DNA , and irreducible complexity

From a debate at TalkOrigins google group:

Talk origins google group


> Your argument is based upon assumptions that the earliest cells were
> similar to those of today and that they would have faced similar
> environmental stresses. It's an extremely dubious assertion about the
> earliest stages of life. You don't know enough about those stages to
> make these claims.


 Scientists call it LUCA, the Last Universal Common Ancestor, but they don’t know much about this great-grandparent of all living things. Many believe LUCA was little more than a crude assemblage of molecular parts, a chemical soup out of which evolution gradually constructed more complex forms. Some scientists still debate whether it was even a cell.

New evidence suggests that LUCA was a sophisticated organism after all, with a complex structure recognizable as a cell, researchers report. Their study appears in the journal Biology Direct.

The study builds on several years of research into a once-overlooked feature of microbial cells, a region with a high concentration of polyphosphate, a type of energy currency in cells. Researchers report that this polyphosphate storage site actually represents the first known universal organelle, a structure once thought to be absent from bacteria and their distantly related microbial cousins, the archaea. This organelle, the evidence indicates, is present in the three domains of life: bacteria, archaea and eukaryotes (plants, animals, fungi, algae and everything else).

The existence of an organelle in bacteria goes against the traditional definition of these organisms, said University of Illinois crop sciences professor Manfredo Seufferheld, who led the study.

http://news.illinois.edu/news/11/1005LUCA_ManfredoSeufferheld_JamesWhitfield_Caetano_Anolles.html

http://dialogue.adventist.org/articles/15_2_ward_e.htm

Leaving aside the technical problems of such chemistry, what would a primordial cell need to survive, replicate, and to get the evolutionary ball rolling? First, a method for capturing energy (e.g.: photosynthetic organisms that make their own food) or a mechanism for utilizing energy derived from pre-formed organic molecules. Both methods involve very complex biochemistry even in the simplest of organisms. Second, a membrane to keep the outside environment separate from the metabolic reactions within the cell. Third, a system by which genetic information can be stored and accessed (DNA). Fourth, a mechanism to convert this information into the molecular tools the cell requires to function. Finally, the all-important requirement for cellular division and self-replication. The stored genetic information must be replicated and passed onto daughter cells in order to produce descendant life forms.



>
> There are all sorts of possibilities. The earliest self-replicating life
> may have been RNA-based, it may have disseminated and persisted due to
> quantity, not quality, and therefore required no sophisticated repair
> mechanisms. It may have evolved for long periods of time under
> conditions that demanded less intensive, or no, repair.


uhmm..... the guesswork is starting... LOL.

OOL theorist Leslie Orgel notes that

an "RNA World" could only form the basis for life, "if prebiotic RNA had two properties not evident today: a capacity to replicate without the help of proteins and an ability to catalyze every step of protein synthesis." The RNA world is thus a hypothetical system behind which there is little positive evidence, and much materialist philosophy:
"The precise events giving rise to the RNA world remain unclear … investigators have proposed many hypotheses, but evidence in favor of each of them is fragmentary at best. The full details of how the RNA world, and life, emerged may not be revealed in the near future.

The best claimed evidence of an "RNA World" includes the fact that there are RNA enzymes and genomes, and that cells use RNA to convert the DNA code into proteins.
However, RNA plays only a supporting role in the cell, and there is no known biochemical system completely composed of RNA.

RNA experts have created a variety of RNA molecules which can perform biochemical functions through what is commonly termed "test tube evolution." However, "test tube evolution" is just a description for what is in reality nothing more than chemical engineering in the laboratory employing Darwinian principles; that does not imply that there is some known pathway through which these molecules could arise naturally.

from my personal virtual library:

http://elshamah.heavenforum.org/t2024-the-rna-world-and-the-origins-of-life



>
> I don't know enough to say for sure, and neither do you. This is the
> point I was making about arguments from ignorance. The fallacy here is
> obvious: the fact that you cannot conceive of a plausible pathway by
> which these mechanisms may have evolved doesn't mean there isn't one,
> nor does the absence of such an explanation support an inference to Design.

Of course it does.

High information content machine-like irreducibly complex and interdependent structures,  of which photosynthesis, the eye, the human body, nitrogenase, the ribosome, the cell, rubisco, photosystem II, the oxygen evolving complex etc. are prime examples, are commonly found in nature.
Since Evolution is unable to  provide a advantage of adaptation in each evolutionary step, and is unable to select it, 1) Darwinism’s prediction is falsified; 2) Design’s prediction is confirmed.


>
> Well, that's certainly the way to bet, regardless of your very powerful
> "LOL" argument.

Sure....

Theist: The DNA code is written by a intelligent mind.
Atheist : Emergent properties, and physical reactions, are perfectly capable to produce the code stored in DNA.
Theist : There is no known natural mechanism ( aka no intelligence involved ) to encode the information stored in DNA
Atheist: God of the gaps argument. Argument from ignorance. Because we don't know yet, does not mean, Godidit.

Theist : "The  sentence you are reading now was written by a intelligent mind"
Atheist: "Emergent properties, and physical reactions  are perfectly capable to screen these letters to the monitor"
Theist : "There is no known natural mechanism ( aka no intelligence involved ) to type these letters and they to appear on the screen"
Atheist: "Argument of the gaps. Argument from ignorance. Because we don't know yet, that does not mean, a intelligence did it"


> First, you'll need to decide whether you want to talk about DNA in
> general, or individual bases. Next, you'll need to think more deeply
> about how irreducible complexity is used by ID "theorists" and whether
> this particular situation really qualifies.

DNA , and irreducible complexity

Individual bases : take away the sugar in the DNA backbone = no function
Take away the phosphate in the backbone = no function
Take away the nucleic acid bases = no function

Evolution is not a driving force at this stage, since replication of the cell depends on DNA.

So the individual DNA molecules are irreducible complex

DNA in general ( the double helix )

Unless the two types, purines, and pyrimidines are present, and so the individual four bases = no function, and no hability of information storage

The the enzymes and proteins for assembly and synthesis of the DNA structure must also be present, otherwise, no DNA double helix......

> No, no laboratory tests have demonstrated that "...Evolution is unable
> to  provide a advantage of adaptation in each evolutionary step." You
> can prove otherwise by citing the pertinent papers.

Of course. I don't make baseless claims.

http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1

In 2011, Ann Gauger and Douglas Axe published a paper in BIO-Complexity, "The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway." They reported results of their laboratory experiments trying to convert one enzyme (Kbl2) to perform the function of a very similar enzyme (BioF2), thought to be very closely related to Kbl2. Because these proteins are both members of the GABA-aminotransferase-like (GAT) family, and are believed to be very closely related, this is the sort of evolutionary conversion that evolutionists say ought to be easily accomplished under the standard co-option model. However, after trying multiple combinations of different mutations, they found otherwise:

We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions.
2010 paper by Axe
Evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

Now in their new study, "Enzyme Families-Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase [GAT] Family," Reeves, Gauger, and Axe examine nine other enzymes from the same GAT family. Once again, the idea was to see if it is possible to convert them to perform the function of BioF2. They tested proteins that are closer to BioF2, or more distant from BioF2, than the enzyme they tested in their prior study (Kbl2). But all of the proteins studied are in the same family, and are thought to be closely related.

First, they sought to determine if the enzymes could be converted to perform the function of BioF2 through a single mutation. They created mutation libraries with every single possible mutation in those nine enzymes. No BioF2 function was ever detected. As they explain:

The present study has added to our previous examination of these problems in several respects. We have shown, based on sequence alignment of α-oxoamine synthases (a subset of the GAT family), that our previous use of rational design did indeed target regions of Kbl2 that are likely to be functionally significant. Furthermore we have now shown that the lack of a simple evolutionary transition to BioF2 function is not at all unique to our initial choice of Kbl2 as the starting point. Single mutations cannot convert any of eight other members of the GAT family to that function, despite the fact that all of these enzymes are regarded as close evolutionary relatives.


>
> As for refutation, you will note that I have been offering the relevant
> responses in the form of pointing out the flaws in both your
> understanding of the science and the logic of your arguments.

I do not recognize anything compelling in your answers so far. And i am explaining you, why.

> No, it cannot, that is merely a reflection of your wishful thinking.
> Design cannot be inferred from any gap in biological data.

Intelligent design is a scientific theory, and as such makes predictions , that can be falsified. Its not based on a gap of understanding, but is based on what we actually DO know.

> All of those elements are characteristic of natural biological
> phenomena.

It has never been observed of chemical reactions to procude coded information. A mind is ALWAYS required.

Furthermore, the removal of the pistone in a car engine makes the engine inoperable. In the same manner, the removal of a protein renders the molecular machine inoperable.  and he biochemical structure of a protein, not embedded and correctly fitting or inserted at the right place has no function, and so there is no survival advantage , and a  stepwise evolutionary pathway is not feasable. Furthermore, in many biological pathways, you need several steps to get the final product, where the intermediate product has no function, and neither so do the enzymes required to sinthesize the specific intermediate product in question. For example, in the biosynthesis pathway of chlorophyll, the enzymes required to synthesize the last 8 steps are uniquely used in that pathway. They could not have been co-opted somewhere else. Say hello to Ken Miller.....


 The only way they can be used to infer a designer is if you
> presume they can only result from Intelligent Design, which is
> tantamount to assuming your conclusion - another logical fallacy.

Is that not what is done in methodological naturalism ? Evolution and natural causes are presumed right from the start. A Designer is excluded a priori.


> Since "specified complexity" is an ambiguous concept that neither
> Dembski nor any other ID proponent has ever rigorously defined, this
> "prediction" is vacuous.

False. Its well described, and well defined.

http://www.arn.org/docs/dembski/wd_idtheory.htm

>
> > ID predicts that, as scientific research progresses, biological
> > complexity will be seen to increase over time, and information will
> > have a more and more central role in the governing of life's
> > operations.
>
> What does that even mean?

In Darwins time, it was thought that cell's were simple. We know today about its enormous complexity. The more science will progress, the more complexity in biological organisms will be discovered. The more we discover, the more the gap between what we do know, and what we do not know, widens.

Furthermore, in the fifties, when DNA and what it contained, was discovered, it was thought that there were just one code stored in DNA. Today we know , that there are overlapping codes, and that information in non coding DNA governs the development of the organism, and gene expression. The more science advances, the more about regulation through information stored in the cell will be discovered. Information is sign of intelligence, not random chemical processes.


>
> > ID predicts the presence
> > of irreducible complexity with respect to macromolecular systems and
> > organelles.
>
> So does "Darwinism." In other words, that's another "prediction" that
> has no necessary relationship with ID.

LOL. Darwinism predicts the exact oposit.