Intelligent Design

Enzymes Complex from the Get-go

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In a seemingly stunning laboratory tour de force, scientists were able to extract ancient enzymatic samples and analyze their structure. From the information so gleaned, they built and tested a synthetic enzyme.

Here’s what they report:

” . . . we found that enzymes that existed in the Precambrian era up to four billion years ago possessed many of the same chemical mechanisms observed in their modern-day relatives.”

And what were their Darwinian expectations?

“Given the ancient origin of the reconstructed thioredoxin enzymes, with some of them predating the buildup of atmospheric oxygen, we expected their catalytic chemistry to be simple.”

And given the ID perspective, what would we have expected?

We would have expected an almost identical degree of complexity simply because the phase space/configuration space of proteins is so immense, and the workings of the cell so complex, that only finely-tuned proteins (enzymes) could operate under these constraints. And we would therefore expect that similar chemical mechanisms would have been at play even at the beginning of cellular life.

Now ask yourself: what would have happened if these scientists had stated this as their purpose when they began: “We want to test ID predictions versus Darwinian predictions (simple systems gradually become complex systems)”?

You see, right now, ID can be put to the test. Yet instead, scientists will test ONLY Darwinian expectations, with the almost sure-fire reaction to their experimental results being, “We were quite surprised to find ………(fill in the blank).” And, as many tests as Darwinism fails, it still remains, in the mind of these scientists, the only working “hypothesis” (theory???) they’ll bring to the lab. Interesting.

14 Replies to “Enzymes Complex from the Get-go

  1. 1
    PaV says:

    Here’s a fine article on where evolutionary theory is today. Hopefully you have limited access to NewScientist.

  2. 2
    DrBot says:

    We would have expected an almost identical degree of complexity simply because the phase space/configuration space of proteins is so immense, and the workings of the cell so complex, that only finely-tuned proteins (enzymes) could operate under these constraints. And we would therefore expect that similar chemical mechanisms would have been at play even at the beginning of cellular life.

    Why would ID predict that? after all an unknown designer with unknown powers could have used a completely different chemical configuration for that era. In fact the various stages of life observed in the fossil record might have been different experimental stages in the design process.

    The only way you can reasonably make an inference about early life chemistry in this way is if you know something of the methods and motives of the designer.

  3. 3
    bornagain77 says:

    Given that this enzyme, which is vital for all lifeforms, was ‘reconstructed’ from a large data set of its supposed ‘descendent modern enzymes’, yet is shown to be more robust than its modern enzymes,,,

    “Further examination of the ancient enzymes revealed some striking features: The enzymes were highly resistant to temperature and were active in more acidic conditions. The findings suggest that the species hosting these ancient enzymes thrived in very hot environments that since then have progressively cooled down, and that they lived in oceans that were more acidic than today.”

    ,,, Then I would say that this study of a vital enzyme conforms to the principle of ‘Genetic Entropy’ in that the ancient enzyme was shown to be more functionally complex than its modern descendents, in as far a direct descendant relationship can be traced, (which won’t be far)! As well, I would also like to point out that this study conforms to the ‘design notion’ of ‘terra-forming’ of the ancient toxic primordial earth into a place habitable for higher life;

    Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. – Paul G. Falkowski – Professor Geological Sciences – Rutgers
    http://www.bioinf.uni-leipzig......g_2008.pdf

  4. 4
    DrBot says:

    It is a bit like looking at modern computers and then saying that the first computers must also have used silicon as the semi-conducting element, when in reality the first ‘computers’ were mechanical, then used valves …

    punctuated equilibrium 😉

  5. 5
    Upright BiPed says:

    Dr Bot,

    In #2 you posted a quote from PAV where he explicitly tells you “why”…then you follow his quote with a question as to “why”.

    Why?

  6. 6
    bornagain77 says:

    DrBot, in so far as we would expect the designer to be God, we would expect that, far from how human technology is arrived at, that ‘when’ the design is implemented we would expect that it would be a ‘optimal design’ with any further ‘natural derivation’ of that initial design to follow ‘entropic’ patterns of deterioration. Which is exactly the pattern we find from all initial data sets.

  7. 7
    DrBot says:

    UB:

    I don’t think you understood my comment.

    An unknown designer with unknown abilities does not have to use the same mechanisms for life back then as it is used in life now. PaV is making a prediction that doesn’t stand up because if you infer an intelligent designer with unknown powers then you can also ‘predict’ that life back then bore no chemical relation to life now, or that it did – it all depends on what the designer was up to at the time so making a clear prediction requires knowledge about their motives and methods.

    If PaV is claiming that life can only function if it uses a chemical configuration that is the same as that which we observe today then he is making quite a strong claim – one that would need some evidence to back it up!

  8. 8
    bornagain77 says:

    DrBot, once again you state;

    ‘if you infer an intelligent designer with unknown powers then you can also ‘predict’ that life back then bore no chemical relation to life now, or that it did – it all depends on what the designer was up to at the time so making a clear prediction requires knowledge about their motives and methods.’

    especially this;

    ‘then you can also ‘predict’ that life back then bore no chemical relation to life now’

    That does not follow, for if we infer God as the designer, which is more than reasonable given the transcendent origin and extreme fine-tuning of the entire universe, then we can infer He has infinite knowledge to be able to arrive at exactly which specific enzymes will be optimal for each specific chemical reaction He wishes to implement in life. Thus since a unique optimal ‘specific amino acid sequence’ can reasonably be expected for each specific enzyme for each specific chemical reaction, then it follows that we can ‘predict’ that life ‘back then’ does indeed bear a ‘chemical relation’ to life today. i.e. the same chemistry is as valid today as it was ‘back then’!

  9. 9
    Mung says:

    It is a bit like looking at modern computers and then saying that the first computers must also have used silicon as the semi-conducting element, when in reality the first ‘computers’ were mechanical, then used valves …

    Excellent point!

    You must be an ID critic.

    Folks, let’s not forget that even ID’ists ought to be free to critique comments about ID made by other ID’ists without immediately being placed into a box labeled ‘enemy.’

  10. 10
    kairosfocus says:

    Dr B:

    But actually, this is what PAV said:

    given the ID perspective, what would we have expected?

    We would have expected an almost identical degree of complexity simply because the phase space/configuration space of proteins is so immense, and the workings of the cell so complex, that only finely-tuned proteins (enzymes) could operate under these constraints. And we would therefore expect that similar chemical mechanisms would have been at play even at the beginning of cellular life.

    In short, in a complex, key-lock environment (the ONLY life environment we have any evidence for) only the parts that fit will work; which will happen as well to be complex. Just as with spare parts for your car.

    And, this is what happened when investigators went and found themselves a minimally complex organism, in the hope they would find a trend of simpler parts; Sci Daily:

    When studying both its proteome [[set of proteins used by an organism] and its metabolome [[the metabolic reaction network that carries out the energy-related chemical life processes of a cell], the scientists found many molecules were multifunctional, with metabolic enzymes catalyzing multiple reactions, and other proteins each taking part in more than one protein complex. They also found that M. pneumoniae couples biological processes in space and time, with the pieces of cellular machinery involved in two consecutive steps in a biological process often being assembled together.

    Remarkably, the regulation of this bacterium’s transcriptome is much more similar to that of eukaryotes — organisms whose cells have a nucleus — than previously thought. As in eukaryotes, a large proportion of the transcripts produced from M. pneumoniae’s DNA are not translated into proteins. And although its genes are arranged in groups as is typical of bacteria, M. pneumoniae doesn’t always transcribe all the genes in a group together, but can selectively express or repress individual genes within each group.

    Cornelius Hunter therefore aptly remarked:

    Many of M. pneumoniae’s molecules are multifunctional.
    ? M. pneumoniae’s transcribed [[DNA] is much more similar to that of eukaryotes. As in eukaryotes, a large proportion of the transcripts produced from M. pneumoniae’s DNA are not translated into proteins.
    ? M. pneumoniae’s gene expression is more complex than expected.
    ? M. pneumoniae is incredibly flexible and readily adjusts its metabolism to drastic changes in environmental conditions. This adaptability and its underlying regulatory mechanisms mean M. pneumoniae has the potential to adapt quickly.
    It is exactly the opposite of what [[materialistic] evolution would expect. Rather than an evolutionary pattern, M. pneumoniae designs are unique, novel, sophisticated and finely-tuned.

    This has been a long day [in which I have had to be looking at a regulatory law that is twice the length of the seriously flawed draft constitution for M/rat, and found predictable errors in approach and philosophy . . . ], and I am finding that it is like the objectors are predictably, consistently wrong, and in ways that seem wrong-headed.

    Why is that?

    From where I sit it looks a lot like there is a systematically wrong perspective at work, that keeps on coming up wrong, but if you are locked into the idea the world “must” be that way . . .

    GEM of TKI

  11. 11
    bornagain77 says:

    Notes on ‘optimality’ found in life;

    Metabolism: A Cascade of Design
    Excerpt: A team of biological and chemical engineers wanted to understand just how robust metabolic pathways are. To gain this insight, the researchers compared how far the errors cascade in pathways found in a variety of single-celled organisms with errors in randomly generated metabolic pathways. They learned that when defects occur in the cell’s metabolic pathways, they cascade much shorter distances than when errors occur in random metabolic routes. Thus, it appears that metabolic pathways in nature are highly optimized and unusually robust, demonstrating that metabolic networks in the protoplasm are not haphazardly arranged but highly organized.
    http://www.reasons.org/metabolism-cascade-design

    Making the Case for Intelligent Design More Robust
    Excerpt: ,,, In other words, metabolic pathways are optimized to withstand inevitable concentration changes of metabolites.
    http://www.reasons.org/making-.....ore-robust

    Also of note; Sometimes evolutionists will point to the Rubisco Enzyme as an example of ‘bad design’, but it turns out the Rubisco Enzyme is indeed optimal for the purpose to which it was created for supporting higher life forms above it. Higher life forms that the Rubisco is not aware of, nor cares about.

    Rubisco is not an example of unintelligent design – David Tyler
    Excerpt: Rubisco’s ability to capture CO2 increases with increasing CO2 content in the atmosphere, so its efficiency rises in a CO2-rich atmosphere. However, increasing oxygen levels in the atmosphere will reduce Rubisco’s ability to capture carbon. So a negative feedback mechanism exists to regulate the relative concentrations of oxygen and carbon dioxide in the atmosphere. This is another example of design affecting the Earth’s ecology,,
    http://www.arn.org/blogs/index.....nintellige

    What I find very persuasive, to the suggestion that the universe was designed with life in mind, is that physicists find many processes in a cell operate at the ‘near optimal’ capacities allowed in any physical system:

    William Bialek – Professor Of Physics – Princeton University:
    Excerpt: “A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,,”
    http://www.princeton.edu/~wbialek/wbialek.html

    Physicists Finding Perfection… in Biology — June 1st, 2009 by Biologic Staff
    Excerpt: “biological processes tend to be optimal in cases where this can be tested.”
    http://biologicinstitute.org/2.....n-biology/

    Further note on ‘chemistry’ being ‘set up’ for life;

    As a sidelight to this, every class of elements that exists on the periodic table of elements is necessary for complex carbon-based life to exist on earth. The three most abundant elements in the human body, Oxygen, Carbon, Hydrogen, ‘just so happen’ to be the most abundant elements in the universe, save for helium which is inert. A truly amazing coincidence that strongly implies ‘the universe had us in mind all along’. Even uranium the last naturally occurring element on the period table of elements is necessary for life. The heat generated by the decay of uranium is necessary to keep a molten core in the earth for an extended period of time, which is necessary for the magnetic field surrounding the earth, which in turn protects organic life from the harmful charged particles of the sun. As well, uranium decay provides the heat for tectonic activity and the turnover of the earth’s crustal rocks, which is necessary to keep a proper mixture of minerals and nutrients available on the surface of the earth, which is necessary for long term life on earth. (Denton; Nature’s Destiny). These following articles and videos give a bit deeper insight into the crucial role that individual elements play in allowing life:

    The Elements: Forged in Stars – video
    http://www.metacafe.com/watch/4003861

    Michael Denton – We Are Stardust – Uncanny Balance Of The Elements – Fred Hoyle Atheist to Deist/Theist – video
    http://www.metacafe.com/watch/4003877

    The Role of Elements in Life Processes
    http://www.mii.org/periodic/LifeElement.php

    Periodic Table – Interactive web page for each element
    http://www.mii.org/periodic/MiiPeriodicChart.htm

    Proteins prove their metal – July 2010
    Excerpt: ‘Nearly half of all enzymes require metals to function in catalysing biological reactions,’ Kylie Vincent, of Oxford University’s Department of Chemistry tells us. ‘Both the metal and the surrounding protein are crucial in tuning the reactivity of metal catalytic centres in enzymes.’ These ‘metal centres’ are hives of industry at a microscopic scale, with metals often held in a special protein environment where they may be assembled into intricate clusters inside proteins.

  12. 12
    PaV says:

    DrBot:

    If PaV is claiming that life can only function if it uses a chemical configuration that is the same as that which we observe today then he is making quite a strong claim – one that would need some evidence to back it up!

    The best thing I can advise is to reread
    what I wrote. I said that because of the
    complexity of the cell, and because of the
    enormous size of the configuration space of
    proteins, that even ab initio a high
    level of complexity would have been
    needed.

    I didn’t say that it would be the “same”
    chemical mechanisms. I implied that it
    would be the same level of complexity with
    “similar” chemical mechanisms.

    However, it is very likely that the chemical mechanisms would be the very very similar; almost the same.

    We are fundamentally dealing with little
    quantum computers when we treat of
    proteins. Protein-protein interactions take place at the quantum level.

    This said, then in order for a great number
    of proteins (quantum computers) to work in
    an integrated fashion will therfore dictate
    that there be very clear quantum differences within the proteins.

    And, yet, those quantum differences cannot
    be huge, or otherwise the kind of bonding
    that would take place would be of such a
    strong type that the cell would lose flexibility in its overall structure(s).

    Therefore, given all of these constraints,
    and given that for all these constraints
    work simultaneously a great level of
    “specificity” is needed, then one would
    expect—simply for life to exist (whether
    ancient or new)—that proteins would be so
    constructed as to provide for clear, but not excessively large, differences amongst all of the proteins present.

    These “specificity” differences would then look like—would have to look like, for the proper operation of the cell—the kind of complex relationships that today hold in cellular life.

    This is a simple, straightforward extrapolation of basic chemistry, and an acknowledgment of the tremendous improbability of actual protein constructions.

  13. 13
    tragic mishap says:

    Or you could be a creationist and predict that animals only reproduce after their kinds and therefore have remained the within certain boundaries throughout history, young earth or old.

  14. 14
    PaV says:

    tragic mishap:

    What if I’m correct? Do you refuse to accept it because it corresponds to what a creationist might think? Is that your basis for rejection of what turns out to be true?

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