Intelligent Design / Evolution

[USincognito]

You seem to be a very angry sort.
I can only imagine your stress in trying to maintain belief while it crumbles around you.

I've seen you try this pathetic Jedi mind trick numerous times.

Does it ever actually work for you?

 

[Zaius137]

Before joining in again to the conversation, I apologize for the late responses. I try to study every post that you participants put out and I admit it is sometimes overwhelming. Lots of good stuff much of it is above my pay grade.

You are conflating a common definition of the word "free" with the statistical one. Sad stuff Z.

Free Parameter definition | Dictionary of Electronic Statistics


Where did you dig this one up? I believe this definition belongs specifically to an engineering tool like “Splice” or some other software.

Also, they are saying "as few as possible" not "none".

Always good for a chuckle.

Because model selection tests directly quantify the evidence for and against competing models, these tests overcome many of the well-known logical problems with Fisherian null-hypothesis significance tests (such as BLAST-style E values).

common descent, yes. universal common descent, no.

The author has overcome the P-values and E-values (supposedly) and is to be congratulated but doesn’t Theobald’s paper deal with verifying a single UCA?

(another layer of statistical error could be introduced at this point).

Really? What's the chance you could be specific. What statistical error layer could be introduced, exactly?

I think that other critical papers may suggest a (type I) error. Specifically at the time, I read the citation my thoughts tended to a “error of definition” but I can not assert that suggestion in an informed manner.

To quantify the evidence supporting the various ancestry hypotheses, I applied three of the most widely used model selection criteria from all major statistical schools: the log likelihood ratio (LLR), the Akaike information criterion (AIC) and the log Bayes factor (LBF).

Good statistical methods but one might ask if the previous assumptions can be overcome to enable some objectivity?

Which assumptions? And what does "enable some objectivity" mean? Perhaps rather than rephrasing your question you could provide an answer? (i.e. what should have been done to overcome these previous assumptions and enable some objectivity).

The impediment and limitations of dishonest statistical evaluation.

Problems should be noted with the Markovian substitution model :
This was also my second problem with the paper. But I basically agree.

I might ask what your first problem was.

A UCA to date has been an intractable proposition to the evolutionist. Before scientists propose such dribble, they must answer the basic questions such as a real molecular mechanism for evolution or actually demonstrate abiogenesis is possible in the first place.

I recommend you listen to the whole song. It's the final thoughts of a man about to be sent to the electric chair ("Mercy Seat")

I know parity is sometimes the bread and butter of rock music but I find it anachronistic and unable to be a comfort.

Except you want me to also deny reality. Not going to happen. I'd also have to give up my day job, and I quite like my day job and its associated pay check.

Denying reality has two faces and as a Newtonian at heart, I find scientific explanation to favor the Christian overall. The overtone of your above statement seems to acknowledge what I have suggested many times, real prejudice is common practice in science against scientific opposition (namely ID).

 

[Blayz]

Sorry Z, I don't like this paper enough to defend it any further, but "free parameter" is a general modelling concept with broader scope than 1 software package.

 

[idscience]

Hey you should be reading that paper!

Ok, I am back again. I have not been able to get the complete paper and like I said I am not an immunity expert.

the absrtact doesn't indicate anything new. Convergent evolution which is an inference to start with, and gene duplication. The abstract doesn't look like the researchers have discovered much new only possible answers like many before them. Maybe you could tell us if thy have indeed found the answers to how the immune system was built step by step, or not.

Is this another one of the same type of papers given to judge Jones?

Here is something also that is interesting on adaptive immunity. This is from Biologos. Kathryn Applegate argues this adaptive evolution from a theistic view and there is Edward Max who also weighed in.
Adaptive Immunity: Chance or Necessity?

 

[Lion Hearted Man]

Ok, I am back again. I have not been able to get the complete paper and like I said I am not an immunity expert.

I know of a another paper that is coming out in response to this one you have cited. It is by an eminent immunologist who ran a research facility for 20 years. He should have it ready shortly as he is working on as we speak.

You can speak to this better having the complete paper but, the absrtact doesn't indicate anything new. Convergent evolution which is an inference to start with, and gene duplication. The abstract doesn't look like the researchers have discovered much new only possible answers like many before them. Maybe you could tell us if thy have indeed found the answers to how the immune system was built step by step, or not.

Is this another one of the same type of papers given to judge Jones?

When I get a copy of the response paper. I will post it. It will be more an exhaustive reply.

Here is something also that is interesting on adaptive immunity. This is from Biologos. Kathryn Applegate argues this adaptive evolution from a theistic view and there is Edward Max who also weighed in.
Adaptive Immunity: Chance or Necessity?

I really don't know why Ewert doesn't publish his dissenting opinions in peer-reviewed journals. Oh, probably because they are just creationist hand waving.

The paper I posted provides phylogenetic evidence and two mechanisms to demonstrate how jawed vertebrates generated their adaptive immune system, and how jawless vertebrates generated theirs. The fact that both lineages developed different adaptive immune systems that are still adaptive immune systems is convergent evolution.

That paper was a review (collected findings of many papers) that simply addressed the adaptive immune system. The innate system, which is present in virtually all living things, is a whole other fascinating story. There is a phylogenetic distribution of immune system components/tactics that is consistent with all other phylogenetic trees.

Nothing Ewert has ever published precludes the natural evolution of the immune system. I will only accept peer-reviewed papers as your counter-evidence. Non peer-reviewed opinion pieces are not reviewed by experts.

 

[RickG]

I really don't know why Ewert doesn't publish his dissenting opinions in peer-reviewed journals. Oh, probably because they are just creationist hand waving.

The paper I posted provides phylogenetic evidence and two mechanisms to demonstrate how jawed vertebrates generated their adaptive immune system, and how jawless vertebrates generated theirs. The fact that both lineages developed different adaptive immune systems that are still adaptive immune systems is convergent evolution.

That paper was a review (collected findings of many papers) that simply addressed the adaptive immune system. The innate system, which is present in virtually all living things, is a whole other fascinating story. There is a phylogenetic distribution of immune system components/tactics that is consistent with all other phylogenetic trees.

Nothing Ewert has ever published precludes the natural evolution of the immune system. I will only accept peer-reviewed papers as your counter-evidence. Non peer-reviewed opinion pieces are not reviewed by experts.

Quite true. ID does not appear in the relative scientific journals specifically because it just doesn't follow scientific methods. Using scientific terms is not following the scientific method.

From the American Association for the advancement of Science (AAAS):

Intelligent design proponents may use the language of science, but they do not use its methodology. They have yet to propose meaningful tests for their claims, there are no reports of current research on these hypotheses at relevant scientific society meetings, and there is no body of research on these hypotheses published in relevant scientific journals. So, intelligent design has not been demonstrated to be a scientific theory. While living things are remarkably complex, scientists have shown that careful, systematic study of them can yield tremendous insights about their functions and origins (as it has in the past).

 

[idscience]

Quite true. ID does not appear in the relative scientific journals specifically because it just doesn't follow scientific methods. Using scientific terms is not following the scientific method.

From the American Association for the advancement of Science (AAAS):

Intelligent design proponents may use the language of science, but they do not use its methodology. They have yet to propose meaningful tests for their claims, there are no reports of current research on these hypotheses at relevant scientific society meetings, and there is no body of research on these hypotheses published in relevant scientific journals. So, intelligent design has not been demonstrated to be a scientific theory. While living things are remarkably complex, scientists have shown that careful, systematic study of them can yield tremendous insights about their functions and origins (as it has in the past).

Your are incorrect Rick. Id is increasing its footprint in the journals. Remember it is a relatively new hypothesis.

I agree, testing for design is a new idea as well but just becuase it has not been nailed down yet doesn't mean it is not valid. There are over 50 peer reviewed papers relating to intelligent design.

Evolution papers make all sorts of claims that show no real evidence just inference. Journals are full of them.

It has also been established that those who dare publish ID friendly papers are diciplined. ID is taboo for Evo scientists and you dare not mention it or else. That has nothing to do with the science.

 

[Lion Hearted Man]

Your are incorrect Rick. Id is increasing its footprint in the journals. Remember it is a relatively new hypothesis.

For any given "new hypothesis" there are typically tons of labs furiously trying to publish the seminal paper that defines a new wave of research. ID has not taken off like that, because as RickG stated, it is not scientific.

I agree, testing for design is a new idea as well but just becuase it has not been nailed down yet doesn't mean it is not valid. There are over 50 peer reviewed papers relating to intelligent design.

Ha, most instances of the phrase "intelligent design" in the literature is when humans intelligently design something. Any others that refer to the creation/evolution "debate" are highly critical of ID. I'd like to see the technical, peer-reviewed papers that could be used as evidence for ID. (The deck is stacked against you, because ID is not science.)

Evolution papers make all sorts of claims that show no real evidence just inference. Journals are full of them.

How would you know? You don't even have access to full length journals by Nature.

It has also been established that those who dare publish ID friendly papers are diciplined. ID is taboo for Evo scientists and you dare not mention it or else. That has nothing to do with the science.

ID is pseudoscience. The methodology used is antithetical to actual science. That's why anyone who attempts to publish a paper that is pro-ID is usually rejected. It's methodology that is the problem, not ideology. Peer reviewers of papers don't cling to evolution like dogma.

It's the same reason astrology papers don't get published. The stuff is junk. ID belongs in the same wastebin as all other pseudoscience.

 

[TeddyReceptus]

Your are incorrect Rick. Id is increasing its footprint in the journals. Remember it is a relatively new hypothesis.

It is a relatively new hypothesis because:

1. It took a long time for the Creationists to realize that shoehorning God into a science classroom wasn't going to work

2. Creationists were getting stymied by the courts (their only way to get creationism into science was to present it to children and the only way to do that was through school boards)

3. So the Creationists latched onto a "god-free" ("god-lite") alternative of "cdesign propentists" (oopsy!) which got it going off the ground.

4. The single greatest aspect of Intelligent Design is that it is almost perfectly UNFALSIFIABLE.

Don't expect the ID scientists to actually develop a falsification criterion for this one. It's too good as it is.

And this is probably the best reason to assume ID isn't "real" science.

I agree, testing for design is a new idea as well but just becuase it has not been nailed down yet doesn't mean it is not valid.

And really the only way to know if the universe is designed is to find another universe that is designed and to see if this one looks like that one. Or maybe find a universe that wasn't designed and compare and contrast!

"Design" is a human attribute. Most of the examples fail ultimately or they require a comparison to a human invention like a mousetrap or a 747.

ID is taboo for Evo scientists and you dare not mention it or else. That has nothing to do with the science.

You make it sound as if ID is being pushed out because it's verboten, not because it simply hasn't risen to the level of actual science.

You see there's a difference. And like ID, it is "unfalsifiable" in the minds of the Intelligent Design folks...just as it is for Creationists.

They see that their non-science is rejected by journals and they think it is because the journals are biased against them.

Actually the journals and science is biased against a blue-sky hypothetical that has no real foundation in standard science (such as falsifiability).

It really is not unlike a "conspiracy theory". It is constructed based on "feelings" and every example given requires that we not accept a more simple explanation.

 

[idscience]

I really don't know why Ewert doesn't publish his dissenting opinions in peer-reviewed journals. Oh, probably because they are just creationist hand waving.

The paper I posted provides phylogenetic evidence and two mechanisms to demonstrate how jawed vertebrates generated their adaptive immune system, and how jawless vertebrates generated theirs. The fact that both lineages developed different adaptive immune systems that are still adaptive immune systems is convergent evolution.

That paper was a review (collected findings of many papers) that simply addressed the adaptive immune system. The innate system, which is present in virtually all living things, is a whole other fascinating story. There is a phylogenetic distribution of immune system components/tactics that is consistent with all other phylogenetic trees.

Nothing Ewert has ever published precludes the natural evolution of the immune system. I will only accept peer-reviewed papers as your counter-evidence. Non peer-reviewed opinion pieces are not reviewed by experts.

I don't know if he has or not. I don't know him. I just know of his debates on biologos and his podcasts. I will see if I can locate some peer reviewed papers on the subject.

 

[idscience]

Ever wonder why so many peer reviewed papers get published that are simply describing possible avenues of evolution? Why are there so few, if any, that actually detail how evolution HAS worked.

It seems that much of the evidence for evolution comes from inference from things that are infered to be evolution. For example, convergence.

Convergence is conjecture not fact. It is assumed and therefore scews any evidence that uses it as a basis for that evidence.

 

[idscience]

I would also like to know if you are aware of any peer reviewed papers that demonstrate how the immune system was built? I know there are plenty with ideas of how it may have, but as many are not interested in "opinions", somebody should have some facts, yes.

 

[idscience]

In several previous posts, there was much debate over the bacterial flagellum. No one came up with a single paper showing how it was built. There were one or two that had general ideas, but nothing that dealt on a biochemical level showing the steps.

Behe is slandered all over and misrepresented continuously. Yet no one has shown how the flagellum or the (TTSS) systems could be built by a Darwinian process.

 

[Lion Hearted Man]

Ever wonder why so many peer reviewed papers get published that are simply describing possible avenues of evolution? Why are there so few, if any, that actually detail how evolution HAS worked.

Maybe you skipped the lectures where you were supposed to learn what science is and isn't, but inductive reasoning (which generates inferences) is the foundation of science. Things are only known to be true within a certain probability.

Science does not operate on deductive reasoning.

It seems that much of the evidence for evolution comes from inference from things that are infered to be evolution. For example, convergence.

Convergence is conjecture not fact. It is assumed and therefore scews any evidence that uses it as a basis for that evidence.

I don't get why you're hung up on convergent evolution. It's a fairly simple concept. It occurs when two branches on an evolutionary tree adopt similar characteristics. For example, bats and birds both have wings, but the structures aren't homologous. Additionally, jawless vertebrates and jawed vertebrates both have adaptive immune systems, but they're different.

Just because you don't understand it doesn't mean it doesn't happen. Like I said before, you can't even read peer-reviewed journals so I don't trust a single thing you say about the current state of evolutionary biology research. You are simply regurgitating PRATTs from professional creationists.

 

[Lion Hearted Man]

In several previous posts, there was much debate over the bacterial flagellum. No one came up with a single paper showing how it was built. There were one or two that had general ideas, but nothing that dealt on a biochemical level showing the steps.

Behe is slandered all over and misrepresented continuously. Yet no one has shown how the flagellum or the (TTSS) systems could be built by a Darwinian process.

The point of the type III secretory system argument was to demonstrate that the bacterial flagellum is not irreducibly complex.

No one knows exactly how the flagellum evolved, but the one testable idea that ID came up with (irreducible complexity) was demolished.

The standard of evidence you require is virtually impossible to meet. Along your line of reasoning, it is impossible to demonstrate that human being can develop from an embryo because we don't know all the steps. It's ludicrous.

 

[idscience]

The point of the type III secretory system argument was to demonstrate that the bacterial flagellum is not irreducibly complex.

No one knows exactly how the flagellum evolved, but the one testable idea that ID came up with (irreducible complexity) was demolished.

The standard of evidence you require is virtually impossible to meet. Along your line of reasoning, it is impossible to demonstrate that human being can develop from an embryo because we don't know all the steps. It's ludicrous.

IC is far from demolished and the flagellum is IC. If you take the ttss from it its broken. Doesn't work. Not only that, but if you just remove the ttss it doesn't work either without changes. So, when you take the TTSS out, you end up with two systems that don't work.

 

[idscience]

What is ludicrous is stating something is demolished when you don't have another answer for it. Just an idea. That is the foundation evolution is built on, ideas, not data.

 

[idscience]

regurgitating PRATTs from professional creationists.

Again, ID and creationism are not the same. The only reason you associate the two is to use creationists non science to slander ID.

ID does not propose anything that is not supported by observation and experimentation.

 

[idscience]

ID is not Creationsim.

• "No. The theory of intelligent design is simply an effort to empirically detect whether the "apparent design" in nature acknowledged by virtually all biologists is genuine design (the product of an intelligent cause) or is simply the product of an undirected process such as natural selection acting on random variations. Creationism typically starts with a religious text and tries to see how the findings of science can be reconciled to it. Intelligent design starts with the empirical evidence of nature and seeks to ascertain what inferences can be drawn from that evidence. Unlike creationism, the scientific theory of intelligent design does not claim that modern biology can identify whether the intelligent cause detected through science is supernatural. Honest critics of intelligent design acknowledge the difference between intelligent design and creationism. University of Wisconsin historian of science Ronald Numbers is critical of intelligent design, yet according to the Associated Press, he "agrees the creationist label is inaccurate when it comes to the ID [intelligent design] movement." Why, then, do some Darwinists keep trying to conflate intelligent design with creationism? According to Dr. Numbers, it is because they think such claims are "the easiest way to discredit intelligent design." In other words, the charge that intelligent design is "creationism" is a rhetorical strategy on the part of Darwinists who wish to delegitimize design theory without actually addressing the merits of its case. " (Intelligent Design)

 

[idscience]

New World Encyclopedia

• "Intelligent design (ID) is the view that it is possible to infer from empirical evidence that "certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection" [1] Intelligent design cannot be inferred from complexity alone, since complex patterns often happen by chance. ID focuses on just those sorts of complex patterns that in human experience are produced by a mind that conceives and executes a plan. According to adherents, intelligent design can be detected in the natural laws and structure of the cosmos; it also can be detected in at least some features of living things."