What Real Science Looks Like

Following up on yesterday’s post, the July 21 issue of Science also contained this review article, entitled “Evolution of the Molecular Machines for Protein Import into Mitochondria.” The authors write:

Here we look at how protein import pathways were established to create mitochondria. The protein import pathway is driven by a set of molecular machines, and these machines are of modular design. Each machine has a core module that seems to be common to all eukaryotes. Additional modules have been added to each machine over time, with these add-ons being common only to particular eukaryotic lineages. The evolution and comparative aspects of the function of these mitochondrial machines provides a blueprint for understanding the evolution of cellular machinery in general and a rich means of determining the precise function of these sophisticated machines. That most of the machinery was created de novo and established in the mitochondrial membranes of the first eukaryote supports the idea that all eukaryotes are descendants of a single ancestor species.

So here we have a complex set of machines importing protein into mitochondria. Indeed, as the remainder of the article makes clear, these machines satisfy the ID definition of irreducible complexity. Yet, while the precise nature of these machines varies from eukaryote to eukaryote, all are merely variations on the same basic theme. I find that rather suggestive.

From here the article goes on to provide a detailed discussion of the likely evolutionary history of the various proteins involved in these systems. Alas, this part is rather dense and short on quotable nuggets, but it does become clear that cooptation of preexisting parts for new functions played an important role. For example:

In the course of transforming from endosymbiont to mitochondria, most of the genes encoding bacterial proteins were transferred into the host nucleus. To ensure the delivery and the assembly of these proteins in the newly established organelle, protein import machinery was needed. Some of the preexisting protein translocation apparatus of the endosymbiont appears to have been commandeered, with molecular chaperones such as mHsp70 and Oxa1 derived from the bacterial chaperones DnaK and YidC, respectively.

The authors close the article with a nice summary and a description of possible directions for future research:

Through looking further afield into the genomes of more and more classes of eukaryotes, it now appears that the molecular machines that drive protein import into mitochondria are of modular design. Core modules representing the translocation channels for each machine are common to all eukaryotes. Additional modules have been added over time, being common only to particular eukaryotic lineages. This provides additional means to analyze the vexing questions in the evolution of eukaryotes. Evolutionary details of the machines also provide a means from which to decipher aspects of machine function, complementing details gained from biochemical studies on the machines of one or more model species. Some exciting questions are being raised from considerations of evolution:

They then list several questions that are more technical than what I wish to include here.

This, you see, is how real scientists respond to the fact of biological complexity. By rolling up their sleeves and getting their hands dirty. This was a short review article, yet it had fifty-seven references. The authors ferreted out the patterns that were emerging from the hard work done by numerous previous scientists and demonstrated that they point to a clear evolutionary scenario for the formation of these complex machines. They then showed how evolutionary reasoning points towards possible furture research.

Compare that to the way ID folks treat complex molecular machines. They just sit there, slack-jawed, never getting beyond childish bleats about how they’re just too darn complex to have evolved. If they respond to this article at all it will only be to dismiss it, unread, as insufficiently detailed for their tastes.

A common refrain from ID folks is that they are not treated respectfully by scientists. One reason for that lack of respect is the fact that there is no respect coming the other way. Countless scientists toil in obscurity to unravel the evoution of one particular set of complex molecular machines. The sheer hard work and brain power leading up to this article is remarkable.

The ID folks don’t care. Instead, Ann Coulter publishes a hundred pages or so of wall-to-wall lies about evolution, and William Dembski brags about being her science consultant. Jonathan Wells writes a book called The Politically Incorrect Guide to Darwinism and Intelligent Design for the right-wing press Regnery. You can be sure it will contain nothing that is both true and important. Michael Behe can only fold his arms and shake his head when confronted with the enormous amount of empirical evidence against his argument (meanwhile making no contributions of his own beyond some breathtakingly unrealistic mathematical models). And the whole lot of them screech, banshee-like, about how ID is going to carry the day, and how Darwinism is just an empty ideology.

Shame on anyone who deals with respectfully with such people.

Comments

  1. #1 Bruce Thompson
    July 28, 2006

    Excited by certain titillating words like molecular machines, the ID proponents will continue pouring through journals looking for pubjacking sources (1). Their behavior is somewhat demeaning but is really just another effort to find a cheap form of entertainment. Common sense and a reading of the journal article instead of looking at the pictures would redirect the blood flow to higher cognitive centers where they would realize that these articles discuss concepts counter to their fantasies.

    Arguments from the data based on an alternative model which generates testable hypotheses would help alleviate the desire to pubjack. The real thing is much more satisfying.

    (1) Mister DNA proposed the term pubjacking in “The State of ID Research” comments section.

  2. #2 Mesk
    July 28, 2006

    The protein import pathway is driven by a set of molecular machines, and these machines are of modular design. Each machine has a core module that seems to be common to all eukaryotes. Additional modules have been added to each machine over time… most of the machinery was created de novo and established in the mitochondrial membranes of the first eukaryote…

    Actually, it’s hard to imagine a paragraph providing better propaganda value to teleologists.

  3. #3 gengar
    July 29, 2006

    Actually, it’s hard to imagine a paragraph providing better propaganda value to teleologists.

    Well, I for one wouldn’t be at all surprised if this isn’t Uncommon Descent’s ‘Superficially Relevent Paper of the Week’.

  4. #4 mark
    July 29, 2006

    Common sense and a reading of the journal article instead of looking at the pictures would redirect the blood flow…

    Somehow this imagery applied to Intelligent Design Creationists seems distasteful. But I wonder, has ID switched from the vision of the watchmaker who designs individual gears to make the watch, to the computer maker who grabs a power module here, a motherboard there, and various other pre-designed modules to assemble his product?

  5. #5 Bruce Thompson
    July 29, 2006

    Somehow this imagery applied to Intelligent Design Creationists seems distasteful.

    It seemed more appropriate than the more descriptive mental mas… that seems to be the stock and trade of many and an easily visualized derivative of pubjacking. ID is capable of generating questions the problem lies in testing those questions. Instead we hear hand waving arguments and rationalizations.

    This behavior is not limited to redefining mainstream publications as ID research. Fundamental approaches to research have been appropriated and redefined as ID concepts by ID proponents. For example, Scott Minnich writes:

    “Behe [17] has proffered the concept of irreducible complexity using the flagellum as a paradigmatic example. It is this very concept that has been the bread and butter of molecular geneticists allowing them to identify genes in any given system by loss of function.”

    Implying the Behe’s IC concept was the impetus for knockout experiments when nothing is further from the truth.

  6. #6 Gerry L
    July 30, 2006

    Aren’t we about due for a 10-year anniversary reissue of Behe’s “Darwin’s Black Box”? Certainly it will be updated to reflect some of the research that was inspired by the book — and Behe’s own work over the past decade. It will be interesting to see the list of new references to papers based on and supporting his work. (sarcarsm)

  7. #7 Male Enhancement
    August 6, 2006

    Interesting article

  8. #8 Marvin E. Kirsh
    August 11, 2006

    Dear Sir; I studied molcular biology many years. When I first read Darwin as an undergraduate,the topic was new and I learned from it. Later in graduate school I learned about protein structure-the genetic code -and last about reverse transcripttion. These things paint a coherent picture from which modern scientists can ask questions and research issues.
    If one starts from another perspective in his questions, how could the complex world come about from evolution-it also seems unfathomable to have happened but to project on verylarge time scales. Creationists do have to do this . Intelligent designers have to find some comflict with this molecular evolution scheme.
    I myself do not think nature is intelligently designed(joking). If one thinks linguistically and defines all things as content container-all the routes to all our behaviors in the same container with all of the possible choices in life – even if you wish to call the content (our behaviors -total daily activities and choices-infinite then the container is infnite. . A container is a container-if you say there is something beyond it -what is-is still part of the container as defined. What then can we say, but that our current views we have constructed from the ground up to be exactly objective,from study, though we are a part of the container itself. yet we are somehow unable to incorporate the two together-ourselves and the universe-external world. Somewhere, along the way inout progressions,though, we must make an adjustment in our orientations when our objectivity becomes obsessive. This has not happened and we are all suffering an especially violitous situation when we are experimenting with nature in the labs fields and medical places-we may have added things up past a line where the real world is. As I ask myself how this could happen?..my answers are extracted from philosophy and the physical sciences and can be summated with the fact that we employ a third objective, third party or point of reference that exists as neutral . We might agree on things -if its’ the same for you it might be the same for me -and maybe it’s the same for everyone-but with the asssumption that no two people or things are the same. Nietzsche relates this idea two centuries ago and even early Greek and Roman writings testify that that no mans’ experience is the same as another’s nor can be discerned from observation-the waters he tread are unknown but to himself. Nature appears to be intelligently designed, because we are intelligent and also have no way to say how intelligence evolved, and there is no way to know from the bits and pieces analysis of science.
    What are we then practicing -in the absence- of a big picture or truthful guiding philosophy -in biology/physics/medicine in nearly all aspects of our societies- -but actions based on historically inherited instinct -mankind in conflict with nature, the stranger, that at its’ roots, are his objective thoughts about himself and the world, viewing nature as separate from himself applied in the name of scientific objectivity. As all history records, as the Arians exported themselves around the world they committed terrible acts when ever beyond their home territorries in the midst of new strangers-evil acts in the eyes of his victums , but only bad appearing when engaged in conflicts within their normal company with known enemies.
    The bottom line is that we have crossed-transcended a neutral division in our scientific pursuits to be functioning on an instinct of itself. This implies with assumptions of likeness or equality of things,that we are tresspassing, crossing borders we did know exist,where assumed equalities and samenessess are really differences. Our activities are themselves autoimmunogenic in nature.
    As an example, if Einsteins equation is correct, but there is no third party to say that the speed of light is a constant-i.e every point in the universe is unequal tothe other, then we do not know what we released when we dropped the bombs on Japan-and may -even if we regret it from from a simple ethical perspective of the human suffering incurred, changed all points in space. We do not see ourselves yet in anyway as Arians with the same ( and equal at its’ very base) instinctual approach to our problems?
    In nature atomic energy can accumulate naturally but never reaches a critical mass because the water evaporates first-nature cannot tolerate release of energy from the glue that holds the atom together. In
    the designed bomb doors from which the water could have vented we anchored in place.
    We still do not know better today in our biology efforts when we seek to change things-dark areas in our knowledge which could change our (very honest and truthfull appearing) asseements, as we are constructing by addition our own painting of nature, are chronically avoided in our instinctual trespassing as we havent even the slightest footing much less scientific connection to establish a route. In current directions, recognition and acknowledgement of mistakes will be arrived at last and not first.
    This is a difficult fact for the most consciencious to accept. In what would appear as a few hours to the year, in mankinds social development, with the applications of a few bold discoveries and intellectual deductions(Newton-Einstein), we are busy dissasembling ourselves in an exactly intelligent manner as we question “this looks exactly intelligently designed-fit”.
    I can express this view, which seems intelligent, also to me, because I know the lesson -it is in part of the content of our environments -in old movies, science fiction, in the moralities and dangers of life taught us. yet we do not recognize it. What is the difference in hurting an animal for prey-food -even out of cruelity vs. destroying it for the purposes of communicating how their biology works. Just animals -are not just animals when treated this way for that purpose. I was once in that position, used mice as an undergraduate (as an aid where I knew little of the research) and a little bit in graduate school for my thesis – though I ultimatley purchased salmon sperm DNA from the fishing industry-drug companies. And lived a very pressured, degree oriented life with the same orientations and directions as anyone currently engaged in research, with an atruism about improving the life of others. From my current perspective, twenty years later, never having gained employment, living very indigently, nearly starved of the same life I lead then, it looks very obvious, the nature and causes of a changing immunological trouble world wide. Is not at the molecular level or especially sexual, but of border and line crossing, hot heads and hotheaded acts, both in thought and action, that how we spend our time-our past ime is tomorrows time-yesterday filters in to our sleep, filters into our dreams, how we live, accept, and indulge in a society flooded with technologies making life easier, the environment easy to change to suit ourselves: blind to a known lesson, philosophy, that goes in any direction the same(to dark or light)-but paints not the same hologram in eiter direction-a shrinking one of a reverse path one way vs a growing one .
    Cannot anyone,scientist or otherwise, come to know this fact..Charity starts at home and so does science where it started-’if for you maybe for we’-but it cannot be added nor projected any further to an absolute, constructions of numbers as science are always insufficient to paint a total view.Nature can be anonomously cruel-an existing fact that we cannot change by “seeking” to change nature -the thought in itself is automunogenic-and breeding a real exisitng worldwide, material pathology, that can only take a reflection and a change in habit to surmount.

    http://www.marvinekirsh.com, http;//www.authorsden.com/marvinelikirsh

  9. #9 kfnyc
    August 14, 2006

    er right….

    “From my current perspective, twenty years later, never having gained employment, living very indigently, nearly starved of the same life I lead then, it looks very obvious, the nature and causes of a changing immunological trouble world wide. Is not at the molecular level or especially sexual, but of border and line crossing,”

    I hate when that happens

  10. #10 marvin kirsh
    August 15, 2006

    dear kfnyc: I imagine my comment looks ridiculous -I am not saying that you cannot pin point exactly all the molecular and genetic changes attributed with the AIDS virus. How do these changes suddenly come about in history. I am saying that the “macro” activities of mankind world wide expressthemselvres this way. I have several additional posts in Aetology if you want to read more of what I think(after traversing the dark sections of the nation no one sees much of-where the reflections of its general functioning surface where those think no one watches-not and idealistic setting-but an expression -compensation for bad problem solving-disturbed thinking reflective of the same-man created obstructions;extensive corruption of which only a little is ever exposed.(that grows from the normal places and streets)..a concealment for the illusion that we have ever conquered any problems at all.

  11. #11 acne information
    September 19, 2009

    Arguments from the data based on an alternative model which generates testable hypotheses would help alleviate the desire to pubjack. The real thing is much more satisfying. i agree..