Evolution: Anyone care to Fill in the Huge Blank?

I supplied some information in a previous post regarding some of the complicated steps necessary in order for life to begin.

I stated that that for the formation of protein that long chains of amino acids would need to join together. Out of the millions of amino acids present, 20 specific types, all left hand, would need to arrange themselves in the correct combinations to form protein.

However, there is still another step that must be accomplished before even this can take place that complicates the process even further.

Before the Long chains of amino acids can become a protein, they must first be joined into "short chains" called peptides. In or order for this to even begin to take place, an amino acid molecule must react with another and become joined through an amide linkage.

This just does not occur naturally, let me qualify that by saying that it has never been observed or demonstrated to occur naturally.

In order for this vital step to take place the amino acid must first activated by attachment to a transfer RNA molecule through an ester bond.

Notice the RNA transfer molecule must already exist! Another interesting point, the ester bond is broken down or destroyed by the presence of water in a process called hydrolysis , eliminating the possibility of the formation of the peptide.

So all of this has to be somehow protected from the very environment claimed necessary to even bring the amino acids together.

And keep in mind that one single strand of peptide or one protein, even if it could somehow miraculously form naturally, is not enough for life to exist, conservative estimates are that at least 200,000 proteins are req'd.

All these amino acids must somehow come together due to whatever environment created them, then taken out of that very environment and protected from it by a membrane that is already made of proteins and is is porous enough to allow food and nutrients to enter, but keep water molecules out.

This is a huge Gap. It is a process that has never been observed to occur naturally, has never been demonstrated in a lab.

And yet, it is accepted as fact by supporters of evolution.

Most people have no idea of the enormous complexity involved. The textbooks gloss over these steps, and give people the impression that if they don't simply accept it, they are ignorant, unenlightened, uneducated, fanatical....and the list goes on and on.

[edit on 13-3-2008 by Sparky63]

Originally posted by Sparky63
I stated that that for the formation of protein that long chains of amino acids would need to join together. Out of the millions of amino acids present, 20 specific types, all left hand, would need to arrange themselves in the correct combinations to form protein.

Maybe they were preselected for a bias towards L-enantiomers?

Science. 1997 Feb 14;275(5302):951-5.

Enantiomeric excesses in meteoritic amino acids.Cronin JR, Pizzarello S.
Collaborators (1)

Cronin JR.
Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA.

Gas chromatographic-mass spectral analyses of the four stereoisomers of 2-amino-2,3-dimethylpentanoic acid (dl-alpha-methylisoleucine and dl-alpha-methylalloisoleucine) obtained from the Murchison meteorite show that the L enantiomer occurs in excess (7.0 and 9.1%, respectively) in both of the enantiomeric pairs. Similar results were obtained for two other alpha-methyl amino acids, isovaline and alpha-methylnorvaline, although the alpha hydrogen analogs of these amino acids, alpha-amino-n-butyric acid and norvaline, were found to be racemates. With the exception of alpha-amino-n-butyric acid, these amino acids are either unknown or of limited occurrence in the biosphere. Because carbonaceous chondrites formed 4.5 billion years ago, the results are indicative of an asymmetric influence on organic chemical evolution before the origin of life.

Which was later enhanced by other processes:

Orig Life Evol Biosph. 2004 Feb;34(1-2):93-110.

Spontaneous onset of homochirality in oligopeptide chains generated in the polymerization of N-carboxyanhydride amino acids in water.

Hitz TH, Luisi PL.
ETH Zürich, Universitätsstr. 6, CH-8092 Zürich, Switzerland.

This article is concerned with the spontaneous onset of homochiral oligopeptide sequences. We will show that the polymerization of hydrophobic NCA (N-carboxyanhydride = cyclic anhydride)-amino acid racemates (i.e. tryptophane, leucine and isoleucine) in aqueous solution yields oligopeptides that are characterized by a high degree of homochiral sequences. Furthermore we will show that quartz enhances efficiently the mole fraction of oligopeptides with homochiral sequence by selectively adsorbing the more stereoregular oligopeptides from an aqueous solution of oligo-D,L-leucine. We find in particular that the mole fraction of the adsorbed homochiral 7mers is 17 times larger than the mole fraction calculated for a theoretical, random process. Experimentally the stereoisomer distribution for each oligomer length can be determined by the use of enantio-labeling and LC-MS (Liquid Chromatography-Mass Spectrometry). Furthermore, if we start the polymerization with an enantiomeric excess (e.e.) of 20% of L-leucine (L-amino acid: D-amino acid = 6:4, molar ratio) we observe a chiral amplification in the enantiomeric homochiral oligopeptides. We think that such processes are relevant to the chemical evolution of single handedness.

ABE: and another...

Space radiation may select amino acids for life
11:24 24 August 2005

Space radiation preferentially destroys specific forms of amino acids, the most realistic laboratory simulation to date has found. The work suggests the molecular building blocks that form the "left-handed" proteins used by life on Earth took shape in space, bolstering the case that they could have seeded life on other planets.

linky

And another:

Published online on May 1, 2001, 10.1073/pnas.101085998
PNAS | May 8, 2001 | vol. 98 | no. 10 | 5487-5490

Geology
Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality
Robert M. Hazen*,, Timothy R. Filley*,, and Glenn A. Goodfriend§

The emergence of biochemical homochirality was a key step in the origin of life, yet prebiotic mechanisms for chiral separation are not well constrained. Here we demonstrate a geochemically plausible scenario for chiral separation of amino acids by adsorption on mineral surfaces. Crystals of the common rock-forming mineral calcite (CaCO3), when immersed in a racemic aspartic acid solution, display significant adsorption and chiral selectivity of D- and L-enantiomers on pairs of mirror-related crystal-growth surfaces. This selective adsorption is greater on crystals with terraced surface textures, which indicates that D- and L-aspartic acid concentrate along step-like linear growth features. Thus, selective adsorption of linear arrays of D- and L-amino acids on calcite, with subsequent condensation polymerization, represents a plausible geochemical mechanism for the production of homochiral polypeptides on the prebiotic Earth.

linky

ABE2: and another...

Chem Commun (Camb). 2005 Apr 21;(15):2047-9. Epub 2005 Mar 1.

Plausible origins of homochirality in the amino acid catalyzed neogenesis of carbohydrates.

Córdova A, Engqvist M, Ibrahem I, Casas J, Sundén H.
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Sweden. [email protected]

The intrinsic ability of amino acids to catalyze the asymmetric formation of carbohydrates, which enzymes have mediated for millions of years, with significant amplification of enantiomeric excess suggests a plausible ancient catalytic process for the evolution of homochirality.

ABE3: I'm getting bored now...another:

Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):12979-80. Epub 2006 Aug 22.

Amplification of enantiomeric concentrations under credible prebiotic conditions.

Breslow R, Levine MS.
Department of Chemistry, Columbia University, New York, NY 10027, USA. [email protected]

Solutions with as little as 1% enantiomeric excess (ee) of D- or L-phenylalanine are amplified to 90% ee (a 95/5 ratio) by two successive evaporations to precipitate the racemate. Such a process on the prebiotic earth could lead to a mechanism by which meteoritic chiral alpha-alkyl amino acids could form solutions with high ee values that were needed for the beginning of biology.

However, there is still another step that must be accomplished before even this can take place that complicates the process even further.

Before the Long chains of amino acids can become a protein, they must first be joined into "short chains" called peptides. In or order for this to even begin to take place, an amino acid molecule must react with another and become joined through an amide linkage.

This just does not occur naturally, let me qualify that by saying that it has never been observed or demonstrated to occur naturally.

Or maybe it has:

Science. 2004 Oct 8;306(5694):283-6.

Carbonyl sulfide-mediated prebiotic formation of peptides.

Leman L, Orgel L, Ghadiri MR.
Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Almost all discussions of prebiotic chemistry assume that amino acids, nucleotides, and possibly other monomers were first formed on the Earth or brought to it in comets and meteorites, and then condensed nonenzymatically to form oligomeric products. However, attempts to demonstrate plausibly prebiotic polymerization reactions have met with limited success. We show that carbonyl sulfide (COS), a simple volcanic gas, brings about the formation of peptides from amino acids under mild conditions in aqueous solution. Depending on the reaction conditions and additives used, exposure of alpha-amino acids to COS generates peptides in yields of up to 80% in minutes to hours at room temperature.

ABE: Another...

A possible primordial peptide cycle.Huber C, Eisenreich W, Hecht S, Wächtershäuser G.

Department for Organic Chemistry and Biochemistry, Technische Universität München, Lichtenbergstrabetae 4, D-85747 Garching, Germany.

alpha-Amino acids can undergo peptide formation by activation with carbon monoxide (CO) under hot aqueous conditions in the presence of freshly coprecipitated colloidal (Fe,Ni)S. We now show that CO-driven peptide formation proceeds concomitantly with CO-driven, N-terminal peptide degradation by racemizing N-terminal hydantoin and urea derivatives to alpha-amino acids. This establishes a peptide cycle with closely related anabolic and catabolic segments. The hydantoin derivative is a purin-related heterocycle. The (Fe,Ni)S-dependent urea hydrolysis could have been the evolutionary precursor of the nickelenzyme urease. The results support the theory of a chemoautotrophic origin of life with a CO-driven, (Fe,Ni)S-dependent primordial metabolism.

The issue here is that we have lots of disparate findings that require integration into a coherent explanation. We have ideas, we have interesting findings, in time they should be more coherent.

Given we only discovered DNA 50 odd years ago, I think we are doing pretty well to uncover a very complex process from scratch.

[edit on 13-3-2008 by melatonin]

reply to post by melatonin



Thanks for the information. This is going to take some time to digest.
It should be noted that there is an enormous difference between oligpeptides and peptides that are necessary for life. For the cell to even begin using a peptide or a protein it would first have to have a set of instruction on how to use them, this would require an existing genetic code.

Regarding the possibility of peptides or amino acids forming around hydothermal vents where it could be exposed to volcanic gas: consider this exerpt from a new York Times article.

A theory that life on earth began at hydrothermal (hot water) vents in the ocean floor has been proved false by recent experiments. “This is probably the most unlikely area for the origin of life to occur,” said chemist Jeffrey L. Bada of the University of California.

The theory had been advanced after the discovery of thriving bacteria and other organisms, such as giant clams and worms, around the hydrothermal vents.

Simulating the temperatures and pressures of the vents, Bada and his colleague, Stanley L. Miller, found that amino acids, the building blocks of life, decomposed rapidly under such conditions. “The combination of amino acids into larger peptide molecules, known as polymerization, was found to be impossible in the presence of water at any temperature,” notes The New York Times. “And more complex molecules carrying the genetic code, a requirement for living organisms, did not last long in the extreme heat.”
According to the Times, the researchers concluded “that the hot waters in the primitive oceans would have destroyed rather than created organic compounds in the primitive oceans.”

query.nytimes.com...

The search continues.





[edit on 13-3-2008 by Sparky63]

I gave you a star for your post, it looks like you did some interesting research.

[edit on 13-3-2008 by Sparky63]

Originally posted by Sparky63
For the cell to even begin using a peptide or a protein it would first have to have a set of instruction on how to use them, this would require an existing genetic code.

But this is jumping the gun. Some even suggest that basic organic metabolism preceded genes. Although not widely accepted.

As I said, lots of ideas, lots of interesting findings, no real coherent explanation. It took us thousands of years for someone to formally develop the theory of evolution, and it may take a while and another 'oddball' scientist to provide a compelling theory to explain abiogenesis.

I gave you a star for your post, it looks like you did some interesting research.

Just a quick search through the academic literature, really. There's lots of stuff out there, that was just what I could find in several minutes. There's a thread by Heronumber1 on this issue, and I think there's a link to a review article in there.

If you are interested, you should read anything by Leslie Orgel (who wrote the review). He was probably the foremost researcher into abiogenesis. Died last year, big loss to science.


[edit on 13-3-2008 by melatonin]

reply to post by Neiby


Dr. Miller is inferring that the fusion of chromosomes is somehow linked with speciation.
This couldn't be further from the truth. Its not the number of the Chromosomes that really matter, but rather, the information contained in them.

For instance he fails to mention that chromosomal rearrangement in animals is quite common. It usually results in no distinguishable differences.

In fact 1 in every 1000 people are born with fused chromosomes. Guess what, they don't become a different species. Most appear
normal, though they may experience fertility problems later in life. Definitely not an advantage you would want to pass on to your offspring.

Also too, although most people have no idea what the difference is between an ape chromosome and a human chromosome, they are worlds apart on the molecular level. Once again the complexity is staggering.

Ken Miller is suggesting that the evidence underpinning human chromosome 2 is a relic of our evolutionary history with other apes.

It was a prediction of evolution. And it was verified.

If we take a faith-based explanation, you could explain the current evidence by saying 'common design', and you could explain anything else by 'common design' or even plain old 'design'.

In other words, it could explain every single situation we could imagine. But, hey, that's magic. Unfalsifiable and applicable to any event. When it can make specific prediction prior to us collecting evidence, it might have some uses. Indeed, the genesis account can be viewed as a real world prediction. However, it is falsified.

But evolution made one specific falsifiable prediction, and it has done the same for pseudogenes and endogenous retroviri. Of course, ID will just say 'common design' like it would for everything else.

Funny enough, I am currently watching a show on the science channel on how use base chemicals, like methane, hydrogene, and so on, combined with water and electricity have created amino acids in a lab. Using that, all it would really take is the right components being in the right lace at the right time, a little spark of lightning or possibly geo thermal heat and poof!!

Melatonin is right. The theory of evolution makes specific predictions that are being proved right. Creation "science" does nothing of the sort. It makes no predictions that are falsifiable. It's simply not science. It's adherents twist the very meaning of science.

Also, interestingly, they're still using the same tired arguments from the 1980s when I was a Creationist. It's almost as if they just can't bother themselves to follow up on continuing scientific research. The theory of evolution becomes more sound every day as research in all sorts of different fields progresses. What about creation "science"? Every day, another nail in the coffin, but its adherents are too stubborn to even notice.

It's difficult to discuss this topic with many creationists because a large majority of them don't even understand what they're saying when they spout off arguments they learned at church in an information movie or whatever. They assume that the people telling them that information are correct, so they feel perfectly comfortable regurgitating the arguments without even understanding them. It's very sad. What's even more sad is that I used to be the same as them. It took years for the truth to sink in. It was like I had to be slowly deprogrammed. But once you see the truth, you can't go back.

The are insurmountable mountains of real scientific evidence backing up the theory of evolution. To deny that is ignorance, not scientific discourse.

Do we know everything? Of course not. But there is no reason to claim "God did it!" whenever we don't know something. That's just silly. It's like growing up but still believing in Santa.

This link here
is very funny

lets go through the steps of this page. "Evidence from Living Organisms" then they go to talk about fossils... uhm fossils are not living last I checked.
"Evidence of Common Ancestry"
in this section they gave perfect example of Micro evolution which has been observed, demonstrated a is indeed scientific and had no contradiction whatsoever with the bible.
"Homologous Structures"
this is just retarted, all these animals also have something called blood too, doesnt mean we all came from the same organic soup. similar structures is a sign of similar design. and just because scientists happen to name these parts the same thing doesnt mean they are utilized in the same way. this is not evidence for anything, all cars have stearing wheels, doesnt mean they evolved from a gokart.
"Vestigial Organs"
now this one is just a straight up lie!
the human tailbone itself is used as an anchor point for 9 muscles and without them you cannot perform a few necessary functions. saying that the human tailbone is vestigal is a lie!
snakes have vestigal hip bones? those bones are used for mating, and are not vestigal, yet another lie!
and the embryo drawings on the side are from the fraudulant so-called scientist Mr. Hackel. again another lie!

wow these are all things that support the theory... i wonder if any other parts of this theory are lies? probably!

date the organism by an index fossil? here

read "1997; King's Holly (Lomatia tasmanica) -"
they use a nearby fossil to date the plant?
this is circular reasoning, not logical at all. not even scientific.

Actually I have done a lot of math....hehe part of doing a physics and chemistry majors as anyone who has done so will agree. As a trained scientist, I have found nothing that contradicts the Bible. We start with a premise, atheistic or theistic and we attempt to do science on that basis, whether we realise it or not. If we are atheistic, we "interpret" what we see on that basis and search for a natural basis only. If we take the premise (and conviction) that the creation is the work of the Almighty God, then we do all our science on that basis.

In my own experience, everything done from this premise makes perfect sense. It explains all the anomolies in the big bang models the physicists don't want you to see (conservation of energy and momentum violated on a scale the size of the universe itself!). Likewise, the wonderful design and complexity we observe in biology is perfectly harmonised with an all wise creator.

This is the creator presented to the nations in Acts 17:24-31

Regards to all

Colin