Phylogenetic trees ultimately fail because the real pattern of life is a mosaic or a web, not a tree.

Were it the case that ALL phylogenetic reconstructions sought ot recontruct the entire history of life, then you might have a point.
Let us look at a more manageable scale – look at your family tree going back, say, ten generations.

Is it a web, or a tree?

So, the phylogenetic trees always end up containing inconclusive and contradictory data.

Always? Really?

The DNA that leads to one tree could just as easily be used to construct an entirely different tree.

This is true, but very misleading. You can constrain tree reconstruction software to produce arrangements contrary to what the data indicate, and in come software packages you can sort of ‘cut and paste’ brnaches to rearrange trees. However, in doing so, the reliability scores for the tree drop significantly. I have seen this done in creationist publications, where programs are constrained to prevent humans from grouping with other apes, since the ‘researhcers’ know that humans and apes are not related. This produces ridiculously low bootstrap values for species that even creationists acknowledge as being related via descent, because it throws the whole tree off, as it were.
Simply letting the program produce the tree as indicated by the data will NOT produce any old tree. To claim so is to admit ignorance of the entire field.

Therefore, in order to make the DNA fit the original assumption that a tree even exists in the first place a procrustean bed is fashioned for the data using the twin excuses of horizontal gene transfer and convergent evolution to cover up the contradictions.

The only instances in which this sort of thing needs ot be done is, again, in the case of creationsit baraminological analyses in which outcomes are constrained to reflect Scriptural criteria.
Please do not assume that all researchers engage in such manipulation.

A third excuse, mutational hot spots can also be used to defend the tree. However, the mutational hot spot explanation must be handled with care because it is a double edge sword that effectively threatens the very assumptions upon which the tree was built in the first place.

A series of largely unsupportable assertions and a misleading claim. Interesting.

…but scientists try to gloss their dogma in the language of probability

So, apparently, do DI Fellows.

Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.

I also noted the title of the paper:

Exceptional Convergent Evolution in a Virus

I’m not sure what Dembski =meant when he wrote:

The actual phylogenies here were experimentally known and yet standard evolutionary theory drew completely wrong conclusions. Oh, but it was a small population, small genomes, and intense selection pressure. Spare me.

So, do fasle positives and false negatives in the EF falsify ID?

Perhaps if the paper had relied on analogies and bogus probability calculations and unsupported assertions, he would have been more impressed?
Heck – maybe we could send a copy to the boys in the ISCID Princeton Office and they could take a look at it…

If all they have to demonstrate is that it can arise without agency, ID is already defeated.

Why? Such a thing has NOT been acomplished.

It is POSSIBLE, that thousands or millions of genetic mutations occur correctly in a single specimen, creating an entirely new species.

YEC accepts speciation.

What’s your point?

Saltation WAS a reality and is believed by this very rational person.

There is absolutely no need for any intervention, supernatural or otherwise, in a goal seeking mechanism such as the Prescribed Evolutionary Hypothesis proposes.

Where is there intervention in ontogeny? There isn’t any.

I had planned to abandon this silly “debate” but I cannot abide idiotic statements such as the one that led to this exchange between joseph and yourself.

There is no need for any allelic mutations to have a occurred to explain evolution. Allelic mutations never had anything to do with evolution except to ensure extinction.

Everything we know pleads for a planned phylogeny now finished.

I have presented my case and I might just as well have been talking to the wall.

This entire thread has been dominated by a half dozen or so unknowns who would rather “debate” with each other than consider an alternative to Darwinian mysticism presented by a real human being. I hope they know whom they are “debating.” I sure don’t and don’t care to find out. Comments from anonymous sources contribute NOTHING, never have and never will.

It is hard to believe isn’t it?

Not at all. Look around. That is exactly all that you see.

“A past evolution is undeniable, a present evolution undemonstrable.”

I diodn’t say anything about a possible pathway.

They have to demonstrate it can arise without agency involvement.

Period.

If all they have to demonstrate is that it can arise without agency, ID is already defeated. Saltation is physically possible. It is POSSIBLE, that thousands or millions of genetic mutations occur correctly in a single specimen, creating an entirely new species. It is astronomically improbable, but still possible. The improbability is why no one believes that actually happened. This is why I say possibility (“can”) should be considered along with probability.

The example of saltation is an extreme, and not believed by any rational person, but it demonstrates the point.

379

JohnADavison

04/17/2009

4:39 am
e i o. y ai y eae, ooa ai e i oei e o ye. y e ae ei a oe o oi e ae i? I i e you y. ey ae o aei o aiia, a’ y.

I i a o eiee i’ i?

380

JohnADavison

04/17/2009

8:28 am
a

I i you ou aao i ae o e a “i iuee” ui you ae oee you auae uie. oee, I o’ ee o you oiy a ae e ie o i.

381

JohnADavison

04/17/2009

1:07 pm
.tfel dna thgir em gniteled erew uoy nehw em ot ti tup uoy sa “flesruoy morf uoy tcetorp ot” gniyrt ylno ma I .laS em natsrednusim t’noD

That is the sort of thing one expects at After The Bar Closes. The last one can at least be read, so please do!

I recommend leaving this sleeping dog alone. If I ever find out who “Davem” is I will expose him to the world as I hope to do with every anonymous blowhard who clutters up internet forums with spiteful, mindless drivel.

As David Springer used to say -

“Got that? Write that down!”

Besides, court cases are not really resolved by debate. If they were there would be no appellate courts, no district courts and no Supreme Court. Even after things finally get “resolved” they are still subject to repeal.

The truth has never been subject to repeal.

“If you tell the truth, you can be certain, sooner or later, to be found out.”
Oscar Wilde

“Truth is incontrovertible, malice my attack it, ignorance may deride it, but in the end, there it is.”
Winston Churchill.

There is not a word in the entire Darwinian fantasy that ever had anything to do with an ascending, goal directed phylogeny which is no longer in progress – not a single word!

“Here I stand. I can do no otherwise.”
Martin Luther

He also said -

“When I pass wind in Wittemburg they can smell it in Rome.”

That is exactly what I have been doing for quite some time.

I love it so!

JohnADavison 218 -
“Court cases are indeed sometimes resolved by debate…”

As chameleons go, Icon, you’ve dodged the ball well. All that’s left for you to deny now is that (S)cience disregards agency as a legitimate cause with evidence to support its consideration.

Oddly enough this is exactly where you came into this discussion. I had asked another commenter on the thread if he would “be joining materialists everywhere calling for an end to the current default assumption that life began by chance and necessity?”

You then took exception to this question by suggesting that ID lacked any real evidence and commented that you “haven’t personally seen any evidence for design in biology” and indeed that you would have “thought that “agency” is readily accepted”.

It’s been a shell game of parsed meanings throughout.

I’ve repeatedly asked you to be specific and repeatedly you’ve bounced out to “non-natural”, and to “cavemen”, and now to whatever Joseph said. Indeed, you may very well be the perfect example of a materialist ideologue – an enabler of a failed paradigm in the face of overwhelming evidence to the contrary.

- – - – - – - – - –

Science celebrates positive and parsimonious descriptions of presumed objectivity. But we must never forget that our knowledge is only “best thus far.” Even the most fundamental laws of physics technically must be viewed as “tentative.” We rightly eschew diatribes of metaphysical pontifications. Science proceeds through open-mindedness and the falsification of null hypotheses, not through the rhetorical pronouncement of dogmas. Popper and many since have exposed the problems associated with trying to prove any positive hypothesis [176, 177]. Neither induction nor deduction is foolproof. Theses that cannot be proven ought not to be proclaimed as positive statements of fact.

At the same time, we have spent much of the last century arguing to the lay community that we have proved the current biological paradigm. Unfortunately, very few in the scientific community seem critical of this indiscretion. One would think that if all this evidence is so abundant, it would be quick and easy to falsify the null hypothesis put forward above. If, on the other hand, no falsification is forthcoming, a more positive thesis might become rather obvious by default. Any positive pronouncement would only be labeled metaphysical by true-believers in spontaneous self organization. Those same critics would disingenuously fail to acknowledge the purely metaphysical nature of the current Kuhnian paradigm rut [178]. A better tact is to thoroughly review the evidence.
Let the reader provide the supposedly easy falsification of the null hypothesis. Inability to do so should cause pangs of conscience in any scientist who equates metaphysical materialism with science. On the other hand, providing the requested falsification of this null hypothesis would once-and-for-all end a lot of unwanted intrusions into science from philosophies competing with metaphysical materialism.

While proof may be evasive, science has an obligation to be honest about what the entire body of evidence clearly suggests. We cannot just keep endlessly labeling abundant evidence of formal prescription in nature “apparent.” The fact of purposeful programming at multiple layers gets more “apparent” with each new issue of virtually every molecular biology journal [179-181]. – The Capabilities of Chaos and Complexity (D. Abel) International Journal of Molecular Sciences. 2009, 10, 247-291