The lie of evolution

"All your verbiage aside which follows your denial, it is true. It is known. In fact that statement is an exact quote from a biochemist in a private email. It is not a layman's analysis, it is a professional analysis."

All the "verbiage" was a small sampling of the data that proves that your assertion is incorrect. I may be a layman doing the reporting on this thread but I provided reference after reference to back up what I was saying.

You make absolutely no response to the actual data that I presented. You brush it off without even a hint at a reason why such examples and mechanisms do not do just what you claimed was impossible. The data refutes you but all we get is a re-assertion of the same thing and an allusion to some private statement by some reputed biochemist.

It does not seem to matter that your private biochemist is on an island disagreeing with essentially every other biochemist out there. It does not matter that examples and mechanisms are given which do provide a path to novel and useful genes.

The facts are that there are known mechanisms to generate novel genes without a loss of previous function and that the literature is full of examples of these mechanisms in action.

Furthermore, the details of the genome that trace how these duplications and mutations happened are without explanation in a YE paradigm.

 

"Don't have to refer to Genesis at all. Here is an example, from a recent email, of the lies professors KNOWINGLY spout to get students to believe in the myth of evolution"

These are anecodotes that have no bearing on the validity of the data and interpretations supporting evolution. At worst, they indicate individual dishonesty. There is nothing to indicate that the researchers generating the data are consistently being dishonest.

Furthermore, these are one side of the story. Take your first example. If someone is still trying to teach Haeckel as Haeckel thought, well they are wrong. I don't think you would have any trouble getting just about any one who accepts evolution to condemn using "ontogony recapitulate phylogeny."

However, there is real value to be gained from ontogeny and it is very easy to confuse what is being said and make a mistake in what you thought you heard.

If you look at the transitional series where mammals evolve from reptiles, you will see that the mammal ear bones evolved from the reptile jaw bones. Now, if you look at the development of reptile and mammal embryos, you will see that they both have an early stage with pharyngeal arches. A part of one of these arches turns into the reptile jaw. The very same part turns into the inner ear of mammals. So you have congruence of data from development and from the fossils.

Often, people will still refer to these arches as "gill slits" which while not the best choice in words, still let's others know what is being discussed. Parts of the arches do turn into gills in fish and there is a superficial resemblance.

But, with all the YE misinformation trying to fallaciously equivocate modern evo-devo with Haeckel, it is a very easy mistake to make and really is the most likely explanation for what happened.

As far as the second example... It seems bad but again we have only an anecdote and one version of it at that. Since we are talking about a written debate, perhaps a transcript of the debate survices somewhere such that we could put it into context. While it sounds bad, I am not sure we have enough data to judge what really happened.

 

All your verbiage aside which follows your denial, it is true. It is known. In fact that statement is an exact quote from a biochemist in a private email. It is not a layman's analysis, it is a professional analysis. </font>[/QUOTE]I'm afraid your biochemist friend was making an extreme overgeneralization. It may be possible that there is a single most superior gene sequence for a protein to do a certain function, and it may be possible that once that sequence has been reached any further mutation is not beneficial. However, this is an extreme hypothetical case--it's far more likely that there is no one superior protein for any application and it's also true that what was an idealish protein for one application may no longer be ideal once conditions (temperature, salt availabilities, energy availability) change. Right now from looking at common proteins among various species we see that their gene sequences are tolerant of variation without loss in function, so it seems clear that we have not reached that apex of specialization that your biochemist friend assumes.

Additionally, somatic hypermutation in B cells does not result in loss of specificity, but is actually required for proper antibody specificity. This is impossible to resolve with the propositions that mutations are always detrimental and always result in loss of specificity.

 

OK Help me out here, Bro. James, so I can answer correctly. Are you asking about how the original code using DNA came to be? Or are you merely asking how species "a" becomes more complex species "b" ?

And for the part about intelligent design - to discuss the intelligent design idea, we have to stop looking at an individual mutation and back up, look at a more abstract level of species change as a whole. So when you ask if mutations are considered intelligent design, you're mixing up levels of abstraction, as if I were to ask you about changing the individual letters of a word and how that affects the theological correctness of your paragraph. In other words, I'm not sure what you asked there. Can you rephrase?

 

Paul, your faith is greater than reality. </font>[/QUOTE]We are both people of great faith, I am sure. One of us is going to tell the other one, in heaven, "I told you so!" Of that I have no doubt. And since we'll both be without sin at that point, don't worry about me rubbing it in to much.

My question to you: What stops the mutations from ever, ever, even in a very rare accidental case from happening to light on a change that is beneficial to the organism? Is it something that God intervenes to prohibit? Is it simply so overwhelmingly improbable that we know it cannot happen? (I'm talking small incremental advantage here, not huge leaps like an arm turning into a wing, but rather like a poorly functioning wing getting just a wee bit better)

 

Got it!! What is the origin of DNA? What is the mechanism of the existence of DNA? Or: how did all that stuff get in the same place at the same time in the right proportions to make even one of the building blocks of life. Please provide the stats as well.

Selah,

Bro. James

 

"Got it!! What is the origin of DNA? What is the mechanism of the existence of DNA? Or: how did all that stuff get in the same place at the same time in the right proportions to make even one of the building blocks of life. Please provide the stats as well."

There are some really great ideas on that topic. When you get a chance, here is some light reading that should help you learn as much as anyone else on how that happened.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15556408&query_hl=1
http://www.pnas.org/cgi/content/full/99/20/12733
http://biotech.icmb.utexas.edu/pages/science/bkup_of_RNA.html
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15217990&query_hl=4

That will get you started. Next, you might want to go to the Proceedings of the National Academy of Sciences of the United States of America. Here are the results you get if you search with "origin of life". I got 153 hits. The second one was

Shelley D. Copley, Eric Smith, and Harold J. Morowitz, A mechanism for the association of amino acids with their codons and the origin of the genetic code, PNAS 2005 102: 4442-4447.

That one sounds intruiging. I am sure you can find other keywords to search under that will yield more information of how they think it all got started.

Once through with that, I have some more papers for you to look up and go through. I'll organize them by topic for you.

A) Composition of the early atmosphere

Genda, Hidenori & Abe, Yutaka
2003 “Survival of a proto-atmosphere through the stage of giant impacts: the mechanical
aspects” Icarus 164, 149-162 (2003).

Holland, Heinrich D.
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Geochemistry Princeton University Press

Holland, Heinrich D.
1999 “When did the Earth’s atmosphere become oxic? A Reply.” The Geochemical
News #100: 20-22 (see Ohmoto 1997 )

Kasting, J. F., J. L. Siefert,
2002 “Life and the Evolution of Earth's Atmosphere” Science 296:1066

Pepin, R. O.
1997 Evolution of Earth's Noble Gases: Consequences of Assuming Hydrodynamic Loss
Driven by Giant Impact Icarus 126, 148-156 (1997).

Rosing, Minik T. and Robert Frei
2003 U-rich Archaean sea-floor sediments from Greenland – indications of &gt;3700 Ma
oxygenic photosynthesis" Earth and Planetary Science Letters, online 6 December 03

B) Formation of the first organic molecules

Amend, J. P. , E. L. Shock
1998 “Energetics of Amino Acid Synthesis in Hydrothermal Ecosystems” Science
Volume 281, number 5383, Issue of 11 Sep , pp. 1659-1662.

Blank, J.G. Gregory H. Miller, Michael J. Ahrens, Randall E. Winans
2001 “Experimental shock chemistry of aqueous amino acid solutions and the cometary
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Chyba, Christopher F., Paul J. Thomas, Leigh Brookshaw, Carl Sagan
1990 "Cometary Delivery of Organic Molecules to the Early Earth" Science Vol.
249:366-373

Engel, Michael H., Bartholomew Nagy,
1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison
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Matthews CN.
1992 Hydrogen cyanide polymerization: a preferred cosmochemical pathway. J. Br.
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Schoonen, Martin A. A., Yong Xu
2001 “Nitrogen Reduction Under Hydrothrmal Vent Conditions: Implications for the
Prebiotic Synthesis of C-H-O-N Compounds” Astrobiology 1:133-142

Miller, Stanley L.,
1953 “A Production of Amino Acids Under Possible Primitive Earth Conditions” Science
vol. 117:528-529

Miller, Stanley, Harold C. Urey
1959 “Organic Compound Synthesis on the Primitive Earth” Science vol 139 Num 3370:
254-251

Weber AL.
1997 Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from
formose substrates (formaldehyde and glycolaldehyde) and ammonia. Origins of Life and
Evolution of the Biosphere 28: 259-270.

Cooper, George, Novelle Kimmich, Warren Belisle, Josh Sarinana, Katrina Brabham,
Laurence Garrel
2001 Carbonaceous meteorites as a source of sugar-related organic compounds for the
early Earth Nature 414, 879 - 883 (20 Dec 2001) Letters to Nature

Cody, George D., Nabil Z. Boctor, Timothy R. Filley, Robert M. Hazen, James H. Scott,
Anurag Sharma, Hatten S. Yoder Jr.
2000 “Primordial Carbonylated Iron-Sulfur Compounds and the Synthesis of Pyruvate”
Science v.289 : 1337-1340

Sephton, Mark A.
2001 Meteoritics: Life's sweet beginnings? Nature 414, 857 - 858 (20 Dec ) News and
Views

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.
2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196 (in Brevia)

Lazcano, Antonio, Stanley L. Miller
1996 “The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World,
and Time” Cell vol 85:793-798

Nelson, K. E., M. Levy, S. L. Miller
2000 “Peptide nucleic acids rather than RNA may have been the first genetic molecule”
PNAS-USA v.97, 3868-3871

Fuller, W. D., Sanchez, R. A. & Orgel, L. E. Studies in prebiotic synthesis. VI. Synthesis
of purine nucleosides. J. Mol. Biol. 67, 25-33 (1972).

Robertson, MP, Miller SL.
1995 An efficient prebiotic synthesis of cytosine and uracil. Nature 375, 772 - 774 ()

Nelson K.E., Robertson M.P., Levy M, Miller S.L.
2001 Concentration by evaporation and the prebiotic synthesis of cytosine. Orig Life
Evol Biosph Jun;31(3):221-229

Deamer, D. W., and Pashley, R. M.
1989. Amphiphilic components of carbonaceous meteorites. Orig. Life Evol. Biosphere
19:21-33.

Krishnamurthy, R., Pitsch, S. & Arrhenius, G. 1999 Mineral induced formation of
pentose-2,4-bisphosphates. Origins Life Evol. Biosph. 29, 139-152 ().

Dworkin, Jason P., David W. Deamer, Scott A. Sandford, and Louis J. Allamandola
2001 “Self-assembling amphiphilic molecules: Synthesis in simulated
interstellar/precometary ices” PNAS 98: 815-819

Pizzarello, Sandra, Yongsong Huang, Luann Becker, Robert J. Poreda, Ronald A.
Nieman, George Cooper, Michael Williams
2001 “The Organic Content of the Tagish Lake Meteorite” Science, Vol. 293, Issue 5538,
2236-2239, September 21, 2001

Segre' D., Ben-Eli D. Deamer D. and Lancet D.
2001 “The Lipid World” Origins Life Evol. Biosphere 31, 119-145.

C) More complex molecules / proto-life

Martin M. Hanczyc, Shelly M. Fujikawa, and Jack W. Szostak
2003 Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth,
and Division Science October 24; 302: 618-622. (in Reports)

D.W. Deamer
1997 "The First Living Systems - A Bioenergetic Perspective", ; Microbiology and
Molecular Biology Reviews, 61(2): 239; June

Chakrabarti, A.C., R.R. Breaker, G.F. Joyce, & D.W. Deamer
1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid
Vesicles Journal of Molecular Evolution 39(6): 555-559 ( December)

Khvorova A, Kwak YG, Tamkun M, Majerfeld I, Yarus M.
1999. RNAs that bind and change the permeability of phospholipid membranes.
Proceedings of the National Academy of the Sciences USA 96:10649-10654.

Yarus M.
1999. Boundaries for an RNA world. Current Opinion in Chemical Biology 3:260-267.

Walter P, Keenan R, Scmitz U.
2000. SRP-Where the RNA and membrane worlds meet. Science 287:1212-1213.

Cronin, J. R. & Pizzarello, S.,
1999. Amino acid enantomer excesses in meteorites: Origin and significance. Advances
in Space Research 23(2): 293-299.

Service, RF,
1999. Does life's handedness come from within? Science 286: 1282-1283.

Antonio Chrysostomou, T. M. Gledhill,1 François Ménard, J. H. Hough, Motohide
Tamura and Jeremy Bailey
2000 "Polarimetry of young stellar objects -III. Circular polarimetry of OMC-1" Monthly
Notices of the Royal Astronomical Society Volume 312 Issue 1 Page 103 - February

Michael H. Engel and Bartholomew Nagy,
1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison
Meteorite", Nature , 296, April 29, , p. 838.

Jeremy Bailey, Antonio Chrysostomou, J. H. Hough, T. M. Gledhill, Alan McCall, Stuart
Clark, François Ménard, and Motohide Tamura
1998 Circular Polarization in Star- Formation Regions: Implications for Biomolecular
Homochirality Science 1998 July 31; 281: 672-674. (in Reports)

Chyba, Christopher F.
1997 Origins of life: A left-handed Solar System? Nature 389, 234- 235 (18 Sep 1997)

Engel, M. H., S. A. Macko
1997 Isotopic evidence for extraterrestrial non- racemic amino acids in the Murchison
meteorite. Nature 389, 265 - 268 (18 Sep) Letters to Nature

Schmidt, J. G., Nielsen, P. E. & Orgel, L. E. 1997 Enantiomeric cross-inhibition in the
synthesis of oligonucleotides on a nonchiral template. J. Am. Chem. Soc. 119, 1494-1495

Saghatelion A, Yokobayashi Y, Soltani K,
Ghadiri MR,
2001"A chiroselective peptide replicator",
Nature 409: 797-51, Feb

Singleton, D A,& Vo, L K,
2002 “Enantioselective Synthsis without Discrete Optically Active Additives” J. Am.
Chem. Soc. 124, 10010-10011

Yao Shao, Ghosh I, Zutshi R, Chmielewski J.
1998 Selective amplification by auto- and cross-catalysis in a replicating peptide system.
Nature. Dec 3;396(6710):447-50.

Hazen, R.M., T.R. Filley, and G.A. Goodfriend.
2001. Selective adsorption of L- and D-amino acids on calcite: Implications for
biochemical homochirality. Proceedings of the National Academy of Sciences 98(May
8):5487.

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.
2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196 (in Brevia)

Pizzarello, Sandra, Arthur L. Weber
2004 Prebiotic Amino Acids as Asymmetric Catalysts Science Vol 303, Issue 5661:
1151, 20 February 2004

Ferris JP, Hill AR Jr, Liu R, and Orgel LE. (1996 May 2). Synthesis of long prebiotic
oligomers on mineral surfaces [see comments] Nature, 381, 59-61.

Lee DH, Granja JR, Martinez JA, Severin K, Ghadri MR.
1996 “A self-replicating peptide.” Nature Aug 8;382(6591):525-8

A.C. Chakrabarti, R.R. Breaker, G.F. Joyce, & D.W. Deamer
1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid
Vesicles Journal of Molecular Evolution 39(6): 555-559 (1994 December)

Smith, J.V.
Biochemical evolution. I. Polymerization on internal, organophilic silica surfaces of
dealuminated zeolites and feldspars Proceedings of the National Academy of Sciences of
the United States of America 95(7): 3370-3375; March 31, 1998

Smith, J.V., Arnold, F.P., Parsons, I., Lee, M.R.
Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal-
hemical modeling, formation of first cells, and geological clues Proceedings of the
National Academy of Sciences of the United States of America 96(7): 3479-3485; March
30, 1999

Blochl, Elisabeth, Martin Keller, Gunter Wächtershäuser , Karl Otto Stetter
1992 “Reactions depending on iron sulfide and linking geochemistry with biochemistry”
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2000 “Origins of hydrogenosomes and mitochondria: evolution and organelle biogensis.”
Current Opinion in Microbiology 3:404-411

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1999 “Elongation of oligopeptides in a simulated submarine hydrothermal system“
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Wow! I was impressed by Ute's posts, were you?

Anyway, what you are in essence now asking for is the start of life, how life was created.

You know, I've said over and over that to me it makes little difference whether God had to jump start the process or whether God prepared the universe in such a way that life would start without requiring special intervention. Whichever way He did it I count it as created by Him.

Science will pursue that angle as far as science can pursue it. They may, indeed, come up with a scenario for a "natural" origin of life, and create life as part of coming up with that scenario. Or, they may not.

Doesn't matter to me. The evidence shows life arose and evolved here on earth over the last 2 to 3 billion years. We cannot (yet!) trace the origin of life but we can trace the evolution of life once it arrived.

Does that address the question you had in mind?

 

Maybe that was too much information at once.

Here are the Cliff notes version.

It is not necessary to think that all of the ingredients in DNA came together all at once and made a working molecule. In fact, most likely there was already something that we would recognize as life before there was DNA. There was a process of making and assembling building blocks leading to this life. We have found that many of the building blocks are catalyzed and stabilized by very common materials, like borates and some clays.

 

the Grand Guessing Game

 

Yes, well, returning to the topic of mutation, how does the fact that B cells undergo somatic hypermutation to result in improved antibody specificity square with the idea that all mutations are detrimental and result in loss of specificity?

 

Impressed? Not really. Dazzled? No. Baffled? Somewhat.

Andrew D. Ellington, in the reference: "Experimental Testing of Theories of An Early RNA World", section entitled: "Ancillary Ribozyme Metabolism", summarized by stating:

"Although these approaches probably do not

resemble events in primordial molecular

evolution, they nevertheless can give us a feel

for how difficult it is to find nucleic acid

catalysts de novo, and what such nucleic acid

catalysts are capable of doing."

Nice try guys--but no cigar.

Are you sure you got the right brand of test tube?

Selah,

Bro. James

[ October 19, 2005, 09:22 PM: Message edited by: Bro. James ]

 

Are you saying God is too weak to do this?

And don't forget about those little B cells, which are happily MUTATING AWAY AS WE SPEAK!!

 

"the Grand Guessing Game"

Who is guessing?

I gave you a long post detailing how your claim that all mutations cause a lack of "specificity" is false.

Between the two posts, I gave at least 6 or 7 different references and gave general descriptions of some mechanisms that can be used to generate novel genetic material and other examples for which references were not provided but could be. The response was merely to call the response verbose, ignore the refutation of your position and to then reassert your claim.

Petrel has done the same thing with the b-cell example which is being happily ignored.

In addition, the implication of the particular pattern that when find in the genome is being ignored. For some gene families, we can even trace the duplications, telling the order by the homology of the genes. Often we even have the same introns and other junk duplicated with the working parts of the gene. The Alu sequences flanking two of the primate opsin genes for example.

 

All your verbiage aside which follows your denial, it is true. It is known. In fact that statement is an exact quote from a biochemist in a private email. It is not a layman's analysis, it is a professional analysis. </font>[/QUOTE]I'm afraid your biochemist friend was making an extreme overgeneralization. It may be possible that there is a single most superior gene sequence for a protein to do a certain function, and it may be possible that once that sequence has been reached any further mutation is not beneficial. However, this is an extreme hypothetical case--it's far more likely that there is no one superior protein for any application and it's also true that what was an idealish protein for one application may no longer be ideal once conditions (temperature, salt availabilities, energy availability) change. Right now from looking at common proteins among various species we see that their gene sequences are tolerant of variation without loss in function, so it seems clear that we have not reached that apex of specialization that your biochemist friend assumes.

Additionally, somatic hypermutation in B cells does not result in loss of specificity, but is actually required for proper antibody specificity. This is impossible to resolve with the propositions that mutations are always detrimental and always result in loss of specificity. </font>[/QUOTE]I neglected to mention this excellent response to the claim about "specificity."

The claim seems to rest on the idea that all genes are at the optimum sequence and cannot be improved upon by any mutation. I do not think that this could be considered a true statement. At least not without some evidence that this is the case.

That is in addition to ignoring other types of mutations.

 

There was no intent to baffle or impress or dazzle or anything else like that. The intent was to show that there are many plausible mechanisms to answer the question you were asking. It is a bit tiresome to repeatedly hear claims that no such mechanisms are known. Providing a long list of references (that are really just the tip of a large iceberg) that show how many different parts of the problem are being addressed is a way to show that the field is not so empty after all.

Now I must ask if you actually read the summary by Dr. Ellington that you quoted from? If anyone wants to read it, it can be found in its entirity here.

http://biotech.icmb.utexas.edu/pages/science/bkup_of_RNA.html

It is a very good summary of the strengths and weaknesses of various proposed solutions to getting to an RNA world. The author is extremely candid which should help put to rest concerns of some that scientists may be less than honest or that they may cover up shortcomings. He tells it like it is.

The problem is, I don't think that the article, when considered as a whole, supports your assertions about the impossibility of abiogenesis. A longer quote.

In any case, most evidence, if not all, that could be used to judge how life on this planet actually arose has been lost to time. But more importantly, quibbling over whether this abiogenesis theory or that one is possible merely serves as a red herring in an attempt to distract from the very real and widespread evidence for common descent.

 

So, UTEOTW, do you believe that God is capable of doing anything that does not require it to follow the physical rules of the universe that He created? If so, give some examples please.

What I am after are examples of God's supernatural intervention in our universe.

I noticed that it is amusing that some evolutionists are now using a "turned around phrase" of: "so, you don't believe God is capable of evolution." ...or at least similar. Isn't this the remark that Creationists should be making, instead?

UTEOW, now is your chance to provide where naturalism ends and God's omnipotence begins. Let's hear your thoughts, OH, and you may use the Bible, if you wish. I notice it is strange that you tend to gloss over faith oriented subjects. Now is your chance for some good ole' fashion testimony of YOUR beliefs in God's power.

 

Guessing has its place in science. It provides directions for the investigations.

 

Guessing has its place in science. It provides directions for the investigations. </font>[/QUOTE]Sure, and that also makes for a lot of dead-ends and retractions as time goes forward. How many scientific theories have been changed in just the past 20 year with the advent of new technology? How many will change in the next 200 years, as we become even wiser?

Theories we were absolutely CONVINCED of have crashed to the ground--we can expect this to increase as technology accelerates at an exponential rate.

 

By the way--for a scientist who is a Christian--would it not make at least a little sense to use what 'God said' when developing a few of those guesses? Is it just possible it could save us a lot of time, instead of flipping coins?