Skeptical

Well, I would reiterate to you that the DNA evidence is quite a bit stronger than you seem to think as has been demonstrated. I don't know why you would continue to argue against the idea that it at least _appears_ that common descent is true when one can easily argue, and theists do all the time, that the mechanism was God, not RM/NS.

This is a rhetorical question, but ask yourself why you were so convinced that common descent was wrong when you joined this board if, by your own admission, you had not thoroughly examined the DNA evidence.

If someone could explain how we can differentiate between non-empirical causes, I'd consider them. I don't know how to go about considering them and no one has ever been able to explain how to do so that doesn't look like anything more than opinion.

I have to admit I have no idea what your talking about here. I haven't been to Yosemite, I'm not even sure I've seen pictures, so I must admit ignorance.

We may draw some conclusions from indirect effects, but we must have some experience that similar effects have occured from known causes. If we see a unique effect (i.e. the universe), and then posit a cause which we have no other evidence for (i.e. God), to me this is nothing more than an opinion. It is true that many people have made inferences of a creator from the "order" they see. However, we now have naturalistic explanations that are plausible for life as we see it. Even if one completely rejects the theories of evolution, this does not mean that one is inevitably required to conclude that God is the necessary reason.

If Earth was the only planet, the Sun the only star and the earth only a few thousand years old, I can see how this argument might hold weight. However, we know there are at least millions, if not hundreds of millions of stars or more, it is also reasonable to conclude that there are hundreds of millions, perhaps even billions of planets. We also know that the universe is billions of years old. These numbers are so large it is difficult for most of us to attach any real meaning to them. The fact that the number of opportunities for life to arise by chance is so large weighs heavily in favor of life arising at least _once_ by chance.

To take an analogy, if I had 100, million sided dice, the odds that on a single roll one of those dice might show up 485,657, is very small indeed. However, suppose that instead of one hundred dice, I rolled 100,000 dice. What are the odds then? Now assume that instead of rolling the dice a single time, I rolled the 100,000 dice 100,000 times? Now the chances that at least once I would get the number 485,657 are pretty good. The problem with assuming that the Earth and life on this planet "couldn't have occured by chance" are that:

1) We don't know how many dice we have (total number of planets)

2) We don't know how many sides they have
(chance of life occuring on a particular planet)

3) We don't know how many times we get to roll them (number of opportunities for organic molecules to combine in such a way that it leads to life plotted against the age of the universe)

However, we do know 1 and 3 are pretty large. 2 may be very large as well and likely is. However, given a sufficiently large 1 and 3 it seems likely that life would occur _somewhere_ on its own. To argue otherwise strikes me as just assuming a priori that we are "special", which just begs the question. "We're the only life we know of, so we must be special". To me, this is no different from assuming the Earth was the center of the universe and nothing more than human arrogance.

No offense, but this seems extraordinarily ironic coming from a theist. I wish at times I could believe that theism made sense, it would certainly make life easier, all the hard questions would be answered for me. Theism seems to be by far the most "comfortable" of the beliefs between theism, deism, agnosticism and atheism.

How do I _know_ they don't? Simple, I don't. How would I know they were from a supernatural cause even if they were? The answer seems simple again, I wouldn't. How do you distinguish what someone thinks is from a "supernatural" cause from something that is just opinion?

Not quite. A reply must make some sort of sense based on what we know about the world and the human brain. If someone wants me to consider non-empirical causes, they must specifically articulate how to do so in a way that allows me to clearly distinguish between reality and opinion. I have not seen any specifics articulated despite having asked repeatedly.

One thing that has suprised me is that despite having made repeated requests for you to specifically articulate how to distinguish non-empirical "knowledge" from opinion, you haven't even tried. As far as I can see, you have dealt only in generalities and every time I have offered a specific example of the problem, you have ignored it or danced around it.

BTW, if someone has researched a topic, examined the evidence and made a conclusion, do you define this as a "preconception"?

[ September 17, 2002: Message edited by: Skeptical ]</p>

Vanderzyden

If I remember correctly, not all of the references referred to prokaryotic trees.

Anyway, my point in presenting them is to indicate that confusion abounds in phylogeny. Please understand that this is my contention.

You may also remember the <a href="http://www.mhhe.com/biosci/pae/zoology/animalphylogenetics/toc.mhtml" target="_blank">summary</a> of problems. Did you read it?

Perhaps yet another article will serve as an example of my general contention--whether one considers prokaryotic or eukaryotic phylogeny:

"Phylogenetic Classification and the Universal Tree", W. Ford Doolittle

[Science, Volume 284, Number 5423 Issue of 25 Jun 1999, pp. 2124 - 2128]

<a href="http://cas.bellarmine.edu/tietjen/Ecology/phylogenetic_classification_and_.htm" target="_blank">http://cas.bellarmine.edu/tietjen/Ecology/phylogenetic_classification_and_.htm</a>

Some interesting section titles:

-- "Methodological Problems"
-- "How Can a Phylogenetic Classification Be Preserved?"
--"LGT Challenges the Conceptual Basis of Phylogenetic Classification"
-- "What If Phylogenetic Classification Is Just Let Go?"


Emphasis mine.

Now, can we agree that there is no universal tree, and that phylogenetic research is inherently problematic?

Vanderzyden

[ September 17, 2002: Message edited by: Vanderzyden ]

[ September 17, 2002: Message edited by: Vanderzyden ]</p>

Vanderzyden

Yes, people have made good points here about significant digits. Fine, yes, I understand that, and realized this after I posted but couldn't return directly to edit it.

My response was meant to make two points:

-- that there is a four decimal place difference in the findings that I cited. (Note that scigirl's reference made reference to "three decimal places", not significant digits.

-- the value of the gravitational constant is very small, requiring a measurement precision that is incomparable to any characteristics of hypothetical phylogenetic tree construction.

Sorry for not making that clear.

Vanderzyden

Doubting Didymus

All of your references refer to levels of organism where horizontal gene transfer and endosymbiosis cause problems for phylogeny AT THOSE LEVELS.

<a href="http://cas.bellarmine.edu/tietjen/Diversity/mix_and_match_in_the_tree_of_lif.htm" target="_blank">This</a> link you quoted from is about horizontal gene transfer and endosymbiosis (here referred to as 'chimerism')

A quote that I think summs up the true point of this article.

Nothing to do with ordinary phylogeny at multicellular levels.

<a href="http://nsmserver2.fullerton.edu/departments/chemistry/evolution_creation/web/PhilipeForterre1999.pdf" target="_blank">This</a> link deals with attempts to revise ancient phylogenies.

Again, the problems and controversies arise from lateral gene transfer and are nothing to do with phylogeny at multicellular levels.

<a href="http://www.pnas.org/cgi/content/full/95/12/6854" target="_blank">This</a> is also nothing to do with traditional multicellular phylogeny, but is an invesigation into the kind of thing the first common ancestor might have been. Again, horizontal gene transfer is an important part of this discussion.

This has all been pointed out to you within a few posts of your original, yet you are still claiming that they are relevant. What will it take? Do we need to get the scientists you are quoting to personally contact you?

Get it strait. primitive ancestral phylogeny is problematic because of gene transfer and 'chimerism' (which includes endosymbiosis). These objections do not apply to phylogeny at other levels, particularly the most relevant to us now: animal phylogeny. OK?

Your most recent quoted article is also about phylogeny problems with the rooting of the tree, referred to here as 'deep' phylogeny.

Get it? you are pointing at problems that have no bearing at all on animals.

Doubting Didymus

We all understand that this is what you are saying, but the 'confusion' that exists in traditional multicellular phylogeny is many orders of magnitude smaller that the discrepancy between values for G, as demonstrated by scigirls marvellous article.

The kind of thing we are looking at is nowhere near the kind of massive discrepancy your quotes imply. One of the current biggies is whether velvetworms should be in with the worms or the arthropods. Big bloody deal. As scigirls article pointed out, this is a very tiny discrepancy considering the number of possible trees that there could be disagreements about.

Yes, animal phylogenies sync up. Pick a protein gene, and you will get a remarkably similar tree. The massive discrepancies you postulate are imaginary. Find us a quote about some area of phylogeny that actually applies, and we might start to consider your idea that there is widespread disagreement.

Vanderzyden

Think about what you have written here. To argue from a "rolling dice" analogy is to argue from a mere opinion, and rejects the "fine-tuning" that has been found in the cosmos and on our planet (size, type, of a bachelor parent star; sufficient distance from the center of the galaxy; strong and weak nuclear force; etc, etc, etc.). And, from what source do you draw the extension out to 100,000 dice? Why are the dice the planets themselves, instead of the combination of cosmological criteria? Furthermore, who is rolling the dice? Who has set up the environment in which the dice may roll? Shall I go on with such questions? This stuff is just pure invention, is it not?

This is to say nothing of your gigantic leap to "human arrogance".

Interesting. You are saying that belief in God, to which one must in someway accountable, is more comfortable to a human. I will tell you from experience and from the comments I've heard from many non-theists that the theist has the rough road, certainly in the terms of moral constraint. I do think that you touch upon the other aspect of belief: justification. It is critical to ask oneself everyday: On what basis are my beliefs warranted? Have I considered everything of importance?

You are affirming my assessment. Based upon your replies so far in this thread, I would think that we should substitute "I" for "we" above. You cannot tell me where the world comes from or how your mind is empircal, and yet you say you know how it is. You are saying, "If I can't see it, it isn't real". But, of course, I have explained at length that you live upon non-empirical assumptions every day. Of course, you deny it, and refuse to admit it directly--for fear that you will then have to concede other non-empirical causes. You have not "seen any specifics" because you refuse to consider them. Instead you hold fast to your "empirical" worldview. Remember, your position is a component of the realist view, which maintains that empircal and non-empirical phenomena are knowable. So, I agree with you by default on empirical knowledge. What you don't realize is that the burden of proof rest upon you to provide an empirical explanation for things that are obviously non-empirical.

Let me reiterate: you define "empirical" too broadly and "non-empirical" too narrowly. In fact, you effectively reject any notion of non-empirical knowledge. Am I correct?

Note: I am still waiting for you to empirically demonstrate the number 2. Starboy hinted at a good example: explain the number 2 on a slide rule.

As seems typical with you, Skeptical, you categorically reject everything I've said. I try to see your position, but you will not try to see mine. My examples are reasonable, but you will not give one inch.

And, here again, you do not answer my inquiry. Is it not reasonable to request that you answer some of my questions now that I have attempted to answer yours?

Please tell me what else, besides any aspect of our dialogue here, has been surprising to your on your quest for knowledge? Has there been any thing of significance that has not met your expectations?

Vanderzyden

Vanderzyden

DD,

I don't see it that way. The article clearly refers to general phylogeny throughout its entire length. Did you read it?

Why didn't you respond to what I highlighted in bold?

Bottom line:

If there are problems at the root of the tree, it becomes a bush. In fact, it is nothing but a scattering of twigs on the ground.

If I put an axe at the root of the tree, it falls. Common descent from a single ancestor comes crashing to the ground.

Vanderzyden

Vanderzyden

Marvellous? I see that you are easily impressed.

Again, I am looking for demonstrations.
You have not shown it, DD. Please do so.

Show me the precision. A simple diagram is hardly evidence.

Vanderzyden

[ September 17, 2002: Message edited by: Vanderzyden ]</p>

Doubting Didymus

The article is definitely referring to phylogeny at the domain level (bacteria, archea and eukaria). Of course I read it.

Your analogy of 'cutting the tree down' is very very stupid. Phylogeny is to do with history. Just because it encounters problems when dealing with extremely ancient history, does not mean it is unreliable for more modern history.

Your analogy is very similar to saying that if carbon dating can not return accurate results from more that 50 000 years ago, we should discard it completely.

Besides, the fact that traditional molecular phylogeny is not a reliable tool for talking about the root of the tree does not imply in the slightest that the root does not exist, or has somehow been destroyed by an axe weilding maniac, does it?

Doubting Didymus

I am not sure what you want to see. The accuracy of molecular phylogeny is well known, as is the remarkable way in which phylogenic trees from various molecules line up with each other.

Would a quote to this effect from a current university approved biology textbook satisfy you? I have a couple of textbooks that say precicely this.