INTELLIGENT DESIGN: DNA just chemicals

[TrueEmpiricism]

[Youtube]
https://www.youtube.com/watch?v=kzySoa14W4w[/Youtube]

Now, of course this video doesn't even begin to scratch the surface. It was just a quick vid conjured up from the top of my head off my phone. I understand all the critiques and multiple sub points that could be added such as information theory genetic algorithms and many other alternatives which have failed repeatedly or are non comparable, at the base explained here I don't think ANYBODY can deny the implications of intelligent design and the data it calls into question. Of course DNA is chemical but its the utilization of this which is the point.

 

[SpecialFrog]

May I suggest a read through this thread?
http://www.leagueofreason.org.uk/viewtopic.php?f=8&t=12191

 

[he_who_is_nobody]

​

Now, of course this video doesn't even begin to scratch the surface. It was just a quick vid conjured up from the top of my head off my phone. I understand all the critiques and multiple sub points that could be added such as information theory genetic algorithms and many other alternatives which have failed repeatedly or are non comparable, at the base explained here I don't think ANYBODY can deny the implications of intelligent design and the data it calls into question. Of course DNA is chemical but its the utilization of this which is the point.

(Fixed embedded player.)

Come back when you have a transcript of this video.

 

[Mugnuts]

:facepalm: Mr. Dunning-Kruger personified makes his comeback.

I watched this while on the loo, and couldn't help but chuckle that we were doing the exact same thing at the same moment, just from different ends.

 

[TrueEmpiricism]

Ah, so mugnuts a troll with no substance behind it. With the reputation of the atheist community can't say I am surprised..

 

[Mugnuts]

Ah Mr. DK. Bring it.

 

[Dave B.]

That was not a straw man. It was an objection to the caller's argument. And it was a valid objection.

Aside from not knowing what a straw man is you, apparently, don't know what an argument from analogy or the affirming the consequent fallacy are, either:

1. Argument from analogy - DNA appears similar to a language therefore it is a language. It's got, like, letters and shit in it! WRONG!

2. Affirming the consequent - English is a language that comes from an intelligent designer. DNA is a "language" so DNA must also come from an intelligent designer. WRONG!

 

[Rumraket]

DNA is not a language. DNA is a molecule.

DNA does not function like a language, it functions according to chemistry and physics. All the reactions that take place inside living cells are due to the physical and chemical properties of the interacting parts, all the way from the 3-dimensional structure of the DNA strand to the distribution of electromagnetic charges around the individual atoms. It's physics all the way down. There is no literal "reader" or "translator" anywhere, these are merely metaphors we use in description of the molecular biochemistry of genetics.

Besides this, we already know that DNA evolved, including everything from the biochemical pathways responsible for synthesizing DNA monomers (they are synthesized from RNA precursors, which is a strong hint that RNA preceded DNA in the history of life), to the translation system responsible for protein synthesis.

How do we know this? Comparative genetics of the individual components of the DNA synthesis pathways (the chains of biochemical reactions that construct the individual components of the deoxyribonucleotides) yield phylogenetic trees that strongly imply these components have distinct evolutionary histories, with some components predating others. Furthermore as mentioned above, there is also strong hints that DNA evolved from an earlier period in the history of life, when genomes of then-life was based on RNA. We know this because the biochemical pathways mentioned above, all construct the DNA from precursors to RNA molecules. That implies the biochemical pathways for synthesizing RNA are older than the ones for synthesizing DNA, which then got subsequently co-opted and modified into making DNA.

 

[Rumraket]

DNA is not a language. DNA is a molecule.

DNA does not function like a language, it functions according to chemistry and physics. All the reactions that take place inside living cells are due to the physical and chemical properties of the interacting parts, all the way from the 3-dimensional structure of the DNA strand to the distribution of electromagnetic charges around the individual atoms. It's physics all the way down. There is no literal "reader" or "translator" anywhere, these are merely metaphors we use in description of the molecular biochemistry of genetics.

Besides this, we already know that DNA evolved, including everything from the biochemical pathways responsible for synthesizing DNA monomers (they are synthesized from RNA precursors, which is a strong hint that RNA preceded DNA in the history of life), to the translation system responsible for protein synthesis.

How do we know this? Comparative genetics of the individual components of the DNA synthesis pathways (the chains of biochemical reactions that construct the individual components of the deoxyribonucleotides) yield phylogenetic trees that strongly imply these components have distinct evolutionary histories, with some components predating others. Furthermore as mentioned above, there is also strong hints that DNA evolved from an earlier period in the history of life, when genomes of then-life was based on RNA. We know this because the biochemical pathways mentioned above, all construct the DNA from precursors to RNA molecules. That implies the biochemical pathways for synthesizing RNA are older than the ones for synthesizing DNA, which then got subsequently co-opted and modified into making DNA.

I thought I'd better dig up a reference, just to show I'm not talking out of my ass here:

http://www.ncbi.nlm.nih.gov/books/NBK6360/
Origin and Evolution of DNA and DNA Replication Machineries
Patrick Forterre, Jonathan Filée, and Hannu Myllykallio.

Origin of DNA

DNA can be considered as a modified form of RNA, since the “normal” ribose sugar in RNA is reduced into deoxyribose in DNA, whereas the “simple” base uracil is methylated into thymidine. In modern cells, the DNA precursors (the four deoxyribonucleoties, dNTPs) are produced by reduction of ribonucleotides di- or triphosphate by ribonucleotide reductases (fig. 1). The synthesis of DNA building blocks from RNA precursors is a major argument in favor of RNA preceding DNA in evolution. The direct prebiotic origin of is theoretically plausible (from acetaldehyde and glyceraldehyde-5-phosphate) but highly unlikely, considering that evolution, as stated by F. Jacob, works like a tinkerer, not an engineer.8,9

Figure 1. Metabolic pathways for RNA and DNA precursors biosynthesis: a palimpsest from the RNA to DNA world transition? The biosynthetic pathways for purine and pyrimidine nucleotides both start with ribose 5-monophosphate.

Figure 1

Metabolic pathways for RNA and DNA precursors biosynthesis: a palimpsest from the RNA to DNA world transition? The biosynthetic pathways for purine and pyrimidine nucleotides both start with ribose 5-monophosphate. The formation of the four bases requires several amino-acids, formate and carbamyl-phosphate. Nucleotide monophosphates (NMP) are converted into RNA precursors (NTP) by NMP kinases (k) and NDP kinases (K). These reactions probably are relics of the RNA-protein world. DNA precursors are produced from NDP and/or NTP by ribonucleotide reductases (RNR), except for dTTP, which results from methylation of dUMP. dTMP is produced from dUMP by Thymidylate synthases (ThyA or ThyX) and converted into dTTP by the same kinases that convert NMP into NTP. dUMP can be produced either by dUTPAse or by dCTP deaminase. In the U-DNA world, it could have been also produced by degradation of U-DNA. The mode of dTMP production clearly suggests that U-DNA was an evolutionary intermediate between RNA and T-DNA. Some viruses contain U-DNA, whereas others contain HMC-DNA (HMC= hydroxymethyl-cytosine). Transformation of C into HMC occurs at the level of dCMP, and conversion of dCMP into dHMCMP is catalyzed by a dCMP hydroxy-methyl transferase (dCMP HM transferase), which is homologue to ThyA (See refs. 11, 14, and 19 for more details).

Metabolic pathways for RNA and DNA precursors biosynthesis: a palimpsest from the RNA to DNA world transition? The biosynthetic pathways for purine and pyrimidine nucleotides both start with ribose 5-monophosphate. The formation of the four bases requires (more...)
The first step in the emergence of DNA has been most likely the formation of U-DNA (DNA containing uracil), since ribonucleotide reductases produce dUTP (or dUDP) from UTP (or UDP) and not dTTP from TTP (the latter does not exist in the cell) (fig. 1). Some modern viruses indeed have a U-DNA genome,10 possibly reflecting this first transition step between the RNA and DNA worlds. The selection of the letter T occurred probably in a second step, dTTP being produced in modern cells by the modification of dUMP into dTMP by thymidylate synthases (followed by phosphorylation).11 Interestingly, the same kinase can phosphorylate both dUMP and dTMP.11 In modern cells, dUMP is produced from dUTP by dUTPases, or from dCMP by dCMP deaminases (fig. 1).11 This is another indication that T-DNA originated after U-DNA. In ancient U-DNA cells, dUMP might have been also produced by degradation of U-DNA (fig. 1).

The origin of DNA also required the appearance of enzymes able to incorporate dNTPs using first RNA templates (reverse transcriptases) and later on DNA templates (DNA polymerases). In all living organisms (cells and viruses), all these enzymes work in the 5' to 3' direction. This directionality is dictated by the cellular metabolism that produces only dNTP 5' triphosphates and no 3' triphosphates. Indeed, both purine and pyrimidine biosyntheses are built up on ribose 5 monophosphate as a common precursor. The sense of DNA synthesis itself is therefore a relic of the RNA world metabolism. Modern DNA polymerases of the A and B families, reverse transcriptases, cellular RNA polymerases and viral replicative RNA polymerases are structurally related and thus probably homologous (for references, see a recent review on viral RNA-dependent RNA polymerases.)12 This suggests that reverse transcriptase and DNA polymerases of the A and B families originated from an ancestral RNA polymerase that has also descendants among viral-like RNA replicases. However, there are several other DNA polymerase families (C, D, X, Y) whose origin is obscure (we will go back to this point below).

If DNA actually appeared in the RNA world, it was a priori possible to imagine that formation of the four dNTPs from the four rNTPs was initially performed by ribozymes. Most scientists, who consider that the reduction of ribose cannot be accomplished by an RNA enzyme, now reject this hypothesis.9,13-19 The removal of the 2' oxygen in the ribose involves indeed a complex chemistry for reduction that requires the formation of stable radicals in ribonucleotide reductases. Such radicals would have destroyed the RNA backbone of a ribozyme by attacking the labile phosphodiester bond of RNA. Accordingly, DNA could have only originated after the invention of modern complex proteins, in an already elaborated protein/DNA world. This suggests that RNA polymerases were indeed available at that time to evolve into DNA polymerases (as well as kinases to phosphorylate dUMP).

Three classes of ribonucleotide reductases (I, II and III) have been discovered so far (for a review, see refs. 9, 16-19) (fig. 1). Although they correspond to three distinct protein families, with different cofactors and mechanisms of action, these mechanisms are articulated around a common theme (radical based chemistry). In all cases, the critical step is the conversion of a cysteine residue into a catalytically essential thiol radical in the active center.18 Recent structural and mechanistic analyses of several RNR at atomic resolution have suggested that all ribonucleotide reductases originated from a common ancestral enzyme, favoring the idea that U-DNA was invented only once.17,18 It has been suggested that either class III (strictly anaerobic) or class II (anaerobic but oxygen tolerant) represent the ancestral form, and that new versions appeared in relation to different lifestyles by recruiting new mechanisms for radical activation (class III in strict anaerobes and class I in aerobes).9,18

The origin of U-DNA in a protein/RNA world logically implies that the second step in the synthesis of DNA precursors, the formation of the letter T, was catalyzed by ancestral thymidylate synthase. For a long time, it was believed that modern thymidylate synthases were all homologues of E. coli ThyA protein, indicating that the letter T was invented only once. However, comparative genomics has revealed recently that ThyA is absent in many archaeal and bacterial genomes, leading to the discovery of a new thymidylate synthase family (ThyX).19 ThyX and ThyA share neither sequence nor structural similarity between each other and have different mechanisms of action,19,20 indicating that thymidylate synthase activity was invented twice independently (fig. 1). T-DNA might have appeared either in two different U-DNA cells, or the invention of a second thymidylate synthase might have occurred in a cell already containing a T-DNA genome. The first possibility would indicate that T-DNA itself has been invented twice, thus suggesting a strong selection pressure to select for uracil modification. In the second case, one should imagine that the new enzyme (either ThyA or ThyX) brought a selective advantage over the previous one in the organism where it appeared first.

 

[Vivre]

Hi TrueEmpiricism,

would you kindly translate the below for me and tell me what of it is the letter 'ὤ' ?

Hvala lijepa!

 

[TrueEmpiricism]

Really?

RAmraket:

DNA is not a language. DNA is a molecule.

DNA does not function like a language, it functions according to chemistry and physics. All the reactions that take place inside living cells are due to the physical and chemical properties of the interacting parts, all the way from the 3-dimensional structure of the DNA strand to the distribution of electromagnetic charges around the individual atoms. It's physics all the way down. There is no literal "reader" or "translator" anywhere, these are merely metaphors we use in description of the molecular biochemistry of genetics.

https://www.youtube.com/watch?v=oF1UzhPA5N8


Editing this to state this, you see I can explain from off the top of my head why it is the case. But the problem is coming from a theist seems to go in one ear and out the other. The facts defy the position of your atheism, how? (A)-theism or (A)-theos means to be without theism. Theism is the belief in a creator behind the influence of the universe which is interactive. SO, your position is without creative intent. The evidence is suggesting creative attributes objectively known to come from creative intelligent thinking minds therefore refuting the premise of your atheism (if you are an atheist) , and become at the very least BENEFICIAL to those that believe in a creator behind these things deism theism ect. Atheism seems to stand outside the circle of the evidence . Its those that believe in creator that has a leg to stand on and is up to them to dispute between among which theological or philosophical belief . Atheism in our generation is a defiance of the evidence and in no way can be justified.

 

[Rumraket]

What the hell does this atheism gibberish have to do with DNA? Either DNA is a language or it is not, whether god exists or not, or whether I believe in that god or not.

Deal with with the evidence I have put forward, stop blathering about irrelevancies.

 

[Deleted member 619]

OK, watching the vid. Crits as I go.

First, you say that Dillahunty is erecting a strawman. Your justification for this, as detailed in the video, is that 'obviously it is'. Yeah, good fucking work. Also incredibly wrong, and an irrelevant tanget. Dillahunty is attacking the argument that DNA is a language by pointing out, quite correctly, that it isn't. That's not a strawman, it's a valid rebuttal to the suggestion that DNA requires a designer because it's a language.

I note you state that no scientist on the intelligent design side denies that there's chemistry involved, which is all very well, apart from one minor niggle. There are NO scientists in intelligent design. There are lying fuckwits in stolen lab coats.

Moving on.

You go on to talk about how DNA is information, citing complexity for some reason known only to yourself. Complexity has exactly zero to do with whether or not something is information. This is horrendously ignorant of what information actually is. Tell me about the complexity of the following:

1

See any complexity there? I certainly don't, but it IS information, and indeed quantifiable information.

Might want to learn something about information theory prior to exposing your ignorance to the entire planet.

Certainly, DNA is information, but so is a sand dune, a dog turd, an incoherent scribble.

You talk about something that Francis Crick hypothesised which was later 'proven as a fact'. Errr, no. nothing is ever 'proven' in science (with a caveat which I will come to). Proof is a formal procedure applicable only to axiomatically complete systems of deductive logic. Science is, by its very nature, inductive. In order to prove something in science you would need to have carried out all possible relevant observations and ruled out the possibility of any falsifying observations. This requires omniscience, which is self-refuting. The only form of proof allowable in science is disproof, also known as falsification.

You say that the type of information is akin to written language, and go on to cite how an alphabet works. Problem is, this is not how DNA works. All there is is chemicals obeying universal rules based on local conditions. What you're actually doing is erecting the fuckwitted argument that he's just debunked. DNA is not a language, it's not a code. It's chemicals.

Ultimately, this entire thread rests on the idea that, because scientists use convenient language as analogy, that language should be taken literally. This is not the case. It's precisely the same as saying that DNA is a code. It isn't. It's analogous to a code (actually, it's analogous to a cipher, in which the individual chemicals are replaced IN OUR TREATMENT THEREOF by symbols signifying said chemicals).

I often use a favourite example to show how analogies work, and this is the best example to employ it on.

Picture yourself in a city you've never been in before. London, say. If you had a map of London that was perfect in every respect, it would be of no more use in navigating London than simply going there and wandering the streets. The map is a much simplified ANALOGY of London, and its value lies in its imperfection, namely the imperfection that it isn't the same scale, and doesn't have the same level of detail, as the real London.

Similarly, when we talk about DNA being a code, we're using shorthand, analogous terminology because it aids our understanding, not because DNA is actually a code. DNA is a code in precisely the same way that London is a map.

Similarly, scientists use terms like 'function', 'adaptation', 'design', 'blueprint', 'design', etc, because it is language that is easily understood, and which aids understanding, not because those terms actually apply, any more than 'code' really applies to DNA, or 'recipe' or 'blueprint' actually apply to organisms, but because they constitute a useful, easily understood shorthand.

In short, the map is not the terrain.

Do yourself a favour and do a full transcript of the video so I can fuck it up the arse properly, but suffice it to say that you're exposing ignorance on a scale that we haven't built a metric large enough to measure. You're talking through your arse from start to finish, and that's just the coherent bits.

 

[he_who_is_nobody]

Really?

RAmraket:

DNA is not a language. DNA is a molecule.

DNA does not function like a language, it functions according to chemistry and physics. All the reactions that take place inside living cells are due to the physical and chemical properties of the interacting parts, all the way from the 3-dimensional structure of the DNA strand to the distribution of electromagnetic charges around the individual atoms. It's physics all the way down. There is no literal "reader" or "translator" anywhere, these are merely metaphors we use in description of the molecular biochemistry of genetics.

https://www.youtube.com/watch?v=oF1UzhPA5N8


Editing this to state this, you see I can explain from off the top of my head why it is the case. But the problem is coming from a theist seems to go in one ear and out the other. The facts defy the position of your atheism, how? (A)-theism or (A)-theos means to be without theism. Theism is the belief in a creator behind the influence of the universe which is interactive. SO, your position is without creative intent. The evidence is suggesting creative attributes objectively known to come from creative intelligent thinking minds therefore refuting the premise of your atheism (if you are an atheist) , and become at the very least BENEFICIAL to those that believe in a creator behind these things deism theism ect. Atheism seems to stand outside the circle of the evidence . Its those that believe in creator that has a leg to stand on and is up to them to dispute between among which theological or philosophical belief . Atheism in our generation is a defiance of the evidence and in no way can be justified.

This is easily the best example of a non sequitur I have ever seen.

 

[Deleted member 619]

Theism is the belief in a creator behind the influence of the universe which is interactive.

No it isn't. Theism is the belief in 1 or more deities. not all deities are creators of the universe. You might want to factor that into your palsied understanding.

SO, your position is without creative intent.

And that's an issue because..?

The evidence is suggesting creative attributes objectively known to come from creative intelligent thinking minds

Well, evolution doesn't create, and nobody suggests that it does, with due caveats regarding how language is used in my previous post.

therefore refuting the premise of your atheism (if you are an atheist) ,

How does one refute something that doesn't constitute a truth claim?

and become at the very least BENEFICIAL to those that believe in a creator behind these things deism theism ect. Atheism seems to stand outside the circle of the evidence .

What evidence is there for your preposterous celestial peeping-tom again?

Its those that believe in creator that has a leg to stand on and is up to them to dispute between among which theological or philosophical belief . Atheism in our generation is a defiance of the evidence and in no way can be justified.

See my last question. The total lack of anything resembling an answer to that is all that is required to justify withholding belief in merely asserted entities. Perhaps you simply don't understand what atheism is, which would hardly be surprising given the paucity of understanding you demonstrate on just about every other topic you've held forth on here.

Atheism is merely the non-acceptance of a specific class of truth claim with regard to the existence of a class of entities. The reasons for said non-acceptance are many and diverse, ranging from never having encountered the concept of said entities to actually having looked closely at the complete lack of any evidential support.

 

[Inferno]

No it isn't. Theism is the belief in 1 or more deities. not all deities are creators of the universe. You might want to factor that into your palsied understanding.

Being absolutely pedantic, I believe it would be correct to say that theism is the belief in one or more deities who also directly intervene in our lives. (Be it by magic, answering prayers, etc.) As opposed to deism, where they're passive.

 

[Mugnuts]

Its those that believe in creator that has a leg to stand on and is up to them to dispute between among which theological or philosophical belief .

I'm not sure if it is the grammar or seemingly missing nouns that make this hard to understand.

What happens when one enters this debate with empirical evidence? And to when the actual true data refutes said philosophical claims/beliefs? Do you still hold to the philosophy regardless of the facts just because they contradict your original theistic or philosophical belief?

Atheism in our generation is a defiance of the evidence and in no way can be justified.

The defiance is marked clearly by the merit of the evidence that is presented. No more than that. Being an atheist is merely not accepting faulty or flawed evidence that has been presented by the believers. If there was actual evidence that can be verified, then I will accept it as so. You could change my mind, but nothing you present gives me any reason to do so.

It sounds like you are trying to borrow from Sye Ten here and presupposing truth because God told you it was true and everything he says is true. Sorry but reality does not work that way.

 

[Mugnuts]

Instead of having the discussion here, he just keeps making videos that are watched by ten to a few hundred times, all the time puffing and posturing up how wrong 'atheists' are.

What I am failing to understand is why the argument settles on regarding his promotion of the DI's assertions as anyone being opposed to the Intelligent Design hypothesis, is an atheist or 'Darwinist'. Ken Miller is no atheist by any means (in a Judea-Christianity sense). He has no issue with Evolutionary theory and the compatibility of his faith. So why doesn't TE have issues with him or others like him that trounce Intelligent Design?

I personally don't take issue with Intelligent Design because of religious implications. I have rejected it because it has been severely debunked over and over again. I hold it in the same light as Deepak Chopra's use of 'Quantum' for his way of looking at things. It's all pseudoscience and has been proven to be so, or so ridiculous that it is unfalsifiable enough to not consider putting much thought into it. Yet I do it anyway because ignoring it won't make it go away on it's own.

Is DNA just chemicals. Yes.
Can we derive information from it. Yes.

Is it complex. Yes and No. It all comes down to what we compare it to, and if it is a comparison to something that shares similar properties then we can better define it's complexity. All the DI uses for it's comparisons are things that we already know to be designed by man (or a mind as they put it). That seems pretty flawed right? But what else can they compare it with if not things that are designed? Should we throw out all such examples just because they were designed? Yes, until you can show the outside mechanism of how it can be created by a mind, then it's a silly argument. Put it to the test. If we can create life in a Lab, and it turns out that naturalistic means were highly unlikely in the process, then you have an argument for design.

How about all the probability calculations put forward? Is showing how improbable something is tantamount to proving it's impossibility? Not even close. If something has a probability no matter how infinitesimal, it can still happen.

My favorite argument is 'If life can come about by itself naturally, how come we don't see it happening all the time?' :facepalm: So...much...wrong with that.

Anyway. TrueEmpiricism, we can have a discussion. I will tame myself and treat you with respect from this point on. No more 'Mr. D-K' name calling etc. I know I started it off that way, but I have rethought my approach in dealing with this type of situation. So, up to you.