Is neo-darwinism a scientific theory?
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05-12-2012, 03:39 PM (This post was last modified: 05-12-2012 04:15 PM by tiagorod84.)
RE: Is neo-darwinism a scientific theory?
The PEER-REVIWED article that I've provided shows interresting data on the evolution of the bacterium flagellum. I've never talked about Ken Miller. What I'm telling you is that evolution explains complex structures by the assembly of smaller components that have different functions. If you don't accept the concept of homology, it's entierely up to you.

If you exclude evolution, then you have to imagine that complexity was totally created. What's new on that?

That's just a F5 on the same argument that Darwin faced himself 150 years ago.

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05-12-2012, 09:45 PM (This post was last modified: 05-12-2012 10:50 PM by THEMAYAN.)
RE: Is neo-darwinism a scientific theory?
(05-12-2012 10:38 AM)tiagorod84 Wrote:  Previous note: Please put your posts in a readable format.

Science aspires to explain the unexplained. That's the driving force. Call it promissory, but it does not make it so!

Irreducible complexity IS a god of the gaps. You don't have an explanation, therefore we may infer it was a design... What kind of science is this?

Anyway in a quick search about the king of irreducibe complexity I've found this article: http://www.plosgenetics.org/article/info...en.1002983

The flagellum is a bad example, because of the TTSS. Now, you'll answer that the TTSS is irreducible complexity example. But, then you'll got to give two things:

1) Flagellum is not a irreducible complex system. There is one component that is funtional in non-flagellar organisms.
2) You see how you can continuously put that god of the gaps argument.

Even blood coagulation there are many articles about the evolution of these systems, here's a good one: http://bloodjournal.hematologylibrary.or.../2589.long

(I'm really not going to waste much more time on that. I really need to finish my PhD thesis... Weeping )

About the creator. It transcends the natural world, it does not transcend the natural. You don't really know. And yet you infer things... Way to go! You can be an open-minded persons to whatever New Age thing you want, but don't call it science.

Once again: science only deals with the natural world. That's the only reality we can aspire to understand.

There's no such thing as empirical proof. There's empirical refutation. And the creator, designer or the one-eyed Sauron (really two eyes would give him perspective on things) is not empirically refutable. Therefore the ID hypothesis is absolutely irrelevant for science!

About your questions: "why do you think that peer review journals would (in this hostile climate to anything ID) publish articles by ID theorist who make a scientific argument based on the observable evidence if it wasn't scientific?" I really don't know... Maybe a very open-minded (in the New Age sense) editor of a theoretical biology journal.

Do you think they were duped or are a part of a Christian conspiracy?
I don't really know the editors, but i have the tendency to be skeptical towards conspiracies.

My questions were not answered... So I guess this debate will continue ad eternum.




The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems


I have to admit, when I saw the T3SS, I jumped to conclusions. I did this because Kenneth Miller has been using the T3SS system as a supposed refutation for the argument of IC concerning the bacterial flagellum for many years. For this mistake I'm sorry. However you are still sadly mistaken if you think this proves your case> It doesn't, and it actually confirms my earlier position. The whole premise of the opposing argument rest on the proposition that the T3SS was a precursor of the BF, and again your citation (while still requiring a certain amount of caution) actually confirms the postion of Behe and mine. If you look at my previous post, I clearly said the proposition lies on the assumption that the T3SS was a precursor to the BF, and again your citation confirms what I said in that it was the other way around, and I also provided article that correlated with yours. I'm not sure who told you that it was a good idea to cite this, but you unwittingly falsified Kenneth Millers argument whether you were actually aware of Miller or not, is irrelevant. Again you unwittingly shot a basket ball in the opposing teams court. Thanks for citation I will definitely file this away for next debate. Those five minute google searches can sometimes back fire. I'm going to contact Behe and ask him if he is aware of this somewhat recent finding. Again thanks a lot for info.
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05-12-2012, 09:58 PM (This post was last modified: 05-12-2012 11:09 PM by tiagorod84.)
RE: Is neo-darwinism a scientific theory?
What this paper tells us is how TT3SS and bacterial flagellum are correlated. You can misinterpret it how you want, it still shows that a component from the bacterial flagellum is able to perform other functions. It still shows the homology between them.

Therefore, that's not backfire at all regarding evolution. As to Ken Miller argumentation, I couldn't care less. That's totally a side question.

But anyway do you really think that the fact that TT3SS evolved from the bacterial flagellum helps your cause?

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05-12-2012, 10:05 PM
RE: Is neo-darwinism a scientific theory?
(05-12-2012 09:45 PM)THEMAYAN Wrote:  
(05-12-2012 10:38 AM)tiagorod84 Wrote:  Previous note: Please put your posts in a readable format.

Science aspires to explain the unexplained. That's the driving force. Call it promissory, but it does not make it so!

Irreducible complexity IS a god of the gaps. You don't have an explanation, therefore we may infer it was a design... What kind of science is this?

Anyway in a quick search about the king of irreducibe complexity I've found this article: http://www.plosgenetics.org/article/info...en.1002983

The flagellum is a bad example, because of the TTSS. Now, you'll answer that the TTSS is irreducible complexity example. But, then you'll got to give two things:

1) Flagellum is not a irreducible complex system. There is one component that is funtional in non-flagellar organisms.
2) You see how you can continuously put that god of the gaps argument.

Even blood coagulation there are many articles about the evolution of these systems, here's a good one: http://bloodjournal.hematologylibrary.or.../2589.long

(I'm really not going to waste much more time on that. I really need to finish my PhD thesis... Weeping )

About the creator. It transcends the natural world, it does not transcend the natural. You don't really know. And yet you infer things... Way to go! You can be an open-minded persons to whatever New Age thing you want, but don't call it science.

Once again: science only deals with the natural world. That's the only reality we can aspire to understand.

There's no such thing as empirical proof. There's empirical refutation. And the creator, designer or the one-eyed Sauron (really two eyes would give him perspective on things) is not empirically refutable. Therefore the ID hypothesis is absolutely irrelevant for science!

About your questions: "why do you think that peer review journals would (in this hostile climate to anything ID) publish articles by ID theorist who make a scientific argument based on the observable evidence if it wasn't scientific?" I really don't know... Maybe a very open-minded (in the New Age sense) editor of a theoretical biology journal.

Do you think they were duped or are a part of a Christian conspiracy?
I don't really know the editors, but i have the tendency to be skeptical towards conspiracies.

My questions were not answered... So I guess this debate will continue ad eternum.




The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems


I have to admit, when I saw the TT3S, I jumped to conclusions. I did this because Kenneth Miller has been using the TT3S system as a supposed refutation for the argument of IC concerning the bacterial flagellum for many years. For this mistake I'm sorry. However you are still sadly mistaken if you think this proves your case> It doesn't, and it actually confirms my earlier position. The whole premise of the opposing argument rest on the proposition that the T3SS was a precursor of the BF, and again your citation (while still requiring a certain amount of caution) actually confirms the postion of Behe and mine. If you look at my previous post, I clearly said the proposition lies on the assumption that the TT3S was a precursor to the BF, and again your citation confirms what I said in that it was the other way around, and I also provided article that correlated with yours. I'm not sure who told you that it was a good idea to cite this, but you unwittingly falsified Kenneth Millers argument whether you were actually aware of Miller or not, is irrelevant. Again you unwittingly shot a basket ball in the opposing teams court. Thanks for citation I will definitely file this away for next debate. Those five minute google searches can sometimes back fire. I'm going to contact Behe and ask him if he is aware of this somewhat recent finding. Again thanks a lot for info.



Irreducible complexity = argument from ignorance

Just because something appears to you as irreducibly complex only illustrates your lack of knowledge or failure of imagination.

Skepticism is not a position; it is an approach to claims.
Science is not a subject, but a method.
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05-12-2012, 10:11 PM
RE: Is neo-darwinism a scientific theory?
Hey, Mayan.

I am now convinced that you are a troll.

For the record, the fact that you cannot comprehend that evolution is not a process wherein the simple becomes the complex demonstrates that you do not understand evolution in any way shape or form. Good luck with trying to prove that ID is scientific. You're gonna need it.
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05-12-2012, 11:13 PM
RE: Is neo-darwinism a scientific theory?
(05-12-2012 09:58 PM)tiagorod84 Wrote:  What this paper tells us is how TT3SS and bacterial flagellum are correlated. You can misinterpret it how you want, it still shows that a component from the bacterial flagellum is able to perform other functions. It still shows the homology between them.

Therefore, that's not backfire at all regarding evolution. As to Ken Miller argumentation, I couldn't care less.

But anyway do you really think that the fact that TT3SS evolved from the bacterial flagellum helps your cause in this debate? That is sad indeed...
False, you don't even know what your talking about. I said before that from a Darwinian perspective the ten proteins in common which the T3SS are considered homologous meaning similar, (but not the same) It says nothing of the bacterial flagellum performing other functions, in fact the title of the paper and the abstract confirms that it speaks of the Bacterial flagellum being the precursor to the T3SS. This not my interpretation. This what your own citation says. Again I'm sorry that you think a five minute crash course is sufficient to argue what has been an on going argument for years and for which your citation actually puts to rest. Again it proves Millers argument wrong and again your trying to use the old heads I win, tails you lose fallacy. All you have to do is look at my previous citation which your confirms. I cite it again.......








  • Evolution. As mentioned, the T3SS is closely related to the bacterial flagellum [11]. It is unresolved, however, exactly how the two are related. There are three competing hypotheses [12]: first, that the flagellum evolved first and the T3SS is derived from that structure, second, that the T3SS evolved first and the flagellum is derived from it, and third, that the two structures are derived from a common ancestor. Current opinion tends to favor the first option, where the T3SS is derived from an early flagellum.
[edit]

^ Saier, M (2004). "Evolution of bacterial type III protein secretion systems". Trends in Microbiology 12 (3): 113–115. doi:10.1016/j.tim.2004.01.003. PMID 15001186.





The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems.


Behe never claimed the T3SS was an IC system. He claimed that the BF was an IC system so the argument of co option fails.


This paper confirms Behes argument that the T3SS was not the precursor to the BF. You dont have to believe me. 'Google Kenneth Miller T3SS' or TTSS,'Kenneth Miller Bacterial Flagellum'
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05-12-2012, 11:22 PM
RE: Is neo-darwinism a scientific theory?
(05-12-2012 09:58 PM)tiagorod84 Wrote:  What this paper tells us is how TT3SS and bacterial flagellum are correlated. You can misinterpret it how you want, it still shows that a component from the bacterial flagellum is able to perform other functions. It still shows the homology between them.

Therefore, that's not backfire at all regarding evolution. As to Ken Miller argumentation, I couldn't care less. That's totally a side question.

But anyway do you really think that the fact that TT3SS evolved from the bacterial flagellum helps your cause?
Please see.....http://www.designinference.com/documents/2003.02.Miller_Response.htm

http://www.evolutionnews.org/2011/03/mic...44801.html

Keep in mind these articles were written before this citation yet still shows the flaws in Millers argument.
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05-12-2012, 11:50 PM
RE: Is neo-darwinism a scientific theory?
(05-12-2012 09:58 PM)tiagorod84 Wrote:  What this paper tells us is how TT3SS and bacterial flagellum are correlated. You can misinterpret it how you want, it still shows that a component from the bacterial flagellum is able to perform other functions. It still shows the homology between them.

Therefore, that's not backfire at all regarding evolution. As to Ken Miller argumentation, I couldn't care less. That's totally a side question.

But anyway do you really think that the fact that TT3SS evolved from the bacterial flagellum helps your cause?






Here is a short list of peer reviewed journaled articles. I also included at least two who were not written by ID theorist yet speak of it favorably in their own work as well as including Myers controversial paper published in
Proceedings of the Biological Society of Washington which resulted in at least one judge being attacked by the NCSE which resulted in his termination for allowing article to get published which includes statement by Dr. Roy McDiarmid, the President of the Biological Society of Washington himself admitting that he reviewed the case personally, and found no wrong doing.


W.A. Dembski, The Design Inference: Eliminating Chance through Small Probabilities (Cambridge: Cambridge University Pres, 1998)


Cambridge University Press and peer-reviewed as part of a distinguished monograph series,

Wells, Jonathan. 2005. Do centrioles generate a polar ejection force? Rivista di Biologia/Biology Forum 98: 37-62.


D. Halsmer, J. Asper, N. Roman, and T. Todd, “The Coherence of an Engineered World,” International Journal of Design & Nature and Ecodynamics, Vol. 4(1):47–65 (2009).


•David L. Abel, “Constraints vs Controls,” The Open Cybernetics and Systemics Journal, Vol. 4:14-27 (January 20, 2010).

Joseph A. Kuhn, “Dissecting Darwinism,” Baylor University Medical Center Proceedings, Vol. 25(1): 41-47 (2012).

David L. Abel, “Is Life Unique?,” Life, Vol. 2:106-134 (2012)


• D.K.Y. Chiu & T.H. Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems, 4(3) (September 2002): 766–77


Lönnig, W.-E. 2004. Dynamic genomes, morphological stasis and the origin of irreducible complexity. In: V. Parisi, V. de Fonzo and F. Aluffi-Pentini, eds. Dynamical Genetics, 101-119. Research Signpost.


Meyer, Stephen. 2004. The origin of biological information and the higher taxonomic categories. Proceedings of the Biological Society of Washington 117: 213-239.

Dr. Roy McDiarmid, the President of the Biological Society of Washington and a scientist at the Smithsonian, later admitted that there was no wrong doing regarding the peer-review process of Meyer's paper

"I have seen the review file and comments from 3 reviewers on the Meyer paper. All three with some differences among the comments recommended or suggested publication. I was surprised but concluded that there was not inappropriate behavior vs a vis [sic] the review process"
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06-12-2012, 01:15 AM (This post was last modified: 06-12-2012 02:35 AM by tiagorod84.)
RE: Is neo-darwinism a scientific theory?
I'm getting tired of repeating myself.

1) I don't care for the Behe vs Miller Argument. I won't waste time on following that debate.

2) If irreducible complexity is set to challenge evolution. This high-quality paper demonstrates that the flagellum evolved into something, so here you have it. If you're rejecting the concept of homology, that's up to you! I cannot do anything about that.

(You'll use part of the paper for whatever you find usefull and forget the rest of the paper... Way to go!!)

3) If by irreducible complexity you mean that, within the same species, a certian complex structure only functions as a whole. Well, I'll say to you that that alone doesn't say anything against evolution (you can say it was designed, I can say it was randomly generated in the computer of the magic goblin), but it may say something about specialization. And I say may, because it is so very common in biology to see a component from a complex cell structure having different functions.

4) Clinging on such specificities and ignoring the majority of the well-studied examples makes ID very feeble. As Ghost said, good luck with that!

5) If you reject evolution, then you have to imagine that it was designed. Same ol' 150 years old argument with biochemestry flavour.

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06-12-2012, 01:53 AM (This post was last modified: 06-12-2012 03:02 AM by tiagorod84.)
RE: Is neo-darwinism a scientific theory?
As to the articles... majorly opinions or mathematical models at the most... Ideas? Yes! Good ideas? Well... you know my opinion about the one-eyed Sauron! New important data? No.

Nonetheless, one caught my attention "Do centrioles generate a polar ejection force?". Hey! they actually can be usefull! They actually pippet things and put stuff in tubes!

What a great disilusion and waste of time!

1) I won't discredit the journal. It would be a feeble argument.

2) No material and methods. It is a review! No bench work!
(Even poor ol' Darwin was in the field trying to do some honest work...)

3) Here's the comment of one reviewer:

"Summary & recommendation.
In this manuscript, the author reviews current knowledge regarding the structure and function of centrioles in animal cells, then proposes a novel role for centrioles in the generation of the polar ejection force. The author's proposal is plausible and testable, but suffers from two weaknesses: 1) the hypothesis is somewhat extravagant, while seeking to fill a knowledge gap that is not similarly dramatic; and 2) the hypothesis is highly speculative and poorly supported by current data. Moreover, the author misrepresents current uncertainty regarding the cause of the polar ejection force, and fails to convincingly establish a strong correlation between presence of polar ejection forces and presence of centrioles. Given the author's stated antipathy toward "neo-Darwinism" it is perhaps not surprising that he omitted the more detailed taxonomic survey that is needed to strengthen the claim of correlation. And the author glosses over the known roles of centrioles in the formation of cilia, structures known to be absent in land plants. Overall, the manuscript is generally clear and well-written, but is weakened by ad hoc swipes at evolutionary theory and some concluding speculation (on cancer biology) that is unacceptably vague and simplistic. Attention to these matters should improve the manuscript such that it will be suitable for publication in Rivista di Biologia, and I recommend that it be published after revision."

4) I've read the article and the revision proposed was not certainly taken into account.

5) Here's a comment of an actual cell biologist (Stephen Matheson) that for me beautifully sumarizes what ID really is:

"Finally, what about this paper could possibly be distinctive as the work of an ID theorist? Only this: that he considered the possibility that tubular structures could be turbines. Now, is that really an ID distinctive? Has Wells noticed how cell biologists refer to motors, cargo, tracks, export, import, zip codes, sorting? Cell biologists regularly identify patterns in biology that make sense through reference to structure-function relationships, and cell biologists are happy to refer to those functions using the vocabulary of design, both literally and metaphorically. If that's all that ID thinkers have to offer, then maybe they should just get back in the lab with the rest of us and try to figure out how all this stuff works."

How did this pathetic attempt to challenge evolution was accepted by the editor, I don't know! But if this is the best the Discovery Institute can produce. Good luck with that!

I'm out...

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