The Truth About Abiogenesis And Probability

[omnevivumexvivo 1]

This is a rebuttal to the points contained at this website:

http://www.talkorigins.org/faqs/abioprob/abioprob.html#r10

Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

 

The problem with that is the fact that, in order to get a good self replicator, you need a very specific set of catalytic properties, and the laws of chemistry and biology have no self-awareness. They'll just govern the formation of polymers from monomers (for the most part, they do so negatively, as even the mineral surface experiments required adenylated amino acids and activated nucleotides) and let chance determine the chemical properties.

 

Secondly, the entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria is given below.

 

The first "living things" could have been a single self replicating molecule, similar to the "self-replicating" peptide from the Ghadiri group [7, 17],

I'm glad you put quotes around self replicating. The peptide in question only was capable of stapling two PRE-ASSEMBLED subunits together. Thirty of the peptide bonds were already in place, all their peptide did was put in the final one.

or the self replicating hexanucleotide [10],

An annoyingly vague abstract. There's nothing I can say to contradict this simply because I have no idea what actually happened in the study.

or possibly an RNA polymerase that acts on itself [12].

This one doesn't even HAVE an abstract.

 

However, I know for a fact that no ribozyme capable of making a complete copy of itself from lone nucleotides has yet been produced in a scientist's lab. If such a molecule existed, the media would have been all over it.

 

Oh, and the title mentioned that the substrates in question were nucleotide TRIPHOSPHATES. While vastly more realistic than pre-assembled subunits, there's no way that polyphosphate chains could have been attached to nucleotides on pre-biotic earth.

 

Another view is the first self-replicators were groups of catalysts, either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle [3, 5, 15, 26, 28]. An example is the SunY three subunit self-replicator [24].

According to the abstract, that self-replicator was only capable of copying ONE of its THREE subunits.

 

No matter whether the first self-replicators were single molecules, or complexes of small molecules, this model is nothing like Hoyle's "tornado in a junkyard making a 747". Just to hammer this home, here is a simple comparison of the theory criticised by creationists, and the actual theory of abiogenesis.

 

Simple Chemicals->Bacteria

 

Simple Chemicals->Polymers->Replicating Polymers->Hypercycle->Protobiont->Bacteria

 

Note that the real theory has a number of small steps, and in fact I've left out some steps (especially between the hypercycle-protobiont stage) for simplicity. Each step is associated with a small increase in organisation and complexity, and the chemicals slowly climb towards organism-hood, rather than making one big leap [4, 10, 15, 28].

So by replacing a tornado with an earthquake and a series of aftershocks makes the odds of getting a Boeng 747 go up?

 

The two major problems with the above hypothesis are as follows: Until you have self replication, you have no natural selection, and thus are relying entirely on chance. That means that until the third step, all you have is chance. The other major issue is that the second law of thermodynamics, which would act on the catalytic units of any hypercycle, tends to spread things out. But based on your illustration of the size and complexity of a protobiont, the lipid membrane would have a diameter of no more than 100 nanometers. How did all of the elements of a hypercycle and a forming lipid membrane managed to get crammed together into the same one-thousandth of a cubic micrometer at the exact same time?

 

Another claim often heard is that there is a "life sequence" of 400 proteins, and that the amino acid sequences of these proteins cannot be changed, for organisms to be alive.

 

This, however, is nonsense. The 400 protein claim seems to come from the protein coding genome of Mycobacterium genetalium, which has the smallest genome currently known of any modern organism [20]. However, inspection of the genome suggests that this could be reduced further to a minimal gene set of 256 proteins [20]. Note again that this is a modern organism. The first protobiont/progenote would have been smaller still [4], and preceded by even simpler chemical systems [3, 10, 11, 15].

The first thing I have to do is acknowledge that recent discoveries have caused the minimum genome size to go down. The simplest organism known today is Hodgkinia cicadicola Dsem, which has only 189 genes, of which 169 code for proteins. HOWEVER, Hodgkinia is an endosymbiont of cicadas, and is only capable of reducing its genome so drastically because it has a host providing it with high concentrations of ready-to-use nucleic acids and amino acids. It's practically an organelle. Mycoplasma(correct spelling) genetalium is also a parasite. The smallest INDEPENDENT organism is the heterotrophic Pelagibacter ubique HTCC1062, which has a whopping 1389 gene products! In order for an organism to survive independently, it would require AT LEAST 1000 gene products.

 

As to the claim that the sequences of proteins cannot be changed, again this is nonsense. There are in most proteins regions where almost any amino acid can be substituted, and other regions where conservative substitutions (where charged amino acids can be swapped with other charged amino acids, neutral for other neutral amino acids and hydrophobic amino acids for other hydrophobic amino acids) can be made.

However, those amino acids in the active site, cysteine, which creates a disulfide bridge, and proline, which causes a kink in the chain, typically cannot be changed without completely impairing the proteins function. Size also plays a role. Clearly, one could not substitute tryptophan for gylcine! The bulky, aromatic side chain would serve as the proverbial monkey wrench in the works. The general properties of the twenty amino acids allow them to be grouped into the following eight groups:

Group1: leucine , isoleucine, valine, alanine, and methionine (do not like water, so they tend to cluster on the inside of the protein).

Group 2: tyrosine, phenylalanine, and tryptophan (very large amino acids that can influence protein folding).

Group 3: aspartate and glutamate (acidic - proton donors, like water).

group 4: histidine, arginine, and lysine (basic - proton acceptors, like water).

Group 5: glutamine and asparagine (charged and like water).

Group 6: serine and threonine (like water, tend to be found on the outside of protein).

Group 7: glycine (very small).

Group 8: proline (introduces a bend into the chain).

Group 9: cysteine (cross links peptide chains).

 

With a handful of rare exceptions, amino acids from different groups are not exchangeable.

Some functionally equivalent molecules can have between 30 - 50% of their amino acids different.

Keep that in mind, because a much lower percentage of amino acids will be fixed in the probability equations in this post.

 

So let's play the creationist game and look at forming a peptide by random addition of amino acids. This certainly is not the way peptides formed on the early Earth, but it will be instructive.

How would non-goal-oriented processes result in anything but random addition of amino acids?

 

I will use as an example the "self-replicating" peptide from the Ghadiri group mentioned above [7]. I could use other examples, such as the hexanucleotide self-replicator [10], the SunY self-replicator [24] or the RNA polymerase described by the Eckland group [12], but for historical continuity with creationist claims a small peptide is ideal. This peptide is 32 amino acids long with a sequence of RMKQLEEKVYELLSKVACLEYEVARLKKVGE and is an enzyme, a peptide ligase that makes a copy of itself from two 16 amino acid long subunits. It is also of a size and composition that is ideally suited to be formed by abiotic peptide synthesis. The fact that it is a self replicator is an added irony.

Only if one defines self replication rather loosely.

The probability of generating this in successive random trials is (1/20)32 or 1 chance in 4.29 x 10⁴⁰. This is much, much more probable than the 1 in 2.04 x 10³⁹⁰ of the standard creationist "generating carboxypeptidase by chance" scenario, but still seems absurdly low.

You've actually vastly understated the difficulties. The real probability equation would have to take into account the fact that different species of amino acid, and even various nucleotides that could be easily spliced into the chain, were present at the time. That's an additional factor of (conservatively) 1/5. Taking the given figure of a 50% degree of divergence, the total to this point is (1/(10 X sq.rt. of 5))^{number of monomers}. Assuming that there is a 1/2 chance that the monomer will be left-handed, and an additional 1/2 chance that the monomer will bind correctly with its neighbors, the overall total is ((sq. rt. of 5)/200)^{number of monomers}. Which means the odds of getting the Ghadiri peptide, which isn't even a true self replicator, are around 1:2.8 X 10⁶², or 3.57 x 10^-63. Impossible! Even if every atom on earth were turned into a chance at getting a 32 aa peptide under the conditions of an absurdly optimistic primordial soup, the odds of one of them being a functional ligase of the type in question are less than one in a billion!

1 chance in 4.29 x 10⁴⁰ is still orgulously, gobsmackingly unlikely; it's hard to cope with this number. Even with the argument above (you could get it on your very first trial) most people would say "surely it would still take more time than the Earth existed to make this replicator by random methods". Not really; in the above examples we were examining sequential trials, as if there was only one protein/DNA/proto-replicator being assembled per trial. In fact there would be billions of simultaneous trials as the billions of building block molecules interacted in the oceans,

In the ocean? The soup would be FAR too dilute for that! Water is RELEASED by polymerization, meaning spontaneous polymerization in plain-old aqueous solution is chemically unrealistic.

or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates [2,15].

Those thousands of kilometers of shorelines would have been exposed to one of the two 100% certain barriers to abiogenesis: oxygen or ultraviolet light. To those of us who aren't familiar with origin of life research, I'm referring to what the community in general calls the "oxygen/ultraviolet paradox." The paradox is this: ultraviolet rays would destroy any biological precursors. Today, the primary thing between us and a 100% chance of dying of melanoma is the ozone layer. The ozone layer is caused by the interaction of certain rays with molecular oxygen, O₂. The issue is that oxygen would also wreak havoc on whatever biological precursors existed on early earth. Either way, if the simple organic molecules were exposed to the air, they'd be completely obliterated.

Yes, one kilogram of the amino acid arginine has 2.85 x 10²⁴ molecules in it (that's well over a billion billion); a tonne of arginine has 2.85 x 10²⁷ molecules. If you took a semi-trailer load of each amino acid and dumped it into a medium size lake, you would have enough molecules to generate our particular replicator in a few tens of years, given that you can make 55 amino acid long proteins in 1 to 2 weeks

Typically, polymers formed on mineral surfaces have a variety of different bonds, not all of them the exclusively peptide bonds needed for organic molecules.

 

So how does this shape up with the prebiotic Earth? On the early Earth it is likely that the ocean had a volume of 1 x 10²⁴ litres. Given an amino acid concentration of 1 x 10^-6 M (a moderately dilute soup, see Chyba and Sagan 1992 [23]), then there are roughly 1 x 10⁵⁰ potential starting chains,

There are only 10⁵⁰ atoms on earth in total. A quick bit of dimensional analysis will show why.

Assuming 1 x 10²⁴ liters, a 1 x 10^-6 molar concentration, and that there are 6.02 x 10²³ molecules per mole, the correct value would be 6.02 x 10⁴¹ amino acids in the soup. Assuming all are locked up in 32 subunit peptides, a truly ridiculous assumption, there would be a maximum of 1.88 x 10⁴⁰ chains in the ocean at any given time.

so that a fair number of efficent peptide ligases (about 1 x 10³¹) could be produced in a under a year, let alone a million years.

Point One: There is a massive difference between "efficient ligase" and "functional self replicator." The former has been developed in the lab. The latter has not.

 

Point Two: Based on the fact that a maximum of 1.88 x 10⁴⁰ 32-amino acid chains existed at any given time, my calculation that the odds of forming even one of the ligases in the presence of competing chemicals are 3.57 x 10^-63, the assertion that the amino acids could all be rearranged 10² times a year(twice a week, a quarter of the time the study he quoted said it took to form 55 subunit polymers), and that there were 10⁹ years for such recombinations to occur, the correct number of ligases would be 6.71 x 10^-12. So the odds of getting even one of the ligases over a billion year period would be less than one in one hundred billion.

 

Point Three: Since this guy wasn't willing to take the competing amino acid species into account, and couldn't even get basic math right, why should we trust him when he says that abiogenesis is a robust theory?

The synthesis of primitive self-replicators could happen relatively rapidly, even given a probability of 1 chance in 4.29 x 10⁴⁰ (and remember, our replicator could be synthesized on the very first trial).

It could be, but realistically it wouldn't be. And again, the Ghardiri peptide is only a ligase, capable of making a single peptide bond out of the 31 in the finished product. Claiming it to be a "self replicator" is a clear case of misrepresentation.

 

Assume that it takes a week to generate a sequence

Perhaps when the amino acids are at absurdly high concentrations in a chemist's flask instead of a primordial soup full of toxic side reactants, such as formaldehyde and cyanide.

Then the Ghadiri ligase could be generated in one week, and any cytochrome C sequence could be generated in a bit over a million years

Provided all of the amino acids are biologically relevant and the effects of aforementioned contaminants, ultraviolet rays, and oxygen gas are conveniently ignored.

(along with about half of all possible 101 peptide sequences, a large proportion of which will be functional proteins of some sort).

I assume by "large proportion" he meant "one in ten to the power of 40-60." Gibberish is so much more common than meaningful information that it boggles the mind.

 

an analysis by Ekland suggests that in the sequence space of 220 nucleotide long RNA sequences, a staggering 2.5 x 10¹¹² sequences are efficent ligases [12]. Not bad for a compound previously thought to be only structural.

Again, there is a HUGE difference between ligase and self-replicator. I know you're probably growing tired of reading that, but I just can't emphasize the fact that being able to string two beads together isn't the same thing as writing a message in Morse code with said beads.

Going back to our primitive ocean of 1 x 10²⁴ litres and assuming a nucleotide concentration of 1 x 10^-7 M [23], then there are roughly 1 x 10⁴⁹ potential nucleotide chains,

Using Avagadro's number, and the supplied figures, the number of nucleotides in the primordial soup would have been 6.02 x 10⁴⁰. The maximum number of 220 nucleotide long chains would be 2.74 x 10³⁸. And, by extrapolation, the maximum number of LIGASES(not replicators) would be 2.41 x 10¹⁸. A good number of them, but there would never be more than one of them in every liter, and they couldn't replicate each other.

so that a fair number of efficent RNA ligases (about 1 x 10³⁴) could be produced in a year, let alone a million years.

At this point, I'm not even going to bother correcting his figures.

 

 

The potential number of RNA polymerases is high also; about 1 in every 10²⁰ sequences is an RNA polymerase [12].

[12] Ekland EH, and Bartel DP, RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature, 383: 192, 1996

Nucleoside triphosphates aren't exactly the most common things to have floating around in a primordial soup.

Similar considerations apply for ribosomal acyl transferases (about 1 in every 10¹⁵ sequences), and ribozymal nucleotide synthesis [1, 6, 13].

Not very useful until there's a simple cell of some sort in the vicinity. Which would require an effective self replicator. Which couldn't come about in a primordial soup.

 

Similarly, of the 1 x 10¹³⁰ possible 100 unit proteins, 3.8 x 10⁶¹ represent cytochrome C alone! [29]

Which means that for every cytochrome c equivalent, there are one hundred thousand billion billion billion billion billion billion billion non-cytochrome c molecules, and that's assuming that all of the primordial soup is made up of 100 amino acid long polypeptides. If a true self replicator is as improbable as cytochrome c, abiogenesis is dead.

There's lots of functional enyzmes in the peptide/nucleotide search space, so it would seem likely that a functioning ensemble of enzymes could be brewed up in an early Earth's prebiotic soup.

But the first one has to be a molecule that can make a COMPLETE replica of itself from NON-ACTIVATED MONOMERS. Until that comes along, natural selection won't do a thing.

 

 

And now, for the coup de gras:

 

These are the issues he claims creationist probability equations have:

1) They calculate the probability of the formation of a "modern" protein, or even a complete bacterium with all "modern" proteins, by random events. This is not the abiogenesis theory at all.

 

2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.

 

3) They calculate the probability of sequential trials, rather than simultaneous trials.

 

4) They misunderstand what is meant by a probability calculation.

 

5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.

 

In response, I quote Professor Arthur V. Chadwick:

 

http://origins.swau.edu/papers/life/chadwick/default.html

 

Let us try another approach---forget the cell, forget the membrane---what would be required as a base minimum just to make a protein molecule. We could imagine proteins smaller than modern proteins, say 100 amino acids long, using less than 20 of the proteinous amino acids, a less than perfect polymerase system, perhaps as few as 100 specific proteins total, maybe even 80. Let’s even suppose they could also use non-proteinous amino acids, and that either enantiomer would work. All of these assumptions are ludicrous. We have no starting materials, not even the right ones. We have no idea how we could make a polymer of 100 amino acids under prebiological conditions. These is no possibility that the ridiculously nonstringent conditions could produce a self-replicating system. But since we are playing this game lets make it even worse. Of the 80 proteins we said we needed, lets let the first 60 have any sequence of amino acids at all. Of the remaining 20 proteins, the first has one amino acid specified. The other 99 can be any amino acid. The second has two specified, and so on until the twentieth has twenty amino acids specified. We will let the ocean be two miles deep over the entire earth and the concentration of amino acids 1 molar for each species. We will divide the ocean into one liter increments and consider the feat accomplished when any one liter produces all of the requisite proteins. We will allow the proteins to be made at the rate of a million tries per liter per second. We will assume the same probability for nucleic acids. With all these assumptions made in favor of producing our exceedingly liberal primitive cell, we will achieve the intended result with a 50% probability once in 10¹⁸⁶ years.

 

So:

1. The proteins in question are primitive, only 100 amino acids long when the average for modern proteins is closer to 200-300. The "cell" in question is also primitive, with only 80 proteins. That could be enough to cover the processes of transcription and translation, but the "cell" would be unable to copy its DNA, distribute its DNA to daughter cells, divide itself, maintain its membrane, or metabolize anything.

 

2. The most specified his proteins get are 20 amino acids. That means that 80% of the sites in the most specified protein are variable. Also, only 20 proteins have ANY specific amino acids.

 

3. The calculation has been adjusted so that every liter of water on earth is producing chains.

 

4. I'm not entirely sure what he meant when he said creationists don't understand the idea of a probability equation. But the above certainly looks like a probability calculation to me.

 

5. 75% of the proteins for this theoretical cell didn't have a single specified amino acid.

 

All this, taken into account with the ridiculously liberal assumptions about competing species of amino acids, the minimal volume in which they could coexist, and the number of non-specified sites that can be allowed, gives an idea of how absurdly improbable abiogenesis really is. In Professor Chadwick's own words:

This figure is of course incomprehensible. To give you an idea of how incomprehensible, I use the following illustration. An amoeba starts out at one side of the universe and begins walking towards the other side, say, 100 trillion light years away. He travels at the rate of one meter per billion years. He carries one atom with him. When he reaches the other side, he puts the atom down and starts back. In 10¹⁸⁶ years, the amoeba will have transported the entire mass of the universe from one side to the other and back a trillion trillion trillion trillion trillion trillion times. That is my definition of impossible. And what resulted from success, if it did occur would not be a living cell or even a promising combination. Spontaneous origin of life on a prebiological earth is IMPOSSIBLE!

 

What more needs to be said?

[KBC id 3]

The second thing I'd like to note is that I've actually already addressed the Hoyle's Fallacy claim on this forum before. No one actually responded to the topic, which was disappointing because I put several days worth of work into it. I called it The Truth About Abiogenesis And Probability.

 

I would like to respond to this quote you made from the thread "Regarding Christian Creationism". and to add to "what more needs to be said"

 

I like everything you wrote and I think it is all quite relevant. I would also like to add something here that I consider empirical backing on the subject of chemical evolution.

 

In case your not familiar with the experiment it is called Spiegelman's monster; http://en.wikipedia.org/wiki/Spiegelman_Monster

 

As an overview I will touch on the significance of the points empirically observed and how its relevant.

Spiegelman introduced RNA from a simple bacteriophage into a solution which contained an RNA replication enzyme along with some free nucleotides and salts in order to observe how replication may advance it over time. What he empirically observed was that it lost information and got shorter over the short time he was able to observe the replication continuity. What started as an original strand with 4,500 nucleotide bases ended with only 218 bases. Other investigators later showed that Spiegelman's monster eventually becomes even shorter and ends up containing only 48 to 54 nucleotides.

 

This is empirical evidence observed in real time. It shows that unless something can come in and immediately be functional and required for optimal replication it will be eliminated in time frames that are observable within our life times and actually much shorter in the case shown. So how does novelty arise? what plays into the origin of novelty? one thing we find in this experiment is speed of replication being a deciding factor, slim and trim is apparently not just an engineering goal. In the end this experiment denies the chemical origin of life.

[ikester7579 19]

Can any evolutionist give an example of where proteins form naturally?

[KBC id 3]

Can any evolutionist give an example of where proteins form naturally?

 

I have asked that same question on other boards and without fail there is an imaginary scenario that is posited to be just right for such things to happen. Peptization, the forming of amino acids via a dehydration reaction into a protein by the elimination of water molecules is quite difficult to accomplish in a water medium and in fact the reverse reaction which breaks them apart is more favorable in the presence of water.

[Ophiolite 0]

Can any evolutionist give an example of where proteins form naturally?

 

Blank, J.G. et al Experimental Shock Chemistry of Aqueous Amino Acid Solutions and the Cometary Delivery of Prebiotic Compounds Origins of Life and Evolution of Biospheres, Volume 31, Numbers 1-2, 15-51, 2001.

 

In experiments duplicating the impact of cometary ices on the primeval Earth amino acids embedded in the ice were energised to form, amongst other things, peptides. As you are probably aware proteins are peptides, just extra large ones.

[KBC id 3]

Blank, J.G. et al Experimental Shock Chemistry of Aqueous Amino Acid Solutions and the Cometary Delivery of Prebiotic Compounds Origins of Life and Evolution of Biospheres, Volume 31, Numbers 1-2, 15-51, 2001.

 

In experiments duplicating the impact of cometary ices on the primeval Earth amino acids embedded in the ice were energised to form, amongst other things, peptides. As you are probably aware proteins are peptides, just extra large ones.

 

They may have duplicated the impact pressures that can be calculated but they didn't duplicate the amount of the reactants;

 

Aqueous solutions containing near-saturation levels of amino acids (lysine, norvaline, aminobutyric acid, proline, and phenylalanine) were sealed inside stainless steel capsules and shocked by ballistic impact.

 

Nor did they test the impact on mixtures of the chemicals together. Read the article. They tested each type individually and at near-saturation levels. How many impactors come in with separated loads of near-saturation level amino acids? They further had the idea that they could say;

 

"Our results support the hypothesis that significant concentrations of organic material could survive a natural impact process."

 

the only thing natural about the experiment was the impact pressures. Everything else was setup intelligently to take advantage of that energy infusion.

[omnevivumexvivo 1]

Blank, J.G. et al Experimental Shock Chemistry of Aqueous Amino Acid Solutions and the Cometary Delivery of Prebiotic Compounds Origins of Life and Evolution of Biospheres, Volume 31, Numbers 1-2, 15-51, 2001.

 

In experiments duplicating the impact of cometary ices on the primeval Earth amino acids embedded in the ice were energised to form, amongst other things, peptides. As you are probably aware proteins are peptides, just extra large ones.

 

In addition to the challenges proposed by KBC, I'd put it to you that even if those unrealistic conditions were overcome, the results would still be meaningless. Did these peptides do anything, or did they just kind of sit there? Did they have any catalytic properties? Could they replicate themselves? If not, what relevance, if any, do these peptides have to the origin of life?

 

Proteins aren't just extra-long peptides. They are INFORMATION CONTAINING extra-long peptides.

[gilbo12345 860]

They may have duplicated the impact pressures that can be calculated but they didn't duplicate the amount of the reactants;

 

Aqueous solutions containing near-saturation levels of amino acids (lysine, norvaline, aminobutyric acid, proline, and phenylalanine) were sealed inside stainless steel capsules and shocked by ballistic impact.

 

Nor did they test the impact on mixtures of the chemicals together. Read the article. They tested each type individually and at near-saturation levels. How many impactors come in with separated loads of near-saturation level amino acids? They further had the idea that they could say;

 

"Our results support the hypothesis that significant concentrations of organic material could survive a natural impact process."

 

the only thing natural about the experiment was the impact pressures. Everything else was setup intelligently to take advantage of that energy infusion.

 

Kinda seems like intellectual dishonesty.... I guess it is as one of my lecturers said, many scientists lack the critical thinking skills to critically analyze their own experiments for flaws.

[Ron 10]

Blank, J.G. et al Experimental Shock Chemistry of Aqueous Amino Acid Solutions and the Cometary Delivery of Prebiotic Compounds Origins of Life and Evolution of Biospheres, Volume 31, Numbers 1-2, 15-51, 2001.

 

In experiments duplicating the impact of cometary ices on the primeval Earth amino acids embedded in the ice were energised to form, amongst other things, peptides. As you are probably aware proteins are peptides, just extra large ones.

 

These “experiments†were based primarily on assumption (unknown cometary ice compositions, unknown primeval Earth conditions, unknown amino acids embedded in the ice etc…) correct? These experiments were driven by said assumptions correct?

 

The bottom line is, these results can in no way be considered “naturalisticâ€ÂÂ, therefore the results cannot be considered “proteins forming naturallyâ€ÂÂ, as Ikester asked for.

[jason777 1]

These “experiments” were based primarily on assumption (unknown cometary ice compositions, unknown primeval Earth conditions, unknown amino acids embedded in the ice etc…) correct? These experiments were driven by said assumptions correct?

 

The bottom line is, these results can in no way be considered “naturalistic”, therefore the results cannot be considered “proteins forming naturally”, as Ikester asked for.

 

Molecules don't assemble themselves and fold themselves into proteins. It's akin to finding crude oil and claiming it could be evidence of the evolution of an automobile.

 

The process of making proteins is no less complex than a GM factory. Not only are there workers assembling the parts but completely different departments ensuring quality control throughout the entire manufacturing process.

 

http://www.youtube.com/watch?v=lpb5s2F1pyM&feature=related

 

 

I have to agree with you and Ikester; They don't form themselves. Essentially, the proteins don't make the organism - The organism makes the proteins.

 

 

 

Enjoy.

[omnevivumexvivo 1]

The barrel-shaped machine in Jason777's video is called a chaperonin. There are other fold-assisting proteins, called chaperones, that bind to the polypeptide and release it once a segment has folded into the proper shape. The interesting thing is that chaperones and chaperonins both need chaperones and chaperonins to fold correctly! It's a chicken-and-egg conundrum, proteins can't fold without chaperones, and chaperones are themselves proteins!

 

Chaperones and chaperonins do more than just make sure proteins fold correctly, they prevent the exposed hydrophobic parts of polypeptides from coming into contact with other hydrophobic polypeptides. In other words, not only do proteins need help before they can fold into the correct shape, if they aren't correctly covered, they can clump together into cell-killing granules! That applies to the polypeptides that fold into chaperones as much as to any other polypeptide, and the cell-killing granules bit applies to protocells as much as it does to modern cells.

[ikester7579 19]

Blank, J.G. et al Experimental Shock Chemistry of Aqueous Amino Acid Solutions and the Cometary Delivery of Prebiotic Compounds Origins of Life and Evolution of Biospheres, Volume 31, Numbers 1-2, 15-51, 2001.

 

In experiments duplicating the impact of cometary ices on the primeval Earth amino acids embedded in the ice were energised to form, amongst other things, peptides. As you are probably aware proteins are peptides, just extra large ones.

 

Problem is, with the earth being hotter back then (according to Old earthers), and atmoshere friction on entering the atmosphere. And cometary ice would be vaporized either while still in the atmosphere, or shortly after it hit the surface.

 

Also, because the atmosphere was in the developing stages (according to old earthers), the barometric pressures would be a lot lower than what they are now. Currently our barometric pressure is 14.7 psi at sea level which makes water boil at a little over 200 degrees F. And example of how the low barometric pressures of a planet effect the boiling point of water is Mars. Mars has 1/4-1/8 the barometric pressure that earth does. This makes water on Mars boil at 50 degree F. This developing atmosphere with lower barometric pressures would ensure that the cometary substance would vaporize and the proteins destroyed.

 

I can guarantee that the experiment conducted did not make a real world condition for such things.

 

1) The earth being hotter with a hot atmosphere.

2) The frictional heat from the comet passing through the atmosphere.

3) The effect on the comet passing through a hot and low barometric pressure atmosphere.

4) If the proteins could survive being vaporized.

 

It just like Miller's experiment were not done in real world conditions. The bolt lightening that is supposed to cause the amino acids to form is several times hotter than the surface of the sun. How does the amino acid keep from being destroyed in such heat? Don't believe lightening gets that hot? Here's a picture of how the heat from a lightening bolt contains so much heat that when it strikes sand it makes glass.

 

 

Miller's electric arc was no where near doing this. But if it was do you think his results would have been the same? Of course not. What would have been made would have been destroyed at the same time from the heat vaporizing it. When scientists don't, or refuse to use real world conditions in their tests it only shows that their ideas and conclusions are flawed. or that they knew real world conditions would not get the results they wanted. so they use unreal world conditions to make sure that they would get the results they wanted while withholding what they did. More or less depending on most of the public being to uneducated to figure this out.

[Ophiolite 0]

In science there is no absolute certainty. If an inherent part of your character requires certainty then perhaps you are best remaining with an approach in which faith plays an integral role. This will enable you to disregard both the scientific process and the provisional findings that arise from it.

 

I was asked if proteins could form by any natural process. I provided an example of research that hints at one possible means of peptide formation.

 

Place that in context. A little over half a century ago we had no idea how amino acids, from which proteins are formed, might appear on a primitive Earth and help set the ball rolling towards abiogenesis. The Miller-Urey experiment, whose results have been overhyped by many and pointlessly criticised by others, offered a potential source. Since then we have learned that amino acids are rather commonplace: they are found in interstellar space, in comets and in meteorites. There are also a number of potential routes to their natural synthesis on or in the primitive Earth.

 

So, we have gone from a position of ignorance – where might the amino acids have come from? – to one of knowledge, with multiple potential sources. The next question is, how might these amino acids link up to form polypeptides and proteins? We don’t have an answer to that yet. As I noted above I gave, as requested, an example of how this might have come about. As research progresses we may expect other possibilities to be identified and eventually one (or more) of these will emerge, on the basis of evidence, as the most probable mechanism.

 

KBCid made an excellent point: the amino acids were concentrated in the test samples and that this was arguably different from the natural situation. That may be correct, but I rather doubt it. To expect an even distribution of amino acids throughout the impacting material would be, frankly, unnatural. Local pockets are much more likely. Speculative? Of course it is, that is the nature of science when attempting initial answers to important questions. As I said at the outset, if you want certainty ‘look away now’.

 

@ikester,

Your objections as to temperature are not valid. You have quite ignored the incoming velocity of the cometary material which would not provide sufficient time for evaporation.

[ikester7579 19]

In science there is no absolute certainty. If an inherent part of your character requires certainty then perhaps you are best remaining with an approach in which faith plays an integral role. This will enable you to disregard both the scientific process and the provisional findings that arise from it.

Not my problem that your side's claim about things concerning evolution do not stand up to scrutiny. I don't disregard scientific processes and findings when they don't go so far out on a limb as to conclude that the impossible can happen just because the impossible conforms to a certain accepted theory that has been deemed already proven. Imply absolutes to a theory means your testing procedures and you conclusions have to be better than what you currently accept. If not then evolution is also not the status that it is claimed to be. it is not the creationists problem that evolutionists claim certain things about their beloved theory then when made to hold to their claims they have to resort to claiming it's a bias on our side.

 

Going outside of science to make a point (Using faith and disregard instead of evidence) is using psychology to prove science not evidence. Having to resort to mind games proves that evolution only exists in the mind of those who wish to believe it,

 

I was asked if proteins could form by any natural process. I provided an example of research that hints at one possible means of peptide formation.

 

And I challenged that possibility with real world conditions of that time. To be scientific you cannot deny that the real world conditions make it impossible for the possibility you presented. Ignoring impossibilities is like claiming plants can grow in sulfuric because: a. I say so, and b. because it conforms to evolution. That's not science. The idea or theory has to remain falsifiable or it;s not a theory. I basically falsified. So are you ignoring that I can do that so you can continue to believe in evolution, or are you willing to ponder what I said and follow the scientific method?

 

Place that in context. A little over half a century ago we had no idea how amino acids, from which proteins are formed, might appear on a primitive Earth and help set the ball rolling towards abiogenesis. The Miller-Urey experiment, whose results have been overhyped by many and pointlessly criticised by others, offered a potential source. Since then we have learned that amino acids are rather commonplace: they are found in interstellar space, in comets and in meteorites. There are also a number of potential routes to their natural synthesis on or in the primitive Earth.

Take and apply fire to the amino acids to see if they survive then we can talk about them surviving atmospheric entry being the cause of the process.

 

So, we have gone from a position of ignorance – where might the amino acids have come from? – to one of knowledge, with multiple potential sources. The next question is, how might these amino acids link up to form polypeptides and proteins? We don’t have an answer to that yet. As I noted above I gave, as requested, an example of how this might have come about. As research progresses we may expect other possibilities to be identified and eventually one (or more) of these will emerge, on the basis of evidence, as the most probable mechanism.

 

A position of ignorance in science is wanting to stay on the side of hope instead of fact. Again you are using psychology to replace the problem of not being able to address things I brought up. You are basically indirectly admitting that your belief cannot meet the challenge or stand up to scrutiny. So instead you make unfounded accusations about me.

 

KBCid made an excellent point: the amino acids were concentrated in the test samples and that this was arguably different from the natural situation. That may be correct, but I rather doubt it. To expect an even distribution of amino acids throughout the impacting material would be, frankly, unnatural. Local pockets are much more likely. Speculative? Of course it is, that is the nature of science when attempting initial answers to important questions. As I said at the outset, if you want certainty ‘look away now’.

You are ignoring the objections to make the evidence conform to evolution. Conformism is not science. You either weigh all for and against and come to a conclusion, or your conclusion is not science.

 

@ikester,

Your objections as to temperature are not valid. You have quite ignored the incoming velocity of the cometary material which would not provide sufficient time for evaporation.

 

Then the shuttle does not need a heat shield because the heat and time of reentry won't burn it up. In fact the one that did burn up on reentry a few years back had nothing to do with "heat" because there was not enough "time", so it was a fluke, right? Your counter argument is so transparent.

 

So if you want to totally debunk what I posted scientifically minus the psychology tactics. Here's what you need to do.

 

1) Prove that a lightening bolt is not as hot as I claim it to be (several time hotter then the surface of the sun) that it would not destroy the amino acids that it created.

2) Prove that a comet would survive entry without being vaporized be showing where comets reach the earth's surface regularly.

3) Prove that a blob of ice is more opt to hit the surface of our planet than a meteor will.

etc...

 

Words, psychology tactics, ignoring real world conditions, refusing to debunk what I claimed with science, and using conformism basically proves that I shot your idea out of the water. If I did not, then use "science" and prove me wrong. If you use more of the same you only prove my point.

[jason777 1]

Hi, Ophiolite.

 

So, we have gone from a position of ignorance – where might the amino acids have come from? – to one of knowledge, with multiple potential sources. The next question is, how might these amino acids link up to form polypeptides and proteins? We don’t have an answer to that yet. As I noted above I gave, as requested, an example of how this might have come about. As research progresses we may expect other possibilities to be identified and eventually one (or more) of these will emerge, on the basis of evidence, as the most probable mechanism.

Some theories aren't testable in real time because of several reasons.

 

1) The experiment may be potentially dangerous.

 

2) The conditions needed for the experiment can't be met.

 

But any ideology and assumption can easily be mathematically shown to be empirically true given the assumptions of the hypothesis. given the fact that they don't even have an assumption that can give a mathematical prediction, is proof to me that the idea is wrong to start with. Without testable predictions there is no theory; Just a belief in an idea.

 

 

 

Enjoy.

[omnevivumexvivo 1]

In science there is no absolute certainty. If an inherent part of your character requires certainty then perhaps you are best remaining with an approach in which faith plays an integral role. This will enable you to disregard both the scientific process and the provisional findings that arise from it.

 

I was asked if proteins could form by any natural process. I provided an example of research that hints at one possible means of peptide formation.

But you haven't even come close to solving the real problems, eg, that contaminating side reactions would destroy both fledgling peptides and the amino acid building blocks themselves, that the aqueous surroundings of any polymer and the energy required to form said polymer would cause it to break down instead of build up, that there is no prebiotically realistic way to account for homeochiralty, and that there is no natural process that causes the generation of information. Until those difficulties are dealt with, you have done nothing for abiogenesis.

 

Place that in context. A little over half a century ago we had no idea how amino acids, from which proteins are formed, might appear on a primitive Earth and help set the ball rolling towards abiogenesis. The Miller-Urey experiment, whose results have been overhyped by many and pointlessly criticised by others, offered a potential source. Since then we have learned that amino acids are rather commonplace: they are found in interstellar space, in comets and in meteorites. There are also a number of potential routes to their natural synthesis on or in the primitive Earth.

Many of the routes to forming ribonucleotides, however, are simply unrealistic. You can't simulate abiogenesis in a clean laboratory jar, you have to do it in a solution of the sludge from the Miller-Urey experiment: tar and all. Monomer formation isn't the problem, monomer preservation is the problem.

 

So, we have gone from a position of ignorance – where might the amino acids have come from? – to one of knowledge, with multiple potential sources. The next question is, how might these amino acids link up to form polypeptides and proteins? We don’t have an answer to that yet. As I noted above I gave, as requested, an example of how this might have come about. As research progresses we may expect other possibilities to be identified and eventually one (or more) of these will emerge, on the basis of evidence, as the most probable mechanism.

There are so many KNOWN physical laws that would preclude further steps, however. Many of these barriers are barriers discovered in the process of seeking knowledge, and said barriers have absolutely demolished abiogenesis as a scientific hypothesis. We know that destructive sludge would have made up easily 90% of the pre-biotic soup based on the Miller-Urey type experiments. We know, based on the laws of chemistry, that polymerization is an energy-intensive process, and that hydrolysis is thermodynamically favored over polymerization simply because of that energy barrier, and that the effect becomes even more pronounced in aqueous solution. We know that information is not a material thing, and as such cannot be accounted for by matter itself.

 

A thousand years from now, when no one even bothers funding experiments in the origin of life field simply because experience over a millennium has taught them that it would be a waste of money, naturalists would be just as justified in dismissing a theist's knowledge based arguments against a natural origin of life as you are today. Why?

 

Because the "God of the gaps" accusation is the REAL argument from ignorance!

 

We can't falsify a theory that hasn't been put forward yet, using such an undiscovered theory is the exact opposite of science! Your attempt to dismiss the evidence for ID is the EPITOME of the argumentum ad ignorantium!

 

KBCid made an excellent point: the amino acids were concentrated in the test samples and that this was arguably different from the natural situation. That may be correct, but I rather doubt it. To expect an even distribution of amino acids throughout the impacting material would be, frankly, unnatural.

The second law of thermodynamics would do a very good job of evening out the concentrations.

 

Local pockets are much more likely.

Perhaps, but pockets purified to the point of saturation as per the experiment? Absolutely ridiculous! Pockets lacking tar and other contaminants? Completely impossible!

 

Speculative? Of course it is, that is the nature of science when attempting initial answers to important questions. As I said at the outset, if you want certainty ‘look away now’.

I don't want certainty. At this point, when dealing with abiogenesis, I'd settle for realism. I can't even find that.

[Ron 10]

In science there is no absolute certainty.

So:

Q 1- Are you saying there are no absolutes?

 

Q 2- Are you saying there are no scientific absolutes?

 

Q 3- Are you absolutely sure in either case?

[Ophiolite 0]

Not my problem that your side's claim about things concerning evolution do not stand up to scrutiny.

This is an irrelevant comment. You have not demonstrated that evolutionist claims do not stand up to scrutiny. My brief post simply noted that certainty is not the province of science. That was the thesis of my opening remarks. If you feel an urge to have certainty then the scientific process is assuredly not for you. And that is not a problem for you if you are happy to live like that.

I don't disregard scientific processes and findings when they don't go so far out on a limb as to conclude that the impossible can happen just because the impossible conforms to a certain accepted theory that has been deemed already proven.

 

You appear not to understand how science works, or to be aware of the vast amount of interlocked research that exists supporting evolution. For one thing it is pure nonsense to speak of a theory being deemed to be already proven. That comment alone establishes that you are ignorant of the scientific method.

 

You appear to have this fairy tale view of a groundless theory being proposed, welcomed with open arms for reasons obscure, then adhered to by generation after generation of unthinking scintists slavishly subordinating their intellects and originality to force everything to fit the mould of that theory.

 

What actually happend? The theory was laboriouusly constructed over decades, then vigorously and rigorously disputed for three quarters of a century before it became accepted as the most plausible explnation for observations. Be honest. The problem is that evolution runs counter to your interpretation of Holy Scripture and must therefore be wrong. I don't have a problem with that. Just don't try to pretend that you are rejecting it on scientific grounds: you lack the knowledge to do that. And that is your choice. I'm not quibbling with your choice.

 

Imply absolutes to a theory means your testing procedures and you conclusions have to be better than what you currently accept. If not then evolution is also not the status that it is claimed to be. it is not the creationists problem that evolutionists claim certain things about their beloved theory then when made to hold to their claims they have to resort to claiming it's a bias on our side.

I'm afraid you have quite lost me here. If this was an important point could you rephrase it please?

 

Going outside of science to make a point (Using faith and disregard instead of evidence) is using psychology to prove science not evidence. Having to resort to mind games proves that evolution only exists in the mind of those who wish to believe it,

I acknowledge I have read this, but it doesn't merit a response.

 

And I challenged that possibility with real world conditions of that time.

It is fascinating to me that creationists routinely use the bits of science that suit them and disregard the ones that don't. How do you know what the real conditions were like at that time? Were you there?

 

I basically falsified. So are you ignoring that I can do that so you can continue to believe in evolution, or are you willing to ponder what I said and follow the scientific method?

You falsified nothing. You established conditions that were they proven to exclusively exist would have blocked this particualr route to polymerisation. So what? I didn't offer this as the bnona fide, only-possible, fundamental route to peptide and protein formation. I introduced it as an example of how proteins may have been formed naturally. (And by the by abiogenesis has nothing to do with evolution. If we could somehow prove abiogenesis tomorrow it would have zero impact on the reality of evolution. The evidence for evolution is wholly independent of the evidence for abiogenesis.)

 

Take and apply fire to the amino acids to see if they survive then we can talk about them surviving atmospheric entry being the cause of the process.

 

If they are embedded in a 1km diameter comet then they are not going to be subject to any fire.

 

A position of ignorance in science is wanting to stay on the side of hope instead of fact. Again you are using psychology to replace the problem of not being able to address things I brought up. You are basically indirectly admitting that your belief cannot meet the challenge or stand up to scrutiny. So instead you make unfounded accusations about me.

I do not understand what you mean by sayting I am using psychology. Perhaps you could expand on this point, which appears to be animportant one. I am also at a loss to know what accusations (founded or unfounded) I have made against you. I have accepted, based upon your statements here and in other posts, that you value certainty and favour absolutes. Have I misread your views in this regard?

 

You are ignoring the objections to make the evidence conform to evolution. Conformism is not science. You either weigh all for and against and come to a conclusion, or your conclusion is not science.

 

And when we weigh everything up we find that the question of abiogenesis remains one of the most exciting ones facing science because there are so many unknowns. The tiny sliver of observation of peptide formation at high impact energies may contribute to our eventual understanding of the process. Or it may not. This is not a problem for me; this is an opportunity for science. But for you it seems to be some imaginary feast of self decpetion on the part of practically the entire scientific community.

 

So if you want to totally debunk what I posted scientifically minus the psychology tactics. Here's what you need to do.

 

1) Prove that a lightening bolt is not as hot as I claim it to be (several time hotter then the surface of the sun) that it would not destroy the amino acids that it created.

2) Prove that a comet would survive entry without being vaporized be showing where comets reach the earth's surface regularly.

3) Prove that a blob of ice is more opt to hit the surface of our planet than a meteor will.

etc...

 

Words, psychology tactics, ignoring real world conditions, refusing to debunk what I claimed with science, and using conformism basically proves that I shot your idea out of the water. If I did not, then use "science" and prove me wrong. If you use more of the same you only prove my point.

 

1. Prove that all amino acids on the Earth's surface would be struck by lightning bolts. Or, to put it another way. Lightning bolts are not relevant to the discussion.

2. You need to prove that it wouldn't. You are the one making the unusual claim.

3. Why would it be relevant whether a meteor or an ice block is more likely to hit the Earth? Not relevant to the problem.

[jason777 1]

In science there is no absolute certainty.

Then it isn't science. Any prediction of a model can be falsified to an absolute certainty. The only people that don't agree with that is the flat earth society and evolutionists. <_>

 

BTW, the president of the flat earth society is an evolutionist, so that is rather ironic that no one can prove anything to him either. It's indicative of a person who has their mind up already no matter what.

 

Try claiming there is no absolute certainty in an advanced chemistry laboratory and you will be quickly told to confirm your results or can them.

 

Since evolution has never been observed but is believed to be true, the term "Faith" is replaced with "Theory" and "Empirical" is replaced with "Inference". It isn't just YEC's that agree that science is empirical and testable. Some of our members are agnostic - never giving any reference to any specific God or age of the earth, but still they claim that ToE has no empirical qualities.

 

"I have come to the conclusion that Darwinism is not a testable scientific theory, but a metaphysical research programme"... Dr. Karl Popper

 

Then you make this statement:

 

2. You need to prove that it wouldn't

That seems to confirm that you believe that science can establish empirical facts, but it only applies to everything except evolution.

 

 

 

 

Enjoy.

[jason 18]

lol. even the idea of retalivism is in the science athiests love.

 

sorry, life demands some level of certainity.

[KBC id 3]

This is an irrelevant comment. You have not demonstrated that evolutionist claims do not stand up to scrutiny. My brief post simply noted that certainty is not the province of science. That was the thesis of my opening remarks. If you feel an urge to have certainty then the scientific process is assuredly not for you. And that is not a problem for you if you are happy to live like that.

As an agnostic mechanical engineer I live within a world defined by empirical evidences that provide certainty whose basis is defined by the scientific method. The certainties provided by scientific method are those defined by 'repeatable' experiment. What does a repeatable experiment provide as a certainty? It shows repatedly what something cannot be. It provides certainty in eliminating so many conjectures and imaginations that you become backed into a corner that typically has a single logical possibility that never seems to be eliminated. It may be true that you can't provide an experiment that would prove something to the point of certainty but by use of the scientific method we provide by repeatable observable evidence with certainty what something cannot be.

Some people try to prove what something is. Others like myself like to prove what something is not because these are the only things you can prove with certainty. "When you have eliminated the impossible, whatever remains, however improbable, must be the truth" Sir Arthur Conan Doyle - Sherlock Holmes

 

A simple question I would ask you at this point; Has the evidences provided by the repeatable tests used to back evolutionary theory eliminated Intelligent design from being a possible explanation for life on this planet? If you believe it has please provide a link to the evidence, if however it has not then such a solution remains on the table until a crucial experiment can be developed that will provide for its elimination.

The facts as I see them from all the evidences I have reviewed do not back the hypothesis of evolution into a proverbial corner as the only logical solution and in fact proper scientific crucial experiments have not even been formed to allow it to acheive the status of theory.

If we were to base a hypothetical solution to how living systems arose based on observable evidence alone what would you be able to observe in the current environment that is capable of forming complex interactive chem-lectro-chanical formations of matter?

 

I observe such a solution daily.

 

Any hypothetical solution that cannot be eliminated from possibility should have equal footing with any other hypothesis. Eliminating possibilities a priori is an error of logic. Materialism is an error of logic.

 

Materialism

1a : a theory that physical matter is the only or fundamental reality and that all being and processes and phenomena can be explained as manifestations or results of matter.

 

This also has had no crucial experiment to eliminate everything from consideration except physical matter. Intelligence is not physical and yet we show empirically that is a causal force and it can produce formations of matter that have many of the traits only observed in living organisms. In fact, we are in a time when we use our intelligence to affect the genetic structure of living organisms to exhibit unique qualities by the infusion of new information into the genetic structure. Do we see any evolutionary forces observed in a repeatable experiment that exhibit this same propensity? At some point we will know enough about the genetic code to actually intelligently design the mechanism within specifiable boundaries.

 

Researchers creating life from scratch

http://www.msnbc.msn.com/id/9005023/ns/technology_and_science-science/t/researchers-creating-life-scratch/

 

Synthetic biology

And man made life

Artificial life, the stuff of dreams and nightmares, has arrived

...It is now possible to conceive of a world in which new bacteria (and eventually, new animals and plants) are designed on a computer and then grown to order...

http://www.economist.com/node/16163154

[ecco 0]

From the OP:

This peptide is 32 amino acids long with a sequence of RMKQLEEKVYELLSKVACLEYEVARLKKVGE … The probability of generating this in successive random trials is … 1 chance in 4.29 x 10⁴⁰ … or ... 1 in 2.04 x 10³⁹⁰.

 

I agree. However, that isn't the way nature works. As an example, I offer the humble water molecule: H₂O – two hydrogen atoms and one oxygen atom combined. Not just combined in any old random way but combined in a very precise way:

 

http://www.aquadyntech.com/watermolecule.html

The water molecule is formed from two hydrogen atoms and one oxygen atom. The bonding angle of the two hydrogens is almost 105 degrees rather than 180 degrees which would make the molecule symmetrical.

 

This causes it to be dipolar, giving it a positive and negative side which accounts for its unique properties. This allows the formation of hydrogen bonds between adjacent molecules. There is a weak intermolecular force of electrostatic attraction between the molecules which is known as van der Waals force. This causes the molecules to act as larger units than the individual molecules.

 

Also when two water molecules combine they also “connect†in a very specific way, not just randomly.

 

Atoms can only “connect†with certain other atoms. Molecules can only “connect†with certain ot molecules.

 

Nature cannot and does not “connect†uranium atoms with oxygen atoms. On the other hand, carbon, hydrogen, nitrogen and oxygen atoms combine readily into various molecules.

 

It's not a random process, it's all about bonding by sharing electrons.

 

Now, let's look at the odds of creating a 32 character string. For ease in demonstrating, let's use ABCDEFGHIJKLMNOPQRSTUVWXYZ123456 to represent a survivable sequence.

 

I wrote a computer program to randomly pick characters 32 times. If the resultant string was ABC...456, it was “survivable†and I stored it, if not I discarded it. Then I repeated the process. I let the program run over night. Not surprisingly, I did not randomly create the ABC...456 string even though the program tried a few million times. The “closest†I got was ABCDEFsomethingelse a few times. Conclusion, I agree that “generating this in successive random trials†borders on the impossible.

 

However, let me repeat, that is not how nature works. The process that bonds atoms to create molecules and bonds molecules to create bigger molecules is at work here.

 

I changed the program to incorporate some basic “physics†into the mix. In my revised program, the right side of an A could only connect to the left side of a B, the right side of a B could only connect to the left side of a C, and so on.

 

I randomly grabbed two letters. If the “connected†(ie. T:U) I stored the “pairâ€ÂÂ, if not I discarded them. I repeated this process several thousand times. For the next step, I randomly grabbed two sets of pairs and determined if they could be connected (ie. OP:RQ). If so, I stored the quad, if not I discarded them. I repeated this process to get eights, sixteens and 32's. Within a few minutes I repeatedly got the survivable sequence ABC...456.

 

That's how nature works. And that's how we get everything from diatomic hydrogen (H2) to peptides to humans.

[Ron 10]

Okay… out of common courtesy, I’ll ask again:

 

In science there is no absolute certainty.

So:

Q 1- Are you saying there are no absolutes?

 

Q 2- Are you saying there are no scientific absolutes?

 

Q 3- Are you absolutely sure in either case?

[omnevivumexvivo 1]

From the OP:

 

 

 

I agree. However, that isn't the way nature works. As an example, I offer the humble water molecule: H₂O – two hydrogen atoms and one oxygen atom combined. Not just combined in any old random way but combined in a very precise way:

 

http://www.aquadyntech.com/watermolecule.html

 

Also when two water molecules combine they also “connect†in a very specific way, not just randomly.

 

Atoms can only “connect†with certain other atoms. Molecules can only “connect†with certain ot molecules.

 

Nature cannot and does not “connect†uranium atoms with oxygen atoms. On the other hand, carbon, hydrogen, nitrogen and oxygen atoms combine readily into various molecules.

 

It's not a random process, it's all about bonding by sharing electrons.

 

Now, let's look at the odds of creating a 32 character string. For ease in demonstrating, let's use ABCDEFGHIJKLMNOPQRSTUVWXYZ123456 to represent a survivable sequence.

 

I wrote a computer program to randomly pick characters 32 times. If the resultant string was ABC...456, it was “survivable†and I stored it, if not I discarded it. Then I repeated the process. I let the program run over night. Not surprisingly, I did not randomly create the ABC...456 string even though the program tried a few million times. The “closest†I got was ABCDEFsomethingelse a few times. Conclusion, I agree that “generating this in successive random trials†borders on the impossible.

 

However, let me repeat, that is not how nature works. The process that bonds atoms to create molecules and bonds molecules to create bigger molecules is at work here.

 

I changed the program to incorporate some basic “physics†into the mix. In my revised program, the right side of an A could only connect to the left side of a B, the right side of a B could only connect to the left side of a C, and so on.

 

I randomly grabbed two letters. If the “connected†(ie. T:U) I stored the “pairâ€ÂÂ, if not I discarded them. I repeated this process several thousand times. For the next step, I randomly grabbed two sets of pairs and determined if they could be connected (ie. OP:RQ). If so, I stored the quad, if not I discarded them. I repeated this process to get eights, sixteens and 32's. Within a few minutes I repeatedly got the survivable sequence ABC...456.

 

That's how nature works. And that's how we get everything from diatomic hydrogen (H2) to peptides to humans.

 

I knew all this ahead of time. In fact, I know enough about the topic to explain to you why the logic you apply to water and incorporated into your computer program doesn't work for amino acids.

 

An amino acid is any molecule with this basic chemical formula: H₂N-CH®-COOH

(The "R" is the side chain, and can have any chemical composition, as you no doubt know, but a layperson reading this may not have been exposed to this subject to the same degree you have)

 

In water, the -COOH ionizes to a -COO^- and an H⁺ ion. That H⁺ ion, or another one like it in solution, is attracted to the H₂N- group, turning it into an H⁺₃N- group.

 

The end result of all this is a zwitterion, or a molecule with a positive charge on one side and a negative charge on the other side. The overall formula is this: H⁺₃N-CH®-COO^- As you can see, the carboxyl group (on the far right) has a negative charge, and the amide group (on the far left) has a positive charge. If there are multiple amino acids in solution, the way they line up will be decided by the amide-carboxyl attraction. What is key is that the positively charged amide group of one amino acid will ALWAYS attract the negatively charged carboxyl group of the other side, REGARDLESS OF SIDE CHAINS. These charges are why certain minerals will catalyze the formation of polypeptides, btw. The alternating positive and negative charges of the ions in the mineral attract carboxyl and amide groups--or any other charged group, for that matter--restricting the motion of the amino acids to one plane, and making it more likely for them to come into contact with one another. Again, this process IS NOT EFFECTED BY THE SIDE CHAINS.

 

Biochemical predestination has been abandoned as the dead end it is. No one really thinks that something inherent in the chemical properties of amino acids that causes them to preferentially form sequences with the capacity to form a hydrophobic core and catylize chemical reactions.

 

Also, when the amide and carboxyl groups attract each other and form a bond, water is released. This means that in aqueous solution, polypeptides have a nasty tendency to spontaneously break apart over time. There is no "process that...bonds molecules to create bigger molecules," but there are pleanty of processes that break molecules apart to form smaller molecules. That is the natural tendency: smaller, less energy content, less information. Polypeptides and oglionucleotides have lots of energy in them, they are usually 70+ monomers in length, and--as they are relevent to living things, at any rate--they have EXTRAORDINARILY HIGH information content. Clearly, something other than natural processes is at work here.

[jason777 1]

Hi, ecco.

 

 

I agree. However, that isn't the way nature works. As an example, I offer the humble water molecule: H₂O – two hydrogen atoms and one oxygen atom combined. Not just combined in any old random way but combined in a very precise way:

 

http://www.aquadyntech.com/watermolecule.html

 

Also when two water molecules combine they also “connect” in a very specific way, not just randomly.

 

Atoms can only “connect” with certain other atoms. Molecules can only “connect” with certain ot molecules.

 

Nature cannot and does not “connect” uranium atoms with oxygen atoms. On the other hand, carbon, hydrogen, nitrogen and oxygen atoms combine readily into various molecules.

 

It's not a random process, it's all about bonding by sharing electrons.

 

Now, let's look at the odds of creating a 32 character string. For ease in demonstrating, let's use ABCDEFGHIJKLMNOPQRSTUVWXYZ123456 to represent a survivable sequence.

 

I wrote a computer program to randomly pick characters 32 times. If the resultant string was ABC...456, it was “survivable” and I stored it, if not I discarded it. Then I repeated the process. I let the program run over night. Not surprisingly, I did not randomly create the ABC...456 string even though the program tried a few million times. The “closest” I got was ABCDEFsomethingelse a few times. Conclusion, I agree that “generating this in successive random trials” borders on the impossible.

 

However, let me repeat, that is not how nature works. The process that bonds atoms to create molecules and bonds molecules to create bigger molecules is at work here.

 

I changed the program to incorporate some basic “physics” into the mix. In my revised program, the right side of an A could only connect to the left side of a B, the right side of a B could only connect to the left side of a C, and so on.

 

I randomly grabbed two letters. If the “connected” (ie. T:U) I stored the “pair”, if not I discarded them. I repeated this process several thousand times. For the next step, I randomly grabbed two sets of pairs and determined if they could be connected (ie. OP:RQ). If so, I stored the quad, if not I discarded them. I repeated this process to get eights, sixteens and 32's. Within a few minutes I repeatedly got the survivable sequence ABC...456.

 

That's how nature works. And that's how we get everything from diatomic hydrogen (H2) to peptides to humans.

 

 

Yes. It is a fact that the laws of chemistry work in precise and predictable reactions with other chemicals. The idea your on to was the basis of the book "Biochemical Predestination" by Dean H. Kenyon Professor Emeritus of Biology at San Francisco State University. The problem that Kenyon and his co author failed to see is the basic problem that separates biological organisms from chemical reactions.

 

"...in 1976, a student gave me a book by A.E. Wilder-Smith, The Creation of Life: A Cybernetic Approach to Evolution. Many pages of that book deal with arguments against Biochemical Predestination, and I found myself hard-pressed to come up with a counter-rebuttal. Eventually, several other books and articles by neo-creationists came to my attention." Dean H. Kenyon

 

The chemicals that make up amino acids are predestined to react and bond if they are in contact with each other and that proves it's no longer a probability, but a scientific fact of chemistry. But, attaching those amino acids into proteins would be a random act without genes that are producing them in repeatable combinations. And proteins themselves aren't under any natural selection since there are no individuals to select, which means we would have nothing but an endless sea of meaningless amino acid combinations without the genome there to guide the process. And that lies in the realm of biology and not chemistry.

 

 

http://www.youtube.com/watch?v=tb6xdaC9hrM&feature=relmfu

 

 

 

Enjoy.