An evolutionary dilemma!!!!

originally posted by: ServantOfTheLamb
a reply to: Noinden

Show proof. DNA self assembles due to chemical potential. There is no need to have a hand of deity involved. Lower energy states are all you need.

DNA carries a semiotic dimension. Codons act as sign vehicles for the ribosomes, this would be the syntax of a progamming language and its environment, and depending on what environment you are in determines whether the the ribosome will produce a functional protein. It may very well look from the human perspective as though DNA self assembled. My claim is not that the parts couldn't have fallen together by suitable conditions but rather, that the abstract information stored in DNA could not have been the product of physical causes and self assembly. I think God spoke things into existence, so its not like I would expect some magical hand of deity. In fact I would simply expect to find a physical process that describes how inorganic matter came to organic matter and then from the information in organic matter we would probably find many body plans arising probably in different areas and places over some period of time and these body plans would have variation among them as natural selection and random mutation took hold. What makes me infer that DNA did not self assemble in the way you speak of it self assembling is its semiotic nature!

Pareidolic dimension you mean? seeing allegory and metaphor and intelligent influence where there is none? figuring out what we want to see and figuring out how to make the evidence look like it supports that? the funniest part here is how you try to sink evolution like its the titanic, then turn around and say "you know what wont sink? my invisible spaceship powered by pentacorn farts!"

originally posted by: Noinden
a reply to: ServantOfTheLamb

Show proof. DNA self assembles due to chemical potential. There is no need to have a hand of deity involved. Lower energy states are all you need.

If that were the ONLY case, then the amount of variation and the speed of its emergence would conform to parameters set by bioinformatic equations such as the Haldane's.

As it is, the rates of genetic change often seem too rapid for the calculated, sometimes on orders of magnitude, and the resultant diversity, far broader than to be expected in the time-frame/s.

So, while the probabilities from chemistry should be enough to calculate reasonable rates, the exceptions to the rules are vexing.

... and there are issues like the efficiency of energy migration from receptor to ATP production in photosynthetic processes which are 'off the board' when compared to the stochastic and Van der Waals forces that should be expected from chemistry alone.

a reply to: TzarChasm

All one needs to do is go to google scholar, Sci-Finder or Reaxys and type "DNA self assembly"

With Reaxys I got over 35K results.

Viz
J Mol Recognit. 2011 Mar-Apr;24(2):137-8.

A Case Study of the Likes and Dislikes of DNA and RNA in Self-Assembly
Zuo, Hua; Wu, Siyu; Li, Mo; Li, Yulin; Jiang, Wen; Mao, Chengde 2015
2015 Angewandte Chemie - International Edition, 2015 , vol. 54, # 50 p. 15118 - 15121

Chromatin assembly during S phase: Contributions from histone deposition, DNA replication and the cell division cycle
Krude; Keller 2001 Cellular and Molecular Life Sciences, 2001 , vol. 58, # 5-6 p. 665 - 672

Synergistic self-assembly of RNA and DNA molecules, Seung Hyeon Ko, Min Su, Chuan Zhang, Alexander E. Ribbe, Wen Jiang & Chengde Mao, Nature Chemistry 2, 1050–1055 (2010)

a reply to: chr0naut

Speaking as someone who holds a degree in Bioinformatics as well as a couple in Chemistry.

Bioiformatics is a blunt instrument. Its great for analysis of DNA (genomics), proteins (proteomics). But its not so crash hot at the thermodynamics, kinetics, let alone the actual chemical mechanisms involved.

Its nice you appear to be cutting and pasting in some words. The intellectually honest thing would be to cite your sources if you are going to do that.

a reply to: Noinden

in the interest of expedience, i thought maybe you could humor some of these folks and post something straight forward as a starting point for their independent studies.

a reply to: TzarChasm

I could, but I'm not going too. I'm not going to assist lazy research. They should go to google scholar, and read it themselves.

originally posted by: Noinden
a reply to: TzarChasm

I could, but I'm not going too. I'm not going to assist lazy research. They should go to google scholar, and read it themselves.

"they' are more interested in dismantling this stuff than reinforcing it.

a reply to: TzarChasm

Then they can go dismantle the 35K papers I've presented the evidence, if they refuse to speak to it, then they can not claim it is wrong with any sense of credibility.

But OK. its lunch time and I don't need to be in plant for an hour

www.ihes.fr...

It states

Molecular self-assembly is the spontaneous organisation of molecules under thermodynamic
equilibrium conditions into a structurally well-defined and rather stable arrangement
through a number of non-covalent interactions

later it says

There are three basic steps that define a process of molecular self-assembly:
1. molecular recognition: elementary molecules selectively bind to others;
2. growth: elementary molecules or intermediate assemblies are the building blocks
that bind to each other following a sequential or hierarchical assembly; cooperativity
and non-linear behavior often characterize this process;
3. termination: a built-in halting feature is required to specify the completion of the
assembly. Without it, assemblies can potentially grow infinitely; in practice, their
growth is interrupted by physical and/or environmental constraints.

originally posted by: Noinden
a reply to: TzarChasm

Then they can go dismantle the 35K papers

I've presented the evidence, if they refuse to speak to it, then they can not claim it is wrong with any sense of credibility.

But OK. its lunch time and I don't need to be in plant for an hour

www.ihes.fr...

It states

Molecular self-assembly is the spontaneous organisation of molecules under thermodynamic
equilibrium conditions into a structurally well-defined and rather stable arrangement
through a number of non-covalent interactions

later it says

There are three basic steps that define a process of molecular self-assembly:
1. molecular recognition: elementary molecules selectively bind to others;
2. growth: elementary molecules or intermediate assemblies are the building blocks
that bind to each other following a sequential or hierarchical assembly; cooperativity
and non-linear behavior often characterize this process;
3. termination: a built-in halting feature is required to specify the completion of the
assembly. Without it, assemblies can potentially grow infinitely; in practice, their
growth is interrupted by physical and/or environmental constraints.

can it be realistically speculated that there is an intelligent component to this process?

a reply to: TzarChasm

How does one demonstrate that there is one? How does one measure an external influence? These are all based upon chemical (and biochemical) calculations.

So I'd say, with the information, one can notconclude that there is an intelligent component involved in the process. While this is not evidence against it, since the absence of evidence (no matter how hard you look) is not evidence against something. You can not imply the hand of deity in this, from the measurable variables.

This last bit is the important part. Just because they can not understand that it is possible that this occurs by itself, it does not mean it must be god. That is a non sequitur. Indeed it is really Argumentum ex Silentio, which is a logical fallacy

Look, machines making machines, let's call it self-organization and forget about what the primary cause is for these capabilities (it's also changing over time and natural forces described by the laws of chemistry and physics also come into play during the process, let's call it a desire to reach equilibrium and talk about energy states rather than the primary cause why these natural forces are interacting in this particular functional manner with the machinery in question):

Self-organization(al) scenarios are old news (involving mythology again, it's still the same storyline regarding the chemical evolution of life by natural forces alone, a.k.a. abiogenesis by natural forces alone), 1 of the Professors that introduced some of them ended up repudiating it himself (and no, changing the terminology to "self-assembly" to conflate the subject with other phenomena isn't going to help you either):

This is what the Professor Emeritus of Biology thinks now after researching the subject others refer to as "self-assembly" (usually leaving out some logical requirements for the complete story while playing the conflation and equivocation game as I described it before regarding the word "endosymbiosis") and he refers to as "we have not the slightest chance of a chemical evolutionary origin for even the simplest of cells", 0:39:

Do Not Be a Victim of Propaganda! Awake!—2000

Use discernment: Discernment is “acuteness of judgment.” It is “the power or faculty of the mind by which it distinguishes one thing from another.” A person with discernment perceives subtleties of ideas or things and has good judgment.

Using discernment, we will be able to recognize those who are merely using “smooth talk and complimentary speech” in order to “seduce the hearts of guileless ones.” (Romans 16:18) Discernment enables you to discard irrelevant information or misleading facts and distinguish the substance of a matter. But how can you discern when something is misleading?

Just to be clear, ServantOfTheLamb was clearly talking about the origin of DNA as it is found in living organisms (including its functionalities and capabilities regarding the reproductive abilities of the organisms and assembly of biomolecular machinery) from nonliving material by natural forces alone when he mentioned: "Neither could DNA Self Assemble."

Pointing to these reproductive and assembly capabilities or pointing to nonfunctional DNA (regarding these functionalities and capabilities) or molecules lumping together (chemically binding) by the forces of nature alone without producing the same functionality and/or using already existing biomolecular machinery and/or the coded instructions to assemble these machines and hope people won't notice what you just did there (no conflation please, when I push and roll a snowball up a snowy hill it's not reproducing or self-assembling* as it accumulates snow, undirected polymerization is also not the equivalent of the assembly of machinery or reproduction in biology) isn't going to cut it. *: in the manner the word "self-assembly" is conflated and confused with "self-organization(al) scenarios" regarding the origin of life or in this case DNA as it is found in living organisms specifically

a reply to: TzarChasm

Nope semiotic.

a reply to: ServantOfTheLamb

Keep clutching at straws. You have yet to demonstrate intelligent design in any shape or form.

a reply to: Noinden

I've done no such thing. I can't help it if you don't like the point I am making. Just saying it is wrong doesn't make it wrong. You need to show that semiotic dimension can be explained from the bottom up.

a reply to: ServantOfTheLamb

Indeed, but you miss the point, you've not demonstrated that your semiotic dimension is actually real. You've never in any of your threads demonstrated proof of intellegent design, you've simply said "this is too complex for it to be natural, thus supernatural", which is logically flawed.

QED you have demonstrated nothing.

a reply to: Noinden

This thread isn't about ID at all. So no I haven't said that. I've most certainly demonstrated it is real with the Mycoplasma and Human cell scenario. You just don't want to accept it.

a reply to: ServantOfTheLamb

However the people pushing semiotic biology seem to all have an ID ax to grind. Given you refuse to acknowledge that nucleic acids are able to undergo auto catalysis, and you refuse acknowledge that there is no actual "evolutionary dilemma" involved in a difference of mitochondrial DNA. One has to assume you are on your usual "god did it" bender.

a reply to: Noinden

I've given sources. Explained what I meant in detail. The people who read my post can decide for themselves.

a reply to: Noinden
Please don't conflate the self-organizational scenarios regarding the origin of DNA as it is found in living organisms (including its functionalities and capabilities in regards to the topic of "life") with so-called "autocatalysis" (like previously explained regarding "self-assembly") and experiments with catalysis resulting in DNA that does not have the same functionalities and capabilities which is ignoring the logical requirements of the story of natural forces alone being the cause for the emergence of DNA as it is found in living organisms (including its functionalities and capabilities); thus also without reverse engineering from biomolecular machinery or already existing codes, or basing your starting code on our knowledge of these existing codes in living organisms, which would not simulate the forces of nature alone or doesn't address the origin of whatever you borrowed from already existing life, not to mention experiments where the endproduct still does not have the same functionalities and capabilities required for the preservation, protection and continuation of life (or not all of them: see some examples of requirements to qualify as "life" in the video below) even with heavy borrowing from already existing life (and their biomolecular machinery and the code that gives the instructions for how this machinery is going to function or how additional machinery is going to be assembled and then interact with the other machinery).

P.S. Taking the strands apart of already existing DNA or sequencing and engineering strands yourself and then observing catalytic reactions (in intelligently picked environmental conditions picked for its properties that are conducive for causing catalytic reactions and preserving the endroduct, more chemical engineering techniques) doesn't say anything about the origin of DNA as it is found in living organisms (caused by natural forces alone). On top of that, DNA on its own is useless when it comes to the topic of "life":