Nested hierarchies and phylogenies

JOHN PAUL John Paul
Main Entry: phy·log·e·ny
Function: noun
Inflected Form(s): plural -nies
Etymology: International Scientific Vocabulary
Date: 1872
1 : the evolutionary history of a kind of organism
2 : the evolution of a genetically related group of organisms as distinguished from the development of the individual organism
3 : the history or course of the development of something (as a word or custom)

and from a website: http://phylogeny.arizona.edu/tree/home.pages/whatisphylogeny.html)

What is phylogeny?

Throughout the evolutionary history of life many things have happened: organisms have consumed, been consumed, made babies, interacted with other organisms, and through the years, they have evolved. An important component of this evolutionary history is the passage of genetic information from parent to offspring.

The genetic connections among organisms within a species that reproduces sexually form a tangled web, through the generations of interbreeding. However, these genetic connections do not extend much between species, and so, through time, each species is descends like a bundle of genetic connections isolated from other such bundles.

Each species is therefore a reproductive community. Occasionally, by various causes, a species might be broken into two isolated reproductive communities. The two isolated reproductive communities become separate species, and each becomes its own isolated bundle of genetic connections.

One species makes two, those two each make more, and so on. This process gives rise of a tree of species lineages descending and splitting. At the same time, some of the species go extinct, thus pruning the growing tree. In the end, this process has produced the many species of organisms we see around us today.

The notion that all of life is genetically connected via a vast phylogenetic tree is one of the most romantic notions to come out of science. How wonderful to think of the common ancestor of humans and beetles. An ancestral worm species was divided in two. Little did they know those hundreds of million years ago that some of their number would end up evolving into beetles, while their brothers and sisters would end up as humans.

This should put an end to people saying using phylogeny as evidence for the ToE is not circular reasoning. Clearly it is circular reasoning. Denying it doesn't make it go away.

EDGE
Who said that?


JOHN PAUL
[ John Paul then proceeds to quote from an earlier exchange:]
John Paul:
As I have stated before, phylogeny is a science that assumes the ToE is indicative of reality. Using phylogeny as evidence for the ToE is therefore circular reasoning.

Ben:
That isn't true. Phylogeny existed before evolution, so how can phylogeny have existed when evolution didn't.
Simple, regardless of how you think creatures came about, it is obvious that their forms and structure form some sort of a tree. This pattern, along with the time pattern of the fossil record and the pattern in DNA lead to the conclusions of evolution.


Also Pat keeps using the phylogeny argument- over and over...


EDGE
As I have stated before, phylogeny is a science that assumes the ToE is indicative of reality. Using phylogeny as evidence for the ToE is therefore circular reasoning.

I see nowhere in your definition that phylogeny is a science.

Your point may be true, but the fact that we CAN produce a phylogeny of organisms that correlates with a relative time scale IS evidence for evolution. Perhaps not very strong, but evidence nonetheless. It is at least as strong as the old irreducibility argument you like to trot out. After all, there is no other way to explain the fossil record in its entirety, if you understand it, that is.


MILAN
The webpage you quoted is good, but it only contains a concise definition of the term; it doesn’t describe the enormous amount of data that supports phylogenetic models.

To put it briefly, phylogeny is the set of ancestor to descendant relationships that connect all things that have ever lived.
From the phylogenetic tree we can make a series of predictions that are confirmed experimentally:

1. the fundamental unity of life (common genetic code, or minor variations thereof, similar metabolic mechanisms, similar chemistry)

2. the nested hyerarchy of species

3. the convergence of independent phylogenies

4. the chronological order of intermediates, as evidenced by the fossil record, etc etc.

That is what people mean when they say that phylogeny supports evolution: that the predictions made by the assumptions of phylogeny are confirmed by the data.

That is the way science works, by building a model that makes predictions. And then making observations or experiments that put the predictions to test. So far no experiment or observation has refuted evolution.
For more info on this fascinating area of reseaarch have a look for instance at www.talkorigins.org.


MR. BEN
From the "History" page of the linean society in London.

The Linnaean Society of London, founded in 1788, takes its name from the Swedish naturalist Carl Linnaeus, whose botanical and zoological collections and library have been in the Society's keeping since 1829, having been purchased for the executor of the Society's first President, Sir James Edward Smith.

Linnaeus was born in 1707, the son of a Lutheran clergyman, at Rashult in Sweden. He began to study medicine at the University of Lund in 1727, transferring to the university of Uppsala the following year. Linnaeus headed an expedition to Lapland in 1732, travelling 4,600 miles and crossing the Scandinavian Peninsula by foot to the Arctic Ocean. On the journey he discovered a hundred botanical species. In 1734, he mounted another expedition to central Sweden. He finished his medical degree at the University of Hardewijk in Holland in 1735, then going to the University of Leiden for further studies. That year, he published Systema Naturae, his classification of plants based on their sexual parts. His method of binomial nomenclature using genus and species names was further expounded when he published Fundmenta Botanica and Classes plantarum. This system used the flower and the number and arrangements of its sexual organs of stamens and pistils to group plants into twenty-four classes which in turn are divided into orders, genera and species.


Phylogenic taxonomy predated any theory of evolution by more than 50 years. In fact, it was the raw data from this effort to classify species which suggested to several people (Darwin included) that there was an underlying pattern to explain the linean branching tree.
We now accept that the pattern behind taxonomy is evolution, and that the obvious similarity between organisms that Linnaeus recognized is not simply by chance.

So, how can a system of classification that existed 'long before' evolution was ever devised somehow be a circular argument for evolution?????


JOHN PAUL
milan:
The webpage you quoted is good, but it only contains a concise definition of the term; it doesnt describe the enormous amount of data that supports phylogenetic models.

John Paul:
All it was supposed to offer is the definition, nothing more.

Milan:
To put it briefly, phylogeny is the set of ancestor to descendant relationships that connect all things that have ever lived.

John Paul:
Right. In other words it assumes the ToE is indicative of reality. That is what I said.

Milan:
From the phylogenetic tree we can make a series of predictions that are confirmed experimentally:
1. the fundamental unity of life (common genetic code, or minor variations thereof, similar metabolic mechanisms, similar chemistry)

John Paul:
The ToE didn't predict living organisms even had a genetic code, so any 'prediction' of its being common is bogus.

2. the nested hyerarchy of species

John Paul:
As assumed by man...

3. the convergence of independent phylogenies

John Paul:
As assumed by man...

4. the chronological order of intermediates, as evidenced by the fossil record, etc etc.

John Paul:
Chronological order? How do you figure? What is your idea on how the fossil record came to be?

Milan:
That is what people mean when they say that phylogeny supports evolution: that the predictions made by the assumptions of phylogeny are confirmed by the data.

John Paul:
Like I said- phylogeny was set up assuming the ToE was indicative of reality.

Milan:
That is the way science works, by building a model that makes predictions. And then making observations or experiments that put the predictions to test. So far no experiment or observation has refuted evolution.

John Paul:
How can any of those experiments be verified? I would love to see an experiment for a procaryotic cell 'evolving' into a eucaryotic cell....

Mr Ben:
Phylogenic taxonomy predated any theory of evolution by more than 50 years. In fact, it was the raw data from this effort to classify species which suggested to several people (Darwin included) that there was an underlying pattern to explain the linean branching tree.

John Paul:
Wow. According to all the sources I have checked, the word 'phylogeny' originated in 1872, which by my math, is13 years after Darwin's 'Origins of species..' was released.

Mr Ben:
We now accept that the pattern behind taxonomy is evolution, and that the obvious similarity between organisms that Linnaeus recognized is not simply by chance.

John Paul:
Linnaeus was a Creationist so I guess the obvious similarity is due to a Common Creator.

Mr Ben:
So, how can a system of classification that existed 'long before' evolution was ever devised somehow be a circular argument for evolution?????

John Paul:
It looks like you are talking about two different things. How could 'phylogeny' exist before the ToE when the ToE came out in 1859 and the word 'phylogeny' came out in 1872? Do the math....


EDGE
Actually, the word was coined in 1866, by Haeckel. But that is not my point. My point is "why is a phylogeny even possible?" If you were correct construction of a phylogeny of fossils with respect to relative time scale should be virtually impossible.


Linnaeus was a Creationist so I guess the obvious similarity is due to a Common Creator.

Like he had a choice! Linneaus died in 1778. How could he be an evolutionist 80 years before the ToE?


MYRMECOS
I think what edge and Mr. Ben mean by "phylogeny" is that biological diversity appears to be organized in a nested hierarchy. This organization was recognized long before Charles Darwin sailed on the Beagle, so I think that edge and Ben do have a valid point. Common descent predicts that life should exist in a nest hierarchy, such that all life forms are not completely novel but merely variations on older groups. Since life broadly fits that pattern, I would regard the nested hierarchy as support for evolution.

However, I would hesitate to call that nested heirachy a "phylogeny", since the folks like Linneaus and Fabricius who established modern nomenclature did not do so with evolutionary relationships in mind. To me, a phylogeny is a fairly specific concept, a schematic representing the evolutionary relationships between organisms. Such a diagram *does* pre-suppose evolution. Point for John Paul.

In short, the nested hierarchy of organisms is evidence of common descent, but phylogenies are not, since they assume descent a priori.

I would add, however, that *congruence* between phylogenies and other data (biogeographic and paleontological) can indicate that common descent is correct, because such congruence is evidence that the assumptions of phylogenetic methods (including common descent) are not violated.


EDGE
Agreed. I have never doubted that the term "phylogeny" per se is dependent upon evolution. Phylogeny is indeed not direct evidence of evolution, though the fact that a phylogeny, with relative timing and actually fossils, can be constructed suggests an underlying cause.

I do ask, however, how a phylogeny can be constructed under the scenario of creationism, or whatever JP believes.


MILAN
John Paul:
Right. In other words it assumes the ToE is indicative of reality. That is what I said.

It seems that you are not understanding the point at all. It would be long to explain it here. Fortunately there are a wide number of webpages that contain excellent discussions on the subject. Have a look for instance at http://www.talkorigins.org/faqs/comdesc/section1.html
for a rather thorough discussion.


THE BARBARIAN
The point is not that supporting phylogenies exist, based on the fossil record, anatomical data, genetics, and biochemistry. The point is that the evidence for each of these phylogenies supports the same conclusions about the relationships among living things.

[For instance] In the late 1800s, birds were associated with dinosaurs on fossil evidence. Then, we found that the genetic evidence also points to that. Now, we have discovered that dinosaur hemoglobin is closer to turkey hemoglobin than snake hemoglobin.


MR. BEN
Taxonomy, or the grouping of all plants and animals into a nested treelike hierarchy, began with the linnean classification system in the 18th century and predates Darwin by more than half a century. This nested ordering of all life is what scientist are talking about when they point to the nested hierarchical pattern of similarities between all of life. That all life could be represented as a nested hierarchy of similar forms was well known before Darwin. It was simple leap for Darwin and Wallace to put that together with the rudimentary fossil record, and Darwins experiences in the Galapagos, and propose a reason 'why' life happens to appear in nested hierarchies.

That evolution was proposed to explain the anomalous treelike pattern of life that was well known long before hand can not possibly be a circular argument.

[ January 08, 2002: Message edited by: Administrator ]