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JudeNebula
Posted 06/20/12 at 08:47 PM Reply with quote  #31 
Quote:
Originally Posted by vmancha


Care to show one article that proves useful DNA information builds over time in the evolutionary scheme of things.

Here are 30

  1. Long, M., Betran, E., Thornton, K. and Wang, W. (2003). "The origin of new genes: glimpses from the young and old." Nature Reviews Genetics. 4(11): 865-875.
  2. Adami et al., 2000. (see below)
  3. Alves MJ, Coelho MM, Collares-Pereira MJ, 2001. Evolution in action through hybridisation and polyploidy in an Iberian freshwater fish: a genetic review. Genetica 111(1-3): 375-385. [2]
  4. Brown CJ, Todd KM, Rosenzweig RF, 1998. Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol. Biol. Evol. 15(8): 931-942. [3]
  5. Decadt, Y. JG, 2000. On the origin and impact of information in evolution paper available on the internet.
  6. Hughes AL, Friedman R, 2003. Parallel evolution by gene duplication in the genomes of two unicellular fungi. Genome Res. 13(6A): 1259-1264.
  7. Knox JR, Moews PC and Frere J-M, 1996. Molecular evolution of bacterial beta-lactam resistance. Chemistry & Biology 3: 937-947.
  8. Lang, D. et al, 2000. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science 289: 1546-1550. See also Miles, E.W. & Davies, D.R., 2000. On the ancestry of barrels. Science 289: 1490.
  9. Lenski, R.E., 1995. in Population Genetics of Bacteria, Society for General Microbiology, Symposium 52, eds. Baumberg, S., Young, J.P.W., Saunders, S.R. & Wellington, E.M.H., Cambridge University Press, UK., pp. 193-215.
  10. Lenski, R., Rose, M.R., Simpson, E.C. & Tadler, S.C., 1991. American Naturalist 138: 1315-1341.
  11. Long M. (2001). "Evolution of novel genes." Curr Opin Genet Dev. 11(6):673-80.
  12. Long, M., Betran, E., Thornton, K. and Wang, W. (2003). "The origin of new genes: glimpses from the young and old." Nature Reviews Genetics. 4(11): 865-875.
  13. Lynch M and Conery JS, 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155. See also Pennisi, E., 2000. Twinned genes live life in the fast lane. Science 290: 1065-1066.
  14. Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL. (1998). "Selective sweep of a newly evolved sperm-specific gene in Drosophila." Nature. 396(6711):572-5.
  15. Ohta T., 2003. Evolution by gene duplication revisited: differentiation of regulatory elements versus proteins. Genetica 118(2-3): 209-216.
  16. Park IS, Lin CH, and Walsh CT, 1996. Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B. Biochemistry 35: 10464-10471.
  17. Prijambada ID et al., 1995. Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution. Applied and Environmental Microbiology 61(5): 2020-2022.
  18. Schneider, T.D., 2000. Evolution of biological information. Nucleic Acids Res 28(14): 2794-2799. [4]
  19. Zhang J, Zhang YP, Rosenberg HF, 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nature Genetics 30(4):411-415. See also: Univ. of Michigan, 2002, How gene duplication helps in adapting to changing environments. [5]
  20. Whitman CP. (2002). "The 4-oxalocrotonate tautomerase family of enzymes: how nature makes new enzymes using a beta-alpha-beta structural motif." Arch Biochem Biophys. 402(1):1-13.PubMed DOI
  21. Bos DH. (2005). "Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication." J Mol Evol. 60(2):221-8. PubMed
  22. Ballicora MA, Dubay JR, Devillers CH, Preiss J. (2005). "Resurrecting the ancestral enzymatic role of a modulatory subunit." J Biol Chem. 280(11):10189-95. PubMed
  23. Todd AE, Orengo CA, Thornton JM. (2002)."Sequence and structural differences between enzyme and nonenzyme homologs." Structure (Camb). 10(10):1435-51. PubMed
  24. Todd AE, Orengo CA, Thornton JM. (2002). "Plasticity of enzyme active sites." Trends Biochem Sci. 27(8):419-26. PubMed
  25. Bartlett GJ, Borkakoti N, Thornton JM. (2003). "Catalysing new reactions during evolution: economy of residues and mechanism." J Mol Biol. 331(4):829-60. PubMed
  26. James LC, Tawfik DS. (2001). "Catalytic and binding poly-reactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution." Protein Sci. 10(12):2600-7. PubMed
  27. Todd AE, Orengo CA, Thornton JM. (2001). "Evolution of function in protein superfamilies, from a structural perspective." J Mol Biol. 307(4):1113-43. PubMed
  28. Raes, J., Van de Peer, Y. (2002). "Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico." Appl Bioinformatics. 2(2):91-101. PubMed
  29. Van de Peer, Y., Taylor, J. S., Braasch, I., Meyer, A. "The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes." J Mol Evol. 53(4-5):436-446.
  30. Carginale, V., Trinchella, F., Capasso, C., Scudiero, R., Riggio, M., Parisi, E. (2004). "Adaptive evolution and functional divergence of pepsin gene family." Gene. 333:81-90.PubMed
CrashTestAuto
Posted 06/21/12 at 08:19 AM Reply with quote  #32 
Quote:
Originally Posted by Equestions
Tell you what Crash. I'll put up the argument I had in the other thread. It's a simplified version and should give you an idea of what it's all about. It has nothing to do with the things you mentioned so it should suffice.

Now.....on another note. I have behind me on my bookshelf Darwin's Origin of Species, 2 of the books by Dawkins, Something From Nothing by Krauss, and about 12 to 14 other pro-evolution books going all the way back to my college days. I'd be interested to find out who, of the atheists on this site, has ever read a book that WASN'T pro evolution. Where I come from that's called 'confirmation bias' which leads to indoctrination, not education. 

It's amazing to me that you are asking us for some simple thing to read or maybe a video to watch that fills you in from an ID perspective and then somehow all you guys think you know the 'truth' about a subject. Without actually reading books (I know, it's not YouTube videos or something you can load into an XBox) on what 'the other side' actually thinks how can you make a well informed rational decision about who's right or wrong? That's like walking into a courtroom. listening ONLY to the prosecution, and then claiming "I'm done! I've heard enough! I could care less what the defense says.....that man is GUILTY!" It's a little intellectually dishonest of all of you guys not to do some real homework on the subject and then make a rational decision based on ALL the evidence.

So I'll post my previous thread but man......you all need to be honest with yourself and do some actual homework. We Christians don't simply believe what we believe because our parents spanked us if we didn't. Believing what we believe is not a 'blind' faith.

Equestions, whilst I respect that you have done your reading, don't underestimate atheists.  I have read about as much of the ID side as the anti-ID side in the actual debate, though obviously done more reading on the actual topic of evolution.

The thing is, and this is not a universal statement, I don't trust ID proponents.  You have shown yourself to be both intelligent, and sincere, so I have asked you for what you consider to be a solid argument.  However, what I have read about is the history of ID.  Whilst we can barter over how much it is rehashed Creationism, it is rehashed Creation Science (see the history of Of Pandas and People).  The history of these two movements is peppered with dishonesty and attempts to get around the First Amendment.  From the trials in the 60s and 70s to Expelled, the movement has simply lost any right to benefit of the doubt, and thus no I don't spend much time listening to its high-profile proponents.

Honestly, I sympathise with theistic opponents to evolution.  Lawless accused me of using a Creationist argument in my 'Santa' defence, but I was actually parodying the theistic evolutionist argument that God could use naturalistic means to achieve His ends.  I don't see why he would, and if I was starting from the premise 'God exists', I would be pretty resistant to the idea that He spent 4 billion years letting us randomly meander towards humans.  However, the evidence for evolution is pretty darn overwhelming at this stage, and I don't know how you can keep up an offence against it.
gregwilson
Posted 06/21/12 at 01:48 PM Reply with quote  #33 
I am agnostic as to the age of the earth. What I don't believe is that we can know with much certainty how old the earth is exactly, but that really isn't pertinent to the discussion.

Dinosaurs existed, probably long ago. Did they live side by side with humans? I'm agnostic to that as well. How do we know our fossil dating is accurate? Do we have a time machine? Essentially we rely on a process which is unverifiable, although not necessarily completely faulty.

As far as fossilized human remains, such as the neaderthals, obviously I believe the fossils to be evidence of humans who lived thousands of years ago. But without more, direct and empirical evidence (such as directly witnessing how they lived, spoke, interacted, used technology), all we have are speculative explanations. I very much doubt we can know with much certainty who these people were. I also believe microevolution to be a process which can lead to a large divergence within a type (kind) of animal. It would appear that a Great Dane and Chihuahua are different animals from just their fossils when they are indeed the same species, or kind of animal. We need more information than just partial fossilized skeletons as it is the interpretation of the fossils which is faulty in my opinion.

It is very presumptuous to claim we know, from scientific endeavors, that all life arose from a single ancestor due to an unguided process over billions of years. It is even more presumptuous to reject design arguments due to naturalistic predispositions, yet that is what Darwinian evolutionists do.
JudeNebula
Posted 06/21/12 at 02:52 PM Reply with quote  #34 
Greg,

You claim to doubt scientific knowledge..but how much do you know about these fields?

Have you read ONE single book on evolution?

Such as Richard Dawkins "The Blind Watchmaker" "The Greatest Show On Earth", or E.O Wilson's "The Diversity of Life", maybe Jerry Coyne's "Why Evolution is true"?

All of these questions you have regarding our dating methods, how we can know about neanderthals are fairly easily explained...etc.. if you actually would give the time of day to learn about them.

Instead you have chosen to dismiss these fields, simply because they don't match up with a collection of ancient mythological tales post hoc assembled in the desert region of modern palestine..


Why not educate yourself? Serious question.

I don't understand why you haven't read a book on evolution. Please explain this to me.


Quote:
It is very presumptuous to claim we know, from scientific endeavors, that all life arose from a single ancestor due to an unguided process over billions of years. It is even more presumptuous to reject design arguments due to naturalistic predispositions, yet that is what Darwinian evolutionists do

Richard Dawkins book The Blind Watchmaker addresses all of these issues specifically.  Why no designer..well for a few reasons, besides having no evidence of a designer..but because there is a TON of bad design that could have only come about through an unguided process.

So why haven't you read that book? Are you not interested in giving yourself a fair and balanced look at the subject? 

Do you prefer to stick with your creationist websites? Do you have too much emotional stake riding on the fact that you need to be right about God/Christianity that you won't even hear the other sides points?

You are smart guy Greg, the only thing keeping you from the truth is your emotional attachment to beliefs that were forced upon you as a child. You haven't read Dawkins because you don't really care about the truth, you simply care about 'proving' what you already believed.
hasbeen
Posted 06/21/12 at 03:04 PM Reply with quote  #35 


1. Has every-bodies toolbar vanished when posting or just mine?

2. in regards to this comment:


It would appear that a Great Dane and Chihuahua are different animals from just their fossils when they are indeed the same species, or kind of animal.

------------

Would you put the Hippo as the same kind as a cow type animal or a whale type?
vmancha
Posted 06/22/12 at 10:54 AM Reply with quote  #36 
Quote:
Originally Posted by JudeNebula
Quote:
Originally Posted by vmancha


Care to show one article that proves useful DNA information builds over time in the evolutionary scheme of things.

Here are 30

  1. Long, M., Betran, E., Thornton, K. and Wang, W. (2003). "The origin of new genes: glimpses from the young and old." Nature Reviews Genetics. 4(11): 865-875.
  2. Adami et al., 2000. (see below)
  3. Alves MJ, Coelho MM, Collares-Pereira MJ, 2001. Evolution in action through hybridisation and polyploidy in an Iberian freshwater fish: a genetic review. Genetica 111(1-3): 375-385. [2]
  4. Brown CJ, Todd KM, Rosenzweig RF, 1998. Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol. Biol. Evol. 15(8): 931-942. [3]
  5. Decadt, Y. JG, 2000. On the origin and impact of information in evolution paper available on the internet.
  6. Hughes AL, Friedman R, 2003. Parallel evolution by gene duplication in the genomes of two unicellular fungi. Genome Res. 13(6A): 1259-1264.
  7. Knox JR, Moews PC and Frere J-M, 1996. Molecular evolution of bacterial beta-lactam resistance. Chemistry & Biology 3: 937-947.
  8. Lang, D. et al, 2000. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science 289: 1546-1550. See also Miles, E.W. & Davies, D.R., 2000. On the ancestry of barrels. Science 289: 1490.
  9. Lenski, R.E., 1995. in Population Genetics of Bacteria, Society for General Microbiology, Symposium 52, eds. Baumberg, S., Young, J.P.W., Saunders, S.R. & Wellington, E.M.H., Cambridge University Press, UK., pp. 193-215.
  10. Lenski, R., Rose, M.R., Simpson, E.C. & Tadler, S.C., 1991. American Naturalist 138: 1315-1341.
  11. Long M. (2001). "Evolution of novel genes." Curr Opin Genet Dev. 11(6):673-80.
  12. Long, M., Betran, E., Thornton, K. and Wang, W. (2003). "The origin of new genes: glimpses from the young and old." Nature Reviews Genetics. 4(11): 865-875.
  13. Lynch M and Conery JS, 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155. See also Pennisi, E., 2000. Twinned genes live life in the fast lane. Science 290: 1065-1066.
  14. Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL. (1998). "Selective sweep of a newly evolved sperm-specific gene in Drosophila." Nature. 396(6711):572-5.
  15. Ohta T., 2003. Evolution by gene duplication revisited: differentiation of regulatory elements versus proteins. Genetica 118(2-3): 209-216.
  16. Park IS, Lin CH, and Walsh CT, 1996. Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B. Biochemistry 35: 10464-10471.
  17. Prijambada ID et al., 1995. Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution. Applied and Environmental Microbiology 61(5): 2020-2022.
  18. Schneider, T.D., 2000. Evolution of biological information. Nucleic Acids Res 28(14): 2794-2799. [4]
  19. Zhang J, Zhang YP, Rosenberg HF, 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nature Genetics 30(4):411-415. See also: Univ. of Michigan, 2002, How gene duplication helps in adapting to changing environments. [5]
  20. Whitman CP. (2002). "The 4-oxalocrotonate tautomerase family of enzymes: how nature makes new enzymes using a beta-alpha-beta structural motif." Arch Biochem Biophys. 402(1):1-13.PubMed DOI
  21. Bos DH. (2005). "Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication." J Mol Evol. 60(2):221-8. PubMed
  22. Ballicora MA, Dubay JR, Devillers CH, Preiss J. (2005). "Resurrecting the ancestral enzymatic role of a modulatory subunit." J Biol Chem. 280(11):10189-95. PubMed
  23. Todd AE, Orengo CA, Thornton JM. (2002)."Sequence and structural differences between enzyme and nonenzyme homologs." Structure (Camb). 10(10):1435-51. PubMed
  24. Todd AE, Orengo CA, Thornton JM. (2002). "Plasticity of enzyme active sites." Trends Biochem Sci. 27(8):419-26. PubMed
  25. Bartlett GJ, Borkakoti N, Thornton JM. (2003). "Catalysing new reactions during evolution: economy of residues and mechanism." J Mol Biol. 331(4):829-60. PubMed
  26. James LC, Tawfik DS. (2001). "Catalytic and binding poly-reactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution." Protein Sci. 10(12):2600-7. PubMed
  27. Todd AE, Orengo CA, Thornton JM. (2001). "Evolution of function in protein superfamilies, from a structural perspective." J Mol Biol. 307(4):1113-43. PubMed
  28. Raes, J., Van de Peer, Y. (2002). "Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico." Appl Bioinformatics. 2(2):91-101. PubMed
  29. Van de Peer, Y., Taylor, J. S., Braasch, I., Meyer, A. "The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes." J Mol Evol. 53(4-5):436-446.
  30. Carginale, V., Trinchella, F., Capasso, C., Scudiero, R., Riggio, M., Parisi, E. (2004). "Adaptive evolution and functional divergence of pepsin gene family." Gene. 333:81-90.PubMed


Not one of these articles shows the development of a new useful gene other than utilizing an old gene. You first have to show the development of a new gene to start with. Show an article in this list that does that.
vmancha
Posted 06/22/12 at 11:52 AM Reply with quote  #37 
Quote:
Originally Posted by vmancha
Quote:
Originally Posted by JudeNebula
Quote:
Originally Posted by vmancha


Care to show one article that proves useful DNA information builds over time in the evolutionary scheme of things.

Here are 30

Here is one from your own links. READ it and understand.


The origin of new genes: glimpses from the young and old.

Long M, Betrán E, Thornton K, Wang W.

Source

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA. mlong@uchicago.edu

Abstract

Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.

PMID:
 
14634634
 
[PubMed - indexed for MEDLINE]


Again no one knows how one single gene originated! Get it? If evolution is such a KNOWN theory with a capital T we should know how information came out of nothing however scientific naturalism simply has no explanation for emergence all the way from the BB to the info in the DNA.
Only a creation perspective gives answers to this end. 
JudeNebula
Posted 06/22/12 at 04:11 PM Reply with quote  #38 
Vmancha,

You clearly have never written a peer-reviewed article. When you do, one of the first things you highlight is WHY your article is important. 

So when the authors write the following ". However, there has been little opportunity to explore how genes with new functions originate and evolve. " They are writing that so they are letting people know,  HEY HERE IS a study about new genes and how they work, not much has been done on it yet so this is going to be worth reading.

Get it? That is exactly what this study is about. New Genes, new genes with new information.  
JudeNebula
Posted 06/22/12 at 04:12 PM Reply with quote  #39 
all of the articles provided what you are asking for, and there are HUNDREDS if not thousands more on PubMed. 
vmancha
Posted 06/22/12 at 05:21 PM Reply with quote  #40 
Quote:
Originally Posted by JudeNebula
Vmancha,

You clearly have never written a peer-reviewed article. When you do, one of the first things you highlight is WHY your article is important. 

So when the authors write the following ". However, there has been little opportunity to explore how genes with new functions originate and evolve. " They are writing that so they are letting people know,  HEY HERE IS a study about new genes and how they work, not much has been done on it yet so this is going to be worth reading.

Get it? That is exactly what this study is about. New Genes, new genes with new information.  







I'm still waiting to see some of your articles. You did write them?
The article here clearly stated they do not know how new genes originate. To hear your side it is a done deal. Again this is another bedtime story article of how's it would be nice if evolution occurs but poses no proof only conjecture in the form of -evolution must have done it. Can you show which gene the article proves came from nothing?
JudeNebula
Posted 06/22/12 at 05:28 PM Reply with quote  #41 
Quote:
Originally Posted by vmancha


I'm still waiting to see some of your articles. You did write them?
The article here clearly stated they do not know how new genes originate. To hear your side it is a done deal. Again this is another bedtime story article of how's it would be nice if evolution occurs but poses no proof only conjecture in the form of -evolution must have done it. Can you show which gene the article proves came from nothing?

I'll keep my anonymity thank you. I don't need some troll going 4chan on me. 

The article does not clearly state that. You are making stuff up.

Obviously new genes do not come from nothing. what are you talking about? 

New genes are mutations of old genes...

Here is an article that will help explain it to you.

Origins of New Genes and Pseudogenes

By: Chitra Chandrasekaran, Ph.D. (Texas Wesleyan University) & Esther Betrán, Ph.D. (Department of Biology, University of Texas, Arlington, TX) © 2008 Nature Education 
Citation: Chandrasekaran , C. & Betrán , E. (2008) Origins of new genes and pseudogenes. Nature Education 1(1)




http://www.nature.com/scitable/topicpage/origins-of-new-genes-and-pseudogenes-835

"There are several mechanism by which new genes are generated. These include gene duplication, transposable element protein domestication, lateral gene transfer, gene fusion, gene fission, and de novo origination."
vmancha
Posted 06/22/12 at 06:11 PM Reply with quote  #42 
Quote:
Originally Posted by JudeNebula
Quote:
Originally Posted by vmancha


I'm still waiting to see some of your articles. You did write them?
The article here clearly stated they do not know how new genes originate. To hear your side it is a done deal. Again this is another bedtime story article of how's it would be nice if evolution occurs but poses no proof only conjecture in the form of -evolution must have done it. Can you show which gene the article proves came from nothing?

I'll keep my anonymity thank you. I don't need some troll going 4chan on me. 

The article does not clearly state that. You are making stuff up.

Obviously new genes do not come from nothing. what are you talking about? 

New genes are mutations of old genes...

Here is an article that will help explain it to you.

Origins of New Genes and Pseudogenes

By: Chitra Chandrasekaran, Ph.D. (Texas Wesleyan University) & Esther Betrán, Ph.D. (Department of Biology, University of Texas, Arlington, TX) © 2008 Nature Education 
Citation: Chandrasekaran , C. & Betrán , E. (2008) Origins of new genes and pseudogenes. Nature Education 1(1)




http://www.nature.com/scitable/topicpage/origins-of-new-genes-and-pseudogenes-835

"There are several mechanism by which new genes are generated. These include gene duplication, transposable element protein domestication, lateral gene transfer, gene fusion, gene fission, and de novo origination."




.
If you are going to swing it around that you have published then you loose your rights. Put up or shut up!
In happy to see its hit you none of your 30 articles prove new information evolved into a first functional gene. Only that a gene can be derived from old information.
As to pseudo genes interesting you should try to claim it proof for evo. When they were deemed junk for 30 yrs your side said see god creates junk and evoists are right that stuff should degrade. But then when scientists showed it was not junk then they claimed see evo did it again. No matter what is found the evos can change and say evo did it. Pseudo genes are not pseudo after all to redefine then and claim this redefinition proves evo ism is typical.
Hows about pointing out in this article a proof of a de novo gene evolution.
Rostos
Posted 06/22/12 at 07:44 PM Reply with quote  #43 

Well, if it can happen as Jade seems to be trying to say it has, Dr Dawkins doesnt know about it...

 
JudeNebula
Posted 06/22/12 at 08:29 PM Reply with quote  #44 
Rostos,

You do know that video was a hoax right?

That the question was overdubbed in editing?

Here's the real story and Richard Dawkins answer to the question..
vmancha
Posted 06/23/12 at 09:51 AM Reply with quote  #45 
Dawkins if he could would have caused the question to backfire by answering it. To claim "I realized they were creationists" does no good for him. The camera was rolling and recorded what he said after a moment of re composure where he fell back into his typical bedtime story mode of evo ism.
The facts remain he could not as Jude can not demonstrate the origin of dna information to a functioning codon s.
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