[_ Old Earth _] Does Anyone Here Know Anything About Molecular Biology?

[Asyncritus]

I've been reading some stuff about molecular biology, and it's findings about the structure of cells, and how they function.

It's nothing short of mind blowing.

For evolution, this has implications that are only slightly less bad that the instinct phenomenon I have been talking about.

But does anyone know anything about the synthesis of proteins for example?

If you do, can you please tell us something about it, and I shall confirm what my author (Michael Denton) says about the subject.

 

[Rhea]

There is a comprehensive discussion of the flaws in Dentons work at TalkOrigins if you are interested in hearing the scientific review of this 25-year old book.

He makes some assumptions and leaps that are not scientific. It is an interesting article and if you are genuinely curious to understand how other people view the evidence, then you will enjoy reading it. Even if you don't agree with the conclusion, you will at least know more accurately how others formed their conclusions.

an exerpt:

Consider, first, the wildly varying plants of the genus Brassica (broccoli, cauliflower, cabbages, kale, and brussel sprouts), which have been derived through artificial selection from a single species of wild mustard (Campbell, 1990, p.432). Anyone who has compared kale with brussel sprouts can see that their structures are extremely different.1 Another example of major structural change is the set of widely variant dog varieties that has resulted from selective breeding.2 Just look at the different varieties of dogs that exist today, and ask whether a Chihuahua and St. Bernard can be connected only by saltations? If such profound change can occur and speciation does, as Denton conceded, occur, then what is to theoretically stop a remote ancestor from evolving into all of the primates? What is theoretically to stop an ancient ungulate from evolving into a whale, or an ancient fish into an amphibian? The fossil record, as we will see later on, provides even more evidence for major structural change, both in skeletal and soft organ characteristics. Yet Denton persists:

While sentences, machines, and other sorts of complex systems can undergo a certain degree of gradual functional change, there is invariably a limit beyond which the system cannot undergo further gradual change. To cross as it were from one "type" to another necessitates a relatively massive reorganization involving the redesign or respecification of all or most of the interacting component subsystems. Systems can undergo gradual microevolution through a succession of minor changes in their component structures but macro-evolution invariably involves a sudden "saltational" change. (Denton, 1985, p. 91)​

In no place does he offer support for this characterization of macroevolution, and for his claim concerning the limits of gradual functional change. Rather, he seems to be taking as self-evident the assertions of Cuvier. Denton does discuss at great length in Chapters 9 and 14 some of the more complex organs in various vertebrates, such as the avian pulmonary system and its lack of a remote counterpart among the reptiles, but these long discussions seem to amount to little more than saying: "We haven't told an evolutionary story for it yet, and it seems difficult to me to believe that such a story could exist, therefore there is not one." This is the type of reasoning that Richard Dawkins has dubbed the "Argument from Personal Incredulity"(Dawkins, 1987, p. 38). Dawkins notes as well as any evolutionist that "anti- evolution propaganda is full of alleged examples of complex systems that 'could not possibly' have passed through a gradual series of intermediates"(Dawkins, 1987, p. 86), and he goes to great lengths to show that accounts can definitely be formulated that explain the development of structures and processes as sophisticated as the human lung and bat echolocation. Perhaps if more evolutionary theorists were around, we would have accounts about every single structure Denton could incredulously point to. But Denton really should be able to formulate such stories himself. The point is, pointing out how impossible it seems, at first glance, for a structure to have evolved gradually, does not constitute evidence that gradual macroevolution is impossible or improbable - it says something rather about one's failure to give hard thought to the possible means whereby complex structures could be generated.

 

[Barbarian]

On Page 276 of Denton's more recent book, Nature's Destiny, he writes:

One of the most surprising discoveries which has arisen from DNA sequencing has been the remarkable finding that the genomes of all organisms are clustered very close together in a tiny region of DNA sequence space forming a tree of related sequences that can all be interconverted via a series of tiny incremental natural steps.

So the sharp discontinuities, referred to above, between different organs and adaptations and different types of organisms, which have been the bedrock of antievolutionary arguments for the past century (3), have now greatly diminished at the DNA level. Organisms which seem very different at a morphological level can be very close together at the DNA level.

In the book, he also says:
it is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science - that the cosmos is a seamless unity which can be comprehended ultimately in its entirety by human reason and in which all phenomena, including life and evolution and the origin of man, are ultimately explicable in terms of natural processes. This is an assumption which is entirely opposed to that of the so-called "special creationist school". According to special creationism, living organisms are not natural forms, whose origin and design were built into the laws of nature from the beginning, but rather contingent forms analogous in essence to human artifacts, the result of a series of supernatural acts, involving the suspension of natural law. Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world - that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies.
Just saying...

 

[Rhea]

Wow, that's pretty unambiguous. Has he undergone an evolution in his views, or was his first book misquoted, do you think?

 

[Barbarian]

A little of each, I think.

 

[Asyncritus]

He has become (in his second book) somewhat more ambivalent and it seems to me, confused and confusing. I don't think he knows what his opinion really is.

On the one hand, as in Evolution: A Theory in Crisis,(pp 212,213) he clearly sees that evolution is impossible, and comes near to actually saying so.

Just how such an utterly different respiratory system could have evolved gradually from standard vertebrate design is fantastically difficult to envisage...

and

"...the avian lung and the feather bring us very close to answering Darwin's challenge:

If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down"

Here's some more from Nature's Destiny which inclines me to the opinion of ambivalency: some of the section headings in chapter 12 'The Tree Of Life':

The Vestiges and Directed Evolution
The Problem of Direction
The Fitness of DNA for Directed Evolution
Directed Mutation and Development
Directed Sequential Change
Other Sources of Direction
Molecular Hints of Direction

It seems pathetic that he cannot see that direction requires intelligence and a director.

Maybe he can, I wouldn't know - but abandoning the idea of a God will force him (as it does everybody) to come down on the side of the idea that life can direct itself into paths of progress: Lamarckism, in other words.

I was tickled to read his quote of Monod, which is fatal to all work on abiogenesis and its daughter, evolution:

"The modern cell's translating machinery consists of at least fifty macromolecular components which are themselves coded in the DNA: the code cannot be translated except by the products of translation. It is the modern expression of omne vivum ex ovo. When and how this circle became closed? It is exceedingly difficult to imagine."

He rocks back and forth between recognising the impossible as above quoted, and weakly falling back into the 'directed evolution' mode.

As I say, he is a confused man: and has lost the clarity of his vision shown in Evolution: A Theory in Crisis.

It may be that pounding from the pro-evolution camp caused this change, as it did with Gould, who hastily backtracked from his punctuated equilibrium theory under pressure (or so it seems to me, anyway).

Poor chap.

 

[Gazelle]

I feel like I only know enough to discuss this topic for 15 minutes...which means I better type quickly. :biglol

Let me give references first, in case my mind goes sooner than that:

1Gráinne McEntee et al., “The Former Annotated Human Pseudogene Dihydrofolate Reductase-like 1 (DHFRL1) Is Expressed and Functional,†Proceedings of the National Academy of Sciences 108, no. 37 (September 13, 2011): 15157–62.

2 John A. P. Rostas and Peter R. Dunkley, “Multiple Forms and Distribution of Calcium/Calmodulin-Stimulated Protein Kinase II in Brain.†Journal of Neurochemistry 59 (October 1992): 1191–202.


This is in reference to what they considered to be a pseudogene (discovered in 1980.) Dihydrofolate reductase-like 1 (DHFRL1) and was considered to be "junk DNA."1

“Why would a creator include non-functional DNA in a genome? This non-functional DNA is present only because the organism inherited it through the evolutionary process.†When supposedly functionless DNA is found to be functional, the argument in favor of evolution is no longer valid.

reasons.org

It was considered dysfunctional because it has no introns, but now that it has been found to be functional, the paradigm needs to be adjusted.

This change may lead to more rapid discoveries of protein-producing pseudogenes and put an end to this argument in favor of evolution.

ibid.

DHFRL1 has the ability to enter the mitochondrion, and it also operates differently than DHFR does, at a different concentration of folate.

This is a mechanism used by the cell in other situations to provide for highly tuned protein functionality.

2

Well, I think I'm outta of time and knowledge.

 

[Asyncritus]

Source: http://belligerentdesign-asyncritus.blogspot.com/2009/10/ervs-function-discovered.html

A recent 2008 paper, "Retroviral promoters in the human genome," in the journal Bioinformatics (Vol. 24(14):1563–1567 (2008)) discusses the fact that "Endogenous retrovirus (ERV) elements have been shown to contribute promoter sequences that can initiate transcription of adjacent human genes. However, the extent to which retroviral sequences initiate transcription within the human genome is currently unknown." The article thus "analyzed genome sequence and high-throughput expression data to systematically evaluate the presence of retroviral promoters in the human genome."

The results were striking:

We report the existence of 51,197 ERV-derived promoter sequences that initiate transcription within the human genome, including 1743 cases where transcription is initiated from ERV sequences that are located in gene proximal promoter or 5' untranslated regions (UTRs).

[…]

Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome. These data suggest that ERVs may regulate human transcription on a large scale.

(Andrew B. Conley, Jittima Piriyapongsa and I. King Jordan, "Retroviral promoters in the human genome," Bioinformatics, Vol. 24(14):1563–1567 (2008).)

So yet another piece of evolution's fairy tales comes to earth with a thud. 'Junk DNA' huh? 90% of the genome, hey?

Visit my blog on that link above for the full story with references.

 

[Barbarian]

"...the avian lung and the feather bring us very close to answering Darwin's challenge:

If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down"

As you learned earlier from a thread you abandoned, the avian lung works as it does in other vertebrate lungs, except that collateral ventilation, which is a secondary function in the lungs of other vertebrates, is the primary function in birds. If you have more to offer, I suggest you go back to the thread you abandoned, and try again.

And seeing as scientists have found that a rather small genetic change will convert scales to feathers, that's not any great mystery, either. You abandoned that thread, as well, after the evidence was presented.

"The modern cell's translating machinery consists of at least fifty macromolecular components which are themselves coded in the DNA: the code cannot be translated except by the products of translation. It is the modern expression of omne vivum ex ovo. When and how this circle became closed? It is exceedingly difficult to imagine."

In other words, "if you can't remove one stone from an arch, without the whole thing collapsing, that proves that it's impossible to build an arch." But people build arches. That should be enough of a hint for you.

It may be that pounding from the pro-evolution camp caused this change, as it did with Gould, who hastily backtracked from his punctuated equilibrium theory under pressure (or so it seems to me, anyway).

You've been had on that belief. Gould's last, most ambitious work, The Structure of Evolutionary Theory still asserts punctuated equilibrium. Surprise.

 

[Barbarian]

Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome. These data suggest that ERVs may regulate human transcription on a large scale.

(Andrew B. Conley, Jittima Piriyapongsa and I. King Jordan, "Retroviral promoters in the human genome," Bioinformatics, Vol. 24(14):1563–1567 (2008).)

So yet another piece of evolution's fairy tales comes to earth with a thud. 'Junk DNA' huh? 90% of the genome, hey?

You've been had on that one, too. When I was an undergrad in the 60s, scientists already knew that some non-coding DNA had functions. On the other hand, it is possible to excise huge stretches of non-coding DNA with no apparent effect whatever:

In yet another twist in the story of understanding "junk DNA," researchers from JGI and Berkeley Lab's Genomics Division have found that deleting large stretches of noncoding DNA can yield surprisingly healthy mice. Mice with the noncoding sequences removed were essentially indistinguishable from wild-type mice, even though the deleted sequences contained many sections that are conserved between mice and humans. This result suggests that some noncoding sequences, even those that persist through the pressures of evolution, may indeed be disposable.
http://www.jgi.doe.gov/science/highlights/nobrega1004.html

Turns out "conserved" may not necessarily indicate "functional." Surprise again.

 

[Asyncritus]

As you learned earlier from a thread you abandoned, the avian lung works as it does in other vertebrate lungs, except that collateral ventilation, which is a secondary function in the lungs of other vertebrates, is the primary function in birds. If you have more to offer, I suggest you go back to the thread you abandoned, and try again.

Sorry. You produced some silly idea that microscopic pores could 'evolve' into an entirely new respiratory system. It doesn't say much for your perspicacity.

And seeing as scientists have found that a rather small genetic change will convert scales to feathers, that's not any great mystery, either. You abandoned that thread, as well, after the evidence was presented.

Oh, because a 'rather small genetic' change will do the trick, that means that that is what happened? Your logic is hopeless, I'm afraid.

And I missed your 'inventions' which explain how the flight instincts a. arose and b. entered the genome - because without them wings, feathers and everything else to do with flight are entirely useless, 'small genetic changes' or not.

In other words, "if you can't remove one stone from an arch, without the whole thing collapsing, that proves that it's impossible to build an arch." But people build arches. That should be enough of a hint for you.

Not quite.

A single bomb can destroy a city - like Hiroshime.

That's what Monod has dropped on you from a great height. The whole of abiogenesis is finished with that single piece of information - and there are others like it too e.g.

life is impossible without enzymes.

Enzymes are proteins.

Proteins can only be produced by living cells with enzyme activity every step of the way.

So without enzymes--->no life.

Without life----> no enzymes.

Chicken or egg?

You've been had on that belief. Gould's last, most ambitious work, The Structure of Evolutionary Theory still asserts punctuated equilibrium. Surprise.

There are mixed opinions on that one. He could see perfectly clearly, that palaeontology supports creation, and had to produce some idea that explained the appearance of bursts of creative activity in the fossils..

Quotes from his works strongly support the idea of creation, even though he didn't dare say so.

When they were so used by us, he backtracked, loudly protesting his innocence and annoyance, that his writings could be and were being used that way.

I published an article on the subject on this forum, and you can go there and look if you like: http://forum.religious-science.com

I don't know who he convinced - but Dawkins definitely wanted to clobber him.

From what he wrote in various places, I got the distinct impression that he was vigorously back-tracking from the PE position.

 

[Asyncritus]

(Andrew B. Conley, Jittima Piriyapongsa and I. King Jordan, "Retroviral promoters in the human genome," Bioinformatics, Vol. 24(14):1563–1567 (2008).)

You've been had on that one, too. When I was an undergrad in the 60s,

The above article was written in 2008.

Got anything more recent than that old junk?

 

[Barbarian]

Barbarian observes:
As you learned earlier from a thread you abandoned, the avian lung works as it does in other vertebrate lungs, except that collateral ventilation, which is a secondary function in the lungs of other vertebrates, is the primary function in birds. If you have more to offer, I suggest you go back to the thread you abandoned, and try again.

Sorry. You produced some silly idea that microscopic pores could 'evolve' into an entirely new respiratory system.

As you learned, just before you bailed out of the thread, it's not an entirely new system. It exists in all vertebrates. It's just become the primary form in birds.

Barbarian observes:
And seeing as scientists have found that a rather small genetic change will convert scales to feathers, that's not any great mystery, either. You abandoned that thread, as well, after the evidence was presented.

Oh, because a 'rather small genetic' change will do the trick, that means that that is what happened?

It means your claims that it can't happen, are in the dumpster.

And I missed your 'inventions' which explain how the flight instincts a. arose

Turns out the same upper limb movments by reptiles that run on two legs, are those that birds use while flying.

Just something old, reworked to do something new. Like bird lungs.

wings, feathers and everything else to do with flight are entirely useless, 'small genetic changes' or not.

The fossil record clearly shows feathers predated flight. That too, is an adaptation. Feathers worked well as insulation and display before they were for flight. We know this, because asymmetrical feathers (necessary for flight) were not the first feathers.

(Argument from irreducible complexity)

Barbarian chuckles:
In other words, "if you can't remove one stone from an arch, without the whole thing collapsing, that proves that it's impossible to build an arch." But people build arches. That should be enough of a hint for you.

Not quite.

For any reasonable person, then. Even Behe now admits that irreducible complexity can evolve. In fact, it has been observed to evolve.

(Sudden attempt to change the subject)

A single bomb can destroy a city - like Hiroshime.

Sorry, no bunny trails.

life is impossible without enzymes.

And...

Enzymes are proteins.

This is going to be fun, I think...

Proteins can only be produced by living cells with enzyme activity

The Murchison meteorite contained, in its interior naturally-occuring peptides (short protein molecules). So you're wrong again.

BTW, evolution doesn't depend on abiogenesis. Darwin, for example, suggested that God just created the first living things.

(Assertion that Gould backed off on punctuated equilibrium)

Barbarian chuckles:
You've been had on that belief. Gould's last, most ambitious work, The Structure of Evolutionary Theory still asserts punctuated equilibrium. Surprise.

There are mixed opinions on that one.

No there aren't. He clearly and unambigously asserts punctuated equilibrium in that book. Never read it, um?

He could see perfectly clearly, that palaeontology supports creation

Nope. In fact, he remained an agnostic. They lied to you about that, too.

and had to produce some idea that explained the appearance of bursts of creative activity in the fossils..

It's not a new idea. Huxley suggested it, for example. Gould's great contribution was demonstrating the evidence for it.

Quotes from his works strongly support the idea of creation, even though he didn't dare say so.

For example, he suggested that maybe the universe produces being like us, because Someone wanted someone to share it with. But that doesn't do your argument any good. That, like Christian belief, is consistent with evolution.

When they were so used by us, he backtracked, loudly protesting his innocence and annoyance, that his writings could be and were being used that way.

Oh yeah. This...

"Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups."
--Stephen Jay Gould, Evolution as Fact and Theory, Hen's Teeth and Horse's Toes: Further Reflections in Natural History, New York: W. W. Norton & Company, 1994, p. 260

Dishonesty or stupidity. Not exactly what I'd be bragging about.

From what he wrote in various places, I got the distinct impression that he was vigorously back-tracking from the PE position.

Show us. I get the distinct impression that you're blowing smoke.

 

[Barbarian]

A quick search on functional non-coding DNA turns up one 33 years old.

Mol Biol (Mosk). 1978 Jan-Feb;12(1):5-35.
[Genome organization in eukaryotes].
[Article in Russian]
Gvozdev VA.
Abstract

The review discussed problems of genome organization in the chromosomes of eukaryotes based on the data of genetical and molecular-biological studies. Particular attention is paid to the peculiarities of organization of genetic material in Drosophila. The main (euchromatic) part of the genome is considered as the totality of separate functional units (chromomere, gene loci), which have in the average a higher excess of DNA compared to the sized of the structural gene. The possible ways of internal organization of these units and the role of different types of DNA sequences in their function are discussed. The features of organization and function of the heterochromatic regions of chromosomes consisting of simple sequences of satellite DNA and tandemly repeated genes (polygenes), that code for general cellular functions (similar to the ribosomal genes) are considered. The instability of the number and even the sites of localization of polygenes in the chromosome, which can be determined by the peculiarities of their functions during differentiation of somatic cells is notes.

 

[abrown9]

life is impossible without enzymes.

A quick note:

Time and time again you bring this concept up as if it in some way relates to evolution. The TOE does not address genesis.

That being said, I know for a fact that I have provided papers to you that demonstrate how RNA can act as as a catalyst, totally negating the need for proteins.

 

[Asyncritus]

A quick note:

Time and time again you bring this concept up as if it in some way relates to evolution. The TOE does not address genesis.

That being said, I know for a fact that I have provided papers to you that demonstrate how RNA can act as as a catalyst, totally negating the need for proteins.

Tut tut.

Apologies for my long absence from this scene, but here's the final damnation of your statement: wiki:

Synthesis of RNA is usually catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription.

And guess what RNA Polymerase is?

You got it. A protein.

And how is DNA, the template, synthesised? You got it again:

In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.

So, no proteins, no DNA or RNA. And no DNA or RNA, no proteins.

Voila. Chicken or egg, sir?

 

[Barbarian]

Turns out, as brown says, some forms of RNA self-polymerize. But even so, we know that peptides form abiotically, so it doesn't matter. Proteins almost certainly predated nucleic acids.

Would you like to see the evidence for that?

 

[Asyncritus]

Peptides are in no way comparable to either RNA and DNA for complexity.

Peptides combine to form proteins eventually. But proteins cannot be formed without enzyme action.

Also, as far as I am aware, they are only formed in living cells at the ribosomes, which are themselves mainly proteins.

For synthesis of protein, a succession of tRNA molecules charged with appropriate amino acids have to be brought together with an mRNA molecule and matched up by base-pairing through their anti-codons with each of its successive codons. The amino acids then have to be linked together to extend the growing protein chain, and the tRNAs, relieved of their burdens, have to be released. This whole complex of processes is carried out by a giant multimolecular machine, the ribosome, formed of two main chains of RNA, called ribosomal RNA (rRNA), and more than 50 different proteins. This molecular juggernaut latches onto the end of an mRNA molecule and then trundles along it, capturing loaded tRNA molecules and stitching together the amino acids they carry to form a new protein chain.[2]

You were saying?

Turns out, as brown says, some forms of RNA self-polymerize. But even so, we know that peptides form abiotically, so it doesn't matter. Proteins almost certainly predated nucleic acids.

RNA self-polymerisation cannot produce a protein. All it can do is produce larger molecules of (RNA)n.

But even so, we know that peptides form abiotically, so it doesn't matter.

Would you like to learn about the differences between proteins and peptides? I think it matters very greatly, because the gulf between the two classes of compounds is simply monumental, as you really should know.

Peptides are easy to synthesise. Proteins are not. I can refer you to some standard texts on the subject if you like.

Proteins cannot be synthesised outside the cell. They cannot be synthesised without enzymes. Enzymes are themselves proteins.

The problem is bigger even than that. Here's a sample of your problems.

- DNA is essential for a single protein to form - DNA cannot form without protein
- Protein cannot form without DNA
- Protein cannot form in the absence of protein
- Sixty separate proteins are needed for a single protein to form
- Protein cannot form in the absence of any one of these
- Protein cannot form with no ribosome
- Protein cannot form with no RNA
- Protein cannot form without ATP
- Protein cannot form without the mitochondria to manufacture ATP
- Protein cannot form without the cell nucleus
- Protein cannot form without the cytoplasm
- Protein cannot form in the absence of a single organelle in the cell
- And proteins are necessary for all the organelles in the cell to exist and function
- There can be no protein without these organelles

Just to rub a bit more salt into the wound, here's Richard Lewontin:

“No living molecule (i.e., biomolecule) is self-producing. Only whole cells may contain all the necessary machinery for self-reproduction... Not only is DNA incapable of making copies of itself, aided or unaided, but it is incapable of ‘making’ anything else... The proteins of the cell are made from other proteins, and without that protein-forming machinery nothing can be made.â€

quoted in Stephen C. Meyer, The Signature in the Cell, Harper One, 2009, p. 132-133

So you're back on the old treadmill.

No proteins ---> no DNA

No DNA ---> no protein.

Chicken or egg, sir?

 

[Asyncritus]

Just to put paid to your simplistic nonsense about peptides and RNA polymers, here is Stephen Meyer again, describing the impossibility of a single protein forming by chance in these words:

Consider the probabilistic hurdles that must be overcome to construct even one short protein molecule of about 100 amino acids in length. First, all amino acids must form a chemical bond known as a peptide bond so as to join with other amino acids in the protein chain. Yet in nature many other types of chemical bonds are possible between amino acids. The probability of building a chain of 100 amino acids in which all linkages involve peptide bonds is roughly 1 chance in 1030.​

Second, in nature every amino acid has a distinct mirror image of itself, one left-handed version or L-form and one right-handed version or D-form. These mirror-image forms are called optical isomers. Functioning proteins tolerate only left-handed amino acids, yet the right-handed and left-handed isomers occur in nature with roughly equal frequency. Taking this into consideration compounds the improbability of attaining a biologically functioning protein. The probability of attaining at random only L-amino acids in a hypothetical peptide chain 100 amino acids long is (1/2)100 or again roughly 1 chance in 1030.

Third and most important of all, functioning proteins must have amino acids that link up in a specific sequential arrangement, just like the letters in a meaningful sentence. Because there are 20 biologically occurring amino acids, the probability of getting a specific amino acid at a given site is 1/20. Even if we assume that some sites along the chain will tolerate several amino acids (using the variances determined by biochemist Robert Sauer of MIT), we find that the probability of achieving a functional sequence of amino acids in several functioning proteins at random is still “vanishingly small,” roughly 1 chance in 1065—an astronomically large number—for a protein only one hundred amino acids in length. (Actually the probability is even lower because there are many nonproteinous amino acids in nature that we have not accounted for in this calculation.)

If one also factors in the probability of attaining proper bonding and optical isomers, the probability of constructing a rather short, functional protein at random becomes so small as to be effectively zero (no more than 1 chance in 10125), even given our multi-billion-year-old universe. Consider further that equally severe probabilistic difficulties attend the random assembly of functional DNA. Moreover, a minimally complex cell requires not 1, but at least 100 complex proteins (and many other biomolecular components such as DNA and RNA) all functioning in close coordination. For this reason, quantitative assessments of cellular complexity have simply reinforced an opinion that has prevailed since the mid-1960s within origin-of-life biology: chance is not an adequate explanation for the origin of biological complexity and specificity.


​

 

[Barbarian]

Would you like to learn about the differences between proteins and peptides? I think it matters very greatly, because the gulf between the two classes of compounds is simply monumental, as you really should know.

Well, let's see... Proteins are chains of amino acids.

And peptides are ... chains of amino acids.

Darn. Turns out we call long chain peptides "proteins." It's a matter of length. So adding more amino acids makes peptides into proteins. But it's kind of a blurred boundary, as you can imagine with two things of identical composition:

The size boundaries which distinguish peptides, polypeptides, and proteins are arbitrary. Long peptides such as amyloid beta can be considered proteins, whereas small proteins such as insulin can be considered peptides.
http://en.wikipedia.org/wiki/Peptide

Surprise.

Meyer, BTW, is speaking of the probability of one long protein of specific amino acid sequence forming by chance. He figures it's too unlikely to have happened. If so, then it's impossible to shuffle a deck of cards. If you do so, you'll find the probability of the result you got is about 1.2397999308571485923950341988946e-68. That's um....
0.00000000000000000000000000000000000000000000000000000000000000000012397999308571485923950341988946.

And yet, it happens every time. Amazing, um? Now, evolutionary theory isn't about the origin of life; it assumes living things and describes how they change. But given God's word in Genesis, and the evidence so far uncovered, it seems that the earth really did bring forth biological life.