Scientific proof of intelligent design? Prove me wrong, please

reply to post by Dispo


i know, i was just putting my thoughts on the table,

everything boils down to math, and math runs deeper than anyone can imagine in both disciples, to me it just seems apparent, since i cant drop a whole scientific processes on you, i dont expect you to believe me, but maybe you may consider what im saying and make your own conclusions. and not believe only the words written in a science book that has been created by man within the past 2000 years give or take.

to me anyone that is a hard core scientist should understand that science has only been around for a ridiculous short time compared to the time line(or loop) of the universe. we know nothing compared to what truly is.

reply to post by DocHolidaze


I appreciate that we know nothing, but the thing is I'd rather no nothing than assume the wrong thing - you cannot teach a man something he thinks he already knows.

If I walk in to every debate with my head empty except for what I've already proven, then I have no bias clouding my judgement.

All I'm saying is, don't believe anything unless you have undeniable, repeatable, concrete evidence. There might be a god, and he might have designed us, and maybe the genetic code is analogous to binary code, but don't just throw suppositions out there and say "well it might be true."

Be more open minded - and I'm not saying "believe what I believe" I'm saying "believe what you can prove."

Originally posted by windlass34
Gentlemen,
current state of Physics states the following:

"The second law of thermodynamics states that the entropy of an isolated system never decreases, because isolated systems spontaneously evolve towards thermodynamic equilibrium—the state of maximum entropy. Equivalently, perpetual motion machines of the second kind are impossible."

en.wikipedia.org...

in other words:

Entropy (state of "disorder") of a closed system always increases, never decreases.

How can we then account for the formation of increasingly complex molecules needed for life from the so-called "primordial soup"? All other planets in Solar system follow this rule - very simple set of chemicals in their atmospheres, rarely anything more complex than basic inorganic stuff. Pretty much all organic molecules are associated with life - created by bacteria or other live organisms.

Can anybody explain this to me, please?

Life has evolved on our planet at the expense of increased entropy in our solar system (more specifically, in the sun).

Originally posted by DocHolidaze
reply to post by windlass34

 

? i always thought the genetic code itself was proof of intellegent design.

To the contrary, the genetic code represents very strong evidence for evolution. I've made a thread about this. Feel free to continue there..

Originally posted by rhinoceros

Originally posted by DocHolidaze
reply to post by windlass34

 

? i always thought the genetic code itself was proof of intellegent design.

To the contrary, the genetic code represents very strong evidence for evolution. I've made a thread about this. Feel free to continue there..

edit on 21-1-2013 by rhinoceros because: (no reason given)

"Evidence" is not proof. Evidence can support different theories. For mathematical evidence that the codon pattern underlying DNA is determined by the sacred geometry of the Tree of Life, the geometrical representation of Adam Kadmon, or Heavenly Man, and in other sacred geometries of various religions, see:
smphillips.8m.com...

reply to post by micpsi


Your link doesn't work.

Evidence are facts that lead to a picture of the whole truth. His point is that evolution has more evidence for it than the 2000 year old word of uneducated sheep herders.

Originally posted by micpsi

Originally posted by rhinoceros

Originally posted by DocHolidaze
reply to post by windlass34

 

? i always thought the genetic code itself was proof of intellegent design.

To the contrary, the genetic code represents very strong evidence for evolution. I've made a thread about this. Feel free to continue there..

edit on 21-1-2013 by rhinoceros because: (no reason given)

"Evidence" is not proof. Evidence can support different theories. For mathematical evidence that the codon pattern underlying DNA is determined by the sacred geometry of the Tree of Life, the geometrical representation of Adam Kadmon, or Heavenly Man, and in other sacred geometries of various religions, see:
smphillips.8m.com...

The article you linked looks like total nonsense to me. In your own words, what do you mean when you say 'the codon pattern underlying DNA'? Also, in my thread about the genetic code, I explain in quite simple terms how the distribution of amino acids and codons in the translation table implies that the genetic code changed over time. If you have a problem with that, go debunk it there. In no way do 'my' observations support your link's new age nonsense.

Main point:

1. Abiotic amino acids (those that exist without biological pathways) are overrepresented in the translation table.
2. Biotic amino acids are underrepresented in the translation table.

If you want to argue for design, then you ought to come out with an explanation why e.g. 6 codons (codon block and a half) encode the abiotic amino acid leucine, but only 1 codon encodes the biotic amino acid methionine. From natural evolution perspective, such observations make a lot of sense..

Originally posted by rhinoceros
If you want to argue for design, then you ought to come out with an explanation why e.g. 6 codons (codon block and a half) encode the abiotic amino acid leucine, but only 1 codon encodes the biotic amino acid methionine.

Funny you should ask, here you go. It's called degeneracy and it is quite elegantly exploited.

In the context of making and analyzing codes, the term "degeneracy" refers to having excess codes that produce the same message. A non-degenerate code, like Morse code, is one for one: each code is unique, producing one and only one output. The genetic code, by contrast, is many-to-one in some cases. For instance, six different codons can produce the amino acid leucine. This would be like having six combinations of dots and dashes to produce the letter A in a "degenerate" version of Morse code. Other amino acids can be coded by 4, 3 or 2 codons, while two (methionine and tryptophan) each have only one unique code. Why is this?

www.pnas.org...
www.evolutionnews.org...

Feedback, regulation, robustness, adaptability. Does this make it look less designed? No it's actually is a good example of another way the code can carry extra information.

BTW There is no way known to create a code without intelligence involved. None. You are forced to believe on faith that the four fundamental forces can create language. Good luck with that.

I recommend you read about all 3 laws of thermodynamics. They don't mean nearly what you think they do. How can you say that the law proves ID while providing zero evidence whatsoever? I don't need to prove you wrong, when you can't even prove yourself right. Stop pigeon holing science into your narrow view of reality and only believing the parts of it that are convenient for your world view. The big picture is much different.

Originally posted by squiz

Originally posted by rhinoceros
If you want to argue for design, then you ought to come out with an explanation why e.g. 6 codons (codon block and a half) encode the abiotic amino acid leucine, but only 1 codon encodes the biotic amino acid methionine.

Funny you should ask, here you go. It's called degeneracy and it is quite elegantly exploited.

In the context of making and analyzing codes, the term "degeneracy" refers to having excess codes that produce the same message. A non-degenerate code, like Morse code, is one for one: each code is unique, producing one and only one output. The genetic code, by contrast, is many-to-one in some cases. For instance, six different codons can produce the amino acid leucine. This would be like having six combinations of dots and dashes to produce the letter A in a "degenerate" version of Morse code. Other amino acids can be coded by 4, 3 or 2 codons, while two (methionine and tryptophan) each have only one unique code. Why is this?

www.pnas.org...
www.evolutionnews.org...

Feedback, regulation, robustness, adaptability. Does this make it look less designed? No it's actually is a good example of another way the code can carry extra information.

BTW There is no way known to create a code without intelligence involved. None. You are forced to believe on faith that the four fundamental forces can create language. Good luck with that.

But you failed to explain why it is (FROM DESIGN PERSPECTIVE) that in three cases six codons encode an abiotic amino acid and in no case a biotic amino acid. FROM EVOLUTION PERSPECTIVE this observation makes sense. BTW it's a translation table, not a code (like a computer code). It's not a language either.

Originally posted by rhinoceros
But you failed to explain why it is (FROM DESIGN PERSPECTIVE) that in three cases six codons encode an abiotic amino acid and in no case a biotic amino acid. FROM EVOLUTION PERSPECTIVE this observation makes sense. BTW it's a translation table, not a code (like a computer code). It's not a language either.

What??? I let the empirical science explain it.

Our study suggests that organisms can exploit degeneracy lifting as a general strategy to adapt protein synthesis to their environment.

Sorry, it makes excellent design sense. It only adds to the design argument. A marvel of molecular logic that would make any engineer drool.
www.evolutionnews.org...

But this arrangement is far from arbitrary. Indeed, the genetic code found in nature is exquisitely tuned to protect the cell from the detrimental effects of substitution mutations. The system is so brilliantly set up that codons differing by only a single base either specify the same amino acid, or an amino acid that is a member of a related chemical group. In other words, the structure of the genetic code is set up to mitigate the effects of errors that might be incorporated during translation (which can occur when a codon is translated by an almost-complementary anti-codon).

For example, the amino acid leucine is specified by six codons. One of them is CUU. Substitution mutations in the 3' position which change a U to a C, A or G result in the alteration of the codons to ones which also specify leucine: CUC, CUA and CUG respectively. On the other hand, if the C in the 5' position is substituted for a U, the codon UUU results. This codon specifies phenylalanine, an amino acid which exhibits similar physical and chemical properties to leucine. The fact in need of explaining is thus that codon assignments are ordered in such a way as to minimize ORF degradation. In addition, most codons specify amino acids that possess simple side chains. This decreases the propensity of mutations to produce codons encoding amino acid sequences which are chemically disruptive.

How many reasons would you like? As above the fact in need of expaining is that they are ordered to minimise error. I find your observation weak and void of evidence as well as lacking explanation of how this random ratio of codons to aa's actually create a high fidelity error protection system?

You asked for a design reason and I gave you one, complete with empirical evidence. I have now given you another. And there are many more indications laid out in the above articles references. Let me ask again, does this amazing advantagous feature make it appear less designed?

On the contrary from an evolution perspective, there is nothing obvious at all. The code and it's development is considered one of the greatest mysteries in all of biology. Personally I have no problem with an evolving code, I have no problem with evolution. Neo darwinism does not have a monopoly on the word evolution.

www.ncbi.nlm.nih.gov...

Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.

A translation table/system is a code. With all the hallmarks of language. Can you explain the difference? Your just playing semantics (pun). Here we go again denying that a code is a code. It is most definately a semantic system, acknowledged as such for decades.

What material force dictates the relationship of codon to amino acid?

Let me rephrase my earlier question? Can the four fundamental forces create a digital system of communication transfer? A code? a sytem of defined symbols representing something else? A semantic system that conforms to shannons communication model?






There is no known way to create semiosis or a code or a coherant translation table/system without intelligence. NONE. You are forced to believe that four material forces can create semiosis. Good luck with that.

reply to post by squiz


A degenerate code allows for protection against mutation. An organism is always mutating, therefore any organism which was more resistant to mutation would have a selection advantage compared to organisms who don't.

Originally posted by Dispo
reply to post by squiz

 

A degenerate code allows for protection against mutation. An organism is always mutating, therefore any organism which was more resistant to mutation would have a selection advantage compared to organisms who don't.

Agreed, but you are missing the point. Organisms mutate because there is a code in place, code is the means of transfering the information but is not the information content itself (genetic information). Mutating a code however will change associations and functional meaning already present. It's not the same thing. From my link above.

Furthermore, the question is naturally raised as to what selective-utility would be exhibited by the new amino acids. Indeed, they would have no utility until incorporated into proteins. But that won't happen until they are incorporated into the genetic code. And thus they must be synthesized by enzymes that lack them. And let us not forget the necessity for the dedicated tRNAs and activating enzymes which are needed for including them in the code.

Functions must first exists for functions to be selected. Selection is not a creative process.

Sorry for getting off topic OP. Here is something to chew on in regards to your topic.
journals.witpress.com...

It has often been asserted that the logical entropy of a non-isolated system could reduce, and thereby new information could occur at the expense of increasing entropy elsewhere, and without the involvement of intelligence. In this paper, we have sought to refute this claim on the basis that this is not a sufficient condition to achieve a rise in local order. One always needs a machine in place to make use of an influx of new energy and a new machine inevitably involves the systematic raising of free energies for such machines to work. Intelligence is a pre-requisite.

Also this,



There has been a long running debate over this rgarding what is quantifiable and what is not, it's very interesting. The bottom line is it doesn't matter, we naturaly can see that something is wrong.

Nothing more to say.

Entropy is a long term process, and as such is the essence of change. Entropy says that all organized behavior will eventually unravel over extreme periods of time. Entropy itself allows for shorter term conditions that actually are responsible for organized behavior.

A good example is a star. They start out with the simplest of elements, hydrogen and helium. The material, through gravity, accumulates to the point of nuclear fusion and the star ignites, and remains in a 'sustainable' state for millions upon billions of years. However, as the hydrogen and helium fuel is consumed, the star begins to manufacture heavier elements, which sink to it;s core and it eventually starts to contract due to the gravitational influence of heavier materials. This is the "Entropy" of the star's organization. One day, there is a supernova, and the star emits most of its materials in a giant explosion. Those elements that it emits range from hydrogen, to iron, lead, gold, uranium, platinum... the entire elemental table, all manufactured by the star during it's "entropy".

But look at what is produced.. Heavy elements of much higher organization that can combine in countless molecules that of course, are the complex molecules needed to create life itself..... All of these creations in turn having their own "Entropy" that will destroy them in the recreation of something new. The concept of Entropy rules the way everything works.

Extremely long term entropy states that even the atomic structure will change. Isotopes will evolve into extremely unstable forms, electrons will fly away with no relationship to quanta, and the protons in the center of atoms will eventually become singularities, with no dimension...... Then, I guess... we are dead. But, then again, what is a universe where nothing exists to experience and observe it?

reply to post by squiz

You are still missing the point. Please try to understand the question before answering. Why so much degeneracy in the case of abiotic amino acids and little to no degeneracy in the case of biotic amino acids?

The more biological a science becomes, the less mathematics and physics can describe accurately. I say this as a holder of a Masters in Biochem and PhD in Organic Synthesis. Oh and 10 years in the Pharma industry..

Originally posted by windlass34
Gentlemen,
current state of Physics states the following:

"The second law of thermodynamics states that the entropy of an isolated system never decreases, because isolated systems spontaneously evolve towards thermodynamic equilibrium—the state of maximum entropy. Equivalently, perpetual motion machines of the second kind are impossible."

en.wikipedia.org...

in other words:

Entropy (state of "disorder") of a closed system always increases, never decreases.

How can we then account for the formation of increasingly complex molecules needed for life from the so-called "primordial soup"? All other planets in Solar system follow this rule - very simple set of chemicals in their atmospheres, rarely anything more complex than basic inorganic stuff. Pretty much all organic molecules are associated with life - created by bacteria or other live organisms.

Can anybody explain this to me, please?

Originally posted by rhinoceros
reply to post by squiz

 

You are still missing the point. Please try to understand the question before answering. Why so much degeneracy in the case of abiotic amino acids and little to no degeneracy in the case of biotic amino acids?

And that's all you have to say? What about my questions? in particular...

Furthermore, the question is naturally raised as to what selective-utility would be exhibited by the new amino acids. Indeed, they would have no utility until incorporated into proteins. But that won't happen until they are incorporated into the genetic code. And thus they must be synthesized by enzymes that lack them. And let us not forget the necessity for the dedicated tRNAs and activating enzymes which are needed for including them in the code.

Answers?

No, I understand what you are saying, you think it evolved from some speculative prebiotic code. Yes it could indicate that, granted. A prebiotic code is still a code. Despite the very difficult problems with that I've already highlighted that you leave unanswered, and there are many more, conceptually I have no problem at all with that. It is irrelevant to my particular design inference and doesn't put a dent in the design argument one bit. It's a mute point on the whole.

As to why the bias, based on the studies I've linked I'd guess it has to do with the bio mechanical properties of the prebiotic AA's as well as availability of raw materials, If you read some of the links further you'd see even the prebiotics seem to be selected for error protection. Evolved or not. Whatever the reason for the particular bias the facts stand the state of degeneracy combines for an exquisite piece of engineering logic.

Does built in error protection and adaptability make it appear less designed?

Can the four fundamental force create a state of semiosis, a system of digital communication?

Of course we don't answer that, intuitively it leads to an uncomfortable place for some.

Originally posted by squiz
What about my questions? in particular...

Furthermore, the question is naturally raised as to what selective-utility would be exhibited by the new amino acids. Indeed, they would have no utility until incorporated into proteins. But that won't happen until they are incorporated into the genetic code. And thus they must be synthesized by enzymes that lack them. And let us not forget the necessity for the dedicated tRNAs and activating enzymes which are needed for including them in the code.

Answers?

Many biotic amino acids are actually by-products of other pathways. So, from evolving code point of view, they were waste products until an advantageous mutation occurred. Such mutation could be e.g. a slightly changed aminoacyl tRNA synthetase, which would effectively capture the codon (and the tRNA) from one amino acid to another, i.e. it would load the unchanged tRNA with the 'new' amino acid..

www.evolutionnews.org...reply to post by rhinoceros


Yes well I Posted a link with dozens of those sort of speculations. There is no shortage of these sorts of guesses, and that's all they are.

Your scenario would result in frameshifting errors more than likely and chaos for the cell, you have to stumble along until you find function without disrupting a change in codon that would change every protein. You also seem to confuse code evolution with regular evolution through code. A mutation as far as a code is concerned may lead to a change in every single protein. Not good.

It stands to reason that before the error correction was in place, the cell would not last long enough to to sample and stumble upon the level of optimization required.

Also you have not in any way accounted for the limitations of protein function with a limited set of AA's. Especially the implimenting enzymes, you have to believe that the enzymes had the specificity to for reliable implimentation of the code. This is what you are assuming without evidence.

You also have to account for the protein parts of the ribosome using even just a narrow selection of AA's. Even if you have 15 or 16 you are going to have a hard time explaining it.

It also stands to reason that if the code went through a selective search as you describe there should be many more variations of the code today. But what we have is a code that is not evolving and with only a few minor variations.

On top of all this much like how even a single simple protein has odds in the order of 10^75 by chance. Well outside of the reach of reason for neodarwinism. The leviathon paradox has been extended to the entire cell. The point being the more components you have the more greater the functional search space becomes. In other words there are vastly more ways of being dead than being alive.

www.evolutionnews.org...

The same is true of the code.

Hubert Yockey, a biophysicist and information theorist, has argued that the number of potential genetic codes is of the order of 1.40 x 10^70. Yockey concedes the extremely conservative figure of 6.3 x 10^15 seconds for the time available for the genetic code to evolve. Note that this assumes that the genetic code has been evolving since the Big Bang. So, how many codes per second would be required to be evaluated in order for natural selection to "stumble upon" the universal genetic code found in nature? The math works out to roughly 10^55 codes per second.

Think about that. Even granting such absurd estimates -- all the time available since the Big Bang -- natural selection would be required to evaluate 10^55 genetic codes per second in order to have a reasonable chance of stumbling across the optimized genetic code found in nature.

No problem evolution dun it!

Your already beginning with a functional code, so it says nothing about the emergence of code or specified information. Interesting but irrelevant to my argument. It's also not the subject of the thread.

Originally posted by squiz
Your scenario would result in frameshifting errors more than likely and chaos for the cell, you have to stumble along until you find function without disrupting a change in codon that would change every protein. You also seem to confuse code evolution with regular evolution through code. A mutation as far as a code is concerned may lead to a change in every single protein. Not good.

Why would it lead to frameshifts? There'd still be a tRNA with a specific anticodon to recognize the codon in the mRNA. The only difference would be that instead of amino acid A, amino acid B would be incorporated into the polypeptide. Yes, proteins would change, but on the other hand not all amino acids of proteins are that important. It's specific domains that matter, and even then you can usually substitute amino acids with others, e.g. a hydrophobic amino acid with another hydrophobic amino acid in a transmembrane domain. Further still, there are examples of genomes in which this exact thing has happened. And finally, we're talking very early stages of evolution, perhaps even pre-DNA era, so it's not like the protein repertoires were very big back then.

Originally posted by squiz
Also you have not in any way accounted for the limitations of protein function with a limited set of AA's. Especially the implimenting enzymes, you have to believe that the enzymes had the specificity to for reliable implimentation of the code. This is what you are assuming without evidence.

Pre-biotic amino acids are: Ala, Asp, Glu, Gly, Ile, Leu, Pro, Ser, Thr and Val. How is this set limited?

Originally posted by squiz
You also have to account for the protein parts of the ribosome using even just a narrow selection of AA's. Even if you have 15 or 16 you are going to have a hard time explaining it.

The protein part of ribosomes is a "new" thing. Primordial ribosomes were in all likelihood pure rRNA. Even today, all the core functions of ribosomes are carried out by the 2-3 rRNAs.

Originally posted by squiz
It also stands to reason that if the code went through a selective search as you describe there should be many more variations of the code today. But what we have is a code that is not evolving and with only a few minor variations.

No. You see, all life on Earth descends from a lineage in which this particular code was "set in stone". None-the-less, unlike you claim, numerous alterations have been uncovered.