Evolution & Intelligent Design; Peer Review

[idscience]

This thread will be postings of peer reviewed evidence that show limits of modern evolutionary synthesis, and research supporting Intelligent Design.

The research papers will be from a variety of sources. One source is a new a journal BioComplexity. Generally the objections will be of a nature that has little to do with the content of the papers. I urge those looking for real answers to look at the research and the critiques of the research, and ignore all the other noise.

The information here will not be debated by the OP​

as to often the thread just fills with opinion. The information will speak for itself for those who are interested in facts and not rhetoric. Feel free to discuss the pro's and con's among yourselves. You can always ask me a question on this thread. http://www.christianforums.com/t7637566-41/

If the thread gets hi-jacked, or filled with noise, there will be a master list of links on this page for all evidence in this thread.

1. The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
2. The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations Interview Audio​
3. EXPERIMENTAL EVOLUTION, LOSS-OF-FUNCTION MUTATIONS,. AND “THE FIRST RULE OF ADAPTIVE EVOLUTION​
4. DNA Codes and Information: Formal Structures and Relational Causes​
   
   
   
   

 

[idscience]

The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway

interview audio

Abstract

Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs--the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations--transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo. We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But 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.

 

[Incariol]

Editorial Team

Vol 2010

Vol 2011

Nice try. Do you honestly expect us to take a "peer-reviewed journal" that publishes articles written by its own editorial board seriously? Anyone who has ever done any reviewing work that you can't have that kind of conflict of interest.

 

[idscience]

The Limits of Complex Adaptation: An Analysis Based on a​

Simple Model of Structured Bacterial Populations

Interview Audio
​

Abstract

To explain life's current level of complexity, we must first explain genetic innovation. Recognition of this fact has generated interest in the evolutionary feasibility of complex adaptations--adaptations requiring multiple mutations, with all intermediates being non-adaptive. Intuitively, one expects the waiting time for arrival and fixation of these adaptations to have exponential dependence on d, the number of specific base changes they require. Counter to this expectation, Lynch and Abegg have recently concluded that in the case of selectively neutral intermediates, the waiting time becomes independent of d as d becomes large. Here, I confirm the intuitive expectation by showing where the analysis of Lynch and Abegg erred and by developing new treatments of the two cases of complex adaptation--the case where intermediates are selectively maladaptive and the case where they are selectively neutral. In particular, I use an explicit model of a structured bacterial population, similar to the island model of Maruyama and Kimura, to examine the limits on complex adaptations during the evolution of paralogous genes--genes related by duplication of an ancestral gene. Although substantial functional innovation is thought to be possible within paralogous families, the tight limits on the value of d found here (d ≤ 2 for the maladaptive case, and d ≤ 6 for the neutral case) mean that the mutational jumps in this process cannot have been very large. Whether the functional divergence commonly attributed to paralogs is feasible within such tight limits is far from certain, judging by various experimental attempts to interconvert the functions of supposed paralogs. This study provides a mathematical framework for interpreting experiments of that kind, more of which will needed before the limits to functional divergence become clear.​

 

[idscience]

EXPERIMENTAL EVOLUTION, LOSS-OF-FUNCTION MUTATIONS,. AND “THE FIRST RULE OF ADAPTIVE EVOLUTION

Abstract

Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

 

[Incariol]

The research papers will be from a variety of sources. One source is a new a journal BioComplexity. Generally the objections will be of a nature that has little to do with the content of the papers. I urge those looking for real answers to look at the research and the critiques of the research, and ignore all the other noise.

Yes, the fact that the authors of every paper published in this BioComplexity "journal" (there's only like 5 articles over two years ROFL) are also the editors does have a great deal to do with the quality of a research journal.

 

[idscience]

DNA Codes and Information: Formal Structures and Relational Causes

Abstract

Recently the terms “codes” and “information” as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any “DNA-centric” reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology.

• By: Staff
  Discovery Institute
  February 1, 2012
• "This article by pro-ID evolutionary biologist Richard Sternberg compares the information processing ability of the cell to computer programming. Sternberg observes that non-physical symbols and codes underlie biology, stating that “There are no chemical constraints or laws that explain the 64-to-20 mapping of codons to amino acids and stop sites -- the relations are ‘arbitrary’ with respect to the molecular components in the sense that mappings can be reassigned.” According to Sternberg, the genetic code is like computer codes in that it contains the following properties: “Redundancy, Error dampening capability, Symbolic and semantic flexibility, Output versatility, Multiple realizability, and Text editing.” There is also a computer-like form of recursivity in molecular biology, “as a protein product can in turn be part of the transcriptional, RNA processing, or translational apparatus -- even binding to its own mRNA.” He explains the interdependent nature of DNA and other biomolecules, stating “Any DNA code is but the domain of a larger system; the larger system in turn depends on DNA codes (at least in part).” The author’s conclusion is that the workings of biology, fundamentally, are not reducible to material molecules but rather resides in information, symbols, and sets of mathematically logical rules: “The mathematical structures that proteins (and RNAs!) are the result of are not ‘in’ a gene. Instead, the DNA sequence is the material platform for the symbol strings that allow information to be accessed. In this sense, then, DNA is less than its Central Dogma interpretation because it is not ontically informational. Yet DNA enables many more code systems tha[n] commonly acknowledged and in this way is more than just a collection of codons.”

 

[Blayz]

This thread will be postings of peer reviewed evidence that show limits of modern evolutionary synthesis, and research supporting Intelligent Design.

So far all you have posted is the usual anit-evolution rubbish. When does the "supporting intelligent design" research get posted here?

 

[Incariol]

So far all you have posted is the usual anit-evolution rubbish. When does the "supporting intelligent design" research get posted here?

My favorite is the "peer-reviewed journal" that only has like 5 papers all published by the editors.