Scientists Claim: They Performed Evolution

Geneticists are in the process of engineering molecules which is great science, but when scientists alter molecules which is not found in nature, are they performing evolution which is a mindless unguided process or intelligent design? Is there any evidence for evolution in the experiment?

The abstract in the paper goes like this…

Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution. It involves the storage and propagation of molecular information and the refinement of that information through experience and differential survival. Heretofore, the only molecules known to be capable of undergoing Darwinian evolution were RNA and DNA, the genetic molecules of biology. But on page 341 of this issue, Pinheiro et al. (1) expand the palette considerably.”

“They report six alternative genetic polymers that can be used to store and propagate information; one of these was made to undergo Darwinian evolution in response to imposed selection constraints. The work heralds the era of synthetic genetics, with implications for exobiology, biotechnology, and understanding of life itself. “

Here the paper uses circular reasoning, “Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution.” There was no observation of nature selecting the defined structures nor the targets, nor the aptamers! It was an international team of scientists who did the selecting! Not only that but their altered molecules “remains relatively inefficient.” unnatural or designed by scientists are poor polymerase substrates at full substitution.

Molecular memory is not a demonstration of evolution rather it’s an assumption of the data.  Scientists invented their own selection strategy which they call  “compartmentalized self-tagging.”  

The conclusion of the paper says…

Our work establishes strategies for the replication and evolution of synthetic genetic polymers not found in nature, providing a route to novel sequence space. The capacity of synthetic polymers for both heredity and evolution also shows that DNA and RNA are not functionally unique as genetic materials.”

“The methodologies developed herein are readily applied to other nucleic acid architectures and have the potential to enable the replication of genetic polymers of increasingly divergent chemistry, structural motifs, and physicochemical properties, as shown here by the acid resistance of HNA aptamers (fig. S17). Thus, aspects of the correlations between chemical structure, evolvability, and phenotypic diversity may become amenable to systematic study. Such “synthetic genetics” — that is, the exploration of the informational, structural, and catalytic potential of synthetic genetic polymers — should advance our understanding of the parameters of chemical information encoding and provide a source of ligands, catalysts, and nanostructures with tailor-made chemistries for applications in biotechnology and medicine.”

Other media makes wild claims that this experiment produces a more understanding about the origin of life which is nothing more than presupposes the existence of DNA. Because without DNA along with its specified information, and proteins to build DNA, nothing happens! Unless scientists are observing this in nature without their tinkering around, this is not evolution rather they are tinkering with something that was intelligently designed by God.  Even if evolution was true, just because it was done in a lab, doesn’t mean nature does it and altering molecules in a lab is not a demonstration on how evolution works rather just like evolution itself, it’s a man-made up story about the experiment.

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36 thoughts on “Scientists Claim: They Performed Evolution

  1. I laugh whenever I see articles like this. It just proves that anything that has to to do with altering DNA needs intervening intelligent input.

    “Here the paper uses circular reasoning, “Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution.” There was no observation of nature selecting the defined structures nor the targets, nor the aptamers! It was an international team of scientists who did the selecting! Not only that but their altered molecules “remains relatively inefficient.” unnatural or designed by scientists are poor polymerase substrates at full substitution.
    Molecular memory is not a demonstration of evolution rather it’s an assumption of the data.”

    Agreed. What you see is desperation. Only the few, critically minded individuals will question it.

  2. Geneticists are in the process of engineering molecules which is great science, but when scientists alter molecules which is [sic] not found in nature, are they performing evolution which is a mindless unguided process or intelligent design? Is there any evidence for evolution in the experiment?

    A seemingly small matter here draws forth Michael’s fundamental misunderstanding of evolution—in fact, his misunderstanding of all of science.

    Michael continues to approach science as though it were religion His basic error here is the “assumption of agency.” He believes that the authors of the Science paper are the agents that cause their new molecules to evolve. This is exactly backward: The authors created the compounds. Then the compounds themselves “perform” the evolution, according to the laws of chemistry and physics. That is, there is no supernatural component in the replication of the XNA compounds. The only outside involvement of any kind is that the authors can specify the fitness function by which their evolutionary success is measured.[1]

    So, yes, evolution of the new XNA molecules is a “mindless unguided process.” It happens all by itself, with no control by the experimenters.

    Until Michael can get his head around this seemingly simple concept, he will not understand anything at all about evolution, and he will continue to make ridiculous statements such as—

    Here the paper uses circular reasoning, “Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution.” There was no observation of nature selecting the defined structures nor the targets, nor the aptamers! It was an international team of scientists who did the selecting!

    It’s not that this is wrong. It’s not even wrong[2] It makes no sense, because it assumes a false premise.[3].

    Of course, Michael is not alone in being unable to shake off the agency delusion. This is one reason that scientists find creationists so ridiculous.

    ====================

    [1] Just as the Lenski experiments used reproductive success in the medium as a fitness function, and the yeast multi-cellular experiment used clumping as the fitness measure. In the wild

    [3] It also has no relation whatever to circular reasoning. Michael does not understand the meaning of circular reasoning. He merely shovels in the term to sound as though he knew what he’s talking about—which he obviously does not. Like “liberal” and “special-interest group” Michael applies “circular reasoning” to any argument he doesn’t like.

    [3] Sort of like saying that the reason dirt is good to eat is that the moon is made of green cheese.

  3. Very Interesting comment….”The authors created the compounds. The authors created the compounds.The authors created the compounds. Then the compounds themselves “perform” the evolution, according to the laws of chemistry and physics” It looks like Michael’s analogy just flew over Olorins head and at any cost, including logic itself. Another word for these so called evolution simulation experiments is called “front loading” In all fairness to Olorin, this often goes over the heads of many. Sometimes even the front loaders themselves. Others like Thaxton, Venture and Szostack are much more up front and honest about this problem in these type of experiments which is not spoken of very often. Doing so publicly seems to interfere with grant money. Even in the end they ended up with a substandard molecule.

  4. It looks like Michael’s analogy just flew over Olorins head and at any cost, including logic itself.

    No\, it did not.. The molecules were “front loaded”. No one denies that. But after the molecules were (human) designed, they were capable of evolving on their own. The authors built the molecules with the capability of evolution—the ability to store, transmit, and modify genetic information. But it is the molecule itself that stores, transmits, and modifies the genetic information. That is, it evolves.

    The concept that Michael does not understand is that the process of evolution requires no external agent—not God, not the designers, not anything. Themayan seems also to have missed this.

    BTW, no one claims that these XNA molecules are as good as DNA or RNA. All of them (except perhaps HNA) require PCR amplification to reproduce, for example. The purpose of the synthesis was to determine whether there are any other NAs that have the capability of storing, transmitting, and modifying genetic information. perhaps these molecules will exhibit novel properties, or be able to bind new targets, or to synthesize compounds other than the biological proteins. They open up new fields of investigation—something that creationism has been utterly incapable of for the past three centuries.

  5. I laugh whenever I see articles like this. It just proves that anything that has to to do with altering DNA needs intervening intelligent input.

    History repeats itself. In the 19thC, the concept of “vitalism” held that certain compounds could be synthesized only by living organisms, and were inherently inexplicable by the laws of physics and chemistry. The concept died hard, even after a major criterion, the artificial synthesis of urea, was attained.

    Creationists repeat this supernatural principle with the idea that there is a magical quality about genetic molecules that is not subject to natural law—or to human intervention. This new result should—but will not—blow the doors off that illusion.

    The mantra of these acolytes is the claim that only an intelligence can create information, citing the 2d law of thermodynamics. There are (at least) two major holes in these arguments. First, the 2d law neither includes nor implies any exception for “intelligence”. In fact, Maxwell’s Demon shows that an intelligent agent cannot generate any information that would otherwise be forbidden by the 2d law.. Second, it is the destruction of information that requires energy under the 2d law. Landauer’s principle, originally posed in 1961, was experimentally confirmed just a month ago.

    So there is nothing magical about information either, and thus no evidence whatever that genetic information is beyond the writ of natural law.

  6. An important point I think is being missed is that it shows other molecules could be used in lieu of DNA. It isn’t necessary for life. Yet for some reason, all life on earth uses DNA. This, surely, is a good indication that life descended from a DNA based common ancestor.

  7. Exactly, Adam. Although DNA could have been one of several at the beginning, or, more likely, evolved later. . For example, RNA is simpler to make, although not as efficient. One of the new molecules, TNA, is also a candidate.

    Several groups o scientists are searching in out-of-the-way places for life forms that may still use other genetic molecules.

    The thing is, every time scientists try something like this, they learn a little more about how things work, and that adds to the mountain that allows us to see farther and farther. Scientists truly do stand on the shoulders of their predecessors.

    As opposed to creationists, who stand on each others feet.

  8. The experimental verification of Landauer’s Principle is published in Berut6, et al., “Experimental Verification of Landauer’s Principle Linking Information and thermodynamics,” Nature 483:187-189.

    Erasing one bit of information require4de 3*10^-17 Joules of heat at room temperature (300K).

    Creating information, on the other hand, requires nothing.

  9. “Erasing one bit of information require4de 3*10^-17 Joules of heat at room temperature (300K).

    Creating information, on the other hand, requires nothing.”

    Olorin seems to believe that these scientist did absolutely nothing, and that this molecule somehow modified itself.
    As for other comments made. I have never heard anyone, (including creationist or ID’ers) say that natural law does not exist, or effect living things, and that molecules could not be synthesized by human agents. I have no idea where Olorin is getting this from. I think he refuses to understand as the author put it. Their desire for….”tailor-made chemistries for applications in biotechnology and medicine.”

    To believe that it requires more energy to go down hill than up hill, says it all. These are how the laws of physics have to be distorted to make this paradigme work. One other thing that Olorin seems to forget, is that Design theory and design theorist are now being used in these new emergent fields of SYSYTEMS biology and BIOinformatics. The question one needs to ask, is why would design theory now be required to learn about something that is in fact is not actually designed, but instead was supposedly put together by purely blind and unguided forces?

  10. To believe that it requires more energy to go down hill than up hill, says it all. These are how the laws of physics have to be distorted to make this paradigme [sic] work.

    Well, now we have someone who deems to understand even less about physics than Michael does. he could have merely Googled “Laudauer Principle” and find that he’s talking about an entirely different subject. And still wrong.

    One other thing that Olorin seems to forget, is that Design theory and design theorist are now being used in these new emergent fields of SYSYTEMS [sic] biology and BIOinformatics.

    Olorin didn’t forget it, because it’s not true. Themayan seems to have the same reckless disregard fro truth that Michael has. As Mark Twain once observed, these two seem to go together.

    Although it’s now almost 50 years old, my master’s degree was in what today would be called systems theory. Well, I have been trying to catch up, recently wit5h a lecture course in the theory of complex systems and reading the journal papers in Science and Nature. Also, the last 5 years of my active career included a fair amount of work in obtaining patents in the field of bioinformatics.[1]

    The thing is, there is no such thing as “design theory.” It is a figment of your febrile imagination.” If you think there is such a thing, please describe its laws and/or principles. Give your sources; creationists are known to make things up.[2]

    Is it really any wonder that scientists don’t take creationists seriously?

    ====================

    [1] Here’s an elementary question: If the distance between A and B is 10 centimorgans, and the difference3 between B and C is 25 centimorgans, approximately how much closer is B to C than it is to A? Non-response will indicate that you have no idea what you’re talking about.

    [2] Recall Scopes Law—that citing Answers in Genesis to support an argument automatically forfeits the argument.

  11. “Olorin didn’t forget it, because it’s not true”

    “The thing is, there is no such thing as “design theory.” It is a figment of your febrile imagination”

    Synthetic and Integrative Biology: Parts and Systems, Design Theory and Applications
    JAMES T GEVONA
    end.

    MIT
    Systems Biology using Axiomatic Design and Complexity Theory
    One of the goals of systems biology is to understand the functions of a biological system in terms of the behavior and interactions of its molecular constituents. The task is difficult because both the physiological functions and the physical and chemical structures of biological systems consist of many levels of aggregation and hierarchy. In this work, we are trying to present a roadmap for establishing the relationship between the high-level functions and molecular-level interactions is presented. It is based on the application of Axiomatic Design theory and complexity theory that have been developed for engineered systems. http://web.mit.edu/pccs/resear… end

    BIOINFORMATICS…..
    Bioinformatics i/ˌbaɪ.oʊˌɪnfərˈmætɪks/ is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software engineering, data mining, image processing, modeling and simulation, signal processing, discrete mathematics, control and system theory, circuit theory, and statistics. Bioinformatics generates new knowledge as well as the computational tools to create that knowledge.
    Commonly used software tools and technologies in this field include Java, XML, Perl, C, C++, Python, R, MySQL, SQL, CUDA, MATLAB, and Microsoft Excel. end.

  12. A scientific theory is defined as a set of principles that explain and predict physical phenomena. “Axiomatic design” is not a scientific theory; it is a methodology—a procedure for coming up with a specific product design given a set of functional requirements as input. One characteristic of a scientific theory is that it makes falsifiable predictions—something which axiomatic design is incapable of.

    Although some of the literature calls this methodology axiomatic design “theory,” the name is inaccurate. One of the characteristics of apologists is to lock onto a specific word, and then to apply it unthinkingly, whether or not the context fits the definition.

    Complexity theory is a loose and not very well defined collection of mathematical concepts for analyzing collections of abstract objects. It is not a theory in the sense of gravitation or quantum theory—it is more like group theory or the theory of graphs. The MIT reference seems to be using the term inaccurately.[1]

    It is ironic that the article mentions “engineered systems,” because a salient characteristic of any complex system is that it evolves. In fact, the theory of complex systems began in large measure as a way to analyze biological evolution. And the evolution of a complex system arises form the emergent behavior of the system itself and does not require any outside agent to initiate or guide it. As noted in Foundations of Complex Systems Theories,[2]

    Downward causation[3] is often accused of being mystical. It is not if it is clearly articulated. There are two dimensions in the interpretation of downward causation. The first regards the effects of the system on the behaviors of its constituents, the second the source of the system’s causal efficacy. Mysticism results if the causal efficacy is credited to independent sources such as vitalism or psychic energy that are totally detached friom the forces among the constituents and stand above them. Such attribution is not necessary.

    The author also cites Stuart Kauffman to show how novel features arise in complex systems—again, without any outside guidance or influence.[4]

    Suppose the Boolean networks represent genomes made up of genes regulating each other. Then, Kauffman argued, those genomes with connectivity that puts them on the edge of chaos have the optimal capacity to evolve. Most mutations have minor effects on those networks, because they are localized in the active islands. However, a few mutations can trigger an avalanche of modification that cascade throughout the system, resulting in emergent evolutionary changes. Thus networks at the edge of chaos are able to evolve both by accumulation of small changes and by dramatic changes in which evolutionary novelties emerge. The emergent changes may be triggered by a random mutation or by a change in the environment. The conditions under which natural selection is most powerful are also those in which self-organization and historical contingency are most likely. [Emphasis in original]

    Thus, to “design” a complex system is self-defeating and is in fact not a good idea.. Once constructed, it will change, perhaps dramatically.[5]

    .Likewise, bioinformatics is strictly an analysis instrument, not a “theory”. If you read the quotation in your comment, it says noting about employing it to “design” new systems.[6]

    Although the link to the MIT reference failed, I found a short precis here. None of the material speaks of using complex systems theory or bioinformatics to “design” synthetic systems. I have followed some of the literature; there seems to be no “theory” or “principles of design” behind the construction of synthetic biologic systems.[7][8]

    .

    Once again, there is no such thing as a scientific “theory of design.”

    =================

    [1] Another instance of latching onto a term without understanding it.

    [2] Sunny Auyang, Cambridge University Press (1998), at 65.

    [3] “Downward causation” refers to the action of the system as a whole upon its own members or upon objects outside the system, action that no component of the system can perform separately

    [4] Id., at 202. Stuart Kauffman is an evolutionary biologist who works in complex systems theory at the Santa Fe Institute.

    [5] Most complex systems are governed by power laws that practically guarantee occasional catastrophic changes. See my eaerlier comment as to why humans avoid complex designs whenever they can.

    [6] None of the software tools mentioned are specific to bioinformatics. They are all general tools used for many applications.

    [7] Again, altho axiomatic design theory may be employed (I haven’t ever run across a reference to it). this is not a “theory” having any laws or predictive power—it is simply a mathematical methodology, like using a Lagrangian instead of a wave function to find the quantum states of an atom.
    [8] For some recent new results, see Pinheiro et al., “Synthetic Genetic Polymers Capable of Heredity and Evolution,” Science 336:341-344 (20 Apr 2012).

  13. Sorry for misattributing the earlier thought to Mark Twain. It was actually Charles Darwin who noted that ignorance and confidence often go together. (Descent of Man, intro., p4)

  14. I have given you examples of design theory being used in Systems biology. As for bioinformatics, engineered systems are also designed systems. The point is that chemistry and physics alone is not sufficient and this is the reason design theory and an engineered systems approach is useful, necessary, and my question of why design theorist are now being used to try to further our understanding of complex biological systems that supposedly occurred as a result of blind unguided chance still stands. Design theory is not a figment of my imagination (as you have now back tracked on with added caveat) and is in the literature. It was actually Mark Twain who said that “A lie could travel half way around the world while the truth is still putting on its shoe’s”

  15. By the way systems biology uses the same statistical theory that evolutionary theory uses. The only difference is the amount inconsistencies. I.e. the known failed predictions that the modern synthesis has.

  16. Correction,……. axiomatic design theory uses the same statistical theory that evolutionary theory uses. The only difference is the amount inconsistencies. I.e. the known failed predictions that the modern synthesis has.

  17. I have given you examples of design theory being used in Systems biology. As for bioinformatics, engineered systems are also designed systems.

    There is no such thing as a scientific “design theory.”

    You gave examples of general-purpose tools and methodologies that can be used to design biological systems.

    Einstein’s theory of gravitation can be employed to design GPS satellites. That does not make Einstein’s theory a scientific “theory of GPS design.”

    The point is that chemistry and physics alone is not sufficient and this is the reason design theory and an engineered systems approach is useful,

    This is of course a load of dingoes kidneys. You have shown nothing that might indicate that biological systems are not governed by the laws of physics and chemistry. Of course engineered systems are designed systems. This is a tautology. Rocket ships and perambulators are engineered and designed systems. Design methods such as axiomatic design theory and unified manufacturing theory con tribute to their design and fabrication Yet no one would claim that rocket ships or perambulators operate beyond the laws of physics—for that reason or for any other reason..

    Themayan is sinking into the modern version of vitalism, the 19thC theory that the functions and reactions of living organisms operate beyond natural law. This theory was debunked a hundred years ago. Apparently the creationists have dug up its rotting corpse and pulled the stake from its heart.

    There is no such thing as a “design theory” that qualifies as a scientific theory.

  18. There is no such thing as a scientific “design theory.”

    Lets stop the knit picking or “Simon didn’t say” bs! Design theory is an acceptable term as is C/K theory. Axiomatic design is just an example of one of a few others.
    I don’t expect everyone to know everything on the topic of cutting edge science.
    I know certainly don’t, but what I would expect is to at least attempt a little research onto the subject. If you had, I don’t believe you would have said that….”There is no such thing as a scientific “design theory.” or that “It is a figment of your febrile imagination” For you to imply that there is no such thing as the science of design, and or scientifically quantifiable design principles, I think speaks louder than any response I could give. Speaking of historical figures, lets not forget Cleopatra who was also the Queen of Denial.

  19. Lets stop the knit [sic] picking or “Simon didn’t say” bs! Design theory is an acceptable term as is C/K theory.

    Design theory is an acceptable term, but it is not a scientific theory such as quantum theory or plate tectonics. This is not a nit, it is a major category error. You are using two different senses of the word “theory” as though they were the same: “Theory” as in a methodology for achieving a desirable result, and “:theory” as a set of explanatory principles governing a physical phenomenon and subject to experiment and falsification. “Design theory” represents the first sense, but the following statement, which generated this topic, invokes the second, different, meaning. There is no such thing as “design theory” in the second sense.

    .

    Design theory and design theorist are now being used in these new emergent fields of SYSYTEMS biology and BIOinformatics. The question one needs to ask, is why would design theory now be required to learn about something that is in fact is not actually designed, but instead was supposedly put together by purely blind and unguided forces

    By the way, this statement obviously false. Design theory (in the first sense of this term) is not “required” to understand biological systems. The use of axiomatic design theory in synthetic biology is to try to improve upon what evolution has come up with. (Complexity theory is not a “design theory” in any sense of that term; it’s a—nascent—branch of mathematics, in the same sense as graph theory or group theory..)

    ==========================

    It may help to define axiomatic design theory, to see what kind of a beast it really is. Quoth Wikipedia—

    Axiomatic design is a systems design methodology using matrix methods to systematically analyze the transformation of customer needs into functional requirements, design parameters, and process variables. Specifically, functional requirements (FRs) are related to design parameters (DPs):

    \begin{bmatrix} FR_1 \\ FR_2 \end{bmatrix} = \begin{bmatrix} A_{11} & A_{12} \\ A_{21} & A_{22} \end{bmatrix} \begin{bmatrix} DP_1 \\ DP_2 \end{bmatrix}

    The method gets its name from its use of design principles or design Axioms (i.e., given without proof) governing the analysis and decision making process in developing high quality product or system designs.

    The highlighted phrases differentiate this design theory from a scientific theory, which has no assumed “axioms,” and which does not involve human thought processes.

    An early major paper lists the axioms ofr this methodology—

    • Axioms of objects
    1. Axiom 1. Everything in the universe is an object.
    2. Axiom 2. There are relations between objects in the universe.
    • Axioms of the human thought
    1. Axiom 3. Human beings are bounded in rationality (Simon, 1969; 1982).
    2. Axiom 4. Human beings do not recognize objects accurately.
    3. Axiom 5. Causal relation is the only plausible relation in all relations between causes and
    effects

    Scientific theories do not involve how to think about anything

  20. The modern synthesis itself is an axiom, however unlike other axioms that can be regarded as correct even though not mathematically quantifiable, the difference is the moderns synthesis as I said before has accumulated so many failed predictions that I have to agree with J Gould, when many years ago he said that the Neo Darwinian/modern synthesis is effectively dead as a theory.
    With the exception of math and a few others, for most scientific subjects, and especially in the historical sciences, theres really no such thing as proof. All we have is evidence. Again, I have provided the fact that design theory is now being used to further our understanding of complex biology systems, and instead of grabbing the bull by the horns and answering my question concerning this reality, you instead chose to play it safe and hide behind your ever growing row of additional goal post and added caveats. This is an old rhetorical game. Its akin to me presenting you with an eyewitness, and then you claiming he or she is irrelevant because you dont like their shoes.

  21. Complexity theory is not a theory of design. So why would themayan claim that it is?

    It seems that axiomatic design theory uses the term “complexity” in a totally different sense from mathematical complexity theory.

    Complexity Theory in Axiomatic Design, defines “complexity” as “a measure of uncertainty in achieving a desired set of functional requirements.”

    Mathematical complexity theory has nothing to do with any form of uncertainty or functional requirements. Rather, a complex system is one characterized by a large number of nodes which have a number of different types of behavior, a specified degree of interconnectedness among the nodes, and the ability to adapt—that is, to change their behavior—in response to other nodes.

    Looks like yet another outbreak of equivocation–using the same term to denote different things without distinguishing between them. This is a common symptom of ignorance of the subject matter.

  22. The modern synthesis itself is an axiom,

    BS. This whopper nails it. You have no idea what you are talking about. Physical sciences do not admit axioms.

    There is no such thing as a scientific axiom.

    Please look up these terms before throwing them around with such reckless abandon.

  23. “There is no such thing as a scientific axiom”

    “Please look up these terms before throwing them around with such reckless abandon”

    I don’t believe I ever used the term “scientific axiom” Although it is a term used from time to time on peer review university level articles. A simple five minute search would have shown you this. Please take time to actually read my post before accusing me of using terms I did not. Again many things you have said do not exist in fact do exist after all.

    You quoted from Wiki earlier, and thats fine. Now I will do the same. Wikipedia-Subject- AXIOM. Under paragraph (Other sciences)……”Axioms play a key role not only in mathematics, but also in other sciences ETC”….. As for my use of the word “axiom” concerning the way the neo Darwinian synthesis has become one in itself, is based on the classical definition…….”a premise so evident as to be accepted as true without controversy” I.e very similar to a dogma. You may not agree, but to teach or to believe something in a non dogmatic view, is not such a bad thing. Again you choose to build straw men and continue to deny and at all cost the reality that axiomatic design theory (which encompasses more than just a tie to the word axiom) and engineering principles, are being used to help us better understand these bio systems. I believe I have made my point.

  24. More of avoiding the original point but so be it. Notice how Olorin continues to accuse me of saying things I never said. He didn’t even understand that C-K theory stands design theory or concept-knowledge theory. He is assuming it stands for complex theory. Yes there are overlapping principles but this has nothing to do with the original subject that he has now changed with his further use of changing the goal post. This is a classic case of metaphysical naturism double speak 101.

    Olorin said…..
    “Complexity theory is not a theory of design. So why would themayan claim that it is? It seems that axiomatic design theory uses the term “complexity” in a totally different sense from mathematical complexity theory. Complexity Theory in Axiomatic Design, defines “complexity” as “a measure of uncertainty in achieving a desired set of functional requirements.”Mathematical complexity theory has nothing to do with any form of uncertainty or functional requirements. Rather, a complex system is one characterized by a large number of nodes which have a number of different types of behavior, a specified degree of interconnectedness among the nodes, and the ability to adapt—that is, to change their behavior—in response to other nodes. Looks like yet another outbreak of equivocation–using the same term to denote different things without distinguishing between them. This is a common symptom of ignorance of the subject matter”

    Again from the same Wikipedia you used recently……..
    Design theory can refer to any theory relating to design in general.
    Design theory may also refer to:
    ▪ Engineering and industrial design
    ▪ C-K theory
    ▪ Design science
    ▪ C-K theory
    ▪ Mathematics
    ▪ Combinatorial design
    ▪ Block design
    ▪ Symmetric design
    ▪ Design of experiments
    ▪ Architecture
    ▪ Interior design
    ▪ Economics
    ▪ Mechanism design
    ▪ Theological argument
    ▪ Intelligent design

    MIT
    AXIOMATIC DESIGN FOR COMPLEX SYSTEMS [2.882s]
    
This course is in development for 2013 or beyond. The below description should be taken as an example of content and is subject to change. If you are interested in this course, please
COURSE SUMMARY
    Learn how the Axiomatic Design (AD) helps top-down thinking when we design complex systems. This course will introduce design principles that will enable you to define problems free from preconceived solutions. The instructors will engage the course participants through interactive discussion using many industrial cases including, where possible, the participants’ own problems.
    Many of today’s engineered systems, whether a very large-scale factory or a small-scale nanoproduct, are complex systems. When designing these systems, most challenging problems manifest at the system level, and decisions need to be made, often in the absence of understanding the complexity. In this course, you will learn how the Axiomatic Design principles enable you to overcome these challenges by identifying and reducing the complexity and by promoting functional, top-down design thinking.
    We will introduce the basics of the Axiomatic Design approach, and will examine how each element of the Axiomatic Design process relates to complex systems design. We will present the latest developments of the Axiomatic Design approach to complex systems as well as a number of case studies and industrial examples ranging from large scale to nano-scale systems, and from design for six sigma to design for health care systems.
    One example of our case studies is Health Care System. The health care delivery system is one of the least studied complex systems. Can we maximize the productivity by streamlining the patient flow while providing the best patient care? We will present ways to understand the complex nature of these interactions, and finding systematic solutions will be presented. Attempts have been made to facilitate the patient flow, to avoid the bottleneck by creating fast tracks in the Emergency Department (ED) of hospitals. We have recently found that the patient flow can be drastically improved by redesigning the fast track system based on Axiomatic Design and the overall patient waiting time could be decreased drastically (~50%).
    In this course you will learn how to:
    • understand the causes of complexity in your project,
    • recognize various mistakes in designing and operating complex systems,
    • understand the benefits of functional, top-down thinking in solving complex design problems,
    • make good decisions in design and operation of complex systems with the Axiomatic Design thinking and processes.

  25. <blockquote.
    I don’t believe I ever used the term “scientific axiom”

    Let’s review the bidding—
    > Themayan said: “The modern synthesis itself is an axiom.”
    > The modern synthesis lies within the physical sciences.
    > Olorin af Valinor said: “Physical sciences do not admit axioms.”
    The chain of implication is farly obvious here. Can you still not see it?

    The rest of your comments represent a compendium of quote-mined keywords, with no understanding of the context or relevance of those words in a scientific setting. Some of them have already been pointed out, but merely disregarded..

    Creationists develop a lot of practice in this area, because the Bible is the mother of all mined quotations.

    In closing, please do not offer to help your children with their science homework.

  26. All I said that was “I don’t believe I ever used the term scientific axiom” I also said…. “Although it is a term used from time to time in peer review university level articles” I also disagree with Olorins statement that axioms are not used in science. This is a blatant falsehood. Remember this is the same guy who said that design theory did not exist.

    Lets take a closer look at this term which is defined….”An “axiom”, in classical terminology, referred to a self-evident assumption common to many branches of science” “Axioms play a key role not only in mathematics, but also in other sciences, notably in theoretical physics In particular, the monumental work of Isaac Newton is essentially based on Euclid’s axioms, augmented by a postulate on the non-relation of spacetime and the physics taking place in it at any moment” These examples are sourced from the same Wikipedia that Olorin used earlier, and which also includes axioms with the science of geometry and mathematics. This shows that Olorin (and apparently you) doesn’t know what he or she is talking about and instead relies on pure rhetoric.
    I say my statement stands. The modern synthesis is a classic example of an axiom. In fact even the out spoken pro evolutionary philosopher Massimo Pigliucci who was a a part of the Altenberg 16 summit which was put together to formulate an extended evolutionary synthesis has called for a relaxing of many of the assumptions of the modern synthesis which I have a list of from the key note adress in Altenberg Austria 2008. Again I point to the change in goal post from the original point of design theory being used in systems biology.

  27. One more correction. I misread the posters named and assumed it was someone other than Olorin. My fault for posting when I’m sleepy.

  28. Massimo Pigliucci who was a a part of the Altenberg 16 summit which was put together to formulate an extended evolutionary synthesis has called for a relaxing of many of the assumptions of the modern synthesis

    Ah. here’s the rub. Themayan is ignorant as to the difference between an axiom and an assumption. All axioms are assumptions, but not all assumptions are axioms.

    Mathematics, and various fields thereof, are based upon axioms. Th reason they are axioms is that their truth cannot be established within the system itself. There is, and can be, no proof that parallel lines never meet. One consequence of this is that axioms can be modified at will—and when they are, they produce a different set of theorems and proofs. Theorems using the old and new axioms are both true, but different. Such as spherical geometry, which says that parallel lines DO meet.[1] As a consequence, the Euclidean theorem about the constant sum of angles in a triangle is not true in spherical geometry.

    Science often employs assumptions. Every scientific hypothesis assumes matters that have not been establishe4d with evidence. If it did not generalize beyond facts that have already been demonstrated, it would have as little value as creationism—that is, no value at all.. It could not make predictions, because it would apply only to facts that are already known. The difference between such an assumption and an axiom is that a scientific assumption can be shown to be true or false (“falsified”) within the system itself.

    An assumption in a scientific theory is a totally different beast from an axiom. Every time I’ve heard scientists apply the term “axiom” to their discipline, the intent was sarcastic: “Dr. Noitall is so smug about his theory of mutant parsnips that he thinks it’s an axiom that stands without proof.”[2]

    “Design theory” is used to design systems, which is its purpose—including to design synthetic biological molecules and processes.. Design theory does not provide scientific explanations for biological systems, or for any other systems. Design theories are used to design perambulators—but they do not explain perambulators.

    There is no such thing as a scientific theory of design. To the extent that any “design theory” is used to analyze a pee-existing system, the only thing it can tell you is whether the system meets the criteria according to the values embedded into that specific theory by its (human) programmer. Values such as minimum cost per function or independence among design components, or graceful failure modes. Therefore, different ones of such design theories will produce different results when analyzing the same system.

    There can be no such thing as a scientific theory based upon human-specified values, or that leads to different results when tested against the same system. So there is no such thing as a scientific design theory. The term “theory” has different meanings in different contexts, and you conflate them without understanding either one. A horse chestnut is not the same as a chestnut horse.

    Again I point to the change in goal post from the original point of design theory being used in systems biology.

    The digression was necessary to point out why your use of “design theory” and other terms is ill-informed, and does not imply that natural chemistry and physics are insufficient to provide scientific explanations of living organisms. Your misunderstandings of science have improperly conflated two entirely different subjects.

    Come back when you have learned a little about what science is and how it works. To start, I would recommend Bowler & Morus, Making Modern Science (U. Chicago Press 2005). For a view into how scientific theories come about, Watson, The Double Helix (Touchstone 2001)[3]

    ==================

    [1] It is possible to assume “axioms” that conflict with each other. However, in that case, at least one of them can be proven to be incorrect within the system, so that it is not in fact an axiom. Or, equivalently, there will be theorems that can be proven to be both true and false, as shown by Godel’s Theorem.)

    [2] The Altenberg 16 conference is widely misconstrued by creationists. I have read all the papers published from that conference. The main import is not that the modern synthesis is falling apart. Rather it is that the past couple of decades have produced many new tools and techniques that the modern synthesis has not yet employed, and may not even know about: For example, evo-devo did not exist when the MS was put together, and it offers many new insights into morphogenesis; natural selection has heretofore considered the environment as a given—but many organisms actually create their own environments, producing a feedback effect that has not been recognized; new sources of novelty have been discovered in gene regulation and gene networks. If all you have seen about Altenberg is from Suzan Muzur, then you not only have twisted interpretations, but you are dealing from a deck of “facts” that are not true.

    [3] Which is subtitled, “A Personal Account of the Discovery of the Structure of DNA.” Bear in mind that Watson is sometimes trenchant, and has been criticized for denigrating the contributions of others.

  29. No, it is you who is wrong. First by saying that design theory does not exist. Then by saying that there is no such thing as a scientific axiom. You are now just offering more red herrings. No thanks buddy. The thing about someone who is knee deep in their own fecal matter, is that after a while, you cant even smell it anymore but everyone else does. Good luck with that kind of rhetoric. Your going to need it.

  30. Design theory does not exist as a scientific theory. For the reasons given.
    The concept of an axiom not exist in the physical sciences. For the reasons given.
    If your overall aim is to imply that biological systems are designed because biologists may use industrial design theories, you are not only wrong , you’re ridiculous. Biologists would laugh at you.

    For half a century, I made a (very comfortable, thank you very much) living working with research scientists in fields from astronomy to zoology., writing extensive descriptions of their projects for government approval. I have a master’s degree in an area of physics that today would be called systems theory.

    Your qualification in this field seem to consist entirely in a certainty that you are right, despite any evidence to the contrary. Truly, as Darwin said, ignorance and self-confidence frequently travel together..

    Again, please do not help your children with their science homework. The US already ranks between Bulgaria and Uzbekistan in science and math. As we become more and more dependent upon citizens’ knowledge for evaluating medical claims, research priorities, and national security, those who do not understand science will become increasingly left behind.

    ——————————————————————-

    Here’s an example. I have come up with a $10 test for a disease that kills 50 Americans every year. The test has a 98% accuracy rate. Should we ask health plans to pay for the test? (This is related to the recent debate on prostate screening.) If you’d like to apply it to national defense,, change “disease” to “terrorist,” and say why we should or should not mandate the test at airports.

    Here’s another. Your school board classes every student into a racial group. They claim that, although the overall average test score for science and math has gone down, the average for every racial group has gone up. How does this happen? Should school policy be changed?

    And an encore. An election poll shows candidate O with 55% positive rating, and candidate R with 45%. What are the odds that R is actually ahead of O?

    if you can’t answer these, your are illiterate to the point that you will affect yourself adversely in some everyday affairs.

    Bon courage.

  31. “Likewise, bioinformatics is strictly an analysis instrument, not a “theory”. If you read the quotation in your comment, it says noting about employing it to “design” new systems.[”

    I never claimed anything about it being employed to design new systems, only that it is being deployed on already existing bio systems. I also asked why are design theorist being used to help us better understand systems that are supposedly non designed and are the result of blind unguided forces? You have yet to answer, and when I proved you wrong concerning the fact that these systems are indeed being used. You then continued to change the goal post and offer red herring and straw man arguments.

    “I have followed some of the literature; there seems to be no “theory” or “principles of design” behind the construction of synthetic biologic systems.[7][8]”

    PENNSTATE
    PhD in Biostatistics ProgramBasic theory and methods for statistical analysis, introduction to bioinformatics,principles and methods of statistical genetics, case-control association studies.

  32. I also asked why are design theorist being used to help us better understand systems that are supposedly non designed and are the result of blind unguided forces? You have yet to answer,

    Apparently the lengthy answers have not penetrated… The shortest answer is that design theories may be applied to designed or natural systems. The source of the system is irrelevant. Design theories cannot be used to understand or to explain biological systems, because design theory cannot explain anything.

    A design theory may be employed to design a new perambulator; it may be used to analyze an existing perambulator, to see whether the theory would or would not consider it to be a “good” design. A design theory may be used to analyze rocks—for example, to judge whether they would make “good” chairs. It makes no difference whether the theory is applied to a rock or to a perambulator. Or to a biological molecule, system, organism, or ecology.

    Therefore,the use of these “design theories” implies nothing at all about how an existing biological system came about.

    You have no understanding of what a design theory is or how it works. Or a scientific theory either. .

    You have supported your points with nothing but a farrago misconstrued quotations and definitions that are contextually inaccurate.

    It’s not even funny anymore. It’s just stupid.

    Go bray at the moon somewhere else.

  33. well the fact is, that scientists have been using different building blocks that have been proven in earlier experiments to form all by themselves..and and used rudimantary fragments of dna , as are to be found everywhere in space.

    now so they “front loaded “ the process with every condition known that would induce some similar reactions as have happened billions of years ago….just becouse we dont have 3,5 billion years to wait for it .

    now the fact that it managed to develope a life using a 6 nucleotide configuration was not engineered…it did it all by ite self…so imof abio …happened ..

    and becouse WE r honest people and not retarded lying fucktards like the religious we just call it “synthetic life“ and not abiogenesis becouse it didnt happen in billions of years..

    so the question to ask to all the retards is : was it there before//// no !
    is it here now/// yes!!

    and its even a better more complex and advanced life as their puny little brainfart god supposedly made .

    end of the god myth,,,, as well all other science has al ready proven..

    now i m curiuos ..of course they will desperatly try to cheat their way out and tell lots of bullshit lies again…

    how they reconcile reality with the fact that their precious buybull says the sun, moon and stars all dangle under giant body of water in the sky.

    HAR HAR HAR HAR HAR HAR HAR HAR HAR HAR HAR HAR HAR HAR ………….

  34. All attempts at creating, as in create, as to create, have all had to use pre existing genetic information. Craig Venture is the leader in this endeavor and admits himself that nature could not have done this particular example on its own as it required selection, purification, chemical coaxing and a whole variety of protocolas that have the human footprint all over it.

    What does this prove? That even with pre-existing genetic information at their disposal an intelligent agent is required to create an augmented cellular machine. Building blocks do not just happen on their own, and contrary to popular belief Stanley Miller was never able to produce non-racemic amino acids as they were all fully racemic and you cannot even produce one protein with a racemic mixture.

    It is physically and chemically impossible and Miller understood this. He also used a trap to prevent the same amino acids he created from being destroyed (which is an old chemist trick that nature does not provide)and this is why these types of contraptions are no longer used. We all make spelling mistakes, but when ever you see anyone using this level of poor grammar and writing skills, bells and whistles should be going off.

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