Extraterrestrial life Intelligent Design Multiverse

The hidden benefits of the pursuit of ET. And the hidden costs.

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Evolution News and Views

Recently, science writer Marcus Chown reviewed a series of books discussing extraterrestrial life, From Dust to Life: The origin and evolution of our solar system, Life Beyond Earth: The search for habitable worlds in the universe, and Alien Universe: Extraterrestrial life in our minds and in the cosmos which, he says, “bring us up to speed on extraterrestrial life, its prospects and possible forms – but it remains ‘queerer than we can suppose.’” He is quoting Darwinian biologist J.B.S. Haldane (1892–1964):

I have no doubt that in reality the future will be vastly more surprising than anything I can imagine. Now my own suspicion is that the Universe is not only queerer than we suppose, but queerer than we can suppose. – Possible Worlds and Other Papers (1927), p. 286

Product DetailsThis thought has been attributed to others as well, and sometimes appears in slightly different forms. Chown writes,

THERE are some 100 billion galaxies in the observable universe, with about 100 billion stars in each of those galaxies. And in recent years, we have discovered that there are probably more planets than there are stars. In fact, there are more planets in the universe than there are sand grains on all the beaches of all the coastlines of all the continents. Yet, in all this immensity, there is only one place where we know there is life – the tiny, fragile “blue dot” we call Earth.

This rather handicaps our speculations about life elsewhere. Not that you would know it, to judge by the hundreds of books published every year about extraterrestrial life, its prospects and possible forms. Some are exuberant and ambitious in scope, other pure entertainment, and still others modest and fact-based.

Actually, lack of information has not handicapped speculation at all. The barest possibility of a fact immediately spawns hundreds of speculations. Even if no exoplanet turns out to be fertile, the human imagination will readily supply the need.

The good news is that many of us might never care to know that phosphorus is one of the CHNOPS, the six elements (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur) most important for life, except that NASA researchers recently claimed that microbes could be got to metabolize arsenic instead (a claim widely dismissed). If so, we were told, life could arise from unexpected chemicals in other parts of the universe.

It’s possible that many people have learned more basic chemistry from following speculations about the origin of life and extraterrestrial life than they ever did in high school chemistry class. So yes, there’s that. The problem is, they also learn an attitude to evidence that skews their thinking about science in general. That is the subject of my Science Fictions series, a light-hearted but deadly serious look at the way in which assertions and assumptions stand in for evidence in cosmology and astrobiology (study of proposals about extraterrestrial life).

In the latest installment, “Multiverse cosmology: Assuming that evidence still matters, what does it say?”, readers will see that the fact that the tide of evidence is decidedly against multiverse cosmology, does not prompt re-examination of basic premises but defensiveness and searches for loopholes:

So the faithful remain. String theory could be tested, we are told, by black holes orbited by pulsars, revealing extra dimensions. In a new bubble universe proposed at Stanford, featuring new laws of physics and a new conception of science, “problems with string theory unification have magically vanished.” Meanwhile, one physicist has proposed abandoning string theory in favor of knot theory, “to delve into the deep recesses of mathematical research” and explain things in “down-to-earth terms that everyone can understand.”

M-theory (the multiverse): Proponent Brian Greene has admitted (2012) that there is no evidence for it: “As of today, we are far from crossing this threshold.” Colleague Roger Penrose sums up, “What is referred to as M-Theory isn’t even a theory, it’s a collection of ideas, hopes, aspirations.”

And what are do we learn by accepting it all anyway? Alan Lightman tells us in Harper’s:

If the multiverse idea is correct, then the historic mission of physics to explain all the properties of our universe in terms of fundamental principles — to explain why the properties of our universe must necessarily be what they are — is futile, a beautiful philosophical dream that simply isn’t true. Our universe is what it is because we are here.

Product DetailsSo the multiverse has little or no explanatory value. But we are told we mustn’t go back either. Leading philosopher of cosmology Tim Maudlin assured us in 2012 that if there is no multiverse, it would be a “terrible mistake” to think that an intelligent designer is the only remaining option. We can adjust our notions of probability instead.

Always, the war on probability. Many of us have hit on a simpler and more reasonable approach by now … More.

Chown concludes, repeating,

But here the fact that we only know about terrestrial biology – and have no idea what is special or general about it – is an enormous handicap. Our speculations inevitably come up against the truth highlighted by the British biologist J. B. S. Haldane: “The universe is not queerer than we suppose,” he said, “it is queerer than we can suppose.” And that is one problem no Star Trek or Star Wars movie can ever seem to escape, even at warp speed.

But is it true?

Think about what the claim means for a moment: No matter how queer something you or I can think up is, the universe is queerer still? Despite the fact that whatever can actually exist in the universe is constrained by various facts and laws that our imaginations can simply dispense with? The claim may be true, but it should not be greeted by so many nods of recognition of a self-evident truth. The claim, after all, may also be false.

Most of what is going wrong in cosmology and astrobiology right now is the multiple protection rackets around ideas that proponents cannot live without even IF they are false. They are too afraid of what they fear to be true.

(See also: Former Canadian defense minister says: Stop wars and space aliens will share technology)

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17 Replies to “The hidden benefits of the pursuit of ET. And the hidden costs.

  1. 1

    Okay, Mr Chown, (and of course, the esteemed Dr. Haldane) I will take you up on it. The one thing that you are constitutionally incapable of supposing, is:

    “Supposing that you are wrong. Suppose there is a Creator of the Universe. Suppose He really doesn’t like you ridiculing his work. Suppose He has told you many times to cease and desist but instead you pretend He isn’t there.”

    Yup, you can’t even come close to supposing THAT.
    Amazing that you understand how much trouble you are in.

  2. 2
    bornagain77 says:

    As to these two quotes:

    If the multiverse idea is correct, then the historic mission of physics to explain all the properties of our universe in terms of fundamental principles — to explain why the properties of our universe must necessarily be what they are — is futile, a beautiful philosophical dream that simply isn’t true. Our universe is what it is because we are here.
    Alan Lightman

    “The universe is not queerer than we suppose,” he said, “it is queerer than we can suppose.”
    J. B. S. Haldane

    Well, contrary to writing physics off as futile, as the first quote indicated, and supposing that the universe will never be grasped by the human mind, as the second quote indicated, I find that the structure of reality is successfully resolved to the enterprise of physics and is grasped by the human mind if we allow that God might possibly be the foundation of physics:

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: Rather, the transcendent reality on which our universe depends must be something that can exhibit agency – a mind that can choose among the infinite variety of mathematical descriptions and bring into existence a reality that corresponds to a consistent subset of them. This is what “breathes fire into the equations and makes a universe for them to describe.” Anything else invokes random miracles as an explanatory principle and spells the end of scientific rationality.,,,

    Mathematics and Physics – A Happy Coincidence? – William Lane Craig – video

    1. If God did not exist the applicability of mathematics would be a happy coincidence.
    2. The applicability of mathematics is not a happy coincidence.
    3. Therefore, God exists.

    Also of note, even if we did have a mathematical ‘theory of everything’ it would still be ‘incomplete’:

    Kurt Gödel – Incompleteness Theorem – video

    Of related note:

    The Mathematics Of Higher Dimensionality – Gauss and Riemann – video

    The Unreasonable Effectiveness of Mathematics in the Natural Sciences – Eugene Wigner – 1960
    Excerpt: We now have, in physics, two theories of great power and interest: the theory of quantum phenomena and the theory of relativity.,,, The two theories operate with different mathematical concepts: the four dimensional Riemann space and the infinite dimensional Hilbert space,

    The Galileo Affair and Life/Consciousness as the true “Center of the Universe”
    Excerpt: I find it extremely interesting, and strange, that quantum mechanics tells us that instantaneous quantum wave collapse to its ‘uncertain’ 3D state is centered on each individual conscious observer in the universe, whereas, 4D space-time cosmology (General Relativity) tells us each 3D point in the universe is central to the expansion of the universe. These findings of modern science are pretty much exactly what we would expect to see if this universe were indeed created, and sustained, from a higher dimension by a omniscient, omnipotent, omnipresent, eternal Being who knows everything that is happening everywhere in the universe at the same time. These findings certainly seem to go to the very heart of the age old question asked of many parents by their children, “How can God hear everybody’s prayers at the same time?”,,, i.e. Why should the expansion of the universe, or the quantum wave collapse of the entire universe, even care that you or I, or anyone else, should exist? Only Theism, Christian Theism in particular, offers a rational explanation as to why you or I, or anyone else, should have such undeserved significance in such a vast universe. [15]

    Psalm 33:13-15
    The LORD looks from heaven; He sees all the sons of men. From the place of His dwelling He looks on all the inhabitants of the earth; He fashions their hearts individually; He considers all their works.

    Moreover, if we allow that God is not only the foundation of physics but that He can also ‘play the role of a person’ as Godel allowed,,,

    The God of the Mathematicians – Goldman
    Excerpt: As Gödel told Hao Wang, “Einstein’s religion [was] more abstract, like Spinoza and Indian philosophy. Spinoza’s god is less than a person; mine is more than a person; because God can play the role of a person.” – Kurt Gödel – (Gödel is considered one of the greatest logicians who ever existed)

    ,,then we find a very credible reconciliation between General Relativity and Quantum Mechanics into a ‘theory of everything’,,

    General Relativity, Quantum Mechanics, Entropy, and The Shroud Of Turin – video

    I have a parallel quote to Haldane’s ‘queerer than we can suppose’ quote,,

    “There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.”
    William Shakespeare – Hamlet

  3. 3
    bornagain77 says:


    Scientists say Turin Shroud is supernatural – December 2011
    Excerpt: And in case there was any doubt about the preternatural degree of energy needed to make such distinct marks, the Enea report spells it out: “This degree of power cannot be reproduced by any normal UV source built to date.”

    The absorbed energy in the Shroud body image formation appears as contributed by discrete values – Giovanni Fazio, Giuseppe Mandaglio – 2008
    Excerpt: This result means that the optical density distribution,, can not be attributed at the absorbed energy described in the framework of the classical physics model. It is, in fact, necessary to hypothesize a absorption by discrete values of the energy where the ‘quantum’ is equal to the one necessary to yellow one fibril.

    Particle Radiation from the Body – July 2012 – M. Antonacci, A. C. Lind
    Excerpt: The Shroud’s frontal and dorsal body images are encoded with the same amount of intensity, independent of any pressure or weight from the body. The bottom part of the cloth (containing the dorsal image) would have born all the weight of the man’s supine body, yet the dorsal image is not encoded with a greater amount of intensity than the frontal image. Radiation coming from the body would not only explain this feature, but also the left/right and light/dark reversals found on the cloth’s frontal and dorsal body images.

    Verses and Music:

    Matthew 16:26
    And what do you benefit if you gain the whole world but lose your own soul? Is anything worth more than your soul?

    Colossians 1:15-20
    The Son is the image of the invisible God, the firstborn over all creation. For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him. He is before all things, and in him all things hold together. And he is the head of the body, the church; he is the beginning and the firstborn from among the dead, so that in everything he might have the supremacy. For God was pleased to have all his fullness dwell in him, and through him to reconcile to himself all things, whether things on earth or things in heaven, by making peace through his blood, shed on the cross.

    Natalie Grant – Alive (Resurrection music video)
    Lyric “Death has lost and Love has won!”

  4. 4
    Jaceli123 says:

    @bornagain77 I cant find a reference you linked about 400 scientists rejecting or questioning the darwinian mechanism of mutations and natural selection!

  5. 5
    bornagain77 says:

    Scientific Dissent From Darwinism List

    A Creationist Interviews Lawrence Krauss – podcast
    Excerpt: – 3,000 scientists and professors, nearly, (most of whom hold a Ph.D. in some field of science) who reject secular Darwinism to varying degrees as named online by Dr. Jerry Bergman
    – 30,000 U.S. public high school biology teachers do not endorse Darwinism in class
    – 100,000 college professors in the U.S. alone who, according to Harvard researchers, agree that “intelligent design IS a serious scientific alternative to the Darwinian theory of evolution.”
    – 570,000 medical doctors in the U.S., specialists in applied science, say God brought about or directly created humans. Whereas Darwinsim is dominated by storytelling, the field of medicine is an actual applied science (see definition and applied science section below) within biology that is practiced by highly educated professionals. Thus it is significant that 60% of all U.S. medical doctors reject the strictly secular Darwinist explanation for our existence, with three of five docs agreeing that either God initiated and guided the process that led to human life or that God specially created human beings as we are.

  6. 6
    Jaceli123 says:

    Thanks @bornagain77 by the way I have to tell you something that happened at my school today. Your not going to believe what happened at school today. My teacher tried to tell us that the belief in God does not stack up to science. That religion is faith based and science is not. He had a attitude that screamed atheism and materialism. He said the ID community believes that God magically made life just poof into existence and that the evidence for darwinian evolution is overwhelming. He then brought up the old atheist spaghetti monster argument. Ill I did was giggle but many kids became skeptical when they questioned Gods existence.this is too much even for a teacher. To tell kids that belief in God is ajoke and then to laugh about it is very wrong. Im pissed at my teacher from every aspect of his lecture. It seems securalism has reeked and snuk its self into the future of society, my generation!

  7. 7
    Timaeus says:


    If you are in a state-funded school, you could in principle launch a complaint against your teacher for violating church and state separation. Of course, you should talk to your parents and others before contemplating any drastic action, but if the teacher persists in this behavior, he is doing exactly what the other side says creationists are trying to do.

    However, I suggest a more cautious approach, one will which not turn your teacher angrily against you. You can very gently embarrass the teacher by asking a very simple question in class: Teacher, can you direct me to an ID-supporting book or article in which it is said that God magically made life poof into existence. Ten to one the teacher cannot name any such book or article. At best he will be able to cite Of Pandas and People, which was not a true ID book but a creationist book slightly edited with ID language. And the publisher has since replaced Of Pandas and People with The Design of Life, which makes no such claims.

  8. 8
    Jaceli123 says:

    Thanks timaeus I really didn’t really have a problem with the teacher but my problem was that fact that he brought the subject up. Were I live in Texas everyone is either a muslim or christian so when a teacher questions gods existence the other students don’t know how to refute it. They have never heard these arguments before like I have so its hard to come up with answers. He said that tomorrow we will watch a video on the flying spaghetti monster argument brought up by atheists on youtube. This has gone to far. Why cant we just discuss the lesson without getting into a philosophical discussion about religion. I thought it was biology class not philosophy basics 101. This just shows that he’s trying to push more than what he’s supposed to!

  9. 9
    bornagain77 says:

    Jaceli123, do you have a way to secretly record him? If so, that would make a very, very, interesting video. Although be forewarned that if he found out that you were the one who recorded his proselytizing in class he probably would retaliate against you by flunking you. Might be best to secretly record him now and wait until you pass his class to release the video this summer of his most flamboyant moments,,, And because of the irrational, over the top, hostility towards ID proponents, it is best at this moment, especially if you are a student, not to directly challenge a Darwinist, but to quietly infiltrate deeper into science and Academia.,,, These resources may be of help for you:

    Preparing Students to Intelligently Question Darwin This Fall – 2009

    A Parent’s Guide to Intelligent Design –


    EXPELLED – Starring Ben Stein – video

    “In the last few years I have seen a saddening progression at several institutions. I have witnessed unfair treatment upon scientists that do not accept macroevolutionary arguments and for their having signed the above-referenced statement regarding the examination of Darwinism. (Dissent from Darwinism list)(I will comment no further regarding the specifics of the actions taken upon the skeptics; I love and honor my colleagues too much for that.) I never thought that science would have evolved like this. I deeply value the academy; teaching, professing and research in the university are my privileges and joys… ”
    Professor James M. Tour – one of the ten most cited chemists in the world

    Slaughter of Dissidents – Book
    “If folks liked Ben Stein’s movie “Expelled: No Intelligence Allowed,” they will be blown away by “Slaughter of the Dissidents.” – Russ Miller

    Origins – Slaughter of the Dissidents with Dr. Jerry Bergman – video

    Slaughter of the Dissidents – Dr. Jerry Bergman – June 2013 – video

  10. 10
    Jaceli123 says:

    @Bornagain77 I was going to do that but I was too late and by the way thanks for the links. By the way do you know what the flying spaghetti atheist video?

  11. 11
    bornagain77 says:

    Well, it should not be too hard to catch him in his proselytizing at some other time if he really is as over the top as you say. As to the FSM video, Not exactly, but I believe the FSM is referenced, and falsified, somewhere in this video;

    Divinely Planted Quantum States – video

  12. 12
    Jaceli123 says:

    Thanks @bornagain77 for the links. BTW my teacher showed me this video
    http://m.youtube.com/watch?v=gJVjTh98aHU want to know your thoughts.

  13. 13
    bornagain77 says:

    As to Shannon information:

    Measuring the functional sequence complexity of proteins – Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors – 2007
    Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families.,,,

    The Evolution-Lobby’s Useless Definition of Biological Information – Feb. 2010
    Excerpt: By wrongly implying that Shannon information is the only “sense used by information theorists,” the NCSE avoids answering more difficult questions like how the information in biological systems becomes functional, or in its own words, “useful.”,,,Since biology is based upon functional information, Darwin-skeptics are interested in the far more important question of, Does neo-Darwinism explain how new functional biological information arises?

    Mutations, epigenetics and the question of information
    Excerpt: By definition, a mutation in a gene results in a new allele. There is no question that mutation (defined as any change in the DNA sequence) can increase variety in a population. However, it is not obvious that this necessarily means there is an increase in genomic information.,, If one attempts to apply Shannon’s theory of information, then this can be viewed as an increase. However, Shannon’s theory was not developed to address biological information. It is entirely unsuitable for this since an increase of information by Shannon’s definition can easily be lethal (and an increase in randomness increases Shannon ‘information’).

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

    Testable hypotheses about FSC

    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.

    Kirk Durston – Functional Information In Biopolymers – video

    (A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
    Excerpt (Page 4): The Probabilities Get Worse
    This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.

    And here is the paper from Durston and company:

    Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring – Kirk K Durston, David KY Chiu, Andrew KC Wong and Gary CL Li – 2012
    The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function.
    Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

    At the 17 minute mark of the following video, Winston Ewert speaks on how functional information is measured in proteins:

    Proposed Information Metric: Conditional Kolmogorov Complexity (Ewert) – July 2012 – video

  14. 14
    bornagain77 says:

    as to Nylonase:

    Nylon Degradation – Analysis of Genetic Entropy
    Excerpt: At the phenotypic level, the appearance of nylon degrading bacteria would seem to involve “evolution” of new enzymes and transport systems. However, further molecular analysis of the bacterial transformation reveals mutations resulting in degeneration of pre-existing systems. The most studied of the nylon degrading bacteria is Arthrobacter sp. K172 (formerly Flavobacterium sp.70). This bacterium employs three enzymes for nylon degradation, EI (NylA), EII (NylB), and EIII (NylC), which are found on the plasmid, pOAD2.71, 72 EI and EIII (also NylC in Agromyces sp.) have been initially characterized.73, 72 They apparently hydrolyze the cyclic forms of some nylons, which provides a linear substrate for EII. However, no detailed analysis of the mutational changes of EI or EIII has yet been performed.
    The mutational changes of EII (6-aminohexanoatedimer hydrolase) have been characterized in detail. This analysis suggests that point mutations in a carboxyesterase gene lead to amino acid substitutions in the enzyme’s catalytic cleft. This altered the enzyme’s substrate specificity sufficiently that it could also hydrolyze linear nylon oligomers.74, 75 Yet, the EII enzyme still possesses the esterase function of the parent esterase. Thus, the mutational alteration results in a reduction of the parent enzyme’s specificity (Figure 4). This enables it to hydrolyze a wider range of oligomers that include nylon oligomers.76
    Nonetheless, reduced specificity of a pre-existing enzyme is biochemically degenerative to the enzyme,77, 78 even if it provides a presumed phenotypic benefit. The “beneficial” phenotype of nylon degradation requires the a priori existence of the enzyme and its specificity. Its degeneration is not a mechanism that accounts for the origin of either the enzyme or its specificity.,,,

    Nylon Eating Bacteria: NOT NEW INFORMATION – video

    The three-dimensional structure of nylon hydrolase and the mechanism of nylon-6 hydrolysis – Seiji Negoro – Dec. 2011
    SUMMARY: We performed x-ray crystallographic analyses of the 6-aminohexanoate oligomer hydrolase (NylC) from Agromyces sp. at 2.0 Å-resolution. This enzyme is a member of the N-terminal nucleophile (N-tn) hydrolase superfamily that is responsible for the degradation of the nylon-6 industry byproduct.
    We observed four identical heterodimers (27kDa+9kDa), which resulted from the autoprocessing of the precursor protein (36kDa) and which constitute the doughnut-shaped quaternary structure. The catalytic residue of NylC was identified as the N-terminal Thr267 of the 9kDa-subunit. Furthermore, each heterodimer is folded into a single domain, generating a stacked (greek symbols) core structure. Amino acid mutations at subunit interfaces of the tetramer were observed to drastically alter the thermostability of the protein. In particular, four mutations (D122G/H130/D36A/E263Q) of wild-type NylC from Arthrobacter sp. (plasmid pOAD2-encoding enzyme), with a heat denaturation temperature of T m=52°C, enhanced the protein thermostability by 36°C (T m=88° C), whereas a single mutation (G111S or L137A) decreased the stability by approximately 10°C. We examined the enzymatic hydrolysis of nylon-6 by the thermostable NylC mutant. Argon-cluster secondary ion mass spectrometry analyses of the reaction products revealed that the major peak of nylon-6 (m/z 10,000-25,000) shifted to a smaller range, producing a new peak corresponding to m/z 1500-3000 after the enzyme treatment at 60°C. In addition, smaller fragments in the soluble fraction were successively hydrolyzed to dimers and monomers. Based on these data, we propose that NylC should be designated as nylon hydrolase (or nylonase). Three potential uses of NylC for industrial and environmental applications are also discussed.

  15. 15
    bornagain77 says:

    as to Lenski’s Citrate:

    Multiple Mutations Needed for E. Coli – Michael Behe
    Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we’ve seen evolution do, then there’s no reason to believe evolution could produce many of the complex biological features we see in the cell.

    Rose-Colored Glasses: Lenski, Citrate, and BioLogos – Michael Behe – November 13, 2012
    Excerpt: Readers of my posts know that I’m a big fan of Professor Richard Lenski, a microbiologist at Michigan State University and member of the National Academy of Sciences. For the past few decades he has been conducting the largest laboratory evolution experiment ever attempted. Growing E. coli in flasks continuously, he has been following evolutionary changes in the bacterium for over 50,000 generations (which is equivalent to roughly a million years for large animals). Although Lenski is decidedly not an intelligent design proponent, his work enables us to see what evolution actually does when it has the resources of a large number of organisms over a substantial number of generations. Rather than speculate, Lenski and his coworkers have observed the workings of mutation and selection.,,,
    In my own view, in retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski’s work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient — that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism.

    Innovation or Renovation? By Ann Gauger – Sept. 24, 2012
    Excerpt: But how significant was this innovation (citrate; Lenski)? In his paper in Quarterly Review of Biology, Dr. Michael Behe pointed out that E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available). He postulated that a change in gene regulation could turn on citrate transport and permit growth on citrate under aerobic conditions.
    After an enormous amount of work, having sequenced the genomes of many clones along the lineages that led to the ability to use citrate, as well as lineages that never did, and testing the phenotypes of identified mutations, Blount et al. have now reported that Behe was largely right. The key innovation was a shift in regulation of the citrate operon, caused by a rearrangement that brought it close to a new promoter.

  16. 16
    bornagain77 says:

    Hemoglobin/gene duplication:

    Gene Duplication and the Origin of Novel Biological Information: A Case Study of the Globins – Jonathan M – 2012
    In summary, we have seen that the scope for evolution of novel genes and proteins by virtue of gene duplication and subsequent divergence or recruitment is very limited, even in facilitating relatively trivial functional innovations. Given the extremely diverse array of protein conformations found in living systems, the likelihood of the relatedness of genes — even within gene families — may be treated with suspicion and healthy skepticism. It is somewhat ironic that biologists are all too willing to accept a statistical argument against two or more proteins with similar sequences arising independently by chance, but are completely unwilling to consider statistical arguments against them arising by chance at all.

    Experimental evolution of gene duplicates in a bacterial plasmid model.- 2007
    The fate of gene duplicates subjected to diversifying selection was tested experimentally in a bacterial system.,,,
    In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow.,,,

    Douglas Axe and Ann Gauger Argue that Design Best Explains New Biological Information – Casey Luskin August 26, 2013
    Excerpt: Axe and Gauger observe that “The most widely accepted explanation for the origin of new enzymes is gene duplication and recruitment.” However, they cite experimental work showing that a duplicate gene is much more likely to be silenced (because of the costly resources expended in transcribing and translating it) than it is to acquire a new function.

    Evolution by Gene Duplication Falsified – December 2010
    Excerpt: The various postduplication mechanisms entailing random mutations and recombinations considered were observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of generating genuinely distinct and entirely novel functionality. Contrary to Darwin’s view of the plasticity of biological features, successive modification and selection in genes does indeed appear to have real and inherent limits: it can serve to alter the sequence, size, and function of a gene to an extent, but this almost always amounts to a variation on the same theme—as with RNASE1B in colobine monkeys. The conservation of all-important motifs within gene families, such as the homeobox or the MADS-box motif, attests to the fact that gene duplication results in the copying and preservation of biological information, and not its transformation as something original.

    The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway – Ann K. Gauger and Douglas D. Axe – April 2011
    Excerpt: 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.

    Can Random Mutations Create New Complex Features? A Response to TalkOrigins – Casey Luskin June 22, 2012
    Excerpt: the (talkorigins) page suggests searching for “gene duplication” on PubMed to find “more than 3000 references” on the topic. These papers, we’re meant to assume, show how evolutionary mechanisms can create new information. But a survey of major review articles on gene duplication I published here on ENV in 2010 revealed that the studies never established that mutations could have produced the complex features in question. After taking a close look at this literature, I found:
    The NCSE’s (and Judge Jones’s) citation bluffs have not explained how neo-Darwinian mechanisms produce new functional biological information. Instead, the mechanisms invoked in these papers are vague and hypothetical at best:

    *exons may have been “recruited” or “donated” from other genes (and in some cases from an “unknown source”);
    *there were vague appeals to “extensive refashioning of the genome”;
    *mutations were said to cause “fortuitous juxtaposition of suitable sequences” in a gene-promoting region that therefore “did not really ‘evolve'”;
    *researchers assumed “radical change in the structure” due to “rapid, adaptive evolution” and claimed that “positive selection has played an important role in the evolution” of the gene, even though the function of the gene was unknown;
    *genes were purportedly “cobbled together from DNA of no related function (or no function at all)”;
    *the “creation” of new exons “from a unique noncoding genomic sequence that fortuitously evolved” was assumed, not demonstrated;
    *we were given alternatives that promoter regions arose from a “random genomic sequence that happens to be similar to a promoter sequence,” or that the gene arose because it was inserted by pure chance right next to a functional promoter.
    *explanations went little further than invoking “the chimeric fusion of two genes” based solely on sequence similarity;
    *when no source material is recognizable, we’re told that “genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors” because they are simply “hypermutable”;
    *we even saw “a striking case of convergent evolution” of “near-identical” proteins.

    To reiterate, in no case were the odds of these unlikely events taking place actually calculated. Incredibly, natural selection was repeatedly invoked in instances where the investigators did not know the function of the gene being studied and thus could not possibly have identified any functional advantages gained through the mutations being invoked. In the case where multiple mutational steps were involved, no tests were done of the functional viability of the alleged intermediate stages. These papers offer vague stories but not viable, plausibly demonstrated explanations for the origin of new genetic information.
    I haven’t gone through all “3000 references” cited by TalkOrigins. Neither, in all likelihood, has the author of the TalkOrigins page. But my strong suspicion is that if you went through many of those pages, you’d reach the same conclusion.
    This 3000-unnamed-paper citation bluff — and much other material on this TalkOrigins page, are not to be taken seriously.

    Hopeless Matzke – David Berlinski & Tyler Hampton (Refutation of all the main examples purporting to show the origination of new information by Darwinian processes) – August 18, 2013

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    Jaceli123 says:

    Wow @bornagain77 thats more information than I thought. Thanks alot sorry for asking you. Thanks again like always! BTW my teacher did not talk about God or the spagheti monster because his computer was not working and I got notes on our subject this month. Its nothing new that Ive never heard before. Anyway thanks again!

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