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UB Strikes Again!

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UB takes down the “life is only fancy chemistry” shibboleth:

AVS:

The transcription and translation processes are entirely based on chemistry.  Can you explain why functional sequence specific DNA cannot be reduced to chemistry?

UB:

Because there is a chemical discontinuity between the nucleic medium and the amino acid effect that must be preserved in order for translation to be obtained.

AVS:

And what is this chemical discontinuity exactly, Upright?

UB:

There is nothing you can do to the nucleic pattern GCA to relate it to Alanine, except translate it. Which is what the cell does.

AVS:

It’s related by another nucleic pattern, bound to alanine, that has a specific sequence that associates with that GCA.

UB:

The base pairing that enables transcription between nucleotides does not establish a relationship to alanine. That relationship is established by the protein aaRS before the transfer RNA ever enters the ribosome.

UB:

AVS, is there an inexorable chemical relationship between pattern GCA and alanine, or is it a contingent relationship? [UD Editors: Instead of “contingent” one might say “arbitrary”]

AVS:

But there is a relationship. You just explained it. The amino acid is associated with the aaRS, which associates with tRNA, which associates with mRNA. This relationship is the product of the evolution of these molecules.

UB:

Correct. The relationship is established in spatial and temporal isolation by the protein aaRS.

So, there is a physical discontinuity between the nucleic pattern and the amino acid, which is contingent on the structure of the protein aaRS. Therefore, there is nothing about the pattern that determines the amino acid, and consequently, chemistry cannot explain the association. It can only explain the operation of the system with the association in place.

AVS:

The association of the tRNA with aaRS determines the amino acid as I said. The chemical evolution that occurred would explain the why these molecules associate in our cells now, an ultimately arbitrary decision, driven by chemical interactions that occurred in early cells.

UB:

The cells decided huh? cool

AVS, there is a chemical discontinuity between the nucleic medium and the amino acid effect, and that discontinuity must be preserved in order for translation to be obtained.

Do you know why?

(…think about it)

AVS:

That chemical discontinuity between nucleotide and protein is bridged by more chemical interactions though, UB, which as I said are the product of evolution. Yes the cells “decided” for lack of a better word. This is one of the problems with you guys, scientists try to put things in the simplest terms an you completely blow these terms out of proportion.

UB:

I’m glad you now recognize the discontinuity.

My question is: Do you know why it’s there, and why the system must preserve it during translation?

(hint: it’s not evolution)

AVS:

It is evolution UB. Early organisms evolved this translating system to carry out more diverse functions with better efficiency. The system we see today is the result of the chemical evolution that occurred in these early organisms and has been conserved to this day.

UB:

This is not an answer to the question. Do you know why it’s there, and why the system must preserve it during translation? There is an identifiable reason. What is it?

AVS:

UB, there obviously needs to be a connection to nucleotide and amino acid that is conserved. The system we have been talking about does this and it does this based on chemical interactions. And the evolution of this system was based on chemical interactions. That’s it. Make your point already.

UB:

AVS,

I was giving you the benefit of the doubt, hoping you could think for yourself. Why would a physical discontinuity be required in a chemo/mechanical system in order to get a particular amino acid presented at the peptide binding site? Why would such a system need to preserve that discontinuity in order to produce the effect?

The physical effect of having a particular amino acid presented at a binding site at a particular point in time is not something that can be derived from physical law – it’s not some innate property to be drawn from, or activated in, the atomic composition of matter. So a discontinuity will naturally exist in any system that produces such an effect. That discontinuity is required in order to allow the input of formal constraint (information) into the system, where it can produce an effect that operates under physical law, but is not determined by it. In other words, it’s an operational necessity to achieve the result.

And the system must preserve that discontinuity for much the same reason. From a purely mechanical standpoint, if the effect were derivable directly from the physical properties of the medium, then it would be so by the forces of inexorable law, and those inexorable forces would limit the system to what can be physically derived from that medium, thus making the input of form (not derived from that medium) impossible to achieve.

However, incorporating the discontinuity by preserving it allows the effect to be determined by a second arrangement of matter operating in the system. This second arrangement establishes a local relationship between the medium and its effect (bridging the discontinuity while preserving it). This relationship then becomes an identifiable regularity of the system, allowing the system the capacity to produce lawful effects not determined by physical law.

UB:

…by the way.

This entire arrangement is a necessary precondition of the genotype-phenotype distinction. It must be in place prior to the onset of Darwinian evolution. To say this system is the product of Darwinian avolution, is to say that a thing that does not yet exist on a pre-biotic earth can cause something to happen.

Which is obviously false.

*crickets*

AVS, where are you? You’re letting down your side. Come on back and tell UB why he’s wrong!

Comments
UprightBiped:"Hello Porthos, sorry I didn’t see your question earlier." Porthos: are you suggesting in the O.P. that chemical evolution by selection can’t happen before the current complex genotype to phenotype translation system is in place? UB:"No, not at all (the OP was a conversation about the operation of the translation system as it is actually exist). I am, however, firmly suggesting that the living cell cannot be organized without translation, which entails a set of relationships being established between the arrangement of an informational medium and the objects to be constrained by that arrangement." Porthos: Suggesting that a translation mechanism would have (necessarily) been in place in the first self-replicators that we might define as cellular life doesn't seem controversial. I don't see how this relates to "intelligent design". (Thanks for the apology, but it was no-one's fault, as I think the board automatically delays first posts for moderation as an understandable spam precaution. I hope you find the linked paper interesting, as it does show that there's an affinity between some Amino Acids and their triplets).porthos
May 24, 2014
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Evolve:
But codons are not a language-like code that represents amino acids without having any physical connection to them.
Upright BiPed would, I think, be among the first to agree with you that codons have a physical effect. DEPENDING. But what is at issue here is also the difference that you seem to think exists between "language-like codes" and presumably, "non-language-like codes." What is a "non-language-like code"? Do tell. Are you aware that there is a mathematical definition of a code that does not depend on whether the code is "language-like" or not?Mung
May 23, 2014
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Evolve @ 104:
The word “table” has no connection to the actual object it represents because language is just a script. It’s a code to represent a real object. But codons are not a language-like code that represents amino acids without having any physical connection to them.
ok, I accept this as a coherent argument. I think it's wrong, but at least it is coherent. So "table" is just a word to identify or describe a physical object, it has no physical effect. So it doesn't matter that there are different words for "table" in different languages. And if I go in to a woodworker and say, build me a table nothing can come of that, because the word "table" cannot, even in principle, bring about a physical effect, regardless of the language understood by the woodworker. Is that correct? That's your argument? And if there is an automated system for constructing tables that allows a user to identify that what is desired is a "table" (in different languages), that doesn't qualify, because when the user says "build me a table" in whatever language happens to be convenient for the user, selecting the word "table" has no physical effect, even if the automated system does in fact produce a table? That's your argument? So if I am at the ATM and I choose "Spanish" rather than "English" that has no physical effect, because "Spanish" and "English" are just words which have no connection to what the words represent?Mung
May 23, 2014
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Evolve:
I don’t intend to “educate” myself with flawed concepts.
This is a recent decision on your part, isn't it. Sadly, you've already "educated" yourself with false concepts and are now using those false concepts to judge how to continue your education.Mung
May 23, 2014
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But you do win the “Elizabeth Liddle Memorial Award for Intellectual Dishonesty”
HAHAHAHAHA!!! Now there's an award worth remembering. How often are we allowed to hand out that award? Can we vote on it?Mung
May 23, 2014
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Charles, how do we know this isn't Chuck? Awesome videos. But still, it's just chemistry, that's all.Mung
May 23, 2014
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Hello Porthos, sorry I didn't see your question earlier.
are you suggesting in the O.P. that chemical evolution by selection can’t happen before the current complex genotype to phenotype translation system is in place?
No, not at all (the OP was a conversation about the operation of the translation system as it is actually exist). I am, however, firmly suggesting that the living cell cannot be organized without translation, which entails a set of relationships being established between the arrangement of an informational medium and the objects to be constrained by that arrangement.Upright BiPed
May 23, 2014
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Charles:
But you do win the “Elizabeth Liddle Memorial Award for Intellectual Dishonesty”
Thank you for making my day. ;) Now back to rowing (machine).Joe
May 23, 2014
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porthos- welcome to UD- Yarus has been discussed at length. For one it is doubtful a living organism could use such a system- too much time required to produce proteins that way. For another there isn't any way to get from that system to the current one- unguided evolution can't produce ribosomes.Joe
May 23, 2014
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Evolve @ 106
I’m sure you got this idea from the ID videos Discovery Institute produces from time to time. A nice assembly line with one "robot" handing over a component to another "robot" in the line.
Hardly. The DNLC.org videos "DNA Transcription (Advanced)" and "mRNA Translation (Advanced)" were produced by Cold Spring Harbor Laboratory: http://www.cshl.edu/about-us/ Cold Spring Harbor Laboratory (CSHL) is a private, not-for-profit research and education institution at the forefront of molecular biology and genetics. The "Translation" video was produced by Garland Science based on their textbook "Essential Cell Biology" 3rd ed. http://www.garlandscience.com/
... We publish textbooks and multimedia for the life sciences, biophysics, and chemistry, and have been producing educational content of the highest quality for nearly three decades. ...
But you do win the "Elizabeth Liddle Memorial Award for Intellectual Dishonesty"Charles
May 23, 2014
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Evolve, In May of 1961 when Nirenberg and Matthaei made the connection between phenylalanine and polyuracile, did they measure a physical property of the uracil triplet and then calculate the connection to phenylalanine? Or, did they have to demonstrate it?Upright BiPed
May 23, 2014
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Psst: The intelligent designer is what’s responsible. Not a measurable force.
No, actually I say: "the relationship between GCA and alanine is established in temporal and spatial isolation by the protein aaRS. It’s a local relationship, not derivable from physical law" And you say: "You will never ever admit your mistakes" ... but then you refuse to make your case, no matter how many time you are asked to do so. You simply repeat your claim, while I am here ready to defend mine with physical evidence taken directly from any biology textbook on the planet. The only one of us here with controversial ideas is you, and you refuse to substantiate them. You have nothing else.Upright BiPed
May 23, 2014
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Strange that if living organisms are just physics and chemistry that no one can produce a living organism using physics and chemistry. Do evolve and AVS think our scientists are a bunch of bumbling idiots?Joe
May 23, 2014
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Upright Biped asks: "The effects of physical laws can be measured in/on an object. Measure them in the nucleic pattern GCA, and demonstrate a relation to alanine from those measurements. Please show your work." This doesn't give you alanine and GCA, but does give you detail of about eight amino acids and their physical relationship to their coding triplets. RNA-Amino Acid Binding I hope there's enough work shown. BTW, are you suggesting in the O.P. that chemical evolution by selection can't happen before the current complex genotype to phenotype translation system is in place?porthos
May 23, 2014
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Evolve:
What’s wrong with you, Joe?
Ignorant evos who cannot focus.
A computer chip requires external coded instructions – SOFTWARE – to do anything.
And DNA requires multiple conditions before it can do anything.
DNA requires no instructions.
That depends on what you require it to do.
It will chemically react with surrounding molecules inside a cell (by well understood physical & chemical principles) to produce functional proteins.
Just cuz you can say so that doesn't make it so. You have been done years ago.Joe
May 23, 2014
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///Well it isn’t DNA on its own. What is wrong with you?/// What's wrong with you, Joe? A computer chip requires external coded instructions - SOFTWARE - to do anything. DNA requires no instructions. It will chemically react with surrounding molecules inside a cell (by well understood physical & chemical principles) to produce functional proteins. I'm done with you, Thank you.Evolve
May 23, 2014
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Evolve:
DNA spontaneously reacts with its surrounding molecules (what we call chemistry) to produce proteins (which carries out life’s functions).
Your bald assertion isn't evidence.Joe
May 23, 2014
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UB: Since they didn't specifically look at GCA -> Alanine, the interactions & forces involved cannot be measured or quantified. That's woo. Psst: The intelligent designer is what's responsible. Not a measurable force.Evolve
May 23, 2014
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And is it really mRNA if it isn't part of transcription and translation? No.Joe
May 23, 2014
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Evolve:
DNA does NOTHING on its own?
That is true.
You take DNA, rabbit reticulocyte lysate and nucleotides in a test tube and leave it at 30C. You’ll make mRNA. What’s that?
Well it isn't DNA on its own. What is wrong with you?Joe
May 23, 2014
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pssst (Evolve, the relationship between GCA and alanine is established in temporal and spatial isolation by the protein aaRS. It's a local relationship, not derivable from physical law)Upright BiPed
May 23, 2014
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pissst (Evolve, then entire scientific community tried for years to make the connection between codons and amino acids. None was found. This is widely distributed knowledge within the biological community)Upright BiPed
May 23, 2014
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None of the links you provided show an inexorable physical connection from the nucleic pattern GCA to amino acid alanine. None. Now what?Upright BiPed
May 23, 2014
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DNA does NOTHING on its own? You take DNA, rabbit reticulocyte lysate and nucleotides in a test tube and leave it at 30C. You'll make mRNA. What's that? It's called chemistry. The same reaction happening inside a living cell can be carried out in a cell-free test tube. DNA spontaneously reacts with its surrounding molecules (what we call chemistry) to produce proteins (which carries out life's functions). No external intervention required. DONE.Evolve
May 23, 2014
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///Measure them in the nucleic pattern GCA, and demonstrate a relation to alanine from those measurements. Please show your work./// The route from GCA to alanine involves molecular properties such as structure & stability as well as interactions like hydrogen bonding and atomic stacking which can be modeled, measured and quantified: http://pubs.acs.org/doi/abs/10.1021/ja993262d http://www.pnas.org/content/92/12/5297.full.pdf http://nar.oxfordjournals.org/content/33/6/1779.full http://pubs.rsc.org/en/Content/ArticleLanding/2007/CP/b703513f#!divAbstract http://www.atdbio.com/content/53/DNA-duplex-stabilityEvolve
May 23, 2014
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Evolve:
But DNA functions on its inherent chemistry, not by external software input.
DNA is inert you twit. Grow up already. DNA does NOTHING on its own.
But codons are not a language-like code that represents amino acids without having any physical connection to them.
Yes codons are language-like with no physical connection to amino acids. Apparently Evolve thinks its ignorance is an argument.Joe
May 23, 2014
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Another flawed analogy, JDD. A computer circuit board will not transmit any information on its own, for that it needs a software input from the human designer. Software is a set of instructions, a code, which tells the hardware what to do. But DNA functions on its inherent chemistry, not by external software input.Evolve
May 23, 2014
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Who said these reactions cannot be measured? All these enzymatic reactions and the parameters under which they work can definitely be measured if they’re studied carefully in detail.
The effects of physical laws can be measured in/on an object. Measure them in the nucleic pattern GCA, and demonstrate a relation to alanine from those measurements. Please show your work.Upright BiPed
May 23, 2014
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Charles, ///No. Amino acids are literally “assembled”, mechanically in a biological assembly line in the cell. They are not created chemically from a codon. /// LOL! You have me in splits here. I'm sure you got this idea from the ID videos Discovery Institute produces from time to time. A nice assembly line with one "robot" handing over a component to another "robot" in the line. ID guys always think anthropocentrically. Cellular machines work like man-made machines. DNA is just like human language. Mutations are directed towards a purpose. Molecules and organs are picked to serve a particular role. A developmental plan was put in place. You won't learn unless you break free from this kind of view, Charles.Evolve
May 23, 2014
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///The important question is what the pattern thymine-adenine-guanine represents to the system in which it operates. We are merely observers of the regulartities within the system. They cannot be measured, only demonstrated./// Who said these reactions cannot be measured? All these enzymatic reactions and the parameters under which they work can definitely be measured if they're studied carefully in detail. ///I once encouraged you to stop pissing on UD and go find a materialist physicists – someone who you can “trust” – someone who has researched semiotic systems and informational control, and READ UP and educate yourself./// Thanks, but no Thanks. I don't intend to "educate" myself with flawed concepts. You will never ever admit your mistakes, UB, because those are the strings you ID guys are clinging onto when you've nearly fallen off the proverbial cliff.Evolve
May 23, 2014
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