How do you reconcile the theory of evolution with the law of thermo-dynamics

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steen

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Smidlee said:
Those scientists in molecular biology better agree with Neo-Darwinism is they will be marked as a heretic / creationist. I don't blame any molecular biologist not speaking out against Dawinism since it not worth losing their job over.
Ah, the "black helicopter" paranoia defense. yeah, whatever.
 
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Late_Cretaceous

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Smidlee said:
Those scientists in molecular biology better agree with Neo-Darwinism is they will be marked as a heretic / creationist. I don't blame any molecular biologist not speaking out against Dawinism since it not worth losing their job over.

Prove that.
 
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Late_Cretaceous

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Smidlee said:
P.S I want to add that there many scientist who doesn't even deal with evolution. Behe made the case that most papers about molecular biology has very little to evolution (seldom mention). Of those papars that I've read does deal with evolution you will find a lot of words like; presumably, likely, probably, perhaps, might have, could have, possibly, apparently, has (some knid of animal) like features,etc so in many ways the scientist are honest enough to add these words to show their views from the actually facts.

Then how do you explain the existance of the Journal of Molecular Biology and Evolution? How about the Journal of Molecular Evolution? How do explain that the University of Princeton has scientists who specialize in the study of evolution employed in their Department of Molecular Biology?


Here is a link to the Journal of Molecular Biology and Evolution, you can aquire copies in pdf form of the papers published in this journal. Perhaps you would take me up the the challenge toreview some articles yourselfl? You could even pick them out yourself based on what you see in the abstracts (you need to be registered to see the entire article). I would be happy to have you point out the freqency of words like "presumably, likely, probably, perhaps, might have, could have, possibly, apparently," in articles of your own choosing. You can read the absracts without registering, but registration is free and you will be able to download entire articles.
 
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rmwilliamsll

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P.S I want to add that there many scientist who doesn't even deal with evolution. Behe made the case that most papers about molecular biology has very little to evolution (seldom mention). Of those papars that I've read does deal with evolution you will find a lot of words like; presumably, likely, probably, perhaps, might have, could have, possibly, apparently, has (some knid of animal) like features,etc so in many ways the scientist are honest enough to add these words to show their views from the actually facts.

I've read a lot of theology over the years.
Oftentimes they use words and phrases like:
"God said", "it is obvious", "it is plainly written", "everyone agrees", "The Bible clearly teaches", "It must be true that"

and you know, i can pick up 3 theology books and get 3 different opinions on almost any topic. And they all use the same words that denote:
certainity, without a doubt, absolutely, must be.

and they all say something different.

You'd think that they would use terms like this quote points out to differentiate between their opinion or their interpretation and what is written in the Scriptures.

OTOH there is remarkable unity across languages, cultures, countries, classes, etc on the elements of the different sciences, in fact, they can agree on lots of little things, where theologians can't seem to agree on even the big things.


so which do you prefer?
certainty with great divisiveness
or tentativeness with extraordinary unity?
 
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Late_Cretaceous

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Here is a listing of the top 12 articles downloaded from the Journal of Molecular Biology (no mention of evolution in the title jut to be fair) from July to Sept 2004

  1. Gene Silencing by Systemic Delivery of Synthetic siRNAs in Adult Mice • Short communication
    Journal of Molecular Biology, Volume 327, Issue 4, 4 April 2003, Pages 761-766
    D.R. Sorensen, M. Leirdal, M. Sioud
  2. Improved Prediction of Signal Peptides: SignalP 3.0 • Article
    Journal of Molecular Biology, Volume 340, Issue 4, 16 July 2004, Pages 783-795
    J. Dyrlov Bendtsen, H. Nielsen, G. von Heijne, S. Brunak
  3. The Protein Folding Network • Article
    Journal of Molecular Biology
    F. Rao, A. Caflisch
  4. A Family-based Approach Reveals the Function of Residues in the Nuclear Receptor Ligand-binding Domain • Review article
    Journal of Molecular Biology
    S. Folkertsma, P. van Noort, J. Van Durme, H.-J. Joosten, E. Bettler, W. Fleuren, L. Oliveira, F. Horn, J. de Vlieg, G. Vriend
  5. The Roles of Ribosomal Proteins in the Structure Assembly, and Evolution of the • Article
    Journal of Molecular Biology
    D.J. Klein, P.B. Moore, T.A. Steitz
  6. GTP Hydrolysis Mechanism of Ras-like GTPases • Review article
    Journal of Molecular Biology, Volume 340, Issue 5, 23 July 2004, Pages 921-932
    G. Li, X.C. Zhang
  7. Structural Modes of Stabilization of Permissive Phosphorylation Sites in Protein Kinases: Distinct Strategies in Ser/Thr and Tyr Kinases • Review article
    Journal of Molecular Biology
    A. Krupa, G. Preethi, N. Srinivasan
  8. Biochemical and Structural Studies of the Interaction of Cdc37 with Hsp90 • Article
    Journal of Molecular Biology
    W. Zhang, M. Hirshberg, S.H. McLaughlin, G.A. Lazar, J.G. Grossmann, P.R. Nielsen, F. Sobott, C.V. Robinson, S.E. Jackson, E.D. Laue
  9. Unique and Conserved Features of Genome and Proteome of SARS-coronavirus, an Early Split-off From the Coronavirus Group 2 Lineage • Article
    Journal of Molecular Biology, Volume 331, Issue 5, 29 August 2003, Pages 991-1004
    E.J. Snijder, P.J. Bredenbeek, J.C. Dobbe, V. Thiel, J. Ziebuhr, L.L.M. Poon, Y. Guan, M. Rozanov, W.J.M. Spaan, A.E. Gorbalenya
  10. In Vivo Selection of Combinatorial Libraries and Designed Affinity Maturation of Polydactyl Zinc Finger Transcription Factors for ICAM-1 Provides New Insights into Gene Regulation • Article
    Journal of Molecular Biology
    L. Magnenat, P. Blancafort, C.F. Barbas
  11. Interaction of the Molecular Chaperone @aB-Crystallin with @a-Synuclein: Effects on Amyloid Fibril Formation and Chaperone Activity • Article
    Journal of Molecular Biology
    A. Rekas, C.G. Adda, J. Andrew Aquilina, K.J. Barnham, M. Sunde, D. Galatis, N.A. Williamson, C.L. Masters, R.F. Anders, C.V. Robinson, R. Cappai, J.A. Carver
  12. Molecular Evolution of a MicroRNA Cluster • Article
    Journal of Molecular Biology, Volume 339, Issue 2, 28 May 2004, Pages 327-335
    A. Tanzer, P.F. Stadler

As you can see, two of the top 12 articles (roughly 17%) deal specifically with evolution. Not exactly rare is it?
 
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Late_Cretaceous

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Smildee said
Of those papars that I've read does deal with evolution you will find a lot of words like; presumably, likely, probably, perhaps, might have, could have, possibly, apparently, has (some knid of animal) like features,etc


Could you please provide the titles of these papers? I would like to read them myself.

I randomly selected an article that delt with evolution and molecular biology. In this case, the article is called The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins. Published by the Journal of Protein Science.
The full version is online, available without registration at the above link..

I recorded the number of occurances of words like "presumably, likely, probably, perhaps, might have, could have, possibly, apparently, has (some knid of animal) like features," as Mr. Smildee stated.

Here is what I found:


presumably,


In order for the reaction to proceed, several divalent metal ions (generally Mg2+ or Mn2+) are required at the active site (Wold and Ballou 1957), presumably to stabilize the carbanion intermediate.

However, the calculated pKa value indicates that the deprotonated form of Lys128 is negligible at physiological pH. Presumably, substrate binding lowers the pKa such that the nucleophilic attack can occur.

Both instances of the occurance of the word presumably have nothing to do with evolution per say. There is some ambiguity regarding the exact role of specific chemicals in certain portions of biochemical pathways. It is totally irrelavent if the author or ready accepts evolution or not in these two cases.


likely (and unlikely)


However, if the pKa is too low, then it is unlikely it will be able to accept a proton.

The catalytic residues of enolase have not been unequivocally determined; however, the conserved Lys357 (again using alignment numbering) is a likely candidate

Again the two occurances of the word likely hardly relate to the validity of evoluionary theory at all. They are used in terms of the chemistry specifically.

probably,

no occurances

perhaps,

no occurances

might have,



could have,

no occurances

possibly,

no occurances

apparently

no occurances

has features (or any variation thereof)

no occurances



It would appear that Mr. Smildee's assertion is quite unfounded in at least this case. The authors of this paper don't seem to have any ambivalence towards the the authenticity of evolution. Perhaps one could argue that the understanding of basic biochemistry is not fully understood (hence the need for research in that area).
 
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Late_Cretaceous

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Here is an example of another article that I found through the previous paper.

Group II introns as phylogenetic tools: structure, function, and evolutionary constraints, published by the American Journal of Botany.
Again, full version available at the link without registration.

recorded the number of occurances of words like "presumably, likely, probably, perhaps, might have, could have, possibly, apparently, has (some knid of animal) like features," that should show that the ideas presented are riddled with uncertainty in regards to evoultion.



presumably,

Failure to properly or efficiently remove the intron from the transcript prevents further transcript processing and translation; the protein is not synthesized, and presumably both the organism and the intron are strongly selected against.

Since it IS research, and research DOES venture into the unkown it is not suprising that they don't exactly know everything there is to know about selective pressure on this particular gene that they studied. Nothing earth shattering there, afterall science does not deal in absolutes.

likely (and unlikely)

We can therefore infer that site-specific mutations that terminate function in one G2 intron will likely have the same effect in other G2 introns if such mutations occur in homologous structural positions.

Domain V is not known to possess any binding sites with the mRNA substrate, and its high degree of conservation is most likely due to its fundamental role in ribozyme folding
Stem nucleotide substitutions may be more likely to persist in group II intron sequences if they are transitions.

This observation certainly does not rule out the parsimony method as a criterion for phylogeny estimation (e.g., Olmstead, Reeves, and Yen, 1998 ; Sanderson and Kim, 2000 )—it merely cautions that equal-weight parsimony as a model of character evolution is unlikely to represent the history of mutational change in group II intron sequences. Instead, the presence of mutational biases in the data suggests a weighted parsimony or maximum likelihood approach to phylogeny estimation (Lockhart et al., 1994 ; Yang, Goldman, and Friday, 1994 ; Swofford et al., 1996 ; Steel and Penny, 2000 ; Conant and Lewis, 2001 ).

As stated above, for group II intron sequences it is unlikely this model will be equal-weight parsimony or Jukes-Cantor

Well, well well. Scientists apparantly admitting that they don't know everything. Tsk tsk. Maybe whats why it's called RESEARCH. Protein folding is being actively studied around the world preciesely because it is not fully understood (besides that has little bearing on evolutionary theory).

Perhpas Mr. Smildee could explain to me how the use of the word "likely " is inappropriate in a research paper.



probably,


The lack of conserved structural motifs in domain IV is probably due to the absence of strong functional constraints on this domain's structure.

Domains II, III, and IV are of lesser importance (Koch et al., 1992 ), although each probably participates either in a particular step of splicing or in enhancing the overall catalytic reaction

Site mutation studies of the D5 loop sequence, GAAA, greatly reduced splicing efficiency (Chanfreau and Jacquier, 1994 ), probably by limiting its {zeta}–{zeta}' tertiary interaction with domain I

And the occurance of the word probably is bad why exactly? Some uncertainty in the area in which research is taking place maybe? Well, if it was fully understood it would not be under investigation would it.

perhaps,

This is perhaps the most dramatic example in the study of a structural partition deviating from an averaged sequence value for a mutation category.

The authors are merely stating that the example given is arguably the best example available .

Base composition in domain V approaches equivalency for all nucleotide states, perhaps due to strong functional constraints resulting in a relative increase in G/C content.

More importantly, perhaps, for mutation dynamics in G2 introns, C-A pairs may be of minimal hindrance in the formation of key stem structures and therefore may not be strongly selected against in certain structural positions.
Therefore, transitions would be more likely to persist in these stem structures, perhaps contributing to the high frequency of transition mutations observed in group II intron stem nucleotides


Oh dear, more examples of research probing into the unkown. Hardly invalidates the theory of evolution though.


might have,

no occurances


could have,


no occurances

possibly,


The legacy of this expectation persists in molecular systematics, possibly due to the absence of readily attainable information to the contrary

The authors are merely pointing out that there is little information available to counter a point they are making.


apparently,

no occurances


has (some knid of animal [plant in this case]) like features

no occurances





I am still at a loss to understand what is wrong with using some of these words in the first place. I am even more confused as to how the occurance of words indicating a degree of uncertainty in inappropriate in research.

If you were exploring a cave and felt a breeze of fresh air and saw a little bit of light what would be wrong with saying "there is probably an opening to the oustide there" or "that is likely a good way to get out of this place"?
 
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Late_Cretaceous

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I managed to look up a few articles in various engineering research journals (nothing whatsoever to do with evolution or biology) and was able to find quite a number of occurances of words like probably, likely, possibly, etc. in any paper I found.

Does that mean that engineering is a fraud? I better not drive over that bridge, it could be a sham !
 
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Smidlee

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Late_Cretaceous said:
I managed to look up a few articles in various engineering research journals (nothing whatsoever to do with evolution or biology) and was able to find quite a number of occurances of words like probably, likely, possibly, etc. in any paper I found.

Does that mean that engineering is a fraud? I better not drive over that bridge, it could be a sham !


Lol. I surely don't see these words as bad words as this shows the scientist being honest which is my whole point. So I actually respect those (even Darwinist) who uses them.
Some parts of evolution isn't in question which is why I prefer ,most of the time, using Darwinism instead.
 
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notto

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Smidlee said:
One of the points I continue to see come up is what was once thought to be "junk" DNA isn't junk after all.

Can you point us to the research article that states this?

What do you think the definition of 'junk' DNA is?

How do they determine that it is or is not 'junk' DNA?

Surely when you see this point brought up, these questions are answered, right?

Of course, even if what you state is true and you understand what you are saying, it doesn't impact the theory of evolution at all.
 
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rmwilliamsll

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Smidlee said:
One of the points I continue to see come up is what was once thought to be "junk" DNA isn't junk after all.

junk is an unfortunate turn of phrase. when you see it in a book, just substitute "dna for which we don't know a function", and you will be ok.

but a lot of it will turn out to be currently junk, long repeats, retroviral inserts etc., so what?
 
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steen

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Smidlee said:
Lol. I surely don't see these words as bad words as this shows the scientist being honest which is my whole point. So I actually respect those (even Darwinist) who uses them.
Some parts of evolution isn't in question which is why I prefer ,most of the time, using Darwinism instead.
Ah, so instead of arguing against the actual science, you are trying to argue against the hypothesis proposed 150 years ago, is that what you are saying? What would be the purpose of this? Trying to have an argument so you feel better about your religion? When you KNOW that your argument is not valid in today's science? Isn't that paradoxical?
 
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