Just Evidence

If you have been paying attention, you might have notices a striking contrast in several of my previous postings about evolution and the genetic code. Let me see if I can make it more clear.

1. Some traits are easy to evolve — formed by many different combinations of mutations. Others are hard to evolve — made from an unlikely genetic recipe. Evolution gives us the easy ones, even when they are not the best.

2. For example, in 1991, evolutionary biologists Laurence Hurst of the University of Bath in England and David Haig of Harvard University showed that of all the possible codes made from the four bases and the 20 amino acids, the natural code is among the best at minimizing the effect of mutations.

3. Furthermore, just as a tinkerer’s creations seem jury-rigged, so too do the products of natural selection.

4. Thus, termination codon sequences are resistant or well-adapted to TM resulting from not only guanine lesions but also cytosine deamination.

5. evolution does not produce rational, perfect, finely-tuned beings. It makes organisms that are good enough.

6. Here, we consider whether robustness to translational frame-shift errors may be linked to the structure of the genetic code. We tested all alternative codes for the mean probability of encountering a stop in a frame-shifted protein-coding message. We find that the real genetic code encounters a stop more rapidly on average than 99.3% of the alternative codes.

It would seem clear to me that an intellectually honest and open-ended approach would have to acknowledge that these rational features of the genetic code count as evidence for its design. Not proof. Not even powerful evidence. Just evidence.

And there is a lot more to come…..

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3 responses to “Just Evidence

  1. Michael, I am enjoying your research.

    I have some questions and wonder how it will impact… “more to come” if at all in the future.

    From Eugene Koonin’s paper…
    “The major evolutionary role assigned to effectively unique events like endosymbiosis is, of course, incompatible with both gradualism and uniformitarianism.”

    http://nar.oxfordjournals.org/cgi/content/full/gkp089v1

    That is an honest assessment and damning one to many Darwinist and all gradualist. Although some say this is not news, it is to most people outside ivory towers.

    “Beyond genomics and metagenomics, one of the hallmarks of the first decade of the new millennium is the progress of research in functional genomics and systems biology.”

    I agree.

    Essentially, biologist must become engineers to save their jobs.

    Meanwhile, I’m being asked to believe that what “appears” to be designed is not. And the most efficient way research will proceed most rapidly is to utilize “what appears to be designed concepts” to “reverse engineer” life yet insist that they’re not using design concepts.

    Um… am I allowed to snicker? Just a little?

    Are research scientist today not living in Absurd Worlds of cognitive dissonance? How long can Orwellian leaders control this area of scientific research where words like “design” must be eliminated? And researchers are afraid to put machine verbage in their papers?

    Koonin continued…
    “A fundamental observation supported by the entire body of evidence amassed by evolutionary genomics is that the sequences and structures of genes encoding proteins and structural RNAs are, generally, highly conserved through vast evolutionary spans.”

    BINGO. But what else does the evidence require? How can Sequences and structures of encoded proteins and RNAs remain conserved? 1) They must have a built in mechanism from start to repair and reliably maintain the structure and to as some point stop evolution or, 2) be superbly made for high selectability against all other random sequences with a stop evolution button somewhere in random time?

    Which is it? A test must confirm there is a reason for high selectibility without “repair.” Failure to produce and repeat such a test is a failure of the hypothesis of natural selection. In fact, I’d argue the very existence of repair mechanisms is big evidence in favor of Design. If you remove the repair mechanism, even the most simple forms of life dive into extinction.

    Koonin continues…
    “From an evolutionary biology perspective, it appears that the sequences of many genes encoding core cellular functions, especially, translation, transcription, replication and central metabolic pathways, are subject to strong purifying selection that remained in place for extended time intervals, on many occasions, throughout the 3.5 billion year history of cellular life.”

    I agree with everything he said in this statement with exception of “strong purifying selection.” Why should anything remain in place for 3.5 billion years that is so fragile as life? Those three words hide the truth imho of exactly what must be done to “strongly” “purify” “selection” for anything, much less conserved information.

    What must be done?

    1) strong attraction of chemicals to self organize in exact sequence?
    2) reading, repair mechanisms to correct/kill bad sequences?
    3) Start/Stop Codons, Frameshift, multi-start positions, multi-use?
    4) Integreation of multiple independent created mechanisms to coordinate all the processes?
    5) conversion of energy
    6) breakdown of energy input
    7) Meta Information about all of the above stored for retrievel?

    Honestly… why do I draw a blank? Is it due to lack of imaigination for the dead to rise? Don’t think so.

    I see macro-evolution as rapid events(fossil records more in line – see Gould). Selection is not required in this scenario, it is instead “enforced” thru a serious of pre-mapped codes and the inherent regulartory processes for each stimuli and resultant trigger from environmental surroundings.

    So, we are looking at pre-coded algorithms, pre-coded triggers, pre-stored object oriented database of calleable subroutines and a master blueprint for reproduction not of one tree, but of multiple trees(see Koonin paper).

    Also, errors are traceable back to storage and give insight into disease. So we are able to compare good code to bad code(mutated-damaged).

    Without stasis, without specificity engineers are lost to cure disease or understand genetic defects.

    We see this with bacteria. So far, they’ve played with the Edges of Bacteria. Not the core process. This is why superbugs exist in specialized care, but cannot survive in nature. In order to understand bacteria, one must understand its original functional design.

  2. Just to follow up…

    “The observations of extensive, ubiquitous and occurring via multiple routes HGT outlined above lead to a fundamental generalization: the genomes of all life forms are collections of genes with diverse evolutionary histories.”

    There’s no way to trace history either. So, you are stuck with a new fundamental method of classification and systems biology based upon function and not history.

    This is a good move for science. It is forced to finally move forward and stop spending money on useless story telling about a past even the most brilliant scientist can never figure out.

    “The corollary of this generalization is that the TOL concept must be substantially revised or abandoned because a single tree topology or even congruent topologies of trees for several highly conserved genes cannot possibly represent the history of all or even the majority of the genes (146–149).”

    Very strong and welcome language. Though he adds the caveat that Darwin’s TOL is still useful. Tree diagrams have always been useful, but the central theory is collapsing in multiiple areas. Gradualism, 1 TOL.

    “Thus, an adequate representation of life’s history is a network of genetic exchanges rather than a single tree, and accordingly, the ‘strong’ TOL hypothesis, namely, the existence of a ‘species tree’ for the entire history of cellular life, is falsified by the results of comparative genomics.”

    again from… Eugene Koonin;

    http://nar.oxfordjournals.org/cgi/content/full/gkp089v1#SEC2

    This favors FL and Design. Engineers often make great leaps and by Horizontal Design Transfer-HDT. Why recreate the wheel?

    No matter what some say however, the wheels are coming off for old school evolution. They’re in trouble and they’re trying desperately to maintain control of a unicycle with a blown tire.

    HGT as once offers them a new mechanism to explain away old problems, yet immediately causes more severe questions to be asked about the original foundation and conjecture made by Darwin.

  3. Hi Curious,

    Thanks big time for drawing my attention to that article. It is definitely worth a few blog postings.

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