Genetics News

Too much of something can be a good thing for ID

Spread the love

One reason I’ve hammered the 500 fair coin illustration and the law of large numbers is that it illustrates how to use the binomial distribution to reject chance as a mechanism. In certain contexts, the law of large numbers is much easier to use than the more generalized design detection methods discussed here. When looking for non-random patterns, excessive appearances of certain symbols may indicate non-randomness, and thus too much of something can be a good thing for ID.

If something is randomly distributed like the DNA bases Adenine, Thymine, Cytosine, Guanine (A,T,C,G), we should see creatures and DNA regions have nearly equal parts of each.

But this is clearly NOT the case on several levels. It sort of crushes Kimura/Nei neutral theory.

Certain creatures have an over abundance of C and G and yet others an overabundance of A and T. From Wiki on CG content

GC content is found to be variable with different organisms….The species problem in prokaryotic taxonomy has led to various suggestions in classifying bacteria, and the ad hoc committee on reconciliation of approaches to bacterial systematics has recommended use of GC ratios in higher level hierarchical classification.[17] For example, the Actinobacteria are characterised as “high GC-content bacteria”.[18] In Streptomyces coelicolor A3(2), GC content is 72%.[19] The GC-content of Yeast (Saccharomyces cerevisiae) is 38%,[20] and that of another common model organism, Thale Cress (Arabidopsis thaliana), is 36%.[21] Because of the nature of the genetic code, it is virtually impossible for an organism to have a genome with a GC-content approaching either 0% or 100%. A species with an extremely low GC-content is Plasmodium falciparum (GC% = ~20%),[22] and it is usually common to refer to such examples as being AT-rich instead of GC-poor.[23]

Take Plasmodium falciparum with a CG-content of 20%. For a genome of about 25 megabases, assuming GG probability is 50%, it’s configuration is 3000 sigma from expectation. 😯 Of course one could say, there must be a bias somewhere. Ok, then how do you explain a creature that has almost the opposite bias like Streptomyces coelicolor that has a deviation of 1349 sigma the other way (for a genome size of 9.4 megabases). You could of course make an ad hoc theory and just use different probability distributions to make the numbers fit for every creature in question.

I discussed the problem of DNA mutation rates in No Universal Transition Transversion Mutation Rates. The problem is if one accepts no universal bias, then how do you explain the existence of bias in certain creatures? If you say there is a bias in one direction (like toward more CG), then how do you explain the examples of creatures with biases in the other direction (like away from CG), or vice versa. The only way out of this problem are special pleadings and ad hoc explanations. Thus it’s a tad humorous that wiki mentions this fact in relation to CG ratios:

The species problem in prokaryotic taxonomy has led to various suggestions in classifying bacteria, and the ad hoc committee on reconciliation of approaches to bacterial systematics has recommended use of GC ratios in higher level hierarchical classification

“Ad hoc” is a good name for solving these peculiarities. How about “the committee for reconciliation of problematic non-random patterns that defy mindless evolutionism through means of special pleading.”

The other level of bias is the CG rich regions in chromosomes themselves. Random evolution should not create such concentrated islands of CG. This is evident in various ways such as Chromsome Bands where the non-randomness of DNA can be seen directly with the Skittle-like patterns:

chromosome bands

One thing I found curious. Google “evolution of chromosome bands” or anything similar. The paucity of evolutionary narratives to explain the CG ratio in the bands as well as the CG ratios between species should tell you something. πŸ˜‰

NOTES

1. As I said, the more minimal ReMine/Sanford neutral theory merely states selection is mostly (not entirely) absent in population dynamics, and that something other that neutral mechanisms or selection created the design of life. This is the form of neutral theory I assent to, not the more general Kimura/Nei neutral theory.

2. photo credits CCBCMD.edu Biotutorials and Proceedings of the National Academy of Sciences (PNAS) In Silico Chromosome Staining

10 Replies to “Too much of something can be a good thing for ID

  1. 1
    NickMatzke_UD says:

    This is a new competitor for Worst Post on UD Ever.

  2. 2
    scordova says:

    This is a new competitor for Worst Post on UD Ever.

    Assuming that is true, it might be informative to the readers to hear why. And here is a bonus, some students that I give talks to will occasionally drop in to read my UD essays.

    Here is your chance to set them straight.

  3. 3
    gpuccio says:

    NickMatzke_UD:

    Yes, I am curious to hear your arguments.

  4. 4
    sixthbook says:

    Not to be outdone, Nick Matzke puts in an entry for worst comment ever.

  5. 5
    Querius says:

    C’mon, Nick. Knock it out of the park. Call someone a doofus (ouch), or an IDiot (arrgh).

    No wait, Larry Moran thought that last one up.

    -Q

  6. 6
    Gordon Davisson says:

    Sal: try searching for “isochore evolution” instead.

    Nick: I am curious to hear your take on this; I just used isochores as an example in this other thread, but I don’t actually know much about them, so I’d like to know if I biffed it.

  7. 7
    scordova says:

    Gordon,

    Actually the demise of Isochore theory inspired this discussion. From wiki on Isochores:

    The rise and fall of the isochore theory

    The isochore theory became one of the most useful theories in molecular evolution for many years. It was the first and most comprehensive attempt to explain the long-range compositional heterogeneity of vertebrate genomes within an evolutionary framework. Despite the interest in the early years in the isochore model, in recent years, the theory’s methodology, terminology, and predictions have been challenged.

    Because this theory was proposed in the past century before complete genomes were sequences, it could not be fully tested for nearly 30 years. In the beginning of the 21st century, when the first genomes were made available it was clear that isochores do not exist in the human genome [29] nor in other mammalian genomes.[30] When failed to find isochores, many attacked the very existence of isochores.[29][31][32][33][34] The most important predictor of isochores, GC3 was shown to have no predictable power [35][36] to the GC content of nearby genomic regions, refuting findings from over 30 years of research, which were the basis for many isochore studies. Isochore-originators replied that the term was misinterpreted [22][37][38] as isochores are not “homogeneous” but rather fairly homogeneous regions with a heterogeneous nature (especially) of GC-rich regions at the 5 kb scale,[39] which only added to the already growing confusion. The reason for this ongoing frustration was the ambiguous definition of isochores as long and homogeneous, allowed some researchers to discover “isochores” and others to dismiss them, although both camps used the same data.

    The unfortunate side effect of this controversy was an “arms race” in which isochores are frequently redefined and relabeled following conflicting findings that failed to reveal “mosaic of isochores.” [22][31][33] The unfortunate outcomes of this controversy and the following terminological-methodological mud were the lost of interest in isochores by the scientific community. When the most important core-concept in isochoric literature, the thermodynamic stability hypothesis, was rejected, the theory lost its appeal. Even today, there is no clear definition to isochores nor is there an algorithm that detects isochores.[40] Isochores are detected manually by visual inspection of GC content curves ,[41] however because this approach lacks scientific merit and is difficult to replicate by independent groups, the findings remain disputed.

  8. 8
    ScuzzaMan says:

    Asking questions, showing skepticism, even trying to refute the theory / hypothesis in question, makes you an enemy of science.

    Popper?

    Popper, who?

  9. 9
    gpuccio says:

    sixthbook:

    Not to be outdone, Nick Matzke puts in an entry for worst comment ever.

    πŸ™‚

    Well, there is great competition for that!

    OK, on both sides, on both sides…

    But is the distribution really random? πŸ™‚

  10. 10
    ppolish says:

    Blind Watchmaker gives us the “appearance of design”.

    Guided Evolution gives us the “appearance of randomness”

    True “Bio Randomness” is not even possible is it? Math randomness ok, but Bio? C’mon, really?

Comments are closed.