Whenever the inference of intelligent design is brought up on this wonderful forum for debate, the usual answer is "there is no evidence for design and your invisible magic man!" I don't take this argument seriously because it is an emotional one, born out of ignorance and personal incredulity. All I will say is look no further than the universal genetic code which is the foundation of life itself. Without it, no cellular organism could even begin to produce the proteins and enzymes that are necessary for its survival. it is essentially a map, as shown in the table below, that assigns trinucleotide "codons" to 20 amino acids and a STOP site. The enzymes that decode the mRNA transcript will identify each codon with its corresponding amino acid and so allow protein translation to take place. These amino acids constitute a chemical "alphabet" out of which peptide sequences are built.



Naturalists have tried to speculate on how this code could have come about purely through the laws of physics and chemistry but have so far failed. But let us avoid any unnecessary speculation and try and determine one thing: is there a strong inference for its purposeful and intelligent design or not? Is it an optimal code or really quite arbitrary in nature?

The genetic code is called redundant or degenerate because there are 4^3 =64 codons for 21 amino acids and a stop site that marks the end of translation. This is an inevitable consequence of having a code with triplets and 4 bases . As such, changing the third base pair of a codon need not result in a change in the amino acid: A good thing for many of us.

As there are 64 codons representing 21 sites, it so happens that there are 1.51 * 10^84 theoretical general codes! But only one exists - it t is universal, albeit with some variation, which indicates it has been around since the time life first began.

Here are some reasons to suppose that the code is optimal and thus the best out of all possible codes:

1) It is a digital and quaternary code. The most widely used digital code we use is binary because we communicate data electronically and there are only two voltage levels (high and low). The genetic code just used 4 symbols (A.C,G,T) instead of 2 binary digits (0,1) to represent information. This is also more efficient as it means less physical space is necessary.

2) The frequency of codons to amino acids accurately reflects the frequency of amino acids in protein sequence with the exception of arginine which is a special case that I won't go into detail here (but note that arginine is over-represented in many important motifs such as the homeobox).

2) It is fault-tolerant. This is partly derived from the fact that most of the 64 codons are synonymous, as explained above, but also due to the fact that a single base pair changes in the 1st and 2nd letters often result in chemically similar amino acids. For example, CTT (leucine) becomes isoleucine when the "C" is substituted for "A". The code therefore dictates the "appropriate distance" between amino acids.

3) It facilitates adaptation. This is because many alkalines and acids are clustered together in the table. Often, a change in the pH level is needed in response to an environmental stimulus. Thus, going from the alkaline lysine (AAA/AAG) to glutamic acid (GAA/GAG) requires only one substitution.

4) It is extremely elegant in that each amino acid is represented by the first two base pairs: the third letter can often be changed but this won't change the amino acid residue.

5) It fully accounts for the transition-transversion bias. Due to molecular mechanisms, the former are twice as likely to occur as the latter. The code recognizes this by ensuring that transitions in the third base pair, but also in the first two, end up with not radically different residues.

6) Just as in asynchronous serial communication, where you have start and stop bits bounding the data frame, so the genetic code incorporates start and stop sites that demarcate the open reading frame (the translated sequence).

Therefore, it is clear that the genetic represents a unique design. So when you look at a table of the genetic code, you are actually staring into the super-intelligent mind of your Creator. It is a religious experience born out of scientific reality.

Just for a minute there I thought you were being serious.

ianryan1 wrote:Just for a minute there I thought you were being serious.

I'd like to see what Cali has to say about this - other than the usual nonsense he normally spouts like "we're still working on finding a solution" that involve no more than chemical bonding.

Atheistoclast wrote:

ianryan1 wrote:Just for a minute there I thought you were being serious.

I'd like to see what Cali has to say about this - other than the usual nonsense he normally spouts like "we're still working on finding a solution" that involve no more than chemical bonding.

Did you post your idea here because you think it's definitive proof, or because you legitimately want to have a discussion about this? Because based on that comment, it seems like you won't take "We're not sure" as an answer, which isn't a good way to enter into a conversation.

matt8819 wrote:

Atheistoclast wrote:

ianryan1 wrote:Just for a minute there I thought you were being serious.

I'd like to see what Cali has to say about this - other than the usual nonsense he normally spouts like "we're still working on finding a solution" that involve no more than chemical bonding.

Did you post your idea here because you think it's definitive proof, or because you legitimately want to have a discussion about this? Because based on that comment, it seems like you won't take "We're not sure" as an answer, which isn't a good way to enter into a conversation.

1) The genetic code is as close to a "proof" of design in life as you will ever find or could possibly hope to find.

2) I would like to know how atheists and naturalists respond to fact of the optimality of the one and universal genetic code. Do they think there was some "simple and sub-optimal precursor" to the present code and what mechanism do they suppose was involved in its evolution?

Atheistoclast wrote:Therefore, it is clear that the genetic represents a unique design. So when you look at a table of the genetic code, you are actually staring into the super-intelligent mind of your Creator. It is a religious experience born out of scientific reality.

And how does looking at the genetic code give rise to:

QED God Did it.

I most certainly do not find it a religious experience. And as to the statement that the comment about there is no sign that god did it is "an emotional one, born out of ignorance and personal incredulity" fatuous. It is yourself who is being credulous and a paucity of imagination in that you have to resort to an outside agency to explain life.

Atheistoclast wrote:

matt8819 wrote:

Atheistoclast wrote:

I'd like to see what Cali has to say about this - other than the usual nonsense he normally spouts like "we're still working on finding a solution" that involve no more than chemical bonding.

Did you post your idea here because you think it's definitive proof, or because you legitimately want to have a discussion about this? Because based on that comment, it seems like you won't take "We're not sure" as an answer, which isn't a good way to enter into a conversation.

1) The genetic code is as close to a "proof" of design in life as you will ever find or could possibly hope to find.

2) I would like to know how atheists and naturalists respond to fact of the optimality of the one and universal genetic code. Do they think there was some "simple and sub-optimal precursor" to the present code and what mechanism do they suppose was involved in its evolution?

I know nothing of genetics, but I do know a sketchy argument when I hear one. How does something being possibly proof of design make it actual proof for design? I would think that the fact that only that one thing supports your argument means your argument is built on a coincidence, more than actual proof.

Does the designer work inside this universe or outside it, say, in a metaphysical manner? Can we find some proof of the method used?

Atheistoclast wrote:Whenever the inference of intelligent design is brought up on this wonderful forum for debate, the usual answer is "there is no evidence for design and your invisible magic man!" I don't take this argument seriously because it is an emotional one, born out of ignorance and personal incredulity. All I will say is look no further than the universal genetic code which is the foundation of life itself. Without it, no cellular organism could even begin to produce the proteins and enzymes that are necessary for its survival. it is essentially a map, as shown in the table below, that assigns trinucleotide "codons" to 20 amino acids and a STOP site. The enzymes that decode the mRNA transcript will identify each codon with its corresponding amino acid and so allow protein translation to take place. These amino acids constitute a chemical "alphabet" out of which peptide sequences are built.



Naturalists have tried to speculate on how this code could have come about purely through the laws of physics and chemistry but have so far failed. But let us avoid any unnecessary speculation and try and determine one thing: is there a strong inference for its purposeful and intelligent design or not? Is it an optimal code or really quite arbitrary in nature?

The genetic code is called redundant or degenerate because there are 4^3 =64 codons for 21 amino acids and a stop site that marks the end of translation. This is an inevitable consequence of having a code with triplets and 4 bases . As such, changing the third base pair of a codon need not result in a change in the amino acid: A good thing for many of us.

As there are 64 codons representing 21 sites, it so happens that there are 1.51 * 10^84 theoretical general codes! But only one exists - it t is universal, albeit with some variation, which indicates it has been around since the time life first began.

Here are some reasons to suppose that the code is optimal and thus the best out of all possible codes:

1) It is a digital and quaternary code. The most widely used digital code we use is binary because we communicate data electronically and there are only two voltage levels (high and low). The genetic code just used 4 symbols (A.C,G,T) instead of 2 binary digits (0,1) to represent information. This is also more efficient as it means less physical space is necessary.

2) The frequency of codons to amino acids accurately reflects the frequency of amino acids in protein sequence with the exception of arginine which is a special case that I won't go into detail here (but note that arginine is over-represented in many important motifs such as the homeobox).

2) It is fault-tolerant. This is partly derived from the fact that most of the 64 codons are synonymous, as explained above, but also due to the fact that a single base pair changes in the 1st and 2nd letters often result in chemically similar amino acids. For example, CTT (leucine) becomes isoleucine when the "C" is substituted for "A". The code therefore dictates the "appropriate distance" between amino acids.

3) It facilitates adaptation. This is because many alkalines and acids are clustered together in the table. Often, a change in the pH level is needed in response to an environmental stimulus. Thus, going from the alkaline lysine (AAA/AAG) to glutamic acid (GAA/GAG) requires only one substitution.

4) It is extremely elegant in that each amino acid is represented by the first two base pairs: the third letter can often be changed but this won't change the amino acid residue.

5) It fully accounts for the transition-transversion bias. Due to molecular mechanisms, the former are twice as likely to occur as the latter. The code recognizes this by ensuring that transitions in the third base pair, but also in the first two, end up with not radically different residues.

6) Just as in asynchronous serial communication, where you have start and stop bits bounding the data frame, so the genetic code incorporates start and stop sites that demarcate the open reading frame (the translated sequence).

Therefore, it is clear that the genetic represents a unique design. So when you look at a table of the genetic code, you are actually staring into the super-intelligent mind of your Creator. It is a religious experience born out of scientific reality.

That's another interesting argument Joe. The million dollar question here, is how it was intelligently designed. Any ideas?

I reckon the intelligent designer manipulates molecules in a metaphysical or inter-dimensional (that is, controlled from dimensions unknown to us) manner so as to offer the impression they are intelligent. It could very well be a masterful, mystical, metaphysical (or inter-dimensional) puppet show.

LucidFlight wrote:Does the designer work inside this universe or outside it, say, in a metaphysical manner? Can we find some proof of the method used?

We don't know, and nor will we ever know because the code was formed billions of years ago. We can speculate as to its origins and how it may have come into being, but science has to be based on some measure of demonstrability. As I said in the post, I am not so much interested in the case of the sudden creation or gradual evolution of the code, but rather on the fact that it is the clearest inference and evidence for design in life that we have. When I look at the code, and see how perfectly the arrangement of codons to amino acids has been mapped, I can't help but marvel at the intelligence and precision behind this. I think anyone else should also feel as sense of wonder.

Gary S. Gaulin wrote:

That's another interesting argument Joe. The million dollar question here, is how it was intelligently designed. Any ideas?

Well, for that you need to understand the translational machinery involved: transfer RNAs, anticodon-binding domains, ribosomes and so on. It is there that the "code" is to be found. There are lots of ideas but little in the way of empirical evidence.

LucidFlight wrote:Does the designer work inside this universe or outside it, say, in a metaphysical manner? Can we find some proof of the method used?

Any designer would have to work within the natural universe. That much is clear: whether space aliens or divine gods, the creator of the code needed to be operating within space and time, though not necessarily part of the continuum (immanent not transcendent).

Atheistoclast wrote:

LucidFlight wrote:Does the designer work inside this universe or outside it, say, in a metaphysical manner? Can we find some proof of the method used?

We don't know, and nor will we ever know because the code was formed billions of years ago. We can speculate as to its origins and how it may have come into being, but science has to be based on some measure of demonstrability. As I said in the post, I am not so much interested in the case of the sudden creation or gradual evolution of the code, but rather on the fact that it is the clearest inference and evidence for design in life that we have. When I look at the code, and see how perfectly the arrangement of codons to amino acids has been mapped, I can't help but marvel at the intelligence and precision behind this. I think anyone else should also feel as sense of wonder.

So the proof is... That you find it impressive?

*cups hand to ear*
What's that tiny flapping sound?



*backs away slowly*

Atheistoclast wrote:

Gary S. Gaulin wrote:

That's another interesting argument Joe. The million dollar question here, is how it was intelligently designed. Any ideas?

Well, for that you need to understand the translational machinery involved: transfer RNAs, anticodon-binding domains, ribosomes and so on. It is there that the "code" is to be found. There are lots of ideas but little in the way of empirical evidence.

I agree. Especially need to better understand molecular intelligence. But with so many in denial that such a thing even exists I doubt we'll see much progress in that area. But maybe we will get lucky and the next generation of scientists will realize its potential then break away from usual crowd, to pioneer the new field.

And I have been meaning to mention that I found your paper on self-organization interesting. It parallels what I have been noticing, where in the life of the average living thing (unless one goes overboard with the term) natural selection has little or no influence. Even in lab evolution experiments the population easily perishes so it's a slow gentle coaxing of the already existing adaptation mechanisms to try a new trick. And if the molecular intelligence cannot find a solution to the problem the researchers give it, then that's the end of their experiment.

Do you think they share an imaginary friend? Or do they each have their own?

I think if we can somehow link the perfection of the designer's work (biological engineering?), intelligent molecules, and chromosome 2 fusion together into a cohesive theory, we'll have a watertight case for ID. Hasta la vista evolutionists!

Perhaps Gary can provide a circuit diagram for this revolutionary theory.