no evolutionary scientist believes life arose by pure chance

[spinoza99]

To answer your question, if you find information, the cause will be intelligence. So let's say you find something that looks like the rosetta stone, you can predict that its cause will be intelligence.

How do you draw this conclusion?

before 1953 we didn't even know information existed in nature. all info before 1953 was produced by intelligence. with the advent of the discovery of a new source of info in 1953,dna, we've had new questions.

[Gawdzilla Sama]

gawdzilla,

i really don't even know what lie you're accusing me of. you know i'm an IDer. all i said was, look, i didn't know evolutionary scientists thought this way, then i asked if people on rationalia think in the same way. basically i was asking a question. not even opening a debate.

You lied.

And so does every evolutionary scientist, I presume.

[drl2]

Loki, what predictions does random mutation make about reality?

Random mutation is not a theory, it's an observed, observable physical process. Theory is about the "how", not the "what". Produce a hypothesis about how random mutation happens, and we can search for evidence that the hypothesis is true.

To answer your question, if you find information, the cause will be intelligence.

Quite an assumption. Prove it.

What I mean by necessity is better described with the word inevitability. If you shine a light, it is inevitable that the photons will cover 300,000 km per second.

Unless a physicist gets her hands on it.

If this is a roundabout way to say that matter and energy seem to reliably follow patterns (which we call "laws"), then sure. Are you assuming intelligent causality there? If so, refer to my reply about "information" above.

[charlou]

To answer your question, if you find information, the cause will be intelligence. So let's say you find something that looks like the rosetta stone, you can predict that its cause will be intelligence.

How do you draw this conclusion?

before 1953 we didn't even know information existed in nature. all info before 1953 was produced by intelligence. with the advent of the discovery of a new source of info in 1953,dna, we've had new questions.

You make a lot of erroneous statements as though they're facts ... and sound like a pulpit preacher spouting dogma with the assumption that people are just going to accept what you say without question or refutation.

What intelligence produced the information for us to find? Where's your evidence?

Stop anthropomorphising and consider that what we discover and learn is not presented to us by any metaphysical intelligence but discovered through the use of our own, which we've developed during our evolution.

[drl2]

gawdzilla,

i really don't even know what lie you're accusing me of. you know i'm an IDer. all i said was, look, i didn't know evolutionary scientists thought this way, then i asked if people on rationalia think in the same way. basically i was asking a question. not even opening a debate.

You lied.

And so does every evolutionary scientist, I presume.

I don't know that I'd go so far as to call him a liar - he stated a presumption he made that's unsupportable, unlikely, and not really even very sensible, but I have no problem accepting that it was an honest unsupportable, unlikely, and not really even very sensible presumption.

[Gawdzilla Sama]

gawdzilla,

i really don't even know what lie you're accusing me of. you know i'm an IDer. all i said was, look, i didn't know evolutionary scientists thought this way, then i asked if people on rationalia think in the same way. basically i was asking a question. not even opening a debate.

You lied.

And so does every evolutionary scientist, I presume.

I don't know that I'd go so far as to call him a liar - he stated a presumption he made that's unsupportable, unlikely, and not really even very sensible, but I have no problem accepting that it was an honest unsupportable, unlikely, and not really even very sensible presumption.

I don't have the least reason to believe he did anything but lie.

[charlou]

I agree with drl, zilla. Getting it wrong =/= lie.

[Feck]

Here we go again when ID gets it wrong they don't add the new evidence to the there probably is no god pile they dismiss it .

They do not care about the truth just the bits of science they can easily turn into Straw men to support their cause .

The shinning hope of ID was the flagellum .no wait it was the Eye no hang it's Dna ........fuck fuck fuck its so hard to follow ID You have to keep learning a new excuse everyday I can't keep track .

If you propose a theory and state that This piece of evidence 'proves ' your theory then either someone explains that it doesn't or new evidence is found that refutes your theory then your theory wasn't anywhere near proven was it ? When more and more evidence stacks up against your theory it's time to abandon it . This is something that ID will not do it cannot . If you start with a list of what proofs the ID crowd had 5 years ago how many have not been refuted

[Gawdzilla Sama]

I agree with drl, zilla. Getting it wrong =/= lie.

Okay, he just has to prove he didn't lie.

[Loki]

So spinoza can't provide any predictions ID makes about reality, preferring obfuscation.

Why is that I wonder?

Also could you please define "intelligence" for me, I may be a bit thick but "whatever makes my waffle sound good to me" doesn't strike me as much of a definition.


Edit: Sorry, I meant "information" not "intelligence", but fuckit, why not define that as well then we might really have an idea what you are talking about

[Feck]

time for this ....look how complicated the picture is look at how much information is in it ,it must be designed ...

[GenesForLife]

Chemistry isn't pure chance, next. Nor is selection, nor are mutagenic processes, the only thing stochastic about mutation is that you cannot predict where a mutation will occur and by which of the several possible processes when they act on a sequence of DNA.

As far as the evolution of the genetic code is concerned, I think I already explained it to you in clear terms before as to what leads to the emergence of information in DNA.
Never mind, I will have another go, and this time I'm reproducing a post I made over on RatSkep, made when responding to an extremely obnoxious liar for doctrine.

[quote="Jireh";p="576535"]
Abiogenesis fails based on various reasons , but the most clear is that DNA contains specified and complex, coded information. No natural mechanism is known to man to create information by chance. This is a clear evidence of intelligent design.[/quote]

Welcome to purely dimwitted assertion session #1190

1) Complementary base pairing isn't chance, nor is the interaction of RNA and amino acid, nor is the formation of peptide bonds.
2) There is no code inherent to DNA.
3) Assertion fail.

The "code" is the result of base pairing between tRNA and mRNA, and the binding of amino acid to tRNA, and the catalysis of a bond in between them. And the fact that mutations in the components of the translational machinery lead to the formation of of divergent genetic codes or alter the fundamental nature of the genetic code is empirically and experimentally demonstrated, in other words, shove your assertions back up the same orifice you produced it out off.

And of course, the fact that the illusion of a code written into DNA is due to the nature of the translational machinery and that altering the latter should change the "code" itself is also an evidentially supported fact.

What follows is some snippets from the extant literature that should cover why the genetic code has evolvability and also demonstrate that there is no code inherent to DNA but that any appearance of a code is a function of the translational apparatus that cells use to process their DNA into proteins.

Translation is a function of ribosomal structure and the way it interacts with mRNA, firstly , and secondly the interactions of tRNA with mRNA held in the ribosome, and the interaction of tRNAs with amino acids, which is affected by the action of enzymes called aminoacyl tRNA synthetases.

Changing these parameters allows the "code" to be modified, and since these components are themselves the result of translation and transcription of their respective genes, mutations in the latter will tend to affect the former.

With this in mind we can now look at some of the literature regarding documented examples of mutant codes resulting from mutant components of the translational machinery.

We investigated directed deviations from the universal genetic code. Mutant tRNAs that incorporate cysteine at positions corresponding to the isoleucine AUU, AUC, and AUA and methionine AUG codons were introduced in Escherichia coli K12. Missense mutations at the cysteine catalytic site of thymidylate synthase were systematically crossed with synthetic suppressor tRNACys genes coexpressed from compatible plasmids. Strains harboring complementary codon/anticodon associations could be stably propagated as thymidine prototrophs. A plasmid-encoded tRNACys reading the codon AUA persisted for more than 500 generations in a strain requiring its suppressor activity for thymidylate biosynthesis, but was eliminated from a strain not requiring it. Cysteine miscoding at the codon AUA was also enforced in the active site of amidase, an enzyme found in Helicobacter pylori and not present in wild-type E. coli. Propagating the amidase missense mutation in E. coli with an aliphatic amide as nitrogen source required the overproduction of Cys-tRNA synthetase together with the complementary suppressor tRNACys. The toxicity of cysteine miscoding was low in all our strains. The small size and amphiphilic character of this amino acid may render it acceptable as a replacement at most protein positions and thus apt to overcome the steric and polar constraints that limit evolution of the genetic code.

http://www.genetics.org/cgi/content/full/150/2/543

In this case, they used mutant tRNAs to encode cysteine instead of isoleucine and methionine, they noted that the inclusion of cysteine instead of the other amino acids was not deleterious because of the nature of the amino acid.
But that is rather superfluous to requirements here, the important thing to note is that mutant tRNAs can cause different amino acids to be incorporated for the same codon on mRNA, they had therefore, by mutation and artificial selection, evolved a new codon assignment, in other words, they'd fundamentally changed the genetic code by evolution.

At this juncture I would also like to cite/present another paper, showing that such an approach is applicable to other amino acids too, in this case Tyrosine.

Abstract.

A unique transfer RNA (tRNA)/aminoacyl-tRNA synthetase pair has been generated that expands the number of genetically encoded amino acids in Escherichia coli. When introduced into E. coli, this pair leads to the in vivo incorporation of the synthetic amino acid O-methyl-L-tyrosine into protein in response to an amber nonsense codon. The fidelity of translation is greater than 99%, as determined by analysis of dihydrofolate reductase containing the
unnatural amino acid. This approach should provide a general method for increasing the genetic repertoire of living cells to include a variety of amino acids with novel structural, chemical, and physical properties not found in the
common 20 amino acids.

The abstract and the full paper can be found here at http://uregina.ca/suhdaey/courses/04%20 ... 20coli.pdf

In this particular case, they chose to reconfigure a stop codon (UAG) into one that would code for Tyrosine.
I now move on to quote what in my opinion are the relevant (to this discussion) snippets of the paper.

What follows is an example of sheer scientific elegance in ensuring that the new modified code was orthogonal (i.e did not affect the translation of the native genetic code in E.coli) and building in selectability.

An orthogonal tRNA/synthetase pair in E.coli can be generated by importing a pair from a different organism if cross-species aminoacylation is inefficient and the anticodon loop is not a key determinant of synthetase recognition. One such candidate pair is the tyrosyl tRNA/synthetase pair of Methanococcus jannaschii, an archaebacterium
whose tRNATyr identity elements differ from those of E. coli tRNATyr (in particular, the first base pair of the acceptor stem is GC in E.coli and CG in M. jannaschii), and whose tyrosyl-tRNA synthetase (TyrRS) has only a minimalist anticodon loop binding domain (13). In addition, the M. jannaschii TyrRS does not have an editing mechanism (14)
and, therefore, should not proofread an unnatural amino acid ligated to the tRNA. We have shown that the M. jannaschii TyrRS efficiently aminoacylates an amber suppressor tRNA derived from its cognate tRNATyr (15), but does not aminoacylate E. coli tRNAs (13). Moreover, the M. jannaschiit RNA [sup]Tyr[/sup] CUA is a poor substrate for the E. coli synthetases but functions efficiently in protein translation in E. coli (15).

[1] The problem of orthogonality was solved by importing the tRNA that carries tyrosine and the coresponding aminoacyl tRNA synthetase pair from the bacterial species Methanococcus jannaschii

[2] This choice was made due to two primary reasons, one - the elements that the synthetase uses to identify the amino acid was different to the one the synthetase present in E.coli uses. In other words, the E.coli native synthetase would not recognize the tRNA from Methanococcus and two- that the said synthetase has minimal interactions with the anticodon loop, which means it could still recognize the tRNA for Tyrosine and attach the amino acid to it. Just to help you grasp the work being discussed you may refer to the diagram of tRNA below.



The anticodon arm binds to mRNA by complementary base pairing, in this case, they had to reconfigure said mRNA by
altering the anticodon loop on the Tyrosine tRNA such that it bound to the amber codon on mRNA instead of the native codon for Tyrosine, and this is where the importance of the second reason becomes apparent.

[3] They subjected these to mutation and selection and evolved the new codon assignment, the method of selection they used follows below.

To further reduce recognition of the M. jannaschii tRNA [sup]Tyr[/sup] CUA by E. coli synthetases, 11 nucleotides of the tRNA that do not interact directly with the M. jannaschii TyrRS (C16, C17, U17a, U20, C32, G37, A38, U45, U47, A59, and U60) were randomly mutated to generate a suppressor tRNA library. This tRNA library
was passed through a negative selection (suppression of amber mutations in the barnase gene), which removes tRNAs that are aminoacylated by E. coli synthetases, and then a positive selection for tRNAs that are efficiently
aminoacylated by M. jannaschii TyrRS (suppression of amber mutations in the b-lactamase gene)

So they generated a library of mutants, which is akin to a gene pool of mutant alleles. They then had two methods they employed for selection.

[1] the expression of barnase is lethal to the cell in the absence of barstar, so whether this is expressed or not can be used for purifying selection. These researchers eliminated those mutant tRNAs that were bound to amino acids by E.coli synthetases (if an amber mutation is suppressed by such activity it would trigger the expression of fully functional barnase and all bacterial colonies that contained that particular gene would go kaput, in other words, non orthologonality was eliminated, and we were left with just those mutant tRNAs which would only react with the imports from M.jannaschii

[2] the expression of beta lactamase would enable bacteria to survive and proliferate in the presence of Beta-lactam antibiotics such as Penicillin. Here, they chose tRNAs that had passed the first round of selection to see if they'd incorporate an amino acid when they met an amber stop codon in a gene for beta lactamase which had a nonsense mutation somewhere in the middle. (in other words, we were now looking at reconfiguring a codon which incorporated nothing previously such that it incorporated an amino acid, allowing the fully functional beta lactamase enzyme to be produced.

Those that were successfully tagged with amino acids by the imported aminoacyl tRNA synthetase allowed their carriers to reproduce. This led to the selection of a set of mutant tRNA/tRNA synthetase pairs that were both orthogonal and capable of introducing amino acids instead of the stop codon.

The following bit leads us to the conclusion they found.

Aminoacylation of a transformed suppressor tRNA by any endogenous E. coli synthetase results in cell growth in the presence of ampicillin. E. coli transformed with the M. jannaschii tRNACUA[sup]Tyr[/sup] and
pBLAM survive at 55 ug/ml ampicillin.

When the best mutant suppressor tRNA (mutRNACUATyr ) selected from the library was
expressed (17), cells survive at only 12 ug/ml ampicillin; similar values are obtained in the absence of any suppressor tRNA. When the M. jannaschii TyrRS is coexpressed with this mutRNACUA [sup]Tyr[/sup] , cells survive at 440 ug/ml ampicillin.

ug = (Mu)g = Micrograms, just thought I should make that clear.

Just expressing the mutant tRNA alone resulted in an extremely low treshold for survival in the presence of ampicillin, and this was no more than the survival if the amber mutation were not suppressed, in other words, the native synthetases from E.coli had no effect (no codon reconfiguration in other words)

Adding both the imported synthetase and the best mutant tRNA they selected from the library led to dose tolerance that was 36 times higher, in other words, reconfiguration successful, new codon assignment successfully evolved.

The paper then goes on to describe the incorporation of unnatural amino acids, but I'll let the discerning reader figure it out themselves :thumbup:

I also said I would illustrate how modifying the ribosome can change the genetic code. I will let Chin et al do the job.

The abstract follows...

The in vivo, genetically programmed incorporation of designer amino acids allows the properties of proteins to be tailored with molecular precision1. The Methanococcus jannaschii tyrosyl-transfer-RNA synthetase–tRNACUA (MjTyrRS–tRNACUA)2, 3 and the Methanosarcina barkeri pyrrolysyl-tRNA synthetase–tRNACUA (MbPylRS–tRNACUA)4, 5, 6 orthogonal pairs have been evolved to incorporate a range of unnatural amino acids in response to the amber codon in Escherichia coli 1, 6, 7. However, the potential of synthetic genetic code expansion is generally limited to the low efficiency incorporation of a single type of unnatural amino acid at a time, because every triplet codon in the universal genetic code is used in encoding the synthesis of the proteome. To encode efficiently many distinct unnatural amino acids into proteins we require blank codons and mutually orthogonal aminoacyl-tRNA synthetase–tRNA pairs that recognize unnatural amino acids and decode the new codons. Here we synthetically evolve an orthogonal ribosome8, 9 (ribo-Q1) that efficiently decodes a series of quadruplet codons and the amber codon, providing several blank codons on an orthogonal messenger RNA, which it specifically translates8. By creating mutually orthogonal aminoacyl-tRNA synthetase–tRNA pairs and combining them with ribo-Q1 we direct the incorporation of distinct unnatural amino acids in response to two of the new blank codons on the orthogonal mRNA. Using this code, we genetically direct the formation of a specific, redox-insensitive, nanoscale protein cross-link by the bio-orthogonal cycloaddition of encoded azide- and alkyne-containing amino acids10. Because the synthetase–tRNA pairs used have been evolved to incorporate numerous unnatural amino acids1, 6, 7, it will be possible to encode more than 200 unnatural amino acid combinations using this approach. As ribo-Q1 independently decodes a series of quadruplet codons, this work provides foundational technologies for the encoded synthesis and synthetic evolution of unnatural polymers in cells.

They developed new orthogonal ribosomes through mutations such that they read in fours instead of threes, firstly, and followed it up by adding two unnatural amino acids to the newly evolved quadruplet code using the new blank codons that were generated. They now have loads of codons to work with just by changing the nature of the code, and they are heralding a new era in synthetic biology where we can write stuff into the genome without affecting any of the native translation of the recipient cells.

The full paper is indeed available for this and I would encourage the discerning reader to read this, and the link is
http://ase.tufts.edu/chemistry/kumar/jc ... n_2010.pdf

Empirical demonstrations of the evolvability of the genetic code, without a mind directing said changes. Just mutation and selection. (the selection here was artificial because they were applying it with a specific purpose in mind, therefore they chose to determine which mutant genetic code would survive.

we have seen evidence that

[1] Mutating the peptidyltransferase subunit of ribosomes as in the work of Chin et al leads to codons being read in fours instead of threes.
[2] Mutant tRNAs incorporate different amino acids even when the same codon assignment is maintained, by virtue of mutability of the chemistry of the interactions of the binding of amino acids with tRNA and their synthetase enzymes.
[3] Mutant tRNAs can incorporate an amino acid in response to another codon assignment.

Varying the chemistry of interaction between the components of the translational machinery and the chemistry of the translational machinery itself explains the origins of the genetic code, thus exposing your manifest false and blatant assertion.

No magic required.

[my_wan]

Last quote first:

I was wondering how many here agree with Cobb

I agree, but you need to get the 10^40,000 rebuttal in the previous thread to understand why, along with the fact that deadly mutations don't die by *accident*.

over at why evolutionistrue.com I came across a rather surprising admission

http://whyevolutionistrue.wordpress.com ... -the-cell/

The keystone argument of Signature of the Cell is that chance, by itself, cannot account for the genetic information found in the genomes of organisms. I agree. And so does every evolutionary scientist, I presume. Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point?

Mathew Cobb

Correct, evolution cannot happen *just* by accident. The mutations that changes base code are *just* accidents, but the accidents that are deadly do not die by accident. It's no accident that a wolf without teeth starves to death. It's no accident that the brains that allows us to soften our food, or make new teeth, allows us to survive without teeth.

Take the nylon bug for instance, which is only 2% efficient at eating nylon, and can eat nothing else. I know of no other organism on Earth that can survive on only 2% efficiency, so why can the nylon bug? Because nylon didn't exist before 1935, and there's nothing else more efficient at eating nylon to compete with it. Just like the Weasel program has survivors that only have 2% of the Weasel sentence correct. As soon as some of the bugs gets more efficient, then the 2% efficient bugs will go extinct. Just like the Weasel program when something comes along that get more than 2% of the Weasel sentence correct.

If we hadn't found this bug before it reached say 40% efficient, many years from now, the anti-evolution crowd would claim that it must have started at 40% efficient, because that's all they see, making evolution impossible. Just like the 10^40,000 odds you quoted pretended that all 20 amino acid sequences was required from the start, along with the 2000 different amino acids commonly found in organisms today, were required for life. We don't see these simpler versions alive, because, like the nylon bug as soon as something more efficient comes along, they'll go extinct. The lack of much much simpler organism does not mean they never existed, but that as soon as some of them evolved better more complex ways to compete, they are driven to extinction.

We see this extinction effect over and over in real organism in the lab, and can track exactly which "simple" mutations lead to the extinction of the original culture in the petri dish. We also see it in artificial self replicators we have created in the lab. And even in sophisticated genetic algorithms that evolve more complex solution than just sentences. Neither are genetic algorithms limited to sentence or food sources we provide for it. They also learn to solve real life satellite orbits and such in ways people never thought of.

The random mutations are "accidents". Which ones live and which ones goes extinct is no accident. It is the result of efficiency and competition, just like the percentage of the Weasel sentence the Weasel program gets right determines which Weasels die. NS has exactly the same (none) information about the real world environment and the Weasel program has about the food sentence. The fact that Weasel can be solved in a few seconds, while evolution has taken 4.5 billion is just a matter of the complexity NS evolved to deal with.

he doesn't say it in the article but I'm pretty sure most scientists believe life arose due to some law, also known as necessity. But I thought many believe that life arose through a combination of chance and necessity.

Life did not arise due to some law. It was merely allowed to arise because there is no law of physics against it. There are many many trillions of times more types of life, both extinct and never existed, that physical laws would allow to exist but doesn't. We might want to remember that there is no law that requires us to exist either.

When odds are quoted for how unlikely species X was to happen by accident, it's should always be remembered that it didn't. The "accidental" mutations that survived was not an accident, but neither was it planned by the mutations. If it hadn't been that species, it would have been something else.

Think of it like throwing darts at a wall with a trillion red checkers squares on it. You throw a dart and hit a red square and say: Wow, there was a 1 in a trillion chance to hit that 1 red dot. But that doesn't mean anything, because if you hadn't hit that red dot you would have hit another one, and you would quote the same 1 in a trillion odds no matter which one you hit. That the game being played with the 10^40,000 odds quote against NS.

[FBM]

I was wondering how many here agree with Cobb

I agree with the main point of the linked article, viz that ID is BS. If you want us to agree with ID, just show us the Intelligent Designer. Can't? Then you've got nothing but ad hoc rationalizations from distorted and incomplete data, designed to wedge in a small space for your favorite imaginary supernatural sky-daddy. No matter how sincere you are in your beliefs, your approach to logical argumentation is disingenuous and unoriginal. Keep trying. Better yet, give up and accept the observable facts.

The linked article, for those who feel disinclined to click:

Francisco Ayala on “Signature in the Cell”
by Matthew Cobb

Jerry, on his way to the Galapagos, asked me to post this. Over at Biologos, “Science and the Sacred” has persuaded Francisco Ayala to write a review of Stephen C. Meyer’s Signature in the Cell. Here it is. There’s a debate going on over there, too.

How should a person of faith respond to Signature of the Cell? I am an evolutionary scientist who would suggest the following considerations.

The keystone argument of Signature of the Cell is that chance, by itself, cannot account for the genetic information found in the genomes of organisms. I agree. And so does every evolutionary scientist, I presume. Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point? It is as if in a book about New York, the author would tell us that New York is not in Europe, and then dedicate most of the book to advancing evidence that, indeed, truly, New York is not in Europe.

Signature of the Cell offers Intelligent Design (ID) as the alternative explanation to chance in order to account for genetic information. This suggestion turns out to be no more convincing than a proposal by the author of the book about New York, who having exhausted all possible ways of telling us that New York is not in Europe, would now offer Peoria as the alternative city to visit. We would rather read about New York’s architecture, splendid avenues, and great parks; about the rich culture and ethnic diversity of the city; about its restaurants, concert venues, theatres, and wonderful sights in and around the city. But regarding natural selection, genetics, ecology, development, physiology, and behavior in the evolution of genetic information, there is nothing substantive in Signature of the Cell.
Christians and other people of faith should be troubled about Signature of the Cell for several reasons. One is that Meyer avoids consideration of the negative implications of ID as an explanation of the origin of genetic information, which is his main subject. According to Meyer, ID provides a more satisfactory explanation of the human genome than evolution does. ID’s explanations envision “discrete or discontinuous intelligent activity in the history of life” (p. 481). Scientists have now obtained the complete DNA sequence of the human genome. The genome has a length of about three billion nucleotides, the “letters” of the DNA alphabet. Scientists have also obtained the complete DNA sequence of the chimpanzee genome—also three billion letters long—and of several hundred other species of organisms. How can we envision the “discrete or discontinuous activity” of the Intelligent Designer? The human and chimpanzee genomes differ from each other in just a few percent of the DNA letters, less than two percent in the genes that code for proteins. Did the Designer tweak the chimpanzee genome to make the human genome? Or, perhaps more likely, did the Designer use a preexisting genome and tweak it a bit to make the human genome and tweak it a different way to make the chimpanzee genome? Did the Designer go on tweaking genomes a bit at a time to design the genome of the gorilla and other primates, and more and more tweaking for other animals, all the way down to mice, and even to fruitflies, with which we share a good fraction of the genome?The human genome includes about twenty-five thousand genes and lots of other (mostly short) switch sequences, which turn on and off genes in different tissues and at different times and play other functional roles. There are also lots and lots of DNA sequences that are nonsensical. For example, there are about one million virtually identical Alu sequences that are each three-hundred letters (nucleotides) long and are spread throughout the human genome. Think about it: there are in the human genome about twenty-five thousand genes, but one million interspersed Alu sequences; forty times more Alu sequences than genes. It is as if the editor of Signature of the Cell would have inserted between every two pages of Meyer’s book, forty additional pages, each containing the same three hundred letters. Likely, Meyer would not think of his editor as being “intelligent.” Would a function ever be found for these one million nearly identical Alu sequences? It seems most unlikely. In fact, we know how these sequences come about: one new Alu sequence appears in the genome for every ten newborns, generation after generation. The Designer at work? Unlikely: many of these sequences damage the genome causing abortion of the fetus during the early weeks of life.

Perhaps one could attribute the obnoxious presence of the Alu sequences to degenerative biological processes that are not the result of ID. But was the Designer incompetent or malevolent in not avoiding the eventuality of this degeneration? Come to think of it: why is it that most species become extinct? More than two million species of organisms now live on Earth. But the fossil record shows that more than ninety-nine percent of all species that ever lived became extinct. That is more than one billion extinct species. How come? Is this dreadful waste an outcome intended by the Designer? Or is extinction an outcome of degeneration of genetic information and biological processes? If so, was the Designer not intelligent enough or benevolent enough to avoid the enormity of this waste? Meyer asserts that the theory of intelligent design has religious implications. “Those who believe in a transcendent God may, therefore, find support for their belief from the biological evidence that supports the theory of intelligent design” (p. 444). I do think that people of faith may find in the world many reasons that support their belief in God. But I don’t think that intelligent design is one of them. Quite the contrary. Indeed, there are good reasons to reject ID on religious grounds, in addition to scientific grounds. The biological information encased in the genome determines the traits that the developing organism will have, in humans as well as in other organisms. But humans are chock-full of design defects. We have a jaw that is not sufficiently large to accommodate all of our teeth, so that wisdom teeth have to be removed and other teeth straightened by an orthodontist. Our backbone is less than well designed for our bipedal gait, resulting in back pain and other problems in late life. The birth canal is too narrow for the head of the newborn to pass easily through it, so that millions of innocent babies—and their mothers—have died in childbirth throughout human history.

I could go on about human features that betray a design that certainly is not intelligent. I will add only one more consideration. More that twenty percent of all human pregnancies end in spontaneous abortion during the first two months of pregnancy. That is because the human genome, the human reproductive system, is so poorly designed. Do I want to attribute this egregiously defective design to God, to the omnipotent and benevolent God of the Christian faith? No, I don’t. It would not do to say that God designed intelligently the human genome and that it then decayed owing to natural processes. If God would have designed the human genome, surely He would have done it so that this enormous misfortune would not happen. Think of it: twenty percent of all human pregnancies amount to twenty million abortions every year. I shudder at the thought of this calamity being attributed to God’s specific design of the human genome. To me, this attribution would amount to blasphemy. Before the scientific revolution of the sixteenth and seventeenth centuries, earthquakes, volcanic eruptions, and the like were attributed to direct action by God, so that the tsunami that five years ago killed two hundred fifty thousand Sumatrans might have been interpreted as God’s punishment. Now we know that these catastrophes are the result of natural processes. Similarly, people of faith would do better to attribute the mishaps caused by defective genomes to the vagaries of natural selection and other processes of biological evolution, rather than to God’s design.

[Ronja]

Spinoza, how can you expect anyone to respect your arguments, if you misattribute material that you wish to use as supporting them?

If the OP is to reflect the sources and their opinions honestly, it should read something like this:

over at why evolutionistrue.com I came across a rather surprising admission a quoted piece by Francisco Ayala, originally from BioLogos http://biologos.org/blog/on-reading-the ... signature/

Mathew Cobb quoted it here: http://whyevolutionistrue.wordpress.com ... -the-cell/

The keystone argument of Signature of the Cell is that chance, by itself, cannot account for the genetic information found in the genomes of organisms. I agree. And so does every evolutionary scientist, I presume. Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point?

Mathew Cobb Francisco Ayala

he doesn't say it in the article but I'm pretty sure most scientists believe life arose due to some law, also known as necessity. But I thought many believe that life arose through a combination of chance and necessity.


I was wondering how many here agree with Cobb Ayala

The first paragraph in the whyevolutionistrue post made it very clear that this was not Cobb's text but something he quoted from elsewhere. Would you care to explain how you came to make such a fundamental mistake in attribution?


Edit: bolded the text I wrote, for clarity