Monday, May 11, 2015

Paper: Water Molecule Harnesses its Electronic Structure to Encode Features

Aristotelianism on Steroids

It’s no secret that the biological world contains all manner of complicated and finely-tuned machines and mechanisms. Even evolutionists admit that life has the appearance of design. But it doesn’t stop there. Biology, for instance, rests on a foundation of chemistry, and there too we find all kinds of fascinations. At the atomic level, matter and its interactions have specific and particular properties that result in a vast set of crucial puzzle pieces. There are the positive and negative ions, such as sodium and chlorine, which result in molecules with ionic bonds, such as salt. There are atoms that can accept or donate electrons, such as carbon, which result in life’s macromolecules, such as carbohydrates and fats. Even quantum mechanics, which may seem like a distant underworld, can be important in biological processes. The fundamental nature of matter and its interactions appear to be ingenious building blocks on which chemistry and biology rely. A good example of this is water, which continues to yield interesting secrets about how nature works.

Every biology student learns that water has a wide range of particular properties that are crucial for life. It expands, rather than contracts, when it freezes leading to ponds merely freezing at the top rather than all the way through, in the winter; it is the universal solvent; and it absorbs heat without increasing much in temperature. Here is how a new research paper summarizes water:

Water is one of the most common substances yet it exhibits anomalous properties important for sustaining life. It has been an enduring challenge to understand how a molecule of such apparent simplicity can encode for complex and unusual behavior across a wide range of pressures and temperatures. … Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water’s crystalline phases and amorphous states.

The paper finds that water’s many properties can be explained with an N-body model with electrostatic forces. And as is so common, the authors use teleological language to describe the phenomena. Watch for the infinitive form:

We show that many-body responses arising from water’s electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states.

So the water molecule harnesses its electronic structure to encode its distinguishing features. Such Aristotelian language and thought are ubiquitous in the natural sciences. This suggests that it is not easy or natural for practitioners to study the natural world strictly from a materialistic perspective. The world didn’t “just happen.”

17 comments:

  1. Waters properties are another fine-tuning argument for certain - I never looked at it from this level. But how many coincidences will it take until materialists will say, OK, something is going on here - without the trap door of the multiverse, where chocolate rivers flow and unicorns abound.. So silly to me.... they gather all this evidence for design and then try and wish it away....WHY?

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  2. Great post as usual! Not much too add except: thank goodness that ice expands so it stays on the water surface during winter. If otherwise we would have lots of angry Canadians.

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    1. As it is, us Canadians walk on water.

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  3. Dr. Hunter,
    I know this comment is way off topic, but I think its an issue that holds a lot of weight as a "no way" for evolution. I'm wondering if you would critique my conjecture (I know it isn't unique to me, but it does seem to be lost as a primary ID case.

    I have been toying around with redundancy and natural selection. It appears that according to the modern evolutionary theory, natural selection plays two roles: purging deleterious mutations, and preserving beneficial mutations. Further, natural selection is the only mechanism available to provide these services. (Yes, I am aware that DNA has various amazing genetic repair mechanisms. These mechanisms are “inside the box”, however. And the box necessitates a certain amount of mutation for organisms to change with.)

    It appears to me that redundant genes are an absolute falsification of natural selection as the only mechanism that maintains genetic quality.

    This thought was brought to me by Denis Noble of “The Music of Life” fame. He said that gene knock out experiments were difficult because knocking out gene A produced no deleterious effects, knocking out gene B also produced no deleterious effects, but knocking out both did. He referred to this as redundancy.

    Let me clearly define my position. If it could be shown that: if the deletion of gene A, or gene B causes no deleterious effects, if knocking out both gene A and gene B produce deleterious effects, and if both gene A and gene B have been around for millions of years then natural selection as the universal agent of gene quality maintenance is falsified.

    My case is simple. Natural selection works on the level of the phenotype. If there is no change in the phenotype of an organism (ie, knocking out gene A or B) then natural selection cares not. Therefore, while gene A and B are both functional, either is available to take a deleterious mutation. That first deleterious mutation has no protection from natural selection. Now, mutations to a particular gene are unlikely to happen in 5 to 10 generations. So it is unlikely that the vulnerability that the other gene takes on will be a factor with sufficient resolution for natural selection to react to.

    Natural selection, therefore, simply cannot protect the redundant aspects of genetics.

    Corollary: Near neutral theory claims that natural selection will allow slightly deleterious mutations to fix in a population. Therefore neutral theory claims that natural selection is not a high precision instrument. This must be factored into the analysis above. If the knocking out of gene A or gene B produces only a slightly deleterious effect, natural selection will still not respond to protect these genes.

    Therefore, to falsify natural selection as the universal preserving agent, the threshold is lowered. If the knocking out of gene A or gene B does not produce greater than “slight” deleterious effects, natural selection as the universal preservative is falsified.

    It is my understanding that genetic redundancy is ubiquitous. I understand the argument that these redundancies may well show deleterious effects in a natural environment where they do not in a laboratory environment. This, therefore, is a potential path of ID research; the ID community needs to create real-world stress tests of known redundancies to show that they are truly redundant outside the lab.

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    1. bFast:

      Yes, I think you make a good point, and I think your point about neutral theory is right on. Merely slightly deleterious effects probably would not be explanatory. But be aware that there are other evidences of the same sort, such as UCEs (ultra conserved elements) which evolutionists have also failed to admit are caustic to their theory.

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    2. Yes, UCEs are the same kind of "this doesn't fit the theory". I know that the excuse for them is the same -- maybe real world creatures in real world scenarios would see benefit from the UCE. Again, the only solution to this challenge is a good, honest experiment.

      I think, however, that the the fact that redundancy is so darn common in DNA, and that the case for redundancy is easy for people to understand makes it a better candidate than UCEs as as a primary case.

      In your opinion, is there any other reasonable explanation for redundancy other than the suggestion that within certain environments both components offer an advantage?

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    3. Well one other explanation I can think of is that the redundancy appeared recently and evolution hasn't gotten around to reckoning with it yet (I realize you already nix'ed that one in your example).

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  4. Hi,
    I don't really think redondancy is a problem for evolution. Think about duplicated genes for example.
    Let's say they are both functional, coding for a vital protein. You could have one of them knocked out without measurable effects of deleteriousness, while knocking them both could result in deleterious consequences because the protein won't be produced at all. This could happen a lot in plants for example, where whole genome duplication are common.

    Also you don't always measure the effect of a mutation based on its deleterious effects, but also about the reduction in fitness (number of offspring) it causes. It can be much more difficult to measure in a lab (needs long time experiment with numerous generations of individuals)

    I don't think what you call redundancy would be a problem.

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    1. First, let me agree with you that duplication can very easily produce redundancy. This is not my point. My point is that once redundancy exists both "redundant" genes are vulnerable to unchecked mutation. Therefore, unchecked mutation should happen given very little time (on an evolutionary scale.)

      Redundancy is very easy to create, redundancy is very difficult to preserve.

      Secondly, I am baffled by your contrast of deleterious effects and "reduction of fitness". I am also baffled that you equate "reduction of fitness" with number of offspring.

      In my view, fitness is the measure of an organism's ability to thrive and reproduce in an environment. If the lack of fitness relates to, say, a plant's ability to withstand heat, a hot summer will kill that plant's population back -- there will be less reproduction. However, this reduction in the number of offspring is an afterthought of the real issue -- the plant's ability to withstand heat. A new inability for a plant community to withstand heat would be, in my understanding, a deleterious effect.

      Therefore I see all deleterious genetic effects to produce a loss of fitness. I see "number of offspring" as an aftereffect of most forms of loss of fitness. Please feel free to show me that I am full of it.

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    2. Calamity,

      Let's say they are both functional, coding for a vital protein. You could have one of them knocked out without measurable effects of deleteriousness

      That's the point. Under evolution there would no purefying selection on one of them. So evolution does not explain the existence of both.

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  5. Hi guys,
    For bFast
    [...]. Therefore, unchecked mutation should happen given very little time
    Don't forget that any mutations will be tested and tried through natural selection anyway, redundancy or not. If mutations are not too severe or neutral they will likely stay in the population. You have actually a good wikipedia article on gene redundancy http://en.wikipedia.org/wiki/Genetic_redundancy with nice article links.
    About fitness :
    However, this reduction in the number of offspring is an afterthought of the real issue. You could define the fitness of an organism as its capacity of producing offspring after selection acts on its phenotype and genotype. Both number of offsprings and "robustness" are important. For example an immortal but sterile individual has a fitness of 0.

    For Mr Hunter :
    Under evolution there would no purefying selection on one of them. You are completely right. That's the mechanism of "pseudogenization" where one of the duplicated genes start to accumulate mutations that stop it from encoding anything. Simply because since the gene is duplicated, one copy is not needed to keep the organism going. But pseudogenization is not the only scenario. There is extensive litterature on the subject if you are interested in.

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    1. Calamity:

      The Wikipedia article states:

      "Taking these notions into account, the very existence of genetic buffering, and the functional redundancies required for it, presents a paradox in light of the evolutionary concepts. On one hand, for genetic buffering to take place there is a necessity for redundancies of gene function, on the other hand such redundancies are clearly unstable in face of natural selection and are therefore unlikely to be found in evolved genomes."

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    2. Thanks for the link. I found the following statement most telling, "Although the functional divergence of paralogous gene pairs can be extremely fast, redundant genes do commonly not mutate faster than essential genes (Winzeler EA et al. 1999; Wagner A, 2000; Kitami T, 2002].

      Did he not just say that it is common for redundant genes to resist mutation as effectively as "essential genes"? If so, how the heck does the current theory hold its head high and claim the status of "fact"?

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  6. I don't know if citing a wikipedia article is the way to go if you want to prove a point ...

    You should check : Evolution of genetic redundancy by Nowak et al. They acknowledge the fact that genetic redundancy should not be evolutionary stable, but provide some examples where it could be.

    The devil is in the detail here. You always have to look closely at the function of those redundant genes.

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    1. Calamity:

      You are contradicting yourself:

      You have actually a good wikipedia article on gene redundancy http://en.wikipedia.org/wiki/Genetic_redundancy


      I don't know if citing a wikipedia article is the way to go if you want to prove a point ...

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    2. I'm just bringing some material for some further discussion, especially with the link provided in the article. Wikipedia is fine for that.
      But you can't justify your view citing an anonymous user on Wikipedia, that's just bad practise.

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    3. So to summarize, you provided a reference, I showed that the reference does not support your position very well, and you responded that it is OK for you to use the reference, but not for me to use it.

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