange genes or become endosymbionts.

Doubting Didymus

I think my last post was quite polite. Are you planning to respond?

Vanderzyden

Yes, it was, and I appreciate it.

This isn't the source I quoted in this <a href="http://iidb.org/ubb/ultimatebb.php?ubb=get_topic&f=58&t=001305&p=1" target="_blank">thread</a>
Actually, Automaton had provided this <a href="http://cas.bellarmine.edu/tietjen/Diversity/mix_and_match_in_the_tree_of_lif.htm" target="_blank">link</a>in response, which is the correct one.

In the opening paragraph, we find:


The concluding remark:

Clearly, the authors are claiming an upset of old paradigms, but then they do nothing to establish a new one. It is speculation.

Other concerns include:

Let me ask you a question:

Are you saying that phylogenetic compilations and comparisons are to any degree reliable? How can they be, since the only real data comes from living things?

My contention is that confusion abounds. Yet phylogeny is touted as solid support for Darwinism. That doesn't make sense.

Vanderzyden

{edited so the links don't distort the page for formatting reason - scigirl}

[ September 12, 2002: Message edited by: scigirl ]</p>

Doubting Didymus

Phylogenetic comparisons are usually reliable, yes. You propose a hypothetical tree based on structural similarity or the fossil record, sequence the genes, and see if the organisms' genes are as similar or different as they should be.

Usually the trees that result from RNA comparison agree with the trees produced by other forms of genetic phylogeny. The case of organisms at the very simple levels of bacteria and archea genetic phylogeny is much more problematic because of things like lateral gene transfer. Even early eukarya have this problem. After all, it is theorised that some of the eukaryotic cells' organelles were once prokaryotic endosymbionts. What would you expect if you tried to compare the genes in the eukaryotic cell with a bacteria that was descended from the same ancestor as the endosymbiont? you would expect some nasty phylogenetic problems. The same problems simply do not occur at the animal level.

You will notice that all of the controversy you cite is to do with these early organisms. The controversy among animal and plant phylogenetics is usually to do with fairly mundane things like whether velvetworms should be arthropods. As I pointed out in other threads, the names of the taxonomic groups are chosen by humans. They mean: 'everthing in this group is descended from the same ancestor'. So its natural than an organism that diverged from the same general area around the same time will be on the 'edge' of a taxonomic group, thus leading to controversy.

This kind of confusion does not detract from evolution. They are almost entirely a matter of semantics.

As for the only evidence coming from living animals, why does this matter? historians could conduct historical research without referring to original texts. Accurate translations and copies will do just fine, thank you.

I am not sure what you think of the modern computer programs that use artificial human selection coupled with random mutaion to produce 'pictures' of animals, but if you were to be shown a group of organisms that were generated in this way, you could conduct a phylogeny on their simulated genes to see which are most related, without using any information from the ancestral forms.

Vanderzyden

Yes, you repeatedly mention the fossil record. However, the global fossil record contains a major obstacle for phylogenetics: the Cambrian boundary, also known as the "explosion". Surely you know that numerous studies have demonstrated the difficulties presented by the abrupt absence of complex biological relics below the Cambrian era. This is perhaps the most devastating contradictory evidence for phylogeny (and one category of positive evidence for directed simultaneous biological instantiation--that is, special creation).

Here is a nice <a href="http://www.mhhe.com/biosci/pae/zoology/animalphylogenetics/toc.mhtml" target="_blank">summary</a>of overall difficulties inhibiting phylo. research, from the publisher McGraw-Hill. Yes, claims of potential future success continue unabated, but immense problems still persist:

-- Molecular phylogenetics refers to any method of inferring evolutionary relationships from similarities or differences in molecular structure.
-- Molecular characters suffer from problems that also afflict morphological characters. For example, neither molecules nor morphology may be able to resolve the phylogeny of evolution that was both ancient and rapid, as in the Cambrian Explosion.
-- Another problem shared by molecular and morphological characters is homoplasy (nonhomologous characters appearing to be similar in different taxa).
-- Other problems shared by molecular and morphological phylogenetics arise from polymorphism (homologous characters appearing differently in the same species). Because of polymorphism, the time of divergence may appear to be earlier than it was.
-- Polymorphism can also result in the incorrect phylogenetic sequence.
-- Similar problems result from different copies of duplicated genes.
-- Another problem with molecular phylogenetics is long-branch attraction: the tendency of fast-evolving molecules to appear more closely related than they actually are.
-- Molecular phylogenetics has gained wide acceptance in spite of these and other problems because it provides a large amount of evidence that is independent of morphology, as well as other advantages.
...
-- Because of long-branch attraction, differences in sequence alignment, limitations in the size of study groups, and different methods of tree reconstruction, conflicting molecular phylogenies have been proposed. As techniques have improved and more molecules from more species have been sequenced, many of the past conflicts have been resolved.

(Several "resolutions" follow in the list, accompanied by even more problems!)

Vanderzyden

ps418

'Complex biological relics' appear well below the base of the Cambrian. They are known both from fossils and trace fossils. The so-called Ediacaran fauna existed for some ~30 million years prior to the Cambrian. The morphologically simplest animal phyla -sponges and cnidarians-- have been identified in Precambrian also, showing that they originated well before the Cambrian.

This is NOT to minimize the magnitude and abruptness of the CE, of course, only to say that more recent paleontology makes it seem a lot more comprehensible. Grotzinger et al (Biostratigraphic and Geochronologic Constraints on Early Animal Evolution, 1995, p. 603-604) write:

Also, I take it that you do not consider bacteria and protists to be 'complex,' since they are known from ~4By and ~2By, respectively, and ruled the world for a long before the first animals showed up.

The use of the word 'simultaneous' is inaccurate. The Cambrian 'Explosion' occurred over millions of years, and was many thousand times longer than all of recorded history. It is 'rapid' only when seen in the context of all of geologic history.

What's more, even within a creationist context, the appearance of many phyla within a few million years does not necessarily indicate special and seperate creation of each phylum rather than, say, directed diversification of the phyla from a common ancestor.

For instance, one could still hold that all of the Cambrian forms are indeed descended from a common animal ancestor (e.g. one of the Ediacaran stock), and that the CE merely represents the intelligent manipulation of that preexisting stock (e.g. by adding or modifying some genes) to produce the diversification of phyla, rather than the seperate creation of the Cambrian phyla seperately. This would be more compatible with the morphological similarities amongst the Cambrian representatives of supposedly seperately-created phyla, as described in the links below.

<a href="http://www.asa3.org/ASA/topics/Evolution/PSCF12-97Miller.html" target="_blank">The Precambrian to Cambrian Fossil Record and Transitional Forms</a>

<a href="http://www.asa3.org/ASA/PSCF/2001/PSCF3-01Morton.html" target="_blank">Transitional Forms and the Evolution of Phyla</a>

<a href="http://cas.bellarmine.edu/tietjen/Ecology/early_animal_evolution.htm" target="_blank">Early Animal Evolution: Emerging Views from Comparative Biology and Geology </a>

Doubting Didymus

PS beat me to the precambrian fossils, but I will address what you consider to be inhibitions to phylogeny.

Do you think that phylogenists just ignore these problems? No, these are well known obstacles that every phylogenist keeps in mind when they are conducting their research. No science is free from hurdles like these, and it is perfectly natural that a historical field trying to discover what happened thousands of millions of years ago is difficult to practice, but as the article says, as techniques improve, past conflicts dissapear.

You could find a list like this addressing any science. Science is always tentative and revisive.

Yes, it's true that there are sometimes modern controversies about phylogenetic trees, but they don't normally last long. The same is true for all science.

Also, I would like to summarise PS's points:

The cambrian explosion is millions of years long.
There are many fossils from well before the cambrian explosion
The cambrian explosion does not represent the sudden appearance of organisms, but only the first organisms that developed a hard body. Naturally, when this first developed, the hardbodied decendants rapidly took over.

I agree that, if the cambrian explosion was what you think it is, it may well be evidence against evolution and for some kind of instantaneous biogenesis. However, what is it about the cambrian that you think suggests the involvement of any kind of designer?

Also, what about the main point of this thread? Can you or can you not see that the quotes you posted have nothing to do with multicellular eukaryotic phylogeny?

Baloo

Phew... glad I'm not the only one able to spot glaringly obvious red herrings. For the sake of amusement, I encourage people to compare and contrast: